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Archive for the ‘Human Immune System in Health and in Disease’ Category

Graft-versus-Host Disease

Writer and Curator: Larry H. Bernstein, MD, FCAP 

 

Introduction

This piece is a follow up to the article on allogeneic transfusion reactions, which extends into transplantation and transplantation outcomes for hematological diseases, both malignant and nonmalignant. The safety of transfusions in Western countries has improved substantially, and the causes for transfusion mishaps has been reduced to unexpected infectious sources, uncommon immune incompatibilities, and errors in processing the blood products.  The greatest risk is incurred in platelet transfusions because of the short shelf-life of the product, and the time needed for testing prior to release.  This portion of the review is concerned with Graft-versus-Host Disease, which is unique to transfusion and transplanting of blood. In other transplantation, there is graft failure because of host versus graft incompatibility or complications.  The reverse order applies to blood.  In this case, on the contrary, the transfused or grafted donor tissue becomes a pursuer after the recipients hematopoietic cells.

Peter Brian Medawar: Father of Transplantation

Thomas E. Starzl, M.D., PH.D., F.A.C.S.
J Am Coll Surg. 1995 Mar; 180(3): 332–336

Most of the surgical specialities can be tracked to the creative vision of a surgeon. Transplantation is an exception. Here, the father of the field is succinctly defined in the dictionary as: “Peter Brian Medawar: a Brazilian born British Zoologist who at the age of 45 shared a 1960 Nobel Prize for his work on acquired immunologic tolerance”. Medawar was mysteriously overwhelming to many colleagues and observers, even when he was young. He was the son of a Lebanese father and an English mother—tall, athletic, abnormally handsome, hypnotically articulate in public, and politely cordial in his personal relations. In September 1969, at the age of 54, he had the first of a series of strokes. These crippled him physically but not in spirit. Although I saw Medawar often professionally and privately over a 22 year period, before and after he was disabled, this sporadic exposure was not enough to understand him. My sense is that no one did, except perhaps Jean, his wife for nearly 50 years.

Medawar’s dazzling personality before and great courage after his strokes was inspirational, but his fame was based on the unique achievement in 1953 captured by the terse dictionary mention of “acquired immunologic tolerance.” The roots leading to this accomplishment had fed on the blood of war. More than 12 years earlier, the recently wed zoologist Medawar—24 years of age and fresh from graduate studies at Oxford University—was assigned to
the service of the British surgeon, Dr. Thomas Gibson, to determine if skin allografts could be used to treat casualties from the Battle of Britain. First,
in human studies with Gibson, and then with simple and logical rabbit experiments, Medawar showed that rejection of the skin was an immunologic phenomenon. This later was shown  to be analogous to the cell-mediated delayed hypersensitivity that confers immunity to diseases such as tuberculosis. The principal evidence in the early studies was that repetitive grafts from the same donor were rejected more rapidly with each successive attempt —the sensitization and donor specificity confirming an earlier clinical observations by Emil Holman of Stanford in skin-grafted burn victims. Once it was established that rejection was an immune reaction, strategies began to evolve to weaken the recipient immune system. By 1953, total body irradiation and adrenal cortical steroids had been shown to delay skin rejection. However, this immunosuppressive effect was either minor if the animals survived, or lethal to the recipient if the grafts were spared.

Bombshell

In the resulting atmosphere of nihilism about clinical applications, a three and one-half page article by Billingham, Brent, and Medawar in the October 3, 1953 issue of Nature describing acquired tolerance, came as a blinding beacon of hope. The three men had learned that donor splenocytes could be engrafted by their intravenous infusion into immunologically immature mice in utero or perinatally. When these inoculated recipients matured, they could accept skin and other tissues from the donor (but from no other) mouse strain. The immune system of the recipients had been populated by the immunocytes of the donor, meaning that they were now chimeras. The race was on to convert this principle to humans. However, the dark side of their accomplishment soon was revealed by the two younger members of Medawar’s team, Billingham and Brent and by the Dane, Simonsen. The engrafted donor cells could turn the tables and reject the defenseless recipient unless the tissue match was a good one. This was the dreaded graft versus host disease (GVHD) in which transplanted donor cells attacked the recipient skin, gastrointestinal tract, lungs, liver, and the bone marrow itself. Medawar’s dream of 1953 was suddenly a nightmare. Or was it?

On the contrary, the work took a straight line to clinical application, after the demonstration by Prehn and Main that similar tolerance could be induced in adult mice rendered immunologically defenseless by total body irradiation before splenocyte (or later bone marrow) infusion. The recipient conditioning, known as cytoablation, also could be accomplished with myelotoxic drugs. However, as Billingham, Brent, and Medawar had predicted, donor specific tolerance could be induced in humans without GVHD only if there was a good tissue (HLA) match. In 1968, 15 years after the epic Billingham, Brent and Medawar publication, Robert Good and Fritz Bach reported the first two successful human bone marrow transplants. Both recipients of well matched bone marrow from blood relatives are still alive. This was a triumph in which the principal clinicians were internists, as summarized 25 years later in the acceptance speech by the 1990 Nobel Laureate Donnall Thomas.

The growth of bone marrow and whole organ transplantation

The growth of bone marrow and whole organ transplantation

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681237/bin/nihms-87975-f0001.gif

The growth of bone marrow (right) and whole organ transplantation (left) from the seed planted by Peter Medawar during World War II. GVHD, Graft versus host disease.

Immunological Tolerance: Medawar Nobel Acceptance Lecture

“Immunological tolerance” may be described as a state of indifference or non-reactivity towards a substance that would normally be expected to excite an immunological response. The term first came to be used in the context of tissue transplantation immunity, i.e. of the form of immunity that usually prohibits the grafting of tissues between individuals of different genetic make-up; and it was used to refer only to a non-reactivity caused by exposing animals to antigenic stimuli before they were old enough to undertake an immunological response. For example, if living cells from a mouse of strain CBA are injected into an adult mouse of strain A, the CBA cells will be destroyed by an immunological process, and the A-line mouse that received them will destroy any later graft of the same origin with the speed to be expected of an animal immunologically forearmed. But if the CBA cells are injected into a foetal or newborn A-line mouse, they are accepted; more than that, the A-line mouse, when it grows up, will accept any later graft from a CBA donor as if it were its own. I shall begin by using the term “immunological tolerance” in the rather restricted sense that is illustrated by this experiment, and shall discuss its more general usage later on.

The experiment I have just described can be thought of as an artificial reproduction of an astonishing natural curiosity, the phenomenon of red-cell chimerism in certain dizygotic twins. The blood systems of twin cattle before birth are not sharply distinct from each other, as they are in most other twins; instead, the blood systems make anastomoses with each other, with the effect that the twins can indulge in a prolonged exchange of blood before birth. In 1945, R.D. Owen2 made the remarkable discovery that most twin cattle are born with, and may retain throughout life, a stable mixture – not necessarily a fifty-fifty mixture – of each other’s red cells; it followed, then, that the twin cattle must have exchanged red-cell precursors and not merely red cells in their mutual transfusion before birth. This is the first example of the phenomenon we came to call immunological tolerance; the red cells could not have “adapted” themselves to their strange environment, because they were in fact identified as native or foreign by those very antigenie properties which, had an adaptation occurred, must necessarily have been transformed. A few years later R.E. Billingham and I3, with the help of three members of the scientific staff of the Agricultural Research Council, showed that most dizygotic cattle twins would accept skin grafts from each other, and that this mutual tolerance was specific, for skin transplanted from third parties was cast off in the expected fashion.

Some properties of the tolerant state

The main points that emerged from our analysis of the tolerant state were these. In the first place, tolerance must be due to an alteration of the host, not to an antigenic adaptation of the grafted cells, for grafts newly transplanted in adult life have no opportunity to adapt themselves, and the descendants of the cells injected into foetal or newborn animals can be shown by N.A. Mitcbison’s methods to retain their antigenic power10. Once established, the state of tolerance is systemic; if one part of the body will tolerate a foreign graft, so will another; we found no evidence that a tolerated graft builds up a privileged position for itself within its own lymphatic territory. The stimulus that is responsible for instating tolerance is an antigenic stimulus – one which, had it been applied to older animals, would have caused them to become sensitive or immune. A plural stimulus can induce plural tolerance; the donor will usually contain several important antigens that are lacking in the recipient, and long-lasting tolerance must imply tolerance of them all. The state of tolerance is specific in the sense that it will discriminate between one individual and another, for an animal made tolerant of grafts from one individual will not accept grafts from a second individual unrelated to the first; but it will not discriminate between one tissue and another from the same donor.

Tolerance and auto-immunity: 50 years after Burnet.

Martini A1, Burgio GR
Eur J Pediatr. 1999 Oct;158(10):769-75.

Fifty years ago Sir F. Macfarlane Burnet published his first fundamental contribution to the theory of immune tolerance he perfected 10 years later. Since then an impressive amount of new information on the function of the immune system has been gathered. As any original meaningful theory, Burnet’s hypothesis on the development of immune tolerance has undergone extensive modifications to take into account all these new findings. An improved understanding of the mechanisms of tolerance has led to new possibilities for the treatment of auto-immune diseases.

Clonal Selection
http://en.wikipedia.org/wiki/Clonal_selection

Clonal selection theory is a scientific theory in immunology that explains the functions of cells (lymphocytes) of the immune system in response to specific antigens invading the body. The concept was introduced by an Australian doctor Frank Macfarlane Burnet in 1957 in an attempt to explain the formation of a diversity of antibodies during initiation of the immune response. The theory has become a widely accepted model for how the immune system responds to infection and how certain types of B and T lymphocytes are selected for destruction of specific antigens.

The theory states that in a pre-existing group of lymphocytes (specifically B cells), a specific antigen only activates (i.e. selection) its counter-specific cell so that particular cell is induced to multiply (producing its clones) for antibody production. In short the theory is an explanation of the mechanism for the generation of diversity of antibody specificity. The first experimental evidence came in 1958, when Gustav Nossal and Joshua Lederberg showed that one B cell always produces only one antibody. The idea turned out to be the foundation of molecular immunology, especially in adaptive immunity.

The fundamental contribution of Robert A. Good to the discovery of the crucial role of thymus in mammalian immunity

Domenico Ribatti
Immunology. 2006 Nov; 119(3): 291–295.
http://dx.doi.org:/10.1111/j.1365-2567.2006.02484.x

Robert Alan Good was a pioneer in the field of immunodeficiency diseases. He and his colleagues defined the cellular basis and functional consequences of many of the inherited immunodeficiency diseases. His was one of the groups that discovered the pivotal role of the thymus in the immune system development and defined the separate development of the thymus-dependent and bursa-dependent lymphoid cell lineages and their responsibilities in cell-mediated and humoral immunity.  Keywords: bursa of Fabricius, history of medicine, immunology, thymus

Robert Alan Good (May 21, 1922 – June 13, 2003) was an American physician who performed the first successful human bone marrow transplant

Robert A. Good began his intellectual and experimental queries related to the thymus in 1952 at the University of Minnesota, initially with pediatric patients. However, his interest in the plasma cell, antibodies and the immune response began in 1944, while still in Medical School at the University of Minnesota in Minneapolis, with his first publication appearing in 1945.

Idiopathic Acquired Agammaglobulinemia Associated with Thymoma (1953)

  • a markedly deficient ability to produce antibodies and significant deficits of all or most of the cell-mediated immunities
  • in no instance did removal of the thymic tumour restore immunological function or correct the protein deficit

Good syndrome: thymoma with immunodeficiency

  • increased susceptibility to bacterial infections by encapsulated organisms and opportunistic viral and fungal infections
  • immunodeficiencies, leukopenia, lymphopenia and eosinophylopenia
  • severely hypogammaglobulinemic rather than agammaglobulinemic

Good and others found that the patients lacked all of the subsequently described immunoglobulins. These patients were found not to have plasma cells or germinal centers in their hematopoietic and lymphoid tissues. They possessed circulating lymphocytes in normal numbers.

Speculation on the reason for immunological failure following neonatal thymectomy has centered on the thymus as a source of cells or humoral factors essential to normal lymphoid development and immunological maturation.

The bursa of Fabricius and the thymus are ‘central lymphoid organs’ in the chicken, essential to the ontogenetic development of adaptive immunity in that species. Studies by Papermaster and co-workers in Good’s laboratory34,35 indicated that bursectomy in the newly hatched chicks did not completely abolish immunological potential in the adult animal but rather produced a striking quantitative reduction insufficient to eliminate the homograft reaction. The failure of thymectomy in newly hatched chicks to alter the immunological potential of the maturing animal probably only reflected the participation of the bursa of Fabricius in the development of full immunological capacity.

Bursectomized and irradiated birds were completely devoid of germinal centers, plasma cells and the capacity to make antibodies yet they had perfectly normal development of thymocytes and lymphocytes elsewhere in the body that mediated cellular immune reactions. On the other hand, thymectomized and irradiated animals were deficient in lymphocytes that mediated cellular immunity as assessed by skin graft rejection, delayed-type hypersensitivity and graft versus host assays, but they still produced germinal centers, plasma cells and circulating immunoglobulins.

 

Graft vs Host Disease

Graft-versus-host disease (GVHD) is a complication that can occur after a stem cell or bone marrow transplant. With GVHD, the newly transplanted donor cells attack the transplant recipient’s body.

Graft-versus-host disease (GVHD) is a common complication following an allogeneic tissue transplant. It is commonly associated with stem cell or bone marrow transplant but the term also applies to other forms of tissue graft. Immune cells (white blood cells) in the tissue (the graft) recognize the recipient (the host) as “foreign“. The transplanted immune cells then attack the host’s body cells. GVHD can also occur after a blood transfusion if the blood products used have not been irradiated or treated with an approved pathogen reduction system.

http://en.wikipedia.org/wiki/Graft-versus-host_disease

Causes

GVHD may occur after a bone marrow or stem cell transplant in which someone receives bone marrow tissue or cells from a donor. This type of transplant is called allogeneic. The new, transplanted cells regard the recipient’s body as foreign. When this happens, the newly transplanted cells attack the recipient’s body.

GVHD does not occur when someone receives his or her own cells during a transplant. This type of transplant is called autologous.

Before a transplant, tissue and cells from possible donors are checked to see how closely they match the person having the transplant. GVHD is less likely to occur, or symptoms will be milder, when the match is close. The chance of GVHD is:

  • Around 30 – 40% when the donor and recipient are related
  • Around 60 – 80% when the donor and recipient are not related

There are two types of GVHD: acute and chronic. Symptoms in both acute and chronic GVHD range from mild to severe.

  • Acute GVHD usually happens within the first 6 months after a transplant.
  • Chronic GVHD usually starts more than 3 months after a transplant, and can last a lifetime.

Bone marrow transplant

A bone marrow transplant is a procedure to replace damaged or destroyed bone marrow with healthy bone marrow stem cells.  Stem cells are immature cells in the bone marrow that give rise to all of your blood cells.

There are three kinds of bone marrow transplants:

  • Autologous bone marrow transplant: The term auto means self. Stem cells are removed from you before you receive high-dose chemotherapy or radiation treatment. The stem cells are stored in a freezer (cryopreservation). After high-dose chemotherapy or radiation treatments, your stems cells are put back in your body to make (regenerate) normal blood cells. This is called a rescue transplant.
  • Allogeneic bone marrow transplant: The term allo means other. Stem cells are removed from another person, called a donor. Most times, the donor’s genes must at least partly match your genes. Special blood tests are done to see if a donor is a good match for you. A brother or sister is most likely to be a good match. Sometimes parents, children, and other relatives are good matches. Donors who are not related to you may be found through national bone marrow registries.
  • Umbilical cord blood transplant: This is a type of allogeneic transplant. Stem cells are removed from a newborn baby’s umbilical cord right after birth. The stem cells are frozen and stored until they are needed for a transplant. Umbilical cord blood cells are very immature so there is less of a need for matching. But blood counts take much longer to recover.

Before the transplant, chemotherapy, radiation, or both may be given. This may be done in two ways:

  • Ablative (myeloablative) treatment: High-dose chemotherapy, radiation, or both are given to kill any cancer cells. This also kills all healthy bone marrow that remains, and allows new stem cells to grow in the bone marrow.
  • Reduced intensity treatment, also called a mini transplant: Patients receive lower doses of chemotherapy and radiation before a transplant. This allows older patients, and those with other health problems to have a transplant.

Histocompatibility antigen:

  • A histocompatibility antigen blood test looks at proteins called human leukocyte antigens (HLAs). These are found on the surface of almost all cells in the human body. HLAs are found in large amounts on the surface of white blood cells. They help the immune system tell the difference between body tissue and substances that are not from your own body.

http://www.nlm.nih.gov/medlineplus/ency/article/001309.htm

Induction of transplantation tolerance in haploidenical transplantation under reduced intensity conditioning: The role of ex-vivo generated donor CD8+ T cells with central memory phenotype

Eran Ophir, Y Eidelstein, E Bachar-Lustig, D Hagin, N Or-Geva, A Lask, , Y Reisner
Best Practice & Research Clinical Haematology 24 (2011) 393–401
http://dx.doi.org:/10.1016/j.beha.2011.05.007

Haploidentical hematopoietic stem cell transplantation (HSCT) offers the advantage of readily available family member donors for nearly all patients. A ‘megadose’ of purified CD34þ hematopoietic stem cells is used to overcome the host’s residual immunity surviving the myeloablative conditioning, while avoiding severe GVHD. However, the number of CD34+ cells that can be harvested is insufficient for overcoming the large numbers of host T cells remaining after reduced intensity conditioning (RIC). Therefore, combining a ‘megadose’ of CD34+ HSCT with other tolerizing cells could potentially support and promote successful engraftment of haploidentical purified stem cell transplantation under a safer RIC. One approach to address this challenge
could be afforded by using Donor CD8 T cells directed against 3rd-party stimulators, bearing an ex-vivo induced central memory phenotype (Tcm). These Tcm cells, depleted of GVH reactivity, were shown to be highly
efficient in overcoming host T cells mediated rejection and in promoting
fully mismatched bone-marrow (BM) engraftment, in HSCT murine models.
This is likely due to the marked lymph node homing of the Tcm, their strong proliferative capacity and prolonged persistence in BM transplant recipients. Thus, combining anti 3rd-party Tcm cell therapy with a ‘megadose’ of purified CD34+ stem cells, could offer a safer RIC protocol for attaining hematopoietic chimerism in patients with hematological diseases and as a platform for organ transplantation or cell therapy in cancer patients.

Induction of tolerance in organ recipients by hematopoietic stem cell transplantation

Eran Ophir, Yair Reisner
International Immunopharmacology 9 (2009) 694–700
http://dx.doi.org:/10.1016/j.intimp.2008.12.009

The use of hematopoietic stem cell transplantation (HSCT) for the establishment of mixed chimerism represents a viable and attractive approach for generating tolerance in transplantation biology, as it generally leads to durable immune tolerance, enabling the subsequent engraftment of organ transplants without the need for a deleterious continuous immunosuppressive therapy. However, in order to apply HSCT to patients in a manner that enables long term survival, transplant-related mortality must be minimized by eliminating the risk for graft-versus-host-disease (GVHD) and by reducing the toxicity of the conditioning protocol. T-cell depleted bone marrow transplants (TDBMT) have been shown to adequately eliminate GVHD. However, even in leukemia patients undergoing supralethal conditioning, mismatched TDBMT are vigorously rejected. This barrier can be overcome through the modulatory activity of CD34 cells, which are endowed with veto activity, by the use of megadose stem cell transplants. In mice, megadoses of Sca+lin– hematopoietic stem cells can induce mixed chimerism following sub-lethal conditioning. Nevertheless, the number of human CD34 cells that can be harvested is not likely to be sufficient to overcome rejection under reduced intensity conditioning (RIC), which might be acceptable in recipients of organ transplantation. To address this challenge, we investigated a novel source of veto cells, namely anti 3rd-party cytotoxic T cells (CTLs) which are depleted of GVH reactivity, combined with megadoses of purified stem cells and a RIC protocol. This approach might provide a safer modality for the induction of durable chimerism.

Intrinsic unresponsiveness of Mertk/B cells to chronic graft-versus-host disease is associated with unmodulated CD1d expression

Wen-Hai Shao, Y Zhen, FD Finkelman, RA Eisenberg, PL Cohen
Journal of Autoimmunity 39 (2012) 412e419
http://dx.doi.org/10.1016/j.jaut.2012.07.001

Activation and migration of marginal zone B (MZB) cells into follicular (FO) regions of the spleen has been proposed as one of the mechanisms that regulate the development of autoreactive B cells. The mer receptor tyrosine kinase (Mertk) mediates apoptotic cell clearance and regulates activation and cytokine secretion. In the well-studied class II chronic GVH model of bm12 cells into B6 hosts, we observed that Mertk deficient B6 mice did not generate autoantibodies in response to this allogeneic stimulus. We posited that Mertk is important in MHC-II-mediated B cell signaling. In the present study, we show that B cells from Mertk-/- mice but not WT B6 mice exhibited decreased calcium mobilization and tyrosine phosphorylation when stimulated by MHC-II cross-linking. The finding that Mertk was important for class II signaling in B cells was further supported by the preponderance of a-allotype autoantibodies in cGVH in RAG-KO mice reconstituted with a mixture of bone marrow from Mertk-/-mice (b-allotype) and C20 mice (a-allotype). MZB cells from Mertk-/-  mice were unable to down regulate surface CD1d expression and subsequent inclusion in the MZ, associated with significantly lower germinal center responses compared to MZB cells from WT. Moreover, Mertk-/- mice treated with an anti-CD1d down regulating antibody responded significantly to bm12 cells, while no response was observed in Mertk-/- mice treated with control antibodies. Taken together, these findings extend the role of Mertk to include CD1d down regulation on MZB cells, a potential mechanism limiting B cell activation in cGVH.

Galectin-9 ameliorates acute GVH disease through the induction of T-cell apoptosis

Kazuki Sakai, Eri Kawata, Eishi Ashihara, Yoko Nakagawa, et al.
Eur. J. Immunol. 2011. 41: 67–75 http://dx.doi.org:/10.1002/eji.200939931

Galectins comprise a family of animal lectins that differ in their affinity for β-galactosides. Galectin-9 (Gal-9) is a tandem-repeat-type galectin that was recently shown to function as a ligand for T-cell immunoglobin domain and mucin domain-3 (Tim-3) expressed on terminally differentiated CD41 Th1 cells. Gal-9 modulates immune reactions, including the induction of apoptosis in Th1 cells. In this study, we investigated the effects of Gal-9 in murine models of acute GVH disease (aGVHD). First, we demonstrated that recombinant human Gal-9 inhibit MLR in a dose-dependent manner, involving both Ca21 influx and apoptosis in T cells. Next, we revealed that recombinant human Gal-9 significantly inhibit the progression of aGVHD in murine BM transplantation models. In conclusion, Gal-9 ameliorates aGVHD, possibly by inducing T-cell apoptosis, suggesting that gal-9 may be an attractive candidate for the treatment of aGVHD.

 

GVHD Prevention: An Ounce Is Better Than a Pound

Pavan Reddy, Gerard Socie, Corey Cutler, Daniel Weisdorf
Biol Blood Marrow Transplant 18:S17-S26, 2012  http://dx.doi.org:/10.1016/j.bbmt.2011.10.034

The pathophysiology of acute graft-versus-host disease (aGVHD) is known to involve donor T cells responding to host histoincompatible allo-antigens presented by the host antigen presenting cells (APCs) and the subsequent induction of pro-inflammatory cytokines and cellular effectors that cause target organ damage. In a more general sense, GVHD can be considered as an immune response against foreign antigens that has gone awry. Similar to all immune responses, GVHD, can be understood as a process that consists of (A) triggers, (B) sensors, (C) mediators, and (D) effectors of GVHD.

Like all immune responses, certain triggers are critical for induction of acute graft-versus-host disease (aGVHD). These include: (1) Disparities between histocompatibility antigens: antigen disparity can be at the level of major histocompatibility complex (MHC), that is, MHC mismatched or at the level of minor histocompatibility antigens (miHA), that is, MHC matched but miHA mismatched. The severity of aGVHD is directly related to the degree of M HC mismatch. In bone marrow transplants (BMT) that are MHC matched but miHA disparate, donor T cells still recognize MHC-peptide derived from the products of recipient polymorphic genes, the miHAs.

Damage induced by conditioning regimens and underlying diseases: under most circumstances, the initiation of an adaptive immune response is triggered by the innate immune response. The innate immune system is triggered by certain exogenous and endogenous molecules. This is likely the case in the induction of aGVHD. Pattern recognition receptors such as Toll-like receptors (TLR), nucleotide-binding oligomerization domain containing 2 (NOD2) play an essential role in innate immunity and in initiating the cellular signaling pathways that activate cytokine secretion, such as NF-kB. Some of their ligands, such as lipopolysaccharide, CpG, and MDP2, which is recognized by TLR-4, TLR-9, and NOD2, respectively, are released by the preparative regimens and contribute to the induction and enhancement of allo-T cell responses. In this way, the conditioning regimens amplify the secretion of proinflammatory cytokines like interleukin (IL)-1, tumor necrosis factor (TNF)-α,  IL-6, and other interferon family members in a process described as a ‘‘cytokine storm.’’

The triggers that initiate an immune response have to be sensed and presented. APCs might be considered the sensors for aGVHD. The APCs sense the DAMPs, present the MHC disparate or miHA disparate protein, and provide the critical secondary (costimulatory) and tertiary (cytokine) signals for activation of the alloreactive T cells, the mediators of aGVHD. APCs sense allo-disparity through MHC and peptide complexes. Dendritic cells (DCs) are the most potent APCs and the primary sensors of allo-disparity.

APCs provide the critical costimulation signals for turning on the aGVHD process. The interaction between the MHC/allopeptide complex on APCs and the T cell receptor of donor T cells along with the signal via T cell costimulatory molecules and their ligands on APCs is required to achieve T cell activation, proliferation, differentiation, and survival and the in vivo blockade of positive costimulatory molecules (such as CD28, ICOS, CD40, CD30, etc.), or inhibitory signals (such as PD-1 and CTLA-4) mitigate or exacerbate aGVHD, respectively.

Evidence suggests that alloreactive donor T cells consist of several subsets with different stimuli responsiveness, activation thresholds, and effector functions.

The allo-antigen composition of the host determines which donor T cells subsets differentiate and proliferate. As mentioned previously, in the majority of HLA-matched HCT, aGVHD may be induced by either or both CD41 and CD81 subsets responses to miHAs. The repertoire and immunodominance of the GVHD-associated peptides presented by MHC class I and class II molecules has not been defined. Donor naive CD62L1 T cells are the primary alloreactive T cells that drive the GVHD reaction while the donor effector memory CD62L2 T cells do not. Interestingly, donor regulatory T cells (Tregs) expressing CD62L are also critical to the regulation of GVHD. We now know that it is possible to modulate the alloreactivity of na€ıve T cells by inducing anergy with costimulation blockade, deletion via cytokine modulation, or mixed chimerism. Donor effector memory T cells that are nonalloreactive do not induce GVHD, yet are able to transfer functional memory. In contrast, memory T cells that are alloreactive can cause severe GVHD.

The effector phase that leads to GVHD target organ damage is a complex cascade that involves cytolytic cellular effectors such as CD8 cytotoxic T lymphocytes (CTLs), CD4 T cells, natural killer cells, and inflammatory molecules such as IL-1β, TNF-α, IFN-ϒ, IL-6, and reactive oxygen species. The cellular effectors require cell-cell contact to kill the cells of the target tissues via activation of perforin granzyme, Fas-FasL (CD95-CD95L), or TNFR TRAIL pathways. Other CTLs killing mechanisms such as TWEAK, and LTβ/LIGHT pathways have also been implicated in GVHD. It is important to note that
CTL pathways are essential for GVL effects as well.

All of the above aspects of the biology of aGVHD have been summarized in the mold of a normal immune response. Although this allows for accessing the biology of GVHD, it is important to note that GVHD is a complicated systemic process with as yet still many unknowns and is not a simplified, linear, or cyclical process.

Kinetics of CD4+ and CD8+ T-cell subsets in graft-versus-host reaction (GVHR) in ginbuna crucian carp Carassius auratus langsdorfii

Yasuhiro Shibasakia, H Todaa, Isao kobayashib, T Moritomoa, T Nakanishia
Developmental and Comparative Immunology 34 (2010) 1075–1081
http://dx.doi.org:/10.1016/j.dci.2010.05.009

We have previously demonstrated the presence of graft-versus-host reaction (GVHR) in fish employing a model system of clonal triploid ginbuna and tetraploid ginbuna-goldfish hybrids. To elucidate the role of CD8+ T cells in the induction of GVHR, we investigate the kinetics of CD4+ and CD8+ T-cell subsets in GVHR along with the pathological changes associated with GVH disease (GVHD) in ginbuna. GVHR was not induced with a leukocyte fraction lacking CD8+ T cells separated by magnetic cell sorting. Ploidy and immunofluorescence analysis revealed that CD4+ and CD8+  T cells from sensitized donors greatly

increased in the host trunk kidney, constituting more than 80% of total cells 1–2 weeks after donor cell injection, while those from non-sensitized donors constituted less than 50% of cells present. The increase of CD4+ T cells was greater and more rapid than that of CD8+ T cells. The number of donor CD4+ and CD8+ T cells was highest in trunk kidney followed by spleen. Increases in donor CD4+ and CD8+ T cells were also found in liver and PBL, although the percentages were not as high. Pathologic changes similar to those in human and murine acute GVHD were observed in the lymphoid organs as well as target organs such as skin, liver and intestine, including the destruction of cells and tissues and massive leukocyte infiltration. The pathologic changes became more severe with the increase of CD8+ T cells. These results suggest that donor-derived CD8+ T cells play essential roles for the induction of acute GVHR/D in teleosts as in mammals.

Fludarabine and Exposure-Targeted Busulfan Compares Favorably with Busulfan/Cyclophosphamide-Based Regimens in Pediatric Hematopoietic
Cell Transplantation: Maintaining Efficacy with Less Toxicity

I.H. Bartelink, E.M.L. van Reij, C.E. Gerhardt, E.M. van Maarseveen, et al
Biol Blood Marrow Transplant 20 (2014) 345e353
http://dx.doi.org/10.1016/j.bbmt.2013.11.027

Busulfan (Bu) is used as a myeloablative agent in conditioning regimens before allogeneic hematopoietic cell transplantation (allo-HCT). In line with strategies explored in adults, patient outcomes may be optimized by replacing cyclophosphamide (Cy) with or without melphalan (Mel) with fludarabine (Flu). We compared outcomes in 2 consecutive cohorts of HCT recipients with a nonmalignant HCT indication, a myeloid malignancy, or a lymphoid malignancy with a contraindication for total body irradiation (TBI). Between 2009 and 2012, 64 children received Flu + Bu at a target dose of 80-95 mg-h/L, and between 2005 and 2008, 50 children received Bu targeted to 74-80 mg-h/L þ Cy. In the latter group, Mel was added for patients with myeloid malignancy (n = 12). Possible confounding effects of calendar time were studied in 69 patients receiving a myeloablative dose of TBI between 2005 and 2012. Estimated 2-year survival and event-free survival were 82% and 78%, respectively, in the FluBu arm and 78% and 72%, respectively, in the BuCy (Mel) arm (P,  not significant). Compared with the BuCy (Mel) arm, less toxicity was noted in the FluBu arm, with lower rates of acute (noninfectious) lung injury (16% versus 36%; P < .007), veno-occlusive disease (3% versus 28%; P < .003), chronic graft-versus-host disease (9% versus 26%; P < .047), adenovirus infection (3% versus 32%; P < .001), and human herpesvirus 6 infection reactivation (21% versus 44%; P < .005). Furthermore, the median duration of neutropenia was shorter in the FluBu arm (11 days versus 22 days; P < .001), and the patients in this arm required fewer transfusions. Our data indicate that Flu (160 mg/m2) with targeted myeloablative Bu (90 mg-h/L) is less toxic than and equally effective
as BuCy (Mel) in patients with similar indications for allo-HCT.

Fibrotic and Sclerotic Manifestations of Chronic Graft-versus-Host Disease

Carrie L. Kitko, Eric S. White, Kristin Baird
Biol Blood Marrow Transplant 18:S46-S52, 2012
http://dx.doi.org:/10.1016/j.bbmt.2011.10.021

Chronic graft-versus-host disease (cGVHD) is a common cause of morbidity
and mortality following allogeneic stem cell transplantation (HCT), with approximately 50% to 60% of long-term HCT survivors developing one or more manifestations of the disorder. Although acute GVHD is typically limited to skin, liver, and gastrointestinal involvement, virtually every organ is at risk for the development of cGVHD. Although the pathophysiology of cGVHD remains poorly understood, some of the most severe organ manifestations are linked by end-organ fibrosis. In particular, fibrotic cutaneous and bronchiolar changes, resulting in scleroderma-like changes and bronchiolitis obliterans syndrome (BOS), respectively, are two of the most devastating outcomes for these patients. Both sclerotic GVHD (ScGVHD) and BOS have been reported in 5% to 15% of patients with cGVHD.

Many of the manifestations of cGVHD share clinical characteristics seen in nontransplant conditions, including systemic sclerosis or pulmonary fibrosis. Thus, understanding the pathophysiology underlying these related conditions may help identify potential mechanisms and ultimately new therapeutic options for patients with cGVHD.

Tyrosine kinase inhibitors (TKIs) have been shown to inhibit two different profibrotic pathways (transforming growth factor β [TGF-β] and platelet-derived growth factor [PDGF]) in various mouse models of fibrotic disease and offer a possible novel treatment approach for cGVHD patients suffering from severe sclerosis. Likewise, overexpression of TNF-α has been shown to induce fibrogenesis in experimental hepatocellular disease and has been linked with human scleroderma-associated interstitial pulmonary fibrosis and profibrotic responses in human osteoarthritic hip joint fibroblasts. The use of TNF antagonists has been examined in some clinical situations associated with fibrosis, suggesting they may also be of some benefit to patients with cGVHD; however, this must first be prospectively tested.

Table. Proposed Modifications to NIH BOS Clinical Definition

  • Absence of infection (no change)
  • Another cGVHD manifestation in another organ (no change)
  • FEV1 <75% predicted (no change) or >10% decline from pre-HCT value (modification)
  • Signs of Obstruction
  • FEV1/SVC ratio <0.7 (modification), or
  • RV >120% predicted (no change), or
  • RV/TLC >120% (modification), and
  • HRCT with evidence of air trapping (no change)

SVC indicates slow vital capacity; RV, residual volume; TLC, total lung capacity; HRCT, high-resolution computed tomography

Figure (not shown)
Effect of etanercept on survival in post-HCT patients with subacute lung injury. (A) Overall 5-year survival by pulmonary function testing defect. Patients with an obstructive defect (solid line) had a 5-year survival of 67% compared with 44% in those with a restrictive lung defect (dashed line) (P 5 .19). (B) Overall 5-year survival by response to therapy. Patients who responded to etanercept therapy (solid line) had a 5-year survival of 90% compared with 55% in patients who failed to respond (dashed line) (P 5.07). (Figures reprinted with permission, Biol Blood and Marrow Trans).

Extensive, sclerotic skin changes with superficial or deep subcutaneous or fascial involvement are seen in approximately 4% to 13% of patients with cGVHD and can be a life-threatening manifestation. ScGVHD of the skin includes several cutaneous presentations characterized by inflammation and progressive fibrosis of the dermis and subcutaneous tissues. These changes can resemble morphea, systemic sclerosis, or eosinophilic fasciitis and may or may not occur in the setting of concurrent overlying epidermal GVHD. When severe, ScGVHD can result in contractures, severe wasting, and chest wall restriction.

Development of clinical trials for patients with cGVHD is difficult because of the complexity and heterogeneity of disease, variable approaches to treatment, and the lack of standardized assessments of disease. In particular, the study of ScGVHD lacks universally accepted measures of disease burden and response. Investigators have used several measures to assess ScGVHD involvement including body surface area, magnetic resonance imaging, ultrasound, and range-of-motion measurements. Additionally, investigators have tried to apply the Rodnan score, the standardmeasure for skin involvement in scleroderma. Thus far, none of these measures has proven
to be completely reliable in the setting of ScGVHD, and it is likely that multiple measures will need to be integrated into the assessment of ScGVHD.

Imatinib mesylate (Gleevec in the US; Glivec in Europe, Australia, and Latin America, marketed by Novartis) is a TKI that has biological activity against both PDGF and TGF-β signaling pathways. Both cytokines have been implicated in the pathogenesis of several fibrosing diseases, including hepatic, renal, and lung, as well as in scleroderma, a disease that closely resembles ScGVHD. In addition, stimulatory antibodies specific for the PDGF receptor (PDGFR) were identified in a series of 39 patients with extensive cGVHD with higher levels detected in those patients with skin involvement. Similar stimulatory antibodies targeting PDGFR have been reported in patients with scleroderma, suggesting an important therapeutic target for these fibrosing conditions. Imatinib mesylate has particularly potent activity against PDGF and is FDA approved in the United States for the treatment of several disorders associated with aberrant PDGFR signaling. The side effect profile of the drug is well established in non-HCT patients, which is helpful in the setting of a therapy for allogenic HCT patients, many of whom have multiorgan system symptoms and possible dysfunction and who will require ongoing immunosuppressive therapy.

Through the efforts of the Chronic GVHD Consortium, led by Stephanie Lee at the Fred Hutchinson Cancer Research Center, there is a multicenter, ongoing prospective evaluation of the NIH diagnostic and assessment tools. This effort has already resulted in several publications that have further refined essential criteria for cGVHD evaluation, including organ-specific manifestations such as BOS and ScGVHD. Currently, the Consortium is conducting a multicenter prospective clinical trial of fluticasone propionate, azithromycin, and montelukast for the treatment of BOS (ClinicalTrials.gov NCT01307462); a separate trial of imatinib versus rituximab for treatment of ScGVHD is also enrolling subjects (ClinicalTrials.gov NCT01309997).

Although cGVHD remains a significant problem for many long-term survivors of HCT, critical advances in cGVHD research and treatment can be achieved by cooperative group efforts such as those put forth by the Chronic GVHD Consortium and the Clinical Trials Network.

Hematopoietic stem cell transplantation (HSCT): An approach to autoimmunity

Carmen Alaez, Mariana Loyola, Andrea Murguıa, Hilario Flores, et al.
Autoimmunity Reviews 5 (2006) 167– 179
http://dx.doi.org:/10.1016/j.autrev.2005.06.003

HSCT provides the opportunity to replace a damaged tissue. It is the most important treatment for high risk hematologic malignant and nonmalignant disorders. An important challenge in the identification of matched donors/patients is the HLA diversity. The Mexican Bone Marrow Registry (DONORMO) has nowadays N5000 donors. The prevalent alleles are Amerindian, Mediterranean (Semitic and Spanish genes) and African. In theory, it is possible to find 11% of 6/6 A–B–DR low resolution matches for 70% of patients with Mexican ancestry. We contributed with 39 unrelated, cord blood and autologous HSCT for patients with malignant, genetic and autoimmune disorders. Overall disease survival was 50% (2–7 years) depending on the initial diagnosis, conditioning, disease evolution or other factors. Clinical studies using autologous and unrelated HSC are performed on patients with refractory autoimmune diseases producing mixed results: mainly, T1D, RA, MS, SLE. Improvement has been observed in skin damage and quality of life in SLE and systemic sclerosis. Disease stabilization in 2/3 of MS patients. However, in RA and T1D, initial benefits have been followed by eventual relapse. With growing clinical experience and protocol improvement, treatment-related mortality is decreasing. Proof efficacy will be achieved by comparing HSCT with standard therapy in autoimmunity.

Monoclonal Antibody-Mediated Targeting of CD123, IL-3 Receptor α Chain, Eliminates Human Acute Myeloid Leukemic Stem Cells

Liqing Jin, Erwin M. Lee, Hayley S. Ramshaw, Samantha J. Busfield, et al.
Cell: Stem Cell 5, 31–42, July 2, 2009
http://dx.doi.org:/10.1016/j.stem.2009.04.018

Leukemia stem cells (LSCs) initiate and sustain the acute myeloid leukemia (AML) clonal hierarchy and possess biological properties rendering them resistant to conventional chemotherapy. The poor survival of AML patients raises expectations that LSC-targeted therapies might achieve durable remissions. We report that an anti-interleukin-3 (IL-3) receptor α chain (CD123)-neutralizing antibody (7G3) targeted AML-LSCs, impairing homing
to bone marrow (BM) and activating innate immunity of nonobese diabetic/ severe-combined immunodeficient (NOD/SCID) mice. 7G3 treatment profoundly reduced AML-LSC engraftment and improved mouse survival.
Mice with preestablished disease showed reduced AML burden in the BM
and periphery and impaired secondary transplantation upon treatment, establishing that AMLLSCs were directly targeted. 7G3 inhibited IL-3-mediated intracellular signaling of isolated AML CD34+ CD38[1] cells in vitro and reduced their survival. These results provide clear validation for therapeutic monoclonal antibody (mAb) targeting of AML-LSCs and for translation of in vivo preclinical research findings toward a clinical application.

Many Days at Home during Neutropenia after Allogeneic Hematopoietic Stem Cell Transplantation Correlates with Low Incidence of Acute Graft-versus-Host Disease

Olle Ringdén, Mats Remberger, Katarina Holmberg, Charlotta Edeskog, et al.
Biol Blood Marrow Transplant 19 (2013) 314e320
http://dx.doi.org/10.1016/j.bbmt.2012.10.011

Patients are isolated in the hospital during the neutropenic phase after allogeneic hematopoietic stem cell transplantation. We challenged this by allowing patients to be treated at home. A nurse from the unit visited and checked the patient. One hundred forty-six patients treated at home were compared with matched hospital control subjects. Oral intake was intensified from September 2006 and improved (P < .002). We compared 4 groups: home care and control subjects before and after September 2006. The cumulative incidence of acute graft-versus-host disease (GVHD) of grades II to IV was 15% in the “old” home care group, which was significantly lower than that of 32% to 44% in the other groups (P <.03). Transplantation-related mortality, chronic GVHD, and relapse were similar in the groups. The “new” home care patients spent fewer days at home (P < .002). In multivariate analysis, GVHD of grades 0 to I was associated with home care (hazard ratio [HR], 2.46; P <.02) and with days spent at home (HR, .92; P < .005) but not with oral nutrition (HR, .98; P = .13). Five year survival was 61% in the home care group as compared with 49% in the control subjects (P < .07). Home care is safe. Home care and many days spent at home were correlated with a low risk of acute GVHD.

Impact on Outcomes of Human Leukocyte Antigen Matching by Allele-Level Typing in Adults with Acute Myeloid Leukemia Undergoing Umbilical Cord Blood Transplantation

Jaime Sanz, Francisco J. Jaramillo, Dolores Planelles, Pau Montesinos, et al.
Biol Blood Marrow Transplant 20 (2014) 106e110
http://dx.doi.org/10.1016/j.bbmt.2013.10.016

This retrospective study analyzed the impact of directional donor-recipient human leukocyte antigen (HLA) disparity using allele-level typing at HLA-A, -B, -C, and -DRB1 in 79 adults with acute myeloid leukemia (AML) who received single-unit umbilical cord blood (UCB) transplant at a single institution. With extended high resolution HLA typing, the donor-recipient compatibility ranged from 2/8 to 8/8. HLA disparity showed no negative impact on nonrelapse mortality (NRM), graft-versus-host (GVH) disease or engraftment. Considering disparities in the GVH direction, the 5-year cumulative incidence of relapse was 44% and 22% for patients receiving an UCB unit matched > 6/8 and < 6/8, respectively (P <.04). In multivariable analysis, a higher HLA disparity in the GVH direction using extended high-resolution typing (Risk ratio [RR] 2.8; 95% confidence interval [CI], 1.5 to 5.1; P ¼.0009) and first complete remission at time of transplantation (RR 2.1; 95% CI, 1.2 to 3.8; P < .01) were the only variables significantly associated with an improved disease-free survival. In conclusion, we found that in adults with AML undergoing single-unit UCBT, an increased number of HLA disparities at allele-level typing improved disease-free survival by decreasing the relapse rate without a negative effect on NRM.

HLA mismatch direction in cord blood transplantation: impact on outcome and implications for cord blood unit selection
Cladd E. Stevens, C Carrier, C Carpenter, D Sung, and A Scaradavou

Blood. 2011; 118(14):3969-3978
http://dx.doi.org:/10.1182/blood-2010-11-317271

Donor-recipient human leukocyte antigen mismatch level affects the outcome of unrelated cord blood (CB) transplantation. To identify possible “permissive” mismatches, we examined the relationship between  direction of human leukocyte antigen mismatch (“vector”) and transplantation outcomes in 1202 recipients of single CB units from the New York Blood Center National Cord Blood Program treated in United States Centers from 1993-2006. Altogether, 98 donor/patient pairs had only unidirectional mismatches: 58 in the graft-versus-host (GVH) direction only (GVH-O) and 40 in the host-versus-graft or rejection direction only (R-O). Engraftment was faster in patients with GVH-O mismatches compared with those with 1 bidirectional mismatch (hazard ratio [HR] = 1.6, P < .003). In addition, patients with hematologic malignancies given GVH-O grafts had lower transplantation-related mortality (HR = 0.5, P < .062), overall mortality (HR = 0.5, P < .019), and treatment failure (HR = 0.5, P < .016), resulting in outcomes similar to those of matched CB grafts. In contrast, R-O mismatches had slower engraftment, higher graft failure, and higher relapse rates (HR = 2.4, P < .010). Based on our findings, CB search algorithms should be modified to identify unidirectional mismatches. We recommend that transplant centers give priority to GVH-O-mismatched units over other mismatches and avoid selecting R-O mismatches, if possible.

Mutation of the NPM1 gene contributes to the development of donor cell–derived acute myeloid leukemia after unrelated cord blood transplantation
for acute lymphoblastic leukemia

G Rodríguez-Macías, C Martínez-Laperche, J Gayoso, V Noriega, .., Ismael Buño
Human Pathology (2013) 44, 1696–1699
http://dx.doi.org/10.1016/j.humpath.2013.01.001

Donor cell leukemia (DCL) is a rare but severe complication after allogeneic stem cell transplantation. Its true incidence is unknown because of a lack of correct recognition and reporting, although improvements in molecular analysis of donor-host chimerism are contributing to a better diagnosis of this complication. The mechanisms of leukemogenesis are unclear, and multiple factors can contribute to the development of DCL. In recent years, cord blood has emerged as an alternative source of hematopoietic progenitor cells, and at least 12 cases of DCL have been reported after unrelated cord blood transplantation. We report a new case of DCL after unrelated cord blood transplantation in a 44-year-old woman diagnosed as having acute lymphoblastic leukemia with t(1;19) that developed acute myeloid leukemia with normal karyotype and nucleophosmin (NPM1) mutation in donor cells. To our knowledge, this is the first report of NPM1 mutation contributing to DCL development.

Graft-versus-leukemia in the bone marrow
Blood, 23 JAN 2014; 123(4)
http://imagebank.hematology.org.

63-year-old female with relapsed acute myeloid leukemia (AML) after allogeneic stem cell transplantation reached CR2 after re-induction therapy followed by consolidation with donor lymphocyte infusions: 3 x 107/kg and 3 x 108/kg after 1 and 2.5 months, respectively. No signs of graft-versus-host disease were observed at this time. At 5 months follow-up, her blood count deteriorated: hemoglobin: 6.9 mmol/L, thrombocytes: 58 x 109/L and leukocytes: 1.37 x 109/L. Bone marrow aspirate was not evaluable. Bone marrow trephine biopsy showed relapse AML with hypercellularity in the H&E staining (340 objective lens, panel A) and 20% CD341 blast cells without any signs of maturation (panel B). Also, a high number of CD3 positive T cells (panel C) was noted, intermingling with the CD34 positive blasts, both staining positively with CD43 (panel D). Only supportive care was given. However, normalization of the blood count was observed in the following months and she developed graft-versus-host disease of the lung, which was treated with ciclosporin and prednisone. A bone marrow aspirate performed 3 months after relapse showed a third remission with 0.8% myeloid blasts. In retrospect, one could therefore consider the picture of the bone marrow trephine biopsy at the second relapse as graft-versus-leukemia in the bone marrow.

GVL- panel A

GVL- panel A

GVL - panel B

GVL – panel B

GVL - panel C

GVL – panel C

GVL - panel D

Long-Term Outcomes of Alemtuzumab-Based Reduced-Intensity Conditioned Hematopoietic Stem Cell Transplantation for Myelodysplastic Syndrome and Acute Myelogenous Leukemia Secondary to Myelodysplastic Syndrome

Victoria T. Potter, Pramila Krishnamurthy, Linda D. Barber, ZiYi Lim, et al.
Biol Blood Marrow Transplant 20 (2014) 111e117
http://dx.doi.org/10.1016/j.bbmt.2013.10.021

Allogeneic hematopoietic stem cell transplantation (HSCT) with reduced-intensity conditioning (RIC) offers a potential cure for patients with myelodysplastic syndrome (MDS) who are ineligible for standard-intensity regimens. Previously published data from our institution suggest excellent outcomes at 1 yr using a uniform fludarabine, busulfan, and alemtuzumab-based regimen. Here we report long-term follow-up of 192 patients with MDS and acute myelogenous leukemia (AML) secondary to MDS (MDS-AML) transplanted with this protocol, using sibling (n = 45) or matched unrelated (n = 147) donors. The median age of the cohort was 57 yr (range, 21 to 72 yr), and median follow-up was 4.5 yr (range, 0.1 to 10.6 yr). The 5-yr overall survival (OS), event-free survival, and nonrelapse mortality were 44%, 33%, and 26% respectively. The incidence of de novo chronic graft-versus-host disease (GVHD) was low at 19%, illustrating the efficacy of alemtuzumab for GVHD prophylaxis. Conversely, the 5-yr relapse rate was 51%. For younger patients (age <50 yr), the 5-yr OS and relapse rates were 58% and 39%, respectively. On multivariate analysis, advanced age predicted significantly worse outcomes, with patients age >60 yr having a 5-yr OS of 15% and relapse rate of 66%. Patients receiving preemptive donor lymphocyte infusions had an impressive 5-yr OS of 67%, suggesting that this protocol may lend itself to the incorporation of immunotherapeutic strategies. Overall, these data demonstrate good 5-yr OS for patients with MDS and MDS-AML undergoing alemtuzumab-based RIC-HSCT. The low rate of chronic GVHD is encouraging, and comparative studies with other RIC protocols are warranted.

Natural killer cell activity influences outcome after T cell depleted stem cell transplantation from matched unrelated and haploidentical donors

Peter Lang, Matthias Pfeiffer,  Heiko-Manuel Teltschik, Patrick Schlegel, et al.
Best Practice & Research Clinical Haematology 24 (2011) 403–411
http://dx.doi.org:/10.1016/j.beha.2011.04.009

Lytic activity and recovery of natural killer (NK) cells was monitored in pediatric patients with leukemias (ALL, AML, CML, JMML) and myelodysplastic syndromes after transplantation of T cell depleted stem cells from matched unrelated (n = 18) and mismatched related (haploidentical, n = 29) donors. CD34+ selection with magnetic microbeads resulted in 8 x 103/kg residual T cells. No post-transplant immune suppression was given. NK cells recovered rapidly after transplantation (300 CD56+/mL at day 30, median), whereas T cell recovery was delayed (median: 12 CD3+/mL at day 90). NK activity was measured as specific lysis of K 562 targets several times (mean: 3 assays per patient). Four temporal patterns of lytic activity could be differentiated: consistently low, consistently high, decreasing and increasing activity. Patients with consistently high or increasing activity had significantly lower relapse probability than patients with consistently low or decreasing levels (0.18 vs 0.73 at 2 years, p < 0.05). The subgroup of patients with ALL showed similar results (0.75 vs 0.14 at 2 years, p < 0.05). Speed of T cell recovery had no influence. These data suggest that both achieving and maintaining a high level of NK activity may contribute to prevent relapse. Since NK activity could be markedly increased by in vitro stimulation with Interleukin 2 (IL-2), in vivo administration should be considered.

Graft-versus-host disease: Pathogenesis and clinical manifestations of graft-versus-host disease

Sharon R. Hymes, Amin M. Alousi,  and Edward W. Cowen
J Am Acad Dermatol  2012; 66: 515.e1-18.

  • Graft-versus-host disease is the primary cause of morbidity and nonerelapse related mortality in patients who undergo allogeneic hematopoietic cell transplantation.
  • Acute graft-versus-host disease manifests as a skin exanthem, liver dysfunction, and gastrointestinal involvement.
  • Chronic graft-versus-host disease of the skin is remarkably variable in its clinical presentation.
  • Chronic graft-versus-host disease is a multisystem disorder that may affect nearly any organ; the most common sites are the skin, oral mucosa, and eyes.

Key points

  • Allogeneic transplantation is in widespread use for hematologic malignancies, but is also increasingly used for marrow failure syndromes, immunodeficiencies, and other life-threatening conditions
  • Graft-versus-host disease is the primary cause of morbidity and nonerelapse related mortality after allogeneic hematopoietic cell transplantation
  • Minimizing graft-versus-host disease without losing the graft-versus-tumor effect is an area of active research
  • The skin is the most common organ affected in patients with graft-versus-host disease

Outcomes of Thalassemia Patients Undergoing Hematopoietic Stem Cell Transplantation by Using a Standard Myeloablative versus a Novel Reduced-Toxicity Conditioning Regimen According to a New Risk Stratification

Usanarat Anurathapan, S Pakakasama, P Mekjaruskul, N Sirachainan, et al.
Biol Blood Marrow Transplant 20 (2014) 2056e2075
http://dx.doi.org/10.1016/j.bbmt.2014.07.016

Improving outcomes among class 3 thalassemia patients receiving allogeneic hematopoietic stem cell transplantations (HSCT) remains a challenge. Before HSCT, patients who were > 7 years old and had a liver size > 5 cm constitute what the Center for International Blood and Marrow Transplant Research defined as a very high risk subset of a conventional high-risk class 3 group (here referred to as class 3 HR). We performed HSCT in 98 patients with related and unrelated donor stem cells. Seventy-six of the patients with age < 10 years received the more conventional myeloablative conditioning (MAC) regimen (cyclophos-phamide, busulfan,  + fludarabine); the remaining 22 patients with age > 10 years and hepatomegaly (class 3 HR), and in several instances additional comorbidity problems, underwent HSCT with a novel reduced-toxicity conditioning (RTC) regimen (fludarabine and busulfan). We then compared the outcomes between these 2 groups (MAC versus RTC). Event-free survival (86% versus 90%) and overall survival (95% versus 90%) were not significantly different between the respective groups; however, there was a higher incidence of serious treatment-related complications in the MAC group, and although we experienced 6 graft failures in the MAC group (8%), there were none in the RTC group. Based on these results, we suggest that (1) class 3HRthalassemia patients can safely receive HSCT with our novel RTC regimen and achieve the same excellent outcome as low/standard-risk thalassemia patients who received the standard MAC regimen, and further, (2) that this novel RTC approach should be tested in the low/standard-risk patient population.

Pharmacological Immunosuppression Reduces But Does Not Eliminate the Need for Total-Body Irradiation in Nonmyeloablative Conditioning Regimens for Hematopoietic Cell Transplantation

Marco Mielcarek, Beverly Torok-Storb, Rainer Storb
Biol Blood Marrow Transplant 17: 1255-1260 (2011)
http://dx.doi.org:/10.1016/j.bbmt.2011.01.003

In the dog leukocyte antigen (DLA)-identical hematopoietic cell transplantation (HCT) model, stable marrow engraftment can be achieved with total-body irradiation (TBI) of 200 cGy when used in combination with postgrafting immunosuppression. The TBI dose can be reduced to 100 cGy without compromising engraftment rates if granulocyte colony-stimulating factor (G-CSF)-mobilized peripheral blood mononuclear cells (G-PBMC) are infused with the marrow. T cell-depleting the G-PBMC product abrogates this effect. These results were interpreted to suggest that the additional T cells provided with G-PBMC facilitated engraftment by overcoming host resistance.We therefore hypothesized that the TBI dose may be further reduced to 50 cGy by augmenting immunosupression either by (1) tolerizing or killing recipient T cells, or (2) enhancing the graft-versus-host (GVH) activity of donor T cells. To test the first hypothesis, recipient T cells were activated before HCT by repetitive donor-specific PBMC infusions followed by administration of methotrexate (MTX) (n 5 5), CTLA4-Ig (n = 4), denileukin diftitox (Ontak; n = 4), CTLA4-Ig 1 MTX (n = 8), or 5c8 antibody (anti-CD154) 1 MTX (n = 3). To test the second hypothesis, recipient dendritic cells were expanded in vivo by infusion of Flt3 ligand given either pre-HCT (n = 4) or pre- and post-HCT (n = 5) to augment GVH reactions. Although all dogs showed initial allogeneic engraftment, sustained engraftment was seen in only 6 of 42 dogs (14% of all dogs treated in 9 experimental groups). Hence, unless more innovative pharmacotherapy can be developed that more forcefully shifts the immunologic balance in favor of the donor, noncytotoxic immunosuppressive drug therapy as the sole component of HCT preparative regimens may not suffice to ensure sustained engraftment.

Pretransplant Immunosuppression followed by Reduced-Toxicity Conditioning and Stem Cell Transplantation in High-Risk Thalassemia: A Safe Approach to Disease Control

Usanarat Anurathapan, S Pakakasama, P Rujkijyanont, N Sirachainan, et al.
Biol Blood Marrow Transplant 19 (2013) 1254e1270
http://dx.doi.org/10.1016/j.bbmt.2013.04.023

Patients with class 3 thalassemia with high-risk features for adverse events after high-dose chemotherapy with hematopoietic stem cell transplantation (HSCT) are difficult to treat, tending to either suffer serious toxicity or fail to establish stable graft function. We performed HSCT in 18 such patients age 7 years and hepatomegaly using a novel approach with pretransplant immunosuppression followed by a myeloablative reduced-toxicity conditioning regimen (fludarabine and i.v. busulfan [Flu-IV Bu]) and then HSCT. The median patient age was 14 years (range, 10 to 18 years). Before the Flu-IV Bu þ antithymocyte globulin conditioning regimen, all patients received 1 to 2 cycles of pretransplant immunosuppression with fludarabine and dexamethasone. Thirteen patients received a related donor graft, and 5 received an unrelated donor graft. An initial prompt engraftment of donor cells with full donor chimerism was observed in all 18 patients, but 2 patients developed secondary mixed chimerism that necessitated withdrawal of immunosuppression to achieve full donor chimerism. Two patients (11%) had acute grade III-IV graft-versus-host disease, and 5 patients had limited chronic graft-versus-host disease. The only treatment-related mortality was from infection, and with a median follow-up of 42 months (range, 4 to 75), the 5-year overall survival and thalassemia-free survival were 89%. We conclude that this novel sequential immunoablative pretransplant-ation conditioning program is safe and effective for patients with high-risk class 3 thalassemia exhibiting additional comorbidities.

Profiling antibodies to class II HLA in transplant patient sera

Curtis McMurtrey, D Lowe, R Buchli, S Daga, D Royer, A Humphrey, et al.
Human Immunology 75 (2014) 261–270
http://dx.doi.org/10.1016/j.humimm.2013.11.015

Immunizing events including pregnancy, transfusions, and transplantation promote strong alloantibody responses to HLA. Such alloantibodies to HLA preclude organ transplantation, foster hyperacute rejection, and contribute to chronic transplant failure. Diagnostic antibody-screening assays detect alloreactive antibodies, yet key attributes including antibody concentration and isotype remain largely unexplored. The goal here was to provide a detailed profile of allogeneic antibodies to class II HLA. Methodologically, alloantibodies were purified from sensitized patient sera using an HLA-DR11 immunoaffinity column and subsequently categorized. Antibodies to DR11 were found to fix complement, exist at a median serum concentration of 2.3 lg/mL, consist of all isotypes, and isotypes IgG2, IgM, and IgE were elevated. Because multimeric isotypes can confound diagnostic determinations of antibody concentration, IgM and IgA isotypes were removed and DR11-IgG tested alone. Despite removal of multimeric isotypes, patient-to patient antibody concentra-tions did not correlate with MFI values. In conclusion, allogeneic antibody responses to DR11 are comprised of all antibody isotypes at differing proportions, these combined isotypes fix complement at nominal serum concentrations, and enhancements other than the removal of IgM and IgA multimeric isotypes may be required if MFI is to be used as a means of determining anti-HLA serum antibody concentrations in diagnostic clinical assays.

Reduced-intensity conditioning and HLA-matched hemopoietic stem-cell transplantation in patients with chronic granulomatous disease: a prospective multicenter study

Tayfun Güngör, P Teira, M Slatter, G Stussi, P Stepensky, D Moshous, et al.
Lancet 2014; 383: 436–48
http://dx.doi.org/10.1016/S0140-6736(13)62069-3

Background In chronic granulomatous disease allogeneic hemopoietic stem-cell transplantation (HSCT) in adolescents and young adults and patients with high-risk disease is complicated by graft-failure, graft-versus-host disease (GVHD), and transplant-related mortality. We examined the effect of a reduced-intensity conditioning regimen designed to enhance myeloid engraftment and reduce organ toxicity in these patients.       Methods This prospective study was done at 16 centers in ten countries worldwide. Patients aged 0–40 years with chronic granulomatous disease were assessed and enrolled at the discretion of individual centers. Reduced-intensity conditioning consisted of high-dose fludarabine (30 mg/m² [infants <9 kg 1∙2 mg/kg]; one dose per day on days –8 to –3), serotherapy (anti-thymocyte globulin [10 mg/kg, one dose per day on days –4 to –1; or thymoglobulin 2·5 mg/kg, one dose per day on days –5 to –3]; or low-dose alemtuzumab [<1 mg/kg on days –8 to –6]), and low-dose (50–72% of myeloablative dose) or targeted busulfan administration (recommended cumulative area under the curve: 45–65 mg/L × h). Busulfan was administered mainly intravenously and exceptionally orally from days –5 to –3. Intravenous busulfan was dosed according to weight-based recommendations and was administered in most centers (ten) twice daily over 4 h. Unmanipulated bone marrow or peripheral blood stem cells from HLA-matched related donors or HLA-9/10 or HLA-10/10 matched unrelated-donors were infused. The primary endpoints were overall survival and event-free survival (EFS), probabilities of overall survival and EFS at 2 years, incidence of acute and chronic GVHD, achievement of at least 90% myeloid donor chimerism, and incidence of graft failure after at least 6 months of follow-up. Findings 56 patients (median age 12∙7 years; IQR 6·8–17·3) with chronic granulomatous disease were enrolled from June 15, 2003, to Dec 15, 2012. 42 patients (75%) had high-risk features (ie, intractable infections and autoinflammation), 25 (45%) were adolescents and young adults (age 14–39 years). 21 HLA-matched related-donor and 35 HLA-matched unrelated-donor transplants were done. Median time to engraftment was 19 days (IQR 16–22) for neutrophils and 21 days (IQR 16–25) for platelets. At median follow-up of 21 months (IQR 13–35) overall survival was 93% (52 of 56) and EFS was 89% (50 of 56). The 2-year probability of overall survival was 96% (95% CI 86∙46–99∙09) and of EFS was 91% (79∙78–96∙17). Graft-failure occurred in 5% (three of 56) of patients. The cumulative incidence of acute GVHD of grade III–IV was 4% (two of 56) and of chronic graft-versus-host disease was 7% (four of 56). Stable (≥90%) myeloid donor chimerism was documented in 52 (93%) surviving patients. Interpretation This reduced-intensity conditioning regimen is safe and efficacious in high-risk patients with chronic granulomatous disease.

Refinement of the Definition of Permissible HLA-DPB1 Mismatches with Predicted Indirectly ReCognizable HLA-DPB1 Epitopes

Kirsten A. Thus, MTA Ruizendaal, TA de Hoop, Eric Borst, et al.
Biol Blood Marrow Transplant 20 (2014) 1705e1710
http://dx.doi.org/10.1016/j.bbmt.2014.06.026

Hematopoietic stem cell transplantation with HLA-DPB1emismatched donors leads to an increased risk of acute graft-versus-host disease (GVHD). Studies have indicated a prognostic value for classifying HLA-DPB1 mismatches based on T cell epitope (TCE) groups. The aim of this study was to determine the contribution of indirect recognition of HLA-DPe derived epitopes, as determined with the Predicted Indirectly ReCognizable HLA Epitopes (PIRCHE) method. We therefore conducted a retrospective single-center analysis on 80 patients transplanted with a 10/10 matched unrelated donor that was HLA-DPB1 mismatched. HLADPB1 mismatches that were classified as GVH nonpermissive by the TCE algorithm correlated to higher numbers of HLA class I as well as HLA class II presented PIRCHE (PIRCHE-I and -II) compared with permissive or host-versus-graft nonpermissive mismatches. Patients with acute GVHD grades II to IV presented significantly higher numbers of PIRCHE-I compared with patients without acute GVHD (P < .05). Patients were divided into 2 groups based on the presence or absence of PIRCHE. Patients with PIRCHE-I or -II have an increased hazard of acute GVHD when compared with patients without PIRCHE-I or -II (hazard ratio [HR], 3.19; 95% confidence interval [CI], 1.10 to 9.19; P <.05; and HR, 4.07; 95% CI, .97 to 17.19; P < .06, respectively). Patients classified as having an HLA-DPB1 permissive mismatch by the TCE model had an increased risk of acute GVHD when comparing presence of PIRCHE-I with absence of PIRCHE-I (HR, 2.96; 95% CI, .84 to 10.39; P < .09). We therefore conclude that the data presented in this study describe an attractive and feasible possibility to better select permissible HLA-DPB1 mismatches by including both a direct and an indirect recognition model.

Treosulfan-Thiotepa-FludarabineeBased Conditioning Regimen for
Allogeneic Transplantation in Patients with Thalassemia Major: A
Single-Center Experience from North India

Dharma Choudhary, SK Sharma, N Gupta,…, Satyendra Katewa
Biol Blood Marrow Transplant 19 (2013) 492e503
http://dx.doi.org/10.1016/j.bbmt.2012.11.007

Hematopoietic stem cell transplantation (HSCT) is the definite treatment
for patients with thalassemia major. A busulfan (Bu) and cyclophosphamide
(Cy)ebased regimen has been the standard myeloablative chemotherapy,
but it is associated with higher treatment-related toxicity, particularly in
patients classified as high risk by the Pesaro criteria. Treosulfan-based
conditioning regimens have been found to be equally effective and less
toxic. Consequently, we analyzed the safety and efficacy of treosulfan/
thiotepa/fludarabine (treo/thio/flu)-based conditioning regimens for
allogeneic HSCT in patients with thalassemia major between February
2010 and September 2012. We compared those results retrospectively
with results in patients who underwent previous HSCT with a Bu/Cy/
antithymocyte globulin (ATG)ebased conditioning regimen. A treo/thio/
flu-based conditioning regimen was used in 28 consecutive patients with
thalassemia major. The median patient age was 9.7 years (range, 2-18
years), and the mean CD34+ stem cell dose was 6.18 x 106/kg. Neutrophil
and platelet engraftment occurred at a median of 15 days (range, 12-23
days) and 21 days (range, 14-34 days), respectively. Three patients
developed veno-occlusive disease, 4 patients developed acute graft
versus-host disease (GVHD), and 2 patients had chronic GVHD. Treatment-
related mortality (TRM) was 21.4%. Two patients experienced secondary
graft rejection. We compared these results with results in patients who
underwent previous HSCT using a Bu/Cy/ATG-based conditioning regimen.
Twelve patients were treated with this protocol, at a median age of 7.2
years (range, 2-11 years). One patient had moderate veno-occlusive disease,
2 patients developed acute GVHD, 2 patients had chronic GVHD, and 2
patients experienced graft rejection. There was no TRM in this group. We
found no significant differences between the 2 groups (treo/thio/flu vs Bu/
Cy/ATG) in terms of the incidence of acute GVHD, chronic GVHD, TRM,
and graft failure, although a trend toward higher TRM was seen with the
treo/thio/flu regimen.

Graft-versus-Host Disease
James L.M. Ferrara, John E. Levine, Pavan Reddy, and Ernst Holler
Lancet. 2009 May 2; 373(9674): 1550–1561
http:dx.doi.org:/10.1016/S0140-6736(09)60237-3

The number of allogeneic hematopoietic cell transplantations (HCT)
continues to increase with more than 25,000 allogeneic transplantations
performed annually. The graft-versus leukemia/ tumor (GVL) effect during
allogeneic HCT effectively eradicates many hematological malignancies.
The development of novel strategies that use donor leukocyte infusions,
non-myeloablative conditioning and umbilical cord blood (UCB)
transplantation have helped expand the indications for allogeneic HCT
over the last several years, especially among older patients. Improvements
in infectious prophylaxis, immunosuppressive medications, supportive care
and DNA-based tissue typing have also contributed to improved outcomes
after allogeneic HCT. Yet the major complication of allogeneic HCT, graft-
versus-host disease (GVHD), remains lethal and limits the use of this
important therapy. Given current trends, the number of transplants from
unrelated donors is expected to double within the next five years,
significantly increasing the population of patients with GVHD. In this
seminar we review advances made in identifying the genetic risk
factors and pathophysiology of this major HCT complication, as well
as its prevention, diagnosis and treatment.

Non-HLA Genetics—Despite HLA identity between a patient and donor,
approximately 40% of patients receiving HLA-identical grafts develop
acute GVHD due to genetic differences that lie outside the HLA loci,
or “minor” histocompatibility antigens (HA). Some minor HAs, such as HY
and HA-3, are expressed on all tissues and are targets for both GVHD
and GVL. Other minor HAs, such as HA-1 and HA-2, are expressed most
abundantly on hematopoietic cells (including leukemic cells) and may
therefore induce a greater GVL effect with less GVHD. Polymorphisms
in both donors and recipients for cytokines that are involved in the
classical `cytokine storm’ of GVHD have been implicated as risk factors
for GVHD. Tumor Necrosis Factor (TNF)-α, Interleukin 10 (IL-10),
Interferon-γ (IFNγ) variants have correlated with GVHD in some, but
not all, studies. Genetic polymorphisms of proteins involved in innate
immunity, such as nucleotide oligomerization domain 2 and Keratin 18
receptors, have also been associated with GVHD.

Future strategies to identify the best possible transplant donor will
probably incorporate both HLA and non-HLA genetic factors. Skin is most
commonly affected and is usually the first organ involved, often coinciding
with engraftment of donor cells. The characteristic maculopapular rash is
pruritic and can spread throughout the body, sparing the scalp. In severe
cases the skin may blister and ulcerate. Apoptosis at the base of epidermal
rete pegs is a characteristic pathologic finding. Other features include
dyskeratosis, exocytosis of lymphocytes, satellite lymphocytes adjacent
to dyskeratotic epidermal keratinocytes, and a perivascular lymphocytic
infiltration in the dermis.

Gastrointestinal tract involvement of acute GVHD usually presents as
diarrhea but may also include vomiting, anorexia, and/or abdominal pain
when severe. The diarrhea of GVHD is secretory and often voluminous
(greater than two liters per day). Bleeding, which carries a poor prognosis,
occurs as a result of mucosal ulceration but patchy involvement of the
mucosa often leads to a normal appearance on endoscopy.

The incidence of the severity of acute GVHD is determined by the extent
of involvement of  three principal target organs. The overall grades are
classified as I (mild), II (moderate), III (severe) and IV (very severe). Severe
GVHD carries a poor prognosis, with 25% long term survival for grade III and
5% for grade IV. The incidence of acute GVHD is directly related to the
degree of mismatch between HLA proteins and ranges from 35-45% in
recipients of full matched sibling donor grafts to 60-80% in recipients of
one-antigen HLA mismatched unrelated donor grafts. The same degree
of mismatch causes less GVHD using UCB grafts and incidence of acute
GVHD is lower following the transplant of partially matched UCB units
and ranges from 35-65%.

Two important principles are important to consider regarding the
pathophysiology of acute GVHD. First, acute GVHD reflects exaggerated
but normal inflammatory mechanisms mediated by donor lymphocytes infused
into the recipient where they function appropriately, given the foreign
environment they encounter. Second, the recipient tissues that stimulate
donor lymphocytes have usually been damaged by underlying disease,
prior infections, and the transplant conditioning regimen. As
a result, these tissues produce molecules (sometimes referred to as
“danger” signals) that promote the activation and proliferation of donor
immune cells.  Based largely on experimental models, the development
of acute GVHD can be conceptualized in three sequential steps or phases:
(1) activation of the APCs; (2) donor T cell activation, proliferation,
differentiation and migration; and (3) target tissue destruction.

Alemtuzumab is a monoclonal antibody that binds CD52, a protein
expressed on a broad spectrum of leukocytes including lymphocytes,
monocytes, and dendritic cells. Its use in GVHD prophylaxis in a
Phase II trial decreased the incidence of acute and chronic GVHD
following reduced intensity transplant.98 In two prospective studies,
patients who received alemtuzumab rather than methotrexate showed
significantly lower rates of acute and chronic GVHD, but experienced
more infectious complications and higher rates of relapse, so that there
was no overall survival benefit. Alemtuzumab may also contribute to
graft failure when used with minimal intensity conditioning regimens.

An alternative strategy to TCD attempted to induce anergy in donor
T cells by ex vivo antibody blockade of co-stimulatory pathways prior
to transplantation. A small study using this approach in haploidentical
HCT recipients was quite encouraging, but has not yet been replicated.
Thus the focus of most prevention strategies remains  pharmacological
manipulation of T cells after transplant.

Administration of anti-T cell antibodies in vivo as GVHD prophylaxis
has also been extensively tested. The best studied drugs are anti-
thymocyte globulin (ATG) or antilymphocyte globulin (ALG) preparations.
These sera, which have high titers of polyclonal antibodies, are made
by immunizing animals (horses or rabbits) to thymocytes or lymphocytes,
respectively. A complicating factor in determining the role of these
polyclonal sera in transplantation is the observation that even different
brands of the same class of sera exert different biologic effects. However,
the side effects of ATG/ALG infusions are common across different
preparations and include fever, chills, headache, thrombocytopenia
(from cross-reactivity to platelets), and, infrequently, anaphylaxis. In
retrospective studies, rabbit ATG reduced the incidence of GVHD in
related donor HSCT recipients without appearing to improve survival.
In recipients of unrelated donor HSCT, addition of ALG to standard
GVHD prophylaxis effectively prevented severe GVHD, but did not
result in improved survival because of increased infections. In a long
term follow-up study, however, pretransplant ATG provided significant
protection against extensive chronic GVHD and chronic lung dysfunction.

As allogeneic transplantation becomes an increasingly attractive therapeutic
option, the need for novel approaches to GVHD has accelerated. The
number of patients receiving transplants from unrelated donors is
expected to double in the next five years, significantly increasing
the population of patients with GVHD. The advent of RIC regimens
has reduced transplant-related mortality and lengthened the period
during which acute GVHD may develop (many new cases present up
to day 200) and the need for close monitoring of patients in this period
has increased. Patients have often returned to the care of their primary
hematologists by this time, increasing the need for these physicians to
collaborate with transplant specialists in the management of GVHD and
its complications.

Identification of biomarkers for GVHD with diagnostic (and possibly
prognostic) significance may eventually make the treatment of GVHD
preemptive rather than prophylactic. The use of cellular component therapy,
such as regulatory T cells that have been expanded ex vivo. will also
enter clinical trials in the near future, but the extensive infrastructure
required for such cellular approaches will likely limit their use initially.

Immunomodulatory Effects of Palifermin (Recombinant Human
Keratinocyte Growth Factor) in 
an SLE-Like Model of Chronic
Graft-Versus-Host Disease

C. A. Ellison, Y. V. Lissitsyn, I. Gheorghiu & J. G. Gartner
Scandinavian Journal of Immunology 2011; 75, 69–76
http://dx.doi.org:/10.1111/j.1365-3083.2011.02628.x

Keratinocyte growth factor (KGF) promotes epithelial cell proliferation
and survival. Recombinant human KGF, also known as palifermin, protects
epithelial cells from injury induced by chemicals, irradiation and acute murine
graft versus-host disease (GVHD). Findings from our studies and others
have shown that palifermin also has immunomodulatory properties. In a
model of acute GVHD, we showed that it shifts the immune response
from one in which Th1 cytokines dominate to mixed Th1 and Th2 cytokine
profile. Using the DBA⁄ 2 fi (C57BL ⁄ 6 · DBA⁄ 2)F1-hybrid model of chronic,
systemic lupus erythematosus-like GVHD, we showed that palifermin
treatment is associated with higher levels of Th2 cytokines, the production
of anti-nuclear antibodies, cryoglobulinemia and the development of more
severe pathological changes in the kidney. The aim of our current study
was to gain a better understanding of the immunobiology of KGF by
further characterizing the palifermin-mediated effects in this model of
chronic GVHD. Because the pathological changes we observed resemble
those seen in thymic stromal lymphopoietin (TSLP) transgenic mice, we
had originally hypothesized that palifermin might augment TSLP levels.
Surprisingly, we did not observe an increase in thymic

TSLP mRNA expression in palifermin-treated recipients. We did, however,
observe some differences in the percentages of CD4+CD25+Foxp3+
regulatory T cells in the spleen at some time points in palifermin-treated
recipients. Most importantly, we found that TGFβ levels were higher in
palifermin-treated recipients early in the GVH reaction, raising the
possibility that KGF might indirectly induce the development of fibrosis
and glomerulonephritis through a pathway involving TGFβ.

Keratinocyte growth factor (KGF) is an epithelial cell growth factor that is
produced by both mesenchymal cells and intraepithelial cdT cells. It is
also known as fibroblast growth factor 7. Its receptor, (KGFR⁄FGF7R), an
alternatively spliced form of FGFR2 ⁄ bek, is found on epithelial cells in
the intestine, mammary glands, ovaries and urinary tract, and on
hepatocytes, keratinocytes and alveolar type II cells. Previously, it
was shown that recombinant human KGF, also known as palifermin,
can protect the lung, bladder or intestine from chemical- or irradiation-
induced injury. This has been attributed to the ability of KGF to reduce
oxidative damage and enhance DNA repair.

Our own studies have provided a better understanding of the immuno-
biological properties of KGF in pathologically distinct models of systemic
disease driven by intense immunological and inflammatory responses.
The acute GVHD that develops in the C57BL ⁄ 6 fi (C57BL ⁄ 6 · DBA⁄ 2)F1-
hybrid model is characterized by the activation of alloreactive donor T cells,
the production of Th1 cytokines and tissue injury in the skin, gastrointestinal
tract, liver, thymus and lung, where epithelia are present. Injury to the
intestinal mucosa permits the translocation of endotoxin into the system,
which, if untreated, leads to the development of endotoxemic shock. We
showed that palifermin treatment protects recipients from epithelial
cell injury, endotoxemia and morbidity in GVH mice. Palifermin also
shifts the immune response away from one that is predominated by Th1
cytokines towards a profile of mixed Th1 and Th2 cytokines, with a
preponderance of Th2 cytokines. The DBA⁄ 2 fi (C57BL ⁄ 6 · DBA⁄ 2)F1-
hybrid model of chronic GVHD is characterized by pathological changes
resembling those seen in systemic lupus erythematosus (SLE). Using this
model, we showed that palifermin treatment augments the production of Th2
cytokines such as IL-4, IL-5 and IL-13 and obviates IFN-c production. Both
untreated and palifermin-treated recipients developed pathological changes
in the kidney, but these changes were more severe in palifermin-treated
recipients. Some of the changes that developed in the palifermin-treated
recipients resemble those seen in thymic stromal lymphopoietin (TSLP)
transgenic mice. These similarities include the presence of ANA in the
sera, the development of cryoglobulinemia and the development of
glomerulonephritis featuring the deposition of immune complexes
consisting of IgG, IgA, IgM and C3 in the mesangium and the glomerular
capillaries. This led us to hypothesize that treating the recipient mice with
palifermin might induce TSLP expression in this model.

In this study, we were interested in determining whether palifermin
treatment was indeed associated with increased TSLP expression.
We were also interested in knowing whether palifermin treatment
changes the percentage of CD4+CD25+FoxP3+ cells in the spleen,
because palifermin treatment has been associated with increased
percentages of CD4+CD25+FoxP3+ cells in other studies including
our own. Lastly, we wished to study the effect of palifermin treatment
on TGFb levels, because this cytokine is known to play a pivotal role
in the development of glomerulonephritis.

We studied the histopathological changes to confirm that the pathological
changes seen in the kidney in this study were the same as those reported
by us previously.We examined kidney sections from both untreated and
palifermin-treated recipients. In these experiments, we were able to
reproduce findings from an earlier study that showed that palifermin-
treated recipients mice in this model of chronic GVHD develop a severe,
extracapillary proliferative glomerular nephritis characterized by epithelial
crescents and hyaline thrombi. These changes were associated with higher
levels of protein in the urine and the development of ascites, presumably
related to the development of nephrotic syndrome, as a consequence
of glomerular injury.

Pathological changes in the kidney

Pathological changes in the kidney. (A) shows a section from a BDF1-hybrid control
mouse that did not receive a graft. (B) shows increased epithelial cellularity within a
glomerulus from an untreated recipient with chronic graft-versus-host disease, on
day 50. No crescents were observed in sections from this group of recipients.
(C and D) show examples of pathological changes observed in kidneys from
palifermin-treated recipients on day 50. Arrows indicate examples of crescentic
glomerulonephritis and the development of protein casts within tubular lumena.
(E and F) show examples of the hyaline thrombi (arrows) seen in the glomeruli
in kidney sections from palifermin-treated recipients on day 50. All sections
were stained with haematoxylin and eosin except for that shown in (F), which
was stained with Masson Trichrome. The concentration of protein measured in
the urine is shown in the lower left corner of each photomicrograph. Original
magnification: ·200 (B–E) and ·400 (A and F).

TGFβ is a highly pleiotropic cytokine with three isoforms, TGFβ1, TGFβ2 and
TGFβ3 . Nearly, all cells have receptors for at least one of these isoforms,
but cells of the immune system primarily express TGFβ1. This cytokine
was implicated in the development of experimental glomerulonephritis in
experiments in which rats were treated with antiserum directed against
TGFβ1. The ability of palifermin to induce TGFβ release and reverse
limited airflow was demonstrated in a mouse model of emphysema. The
authors further showed that palifermin induced the release of TGFβ1
from primary cultures of mouse alveolar type 2 cells. Our results show
that palifermin treatment is associated with a rise in splenic TGFβ levels
during the first month of the GVH reaction. It is possible that by inducing
TGFβ production shortly after transplantation, palifermin treatment is able
to promote the development of the severe, crescentic glomerulonephritis
that we observed at later time points. As such, our findings raise the
possibility that endogenous KGF might play a role in the development
of glomerulonephritis and ⁄ or other autoimmune phenomena associated
with chronic GVHD and ⁄ or SLE.

T cells, murine chronic graft-versus-host disease and autoimmunity

Robert A. Eisenberg, Charles S. Via
Journal of Autoimmunity 39 (2012) 240e247
http://dx.doi.org:/10.1016/j.jaut.2012.05.017

The chronic graft-versus-host disease (cGVHD) in mice is characterized by
the production of autoantibodies and immunopathology characteristic of
systemic lupus erythematosus (lupus). The basic pathogenesis involves
the cognate recognition of foreign MHC class II of host B cells by alloreactive
CD4 T cells from the donor. CD4 T cells of the host are also necessary for
the full maturation of host B cells before the transfer of donor T cells.
CD8 T cells play critical roles as well. Donor CD8 T cells that are highly
cytotoxic can ablate or prevent the lupus syndrome, in part by killing
recipient B cells. Host CD8 T cells can reciprocally downregulate donor
CD8 T cells, and thus prevent them from suppressing the autoimmune
process. Thus, when the donor inoculum contains both CD4 T cells and
CD8 T cells, the resultant syndrome depends on the balance of activities
of these various cell populations. For example, in one cGVHD model
(DBA/2 (C57BL/6xDBA/2)F1, the disease is more severe in females, as
it is in several of the spontaneous mouse models of lupus, as well as in
human disease. The mechanism of this female skewing of disease
appears to depend on the relative inability of CD8 cells of the female host
to downregulate the donor CD4 T cells that drive the autoantibody response.
In general, then, the abnormal CD4 T cell help and the modulating roles
of CD8 T cells seen in cGVHD parallel the participation of T cells in
genetic lupus in mice and human lupus, although these spontaneous
syndromes are presumably not driven by overt alloreactivity.

Systemic lupus erythematosus (SLE) is characterized by a spectrum of auto-
antibodies that targets multiple normal cellular components, particularly
nucleic acids or proteins that are physiologically bound to nucleic acids.
Although SLE is highly diverse in its manifestations, a common theme
is the loss of B cell tolerance to these cellular autoantigens. More than
for any other human condition, several spontaneously arising mouse
models for SLE have been described, beginning with the New Zealand
strains in 1959. These models are largely genetic. In some cases, an
individual gene such as fas or Yaa plays a major role in driving the loss
of tolerance. However, in general the genetic contribution is complex and
involves multiple loci, which are not yet fully defined.

Despite extensive investigations, the failures in immunoregulation that
underlie the genetic SLE models remain poorly understood. It is not known
for sure which B cell tolerance checkpoints are breached in a given model,
and why. The autoantibody response to DNA, Sm, and other autoantigens
resembles the normal response to exogenous antigens: it involves clonal
expansion, somatic mutation, and a pattern of isotype use characteristic of
a T-cell dependent immunization. Thus the cellular dynamics of the response
may be basically normal. Yet the B-cell repertoire is abnormally autoreactive.

In this review we wish to focus more on the role of the T cell in SLE. As
stated above, the loss of B cell tolerance in SLE does appear in general
to require the participation of T cells. Multiple T cells abnormalities have
been described in human and in murine SLE, although in most cases it is
not clear if these are primary or secondary manifestations. Nevertheless,
it is striking how difficult it has been to demonstrate definitively the specificity
of the T cells that provide help for autoantibody production.

The key cellular mechanism in the cGVHD that results in the loss of B cell
tolerance and the production of the autoantibodies typical of SLE is the
cognate interaction of CD4 T cells with an MHC class II determinant on
the B cell surface. A variety of protocols have achieved this interaction.
In general, either the donor/recipient strains are paired in such away
that they only differ at the MHC class II loci, or the CD4 cells are isolated
free of CD8 cells that would recognize MHC class I. If the allorecognition
involves both CD4 T cell interaction with MHC II and CD8 interaction with
MHC I, an acute GVHD occurs, which is immunosuppressive, rather than
immunostimulatory. The DBA/2 (C57BL/6 DBA/2)F1 (B6D2F1) and the
BALB/c (BALB/c A/J)F1 models are exceptions to this rule. The former
has been investigated extensively for a deficiency in CD8 cytotoxic
lymphocytes.

The MHC class II recognition may be at either the I-A or the I-E locus.
However, the autoantibody specificities seen and the degree of immuno-
pathology differ depending on the locus targeted. In one set of experiments,
F1 mice were bred between either B6 or coisogenic bm12 mice and
B10.A(2R) or B10.A(4R) MHC recombinant congenics. The MHC class II
of B6 is I-Ab, while that of bm12 is I-Abm12. These two alleles differ by
only three amino acids, which is sufficient for a full strength MLR (mixed
lymphocyte reaction) between the two strains. Otherwise B6 and bm12
are identical. B10.A(2R) and B10.A(4R) differ only by the expression of
I-E in the former strain, but not in the latter strain. Thus, donor/recipient
combinations could be employed that provided for allogeneic differs only
at I-A, only at I-E, or at both loci.

Results from Busser et al. delineate requirements for this MHC class II
recognition. Utilizing several transgenic mouse strains that express a
more or less constricted CD4 autoreactive repertoire, they showed that
a diverse repertoire was essential to the production of SLE autoantibodies
by MHC II recognition. On the other hand, the non-specific, early polyclonal
B cell activation phase of cGVHD occurred even with a limited CD4 repertoire.

Figure not shown. Chronic GVHD in bm12 C57BL/6 mice. The MHC of the
bm12 donor differs from the MHC of the C57BL/6 recipient just in three
amino acids in the I-A class II molecule. Thus donor CD4 T cells recognize
MHC IIþ B cells as foreign. Donor CD8 T cells see only self MHC I. All T
cells do not express MHC II. Polyclonal activation and specific lupus
autoantibody responses ensue..

Lupus can result from unchecked CD4 T cell cognate help to a polyclonal
population of B cells. CD8 T cells can downregulate this CD4 driven B-cell
hyperactivity through CD8 CTL effectors and can maintain remission,
possibly through memory CD8 T cells. Whether CD8 CTL actually prevent
lupus in normals and fail in lupus prone individuals is not known; however,
data from the P F1 model suggest that therapeutic induction of CD8 CTL
and possibly long term memory cells may be beneficial in preventing or
limiting disease expression. The potential major role played by either
IFNa and IL-21 in both lupus expression and CD8 CTL function remains
to be further defined, but already these cytokines are being targeted in
human or murine lupus.

It is not surprising that the T cells have been shown to have diverse roles in
the autoimmune cGVHD in mice. Donor CD4 T cells drive the host B cell
activation, while host CD4 T cells are required to mature these B cells prior
to their encounter with donor T cells. Donor CD4 T cells also help activate
donor CD8 T cells, which in turn can downregulate or even ablate the
autoimmune response. Donor CD4 T cells license host DC cells, which in
turn can interact with donor CD8 T cells. Host CD8 T cells can suppress
the activity of donor CD8 T cells, and thereby favor the development of
the lupus syndrome. Although the precise mechanisms of T cell participation
in spontaneous lupus are still being defined, it seems reasonable to probe
these syndromes in humans and in mice for T cell mechanism that have
been shown to participate in cGVHD, CD4-B cell interactions almost
certainly are central to the pathogenesis of spontaneous lupus, and they
have been a target of investigation for several decades. If we understood
the peptide specificity of the alloreactive CD4 T cells that drive the formation
of the characteristic lupus autoantibodies, we would have a much clearer
idea where to look for such epitopes in spontaneous disease. Much less
is known about the other T cell activities defined in cGVHD, particularly
those that involve CD8 T cells. This area should invite further detailed
investigation. For example, the striking role of CD8 T cells in the stronger
female disease in the DBA BDF1 model clearly demands that similar
mechanisms be sought for in spontaneous disease.

Understanding Chronic GVHD from Different Angles

Bruce Blazar, Eric S. White, Daniel Couriel
Biol Blood Marrow Transplant 18:S184-S188, 2012
http://dx.doi.org:/10.1016/j.bbmt.2011.10.025

Whereas acute graft-versus-host disease (aGVHD) rates have decreased
with more intensive GVHD preventive agents and use of single and double
umbilical cord blood units as a source of donor cells in adult recipients,
significant chronic GVHD (cGVHD) rates unexpectedly have remained high.
Moreover, granulocyte colony stimulating factor mobilized peripheral blood
stem cell grafts have been associated with an increased overall risk of
cGVHD. As such, cGVHD has emerged as a primary cause of morbidity
and mortality following allogeneic hematopoietic stem cell transplantation.
Progress in developing cGVHD interventional strategies has been hampered
by variable onset and clinical and pathological manifestations of cGVHD, now
better defined by the National Institutes of Health (NIH) consensus conference,
and a dearth of preclinical models that closely mimic the conditions in which
cGVHD is generated and manifested. Although the exact causes of cGVHD
remain unknown, higher antibody levels have been associated with auto-
immunity and implicated in cGVHD. Newly diagnosed patients with
extensive cGVHD had elevated soluble B cell activating factor levels and
anti-double-strand DNA antibodies were found, which was associated with
higher circulating levels of pregerminal center (GC) B cells and post-GC
plasmablasts. B cells from cGVHD patients were hyperresponsive to Toll-like
receptor-9 signaling and have up-regulated CD86 levels.

By using a Cy and low doses of donor T cells, aGVHD was avoided and
cGVHD with BO favored. Histologic changes were similar to the findings in
human cGVHD with peribronchiolar and perivascular cuffing and infiltration
of the airway epithelium. The liver had inflammation and lymphocytic
infiltration, along with collagen deposition. The parotid and submandibular
salivary glands displayed lymphocytic infiltrates in both the bone marrow
and cGVHD groups, likely because of transplantation conditioning.

Treatment of steroid refractory cGVHD patients with rituximab, a B cell–
depleting anti-CD20 monoclonal antibody, has shown a beneficial role in
resolution of the autoimmune disorders such as systemic lupus erythmatosus
and rheumatoid arthritis, andcGVHD, with overall response rates of 29%
to 36% for oral, hepatic, gastrointestinal, and lung cGVHD, and 60% for
cutaneous cGVHD in aggregate data from multiple trials. Thus, we recently
undertook studies to identify the presence of CD41 T helper cells and B2201
B cells in the airways of mice that had BO, tissue-specific antibodies from sera,
and alloantibody deposition in the lung and liver of cGVHD recipients. cGVHD
development was associated with IgG2c deposition in the lung and liver,
abrogated if the donor bone marrow was deficient in mature B cells or
incapable of producing antihost reactive IgG. Robust GC formation was
seen in mice with cGVHD. Alleviation of symptoms in mice that received
B cell–deficient bone marrow confirms the requirement of B cells for lung
dysfunction and inflammation and fibrosis in the lung and liver.

Given a role for IgG antibodies, allo- or auto-Ab binding to the cGVHD organs
could enable tissue destruction or the pathology could be defined by the
specific function of these secreted antibodies. Pathogenic antibody production
therefore is likely to be an important inducer of cGVHD, and targeting this
specific function of the B cells is an attractive strategy for cGVHD. Because
GC B cells display lower susceptibility to rituximab-mediated clearance, probably
because they reside in a nonoptimal environment for antibody-based depletion,
our observation that GC B cells are critical to the development of cGVHD
suggests that agents that are more effective at disrupting the GC might be
more clinically useful. Treatment with LTbR-Ig, a fusion protein that blocks
interactions between LTbR and its ligands, had a direct effect on the
symptoms of cGVHD, at least in part by blocking GC formation and suggest
that LTbR-Ig could be a potential clinical interventional strategy for prevention
and therapy of cGVHD.

Fibrosis is the end result of a number of inflammatory and other injurious events,
resulting in replacement of normal tissue with a dense extracellular matrix (ECM)
scar composed primarily of collagens. While some degree of tissue fibrosis is
considered protective (e.g. in the setting of cutaneous wound healing),
exaggerated or unrelenting ECM deposition with replacement of the normal
tissue architecture is considered pathologic. Fibroproliferative disorders as
a class involving multiple organs (e.g. cGVHD following hematopoietic stem
cell transplant [affecting up to 30% of recipients surviving more than 100 days,
scleroderma [estimated to affect 70,000 in the US], idiopathic pulmonary fibrosis
[estimated to affect 200,000 in the US], hepatic cirrhosis [estimated to affect
up to 400,000 in the US], and renal fibrosis due to diabetic nephropathy and
other causes [estimated to affect over 400,000 in the US]) are a major cause
of morbidity and mortality. Combined, these disorders alone are conservatively
estimated to affect approximately 1 in 300 persons in the United States. When
coupled with a host of other disorders in which tissue fibrosis contributes to
morbidity (e.g. fibroproliferative acute respiratory distress syndrome,
hypersensitivity pneumonitis, solid organ transplant rejection), that estimate
is likely to be much greater.

Wound healing occurs by a highly orchestrated, complex process that has
been well defined. In general, wound repair occurs in 4 stages which overlap
considerably: clotting/coagulation, inflammation, fibroproliferation, and tissue
remodeling. The initial injury leads to a local disruption of epithelial and
endothelial barriers resulting in the elaboration of inflammatory mediators and
extravasation of cells and plasma proteins that serve to achieve hemostasis
and provide a provisional fibrin-rich matrix for the influx of inflammatory and
other reparative cells. Simultaneously, platelet degranulation provides a local
“boost” of vasodilators, growth factors, and ECM proteins that aid in the wound
healing response. Inflammatory cell influx occurs next, with polymorphonuclear
leukocytes (PMNs) arriving first. Following PMN degranulation, mononuclear
cells (macrophages and lymphocytes) arrive next and, along with PMN derived
products, sterilize and remove foreign materials from the wound. This process
also results in the elaboration of cytokines and chemokines designed to
augment the inflammatory response, to promote angiogenesis (allowing for
enhanced nutrient and oxygen delivery to the wound bed), and to recruit
fibroblasts to the wound bed. Fibroblast recruitment and transdifferentiation to
myofibroblasts (or recruitment of already-differentiated myofibroblasts or
fibroblast precursors; this point is still controversial) marks the fibroproliferative
stage, with the result being the elaboration of ECM proteins (collagens,
fibronectins) to repair the tissue defect.

Vorinostat plus tacrolimus and mycophenolate to prevent graft-versus-host
disease after related-donor reduced-intensity conditioning allogeneic
hemopoietic 
stem-cell transplantation: a phase 1/2 trial

Sung Won Choi, T Braun, L Chang, JLM Ferrara, A Pawarode, et al.
Lancet Oncol 2014; 15: 87–95
http://dx.doi.org/10.1016/S1470-2045(13)70512-6

Background Acute graft-versus-host disease (GVHD) remains a barrier to more
widespread application of allogeneic hemopoietic stem-cell transplantation.
Vorinostat is an inhibitor of histone deacetylases and was shown to attenuate
GVHD in preclinical models. We aimed to study the safety and activity of
vorinostat, in combination with standard immunoprophylaxis, for prevention of
GVHD in patients undergoing related-donor reduced-intensity conditioning
hemopoietic stem-cell transplantation. Methods Between March 31, 2009,
and Feb 8, 2013, we did a prospective, single-arm, phase 1/2 study at two
centers in the USA. We recruited adults (aged ≥18 years) with high-risk
hematological malignant diseases who were candidates for reduced-intensity
conditioning hemopoietic stem-cell transplantation and had an available 8/8
or 7/8 HLA matched related donor. All patients received a conditioning regimen
of fl udarabine (40 mg/m² daily for 4 days) and busulfan (3·2 mg/kg daily for
2 days) and GVHD immunoprophylaxis of mycophenolate mofetil (1 g three
times a day, days 0–28) and tacrolimus (0·03 mg/kg a day, titrated to a goal
level of 8–12 ng/mL, starting day –3 until day 180). Vorinostat (either 100 mg
or 200 mg, twice a day) was initiated 10 days before haemopoietic stem-cell
transplantation until day 100. The primary endpoint was the cumulative
incidence of grade 2–4 acute GVHD by day 100. This trial is registered with
ClinicalTrials.gov, number NCT00810602.
Findings 50 patients were assessable for both toxic effects and response;
eight additional patients were included in the analysis of toxic effects. All
patients engrafted neutrophils and platelets at expected times after
hemopoietic stem-cell transplantation. The cumulative incidence of grade
2–4 acute GVHD by day 100 was 22% (95% CI 13–36). The most common
non-hematological adverse events included electrolyte disturbances (n=15),
hyperglycemia (11), infections (six), mucositis (four), and increased activity
of liver enzymes (three). Non-symptomatic thrombocytopenia after
engraftment was the most common hematological grade 3–4 adverse
event (nine) but was transient and all cases resolved swiftly.
Interpretation Administration of vorinostat in combination with standard
GVHD prophylaxis after related-donor reduced-intensity conditioning
hemopoietic stem-cell transplantation is safe and is associated with a
lower than expected incidence of severe acute GVHD. Future studies
are needed to assess the effect of vorinostat for prevention of GVHD in
broader settings of hemopoietic stem-cell transplantation.

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Allogeneic Transfusion Reactions

Writer and Curator: Larry H. Bernstein, MD, FCAP 

 

Introduction

Transfusion Medicine owes much to the discovery of the ABO Blood Groups
by Landsteiner. This was a landmark in the history of immunology.  The next
important discovery was the RhD system in immune hemolytic anemia of the
newborn, which was important in the history of neonatology.  As blood banking
became critical in the preparation, storage, transport, and transfusion of blood
during the Second World War, there was the elucidation of the Kell, MNSs,
Kidd, Duffy, Lewis, and other red cell antigenic systems.  The type and screen
for antibodies, and for red cell compatibility in the crossmatch became routine,
and a formal classification of the antigenic components was created.
Incompatibilities in transfusion mediated reactions were expressed as
allogeneic transfusion reactions.  The red cell was not the only component,
as whole blood was ultimately broken into red cell units, plasma, and platelets,
and eventually a neutrophilic component.  With the development of solid organ
transplantation, the definition of the HLA antigen was a large focus for
compatibility.  Today, the traditional problems of transfusion immuno-compatibility have become displaced in large measure by transplantation
issues.  This piece and that which follows will address allogeneic
transplantation reactions and graft-versus-host disease.

Blood Groups

Although all blood is made of the same basic elements, not all blood is
alike. In fact, there are eight different common blood types, which are
determined by the presence or absence of certain antigens – substances that can trigger an immune response if they are foreign
to the body. Since some antigens can trigger a patient’s immune system
to attack the transfused blood, safe blood transfusions depend on careful
blood typing and cross-matching.

There are four major blood groups determined by the presence or absence
of two antigens – A and B – on the surface of red blood cells:

  • Group A – has only the A antigen on red cells (and B antibody in the plasma)
  • Group B – has only the B antigen on red cells (and A antibody in the plasma)
  • Group AB – has both A and B antigens on red cells (but neither A nor B
    antibody in the plasma)
  • Group O – has neither A nor B antigens on red cells (but both A and B
    antibody are in the plasma)

There are very specific ways in which blood types must be matched for a
safe transfusion. See the chart below:

http://www.redcrossblood.org/sites/arc/files/images/ab_top.gif

In addition to the A and B antigens, there is a third antigen called the
Rh factor, which can be either present (+) or absent ( – ). In general,
Rh negative blood is given to Rh-negative patients, and Rh positive blood
or Rh negative blood may be given to Rh positive patients.

O positive is the most common blood type. Not all ethnic groups have the
same mix of these blood types. Hispanic people, for example, have a relatively
high number of O’s, while Asian people have a relatively high number of B’s.
The mix of the different blood types in the U.S. population is:

Caucasians African American Hispanic Asian
O + 37% 47% 53% 39%
O – 8% 4% 4% 1%
A + 33% 24% 29% 27%
A – 7% 2% 2% 0.5%
B + 9% 18% 9% 25%
B – 2% 1% 1% 0.4%
AB + 3% 4% 2% 7%
AB – 1% 0.3% 0.2% 0.1%

Some patients require a closer blood match than that provided by the ABO
positive/negative blood typing. For example, sometimes if the donor and
recipient are from the same ethnic background the chance of a reaction
can be reduced. That’s why an African-American blood donation may be
the best hope for the needs of patients with sickle cell disease, 98 percent
of whom are of African-American descent.

http://www.redcrossblood.org/learn-about-blood/blood-types

Whether your blood group is type A, B, AB or O is based on the blood types
of your mother and father.

This chart shows the potential blood types you may inherit.

Parent 1 AB AB AB AB B A A O O O
Parent 2 AB B A O B B A B A O
Possible
blood
type
of
child
O X X X X X X
A X X X X X X X
B X X X X X X X
AB X X X X

A blood type (also called a blood group) is a classification of blood based on
the presence or absence of inherited antigenic substances on the surface of
red blood cells (RBCs). These antigens may be proteins, carbohydrates,
glycoproteins, or glycolipids, depending on the blood group system. Some of
these antigens are also present on the surface of other types of cells of
various tissues. Several of these red blood cell surface antigens can stem
from one allele (or very closely linked genes) and collectively form a blood
group system. Blood types are inherited and represent contributions from
both parents. A total of 33 human blood group systems are now recognized
by the International Society of Blood Transfusion (ISBT). The two most
important ones are ABO and the RhD antigen; they determine someone’s
blood type (A, B, AB and O, with +, − or Null denoting RhD status).

Many pregnant women carry a fetus with a blood type which is different from
their own, and the mother can form antibodies against fetal RBCs. Sometimes
these maternal antibodies are IgG, a small immunoglobulin, which can cross
the placenta and cause hemolysis of fetal RBCs, which in turn can lead to
hemolytic disease of the newborn called erythroblastosis fetalis, an illness
of low fetal blood counts that ranges from mild to severe. Sometimes this is
lethal for the fetus; in these cases it is called hydrops fetalis.

ABO_blood_type.svg

ABO_blood_type.svg

http://upload.wikimedia.org/wikipedia/commons/thumb/3/32/ABO_blood_type.svg/824px-ABO_blood_type.svg.png

Blood type (or blood group) is determined, in part, by the ABO blood group antigens

A complete blood type would describe a full set of 30 substances on the surface
of RBCs, and an individual’s blood type is one of many possible combinations
of blood-group antigens. Across the 33 blood groups, over 600 different blood-
group antigens have been found, but many of these are very rare, some being
found mainly in certain ethnic groups.

Almost always, an individual has the same blood group for life, but very rarely
an individual’s blood type changes through addition or suppression of an
antigen in infection, malignancy, or autoimmune disease. Another more
common cause in blood type change is a bone marrow transplant. Bone-marrow transplants are performed for many leukemias and lymphomas,
among other diseases. If a person receives bone marrow from someone
who is a different ABO type (e.g., a type A patient receives a type O bone
marrow), the patient’s blood type will eventually convert to the donor’s type.

Some blood types are associated with inheritance of other diseases; for example,
the Kell antigen is sometimes associated with McLeod syndrome. Certain
blood types may affect susceptibility to infections, an example being the
resistance to specific malaria species seen in individuals lacking the Duffy
antigen. The Duffy antigen, presumably as a result of natural selection, is
less common in ethnic groups from areas with a high incidence of malaria.

The Rh system (Rh meaning Rhesus) is the second most significant blood-
group system in human-blood transfusion with currently 50 antigens.
The most significant Rh antigen is the D antigen, because it is the most
likely to provoke an immune system response of the five main Rh antigens.
It is common for D-negative individuals not to have any anti-D IgG or
IgM antibodies, because anti-D antibodies are not usually produced
by sensitization against environmental substances. However, D-negative
individuals can produce IgG anti-D antibodies following a sensitizing event:
possibly a fetomaternal transfusion of blood from a fetus in pregnancy or
occasionally a blood transfusion with D positive RBCs. Rh disease can
develop in these cases. Rh negative blood types are much less common
in proportion of Asian populations (0.3%) than they are in White (15%).
The presence or absence of the Rh antigens is signified by the + or − sign,
so that for example the A− group does not have any of the Rh antigens.

http://en.wikipedia.org/wiki/Blood_type

Allogeneic blood transfusions: benefit, risks and clinical indications
in countries with a low or high human development index

Carlos Marcucci, Caveh Madjdpour and Donat R. Spahn
Br Med Bull (2004) 70 (1): 15-28. http://dx.doi.org:/10.1093/bmb/ldh023

The risks associated with allogeneic red blood cell (RBC) transfusions differ
significantly between countries with low and high human development indexes
(HDIs). In countries with a low HDI, the risk of infection (HIV, HBV, HCV and
malaria) is elevated. In contrast, in countries with a high HDI, immunological
reactions (hemolytic transfusion reactions, alloimmunization and immuno-suppression) are predominant. Therefore the overall risk associated with RBC
transfusions in low HDI countries is much more significant than that in high HDI
countries. In view of these risks, the limited efficacy of RBC transfusion and its
high costs, this procedure should be used sparingly and rationally.

Red blood cell (RBC) transfusions originating from an unrelated donor are known
as allogeneic RBC transfusions. In the West, i.e. in countries with a high human
development index (HDI), which is an index based on life expectancy, literacy,
enrolment in further education and per capita income, >50% of RBC transfusions
are used in trauma and surgery to compensate for major blood loss.

RBC transfusions are certainly beneficial in specific situations, but are accompanied
by many risks and side effects. Several recent studies have suggested that RBC
transfusions are associated with major adverse outcomes and high costs. In addition,
RBC transfusions are a limited resource and blood shortages can occur at times.

The risk of viral transmission via RBC transfusions has decreased considerably
in recent years in high HDI countries, although new transfusion-transmitted
viruses have been discovered.14 In contrast, in countries with medium or low
HDIs, the risk of transmission of infectious diseases may still be extremely high.

Most reviews consider risks on transfusion-transmissible infections and
immunological reactions, associated with RBC transfusions, that are only
applicable to Western countries, i.e. countries with a high HDI. Although 83%
of the global population live in countries with medium and low HDIs, they
have access to only 40% of the global blood supply. Most notably, all blood
donations in high HDI countries are screened for transfusion-transmissible
infections, whereas only 57% of blood donations in medium and low HDI
countries are tested. In addition, the tests used for blood screening are
not always comparable. For example, only four of the 19 countries
participating in the ‘Workshop of the Directors of National Blood Transfusion
Services’, held in Harare, Zimbabwe, in 2000, used p24 antigen testing for
HIV blood screening.18 Moreover, the blood donation rate per 1000 population
is almost 20 times higher in developed countries than in countries with a low HDI.
Regular non-remunerated volunteers, who are the safest donors, provide 98%
of donations in high HDI countries. In contrast, such donors are a minority in
low HDI countries where up to 60% of donated blood comes from relatives of
the anemic patient or from paid donors.

Acute extravascular hemolytic transfusion reaction due to
anti-Kpa antibody missed by electronic crossmatch

Ruth Padmore, Philip Berardi, …, Doris Neurath, Elianna Saidenberg
Transfusion and Apheresis Science 51 (2014) 168–171
http://dx.doi.org/10.1016/j.transci.2014.08.011

Background: Kpa antigen is a low incidence red blood cell antigen within the Kell
system. Anti-Kpa alloantibody may be associated with acute and delayed hemolytic
transfusion reactions.
Case Study: We report a case of a clinically significant acute extravascular
hemolytic transfusion reaction mediated by previously unrecognized (and
undetected) anti-Kpa alloantibody. This reaction occurred in a patient who
met all criteria for electronic crossmatch, resulting in the transfusion of an
incompatible red cell unit.
Results: Post-transfusion investigation showed the transfused red cell unit
was crossmatch compatible at the immediate spin phase but was 3 + incompatible
at the antiglobulin phase.No evidence of intravascular hemolysis was observed
upon visual comparison of the pre and post-transfusion peripheral blood plasma.
Further testing showed the presence of anti-Kpa antibody. The clinical course
of the patient included acute febrile and systemic reaction.
Conclusion: Acute extravascular hemolytic transfusion reaction may occur due
to undetected anti-Kpa alloantibody. Various strategies for crossmatching are
discussed in the context of antibodies to low incidence antigens.

Transfusion-related mortality: the ongoing risks of allogeneic blood
transfusion and the available strategies for their prevention

Eleftherios C. Vamvakas and Morris A. Blajchman
Blood. 2009; 113: 3406-3417
http://dx.doi.org:/10.1182/blood-2008-10-167643

As the risks of allogeneic blood transfusion (ABT)–transmitted viruses were
reduced to exceedingly low levels in the US, transfusion-related acute lung injury
(TRALI), hemolytic transfusion reactions (HTRs), and transfusion-associated
sepsis (TAS) emerged as the leading causes of ABT related deaths. Since 2004,
preventive measures for TRALI and TAS have been implemented, but their
implementation remains incomplete. Infectious causes of ABT-related deaths
currently account for less than 15% of all transfusion-related mortality, but the
possibility remains that a new transfusion-transmitted agent causing a fatal
infectious disease may emerge in the future. Aside from these established
complications of ABT, randomized controlled trials comparing recipients of
non–white blood cell (WBC)–reduced versus WBC-reduced blood components
in cardiac surgery have documented increased mortality in association with
the use of non-WBC–reduced ABT. ABT-related mortality can thus be further
reduced by universally applying the policies of avoiding prospective donors
alloimmunized to WBC antigens from donating plasma products, adopting
strategies to prevent HTRs, WBC-reducing components transfused to patients
undergoing cardiac surgery, reducing exposure to allogeneic donors through
conservative transfusion guidelines and avoidance of product pooling, and
implementing pathogen-reduction technologies to address the residual risk of TAS as well as the potential risk of a transfusion transmitted agent to emerge
in the foreseeable future.

Red blood cell-incompatible allogeneic hematopoietic progenitor cell
transplantation

S D Rowley, M L Donato and P Bhattacharyya
Bone Marrow Transplantation (2011) 46, 1167–1185; http://dx.doi.org:/10.1038/bmt.2011.135

Transplantation of hematopoietic progenitor cells from red cell-incompatible
donors occurs in 30–50% of patients. Immediate and delayed hemolytic
transfusion reactions are expected complications of red cell-disparate
transplantation and both ABO and other red cell systems such as Kidd
and rhesus can be involved. The immunohematological consequences of
red cell-incompatible transplantation include delayed red blood cell recovery,
pure red cell aplasia and delayed hemolysis from viable lymphocytes carried
in the graft (‘passenger lymphocytes’). The risks of these reactions, which
may be abrupt in onset and fatal, are ameliorated by graft processing and
proper blood component support. Red blood cell antigens are expressed on
endothelial and epithelial tissues in the body and could serve to increase
the risk of GvHD. Mouse models indicate that blood cell antigens may
function as minor histocompatibility antigens affecting engraftment. Similar
observations have been found in early studies of human transplantation
for transfused recipients, although current conditioning and immuno-suppressive regimens appear to overcome this affect. No deleterious effects
from the use of red cell-incompatible hematopoietic grafts on transplant
outcomes, such as granulocyte and platelet engraftments, the incidences
of acute or chronic GvHD, relapse risk or OS, have been consistently
demonstrated. Most studies, however, include limited number of patients,
varying diagnoses and differing treatment regimens, complicating the
detection of an effect of ABO-incompatible transplantation. Classification
of patients by ABO phenotype ignoring the allelic differences of these
antigens also may obscure the effect of red cell-incompatible transplantation
on transplant outcomes.

Severe hemolytic transfusion reaction due to anti-A1 following allogeneic
stem cell transplantation with minor ABO incompatibility

Çiğdem Akalın Akkok, Håkon Haugaa, Anders Galgerud, Lorentz Brinch
Transfusion and Apheresis Science 2013; 48(1), Pages 63–66
http://dx.doi.org/10.1016/j.transci.2012.07.006

Blood components should be compatible both with the recipient and the
donor in the ABO incompatible allogeneic stem cell transplantation setting.
A patient with blood type A2 received peripheral blood stem cells from a
blood type O donor. The patient was in critical condition due to treatment-
related toxicity. He had acquired anti-A1 that was unfortunately overlooked.
Following transfusion of A1 red blood cells in error, he developed a severe
hemolytic transfusion reaction. Anti-A1 is rarely clinically significant.
We discuss the role of passenger lymphocytes in development of the anti-A1, and stress the importance of investigating unusual/atypical reactions
in blood typing.

Transfusion Support of Allogeneic Stem Cell Transplant Recipients

Kate Chipperfield MD FRCPC  21 Feb 2012

After this session, the learner will be able to:

  1. Provide an overview of transfusion issues in allogeneic stem cell transplant.
  2. Discuss the potential consequences of ABO mismatch between recipient
    and donor.
  3. Understand the rationale for ABO/D group selection of blood product support
    peri-stem cell transplant.
  4. Appreciate the special impact of umbilical cord blood stem cell transplant.
  5. Briefly outline variable practices in transfusion support of stem cell
    transplantation.

Pre-transplant

  • Leukocyte Reduction

– reduction in HLA Alloimmunization (TRAP study)

– reduction in CMV infection in seronegative candidates*

  • Avoidance of directed donations
  • Irradiation of cellular blood products

– Only from start of SCT conditioning (to end of GVHD prophylaxis or
lymphs >1 x 109/L)

  • Issues with this

– as soon as identified as potential SCT recipient*

– prevention of microchimerism in intended recipient (donor lymphocytes)

 

ABO and SCT

  • Any allogeneic SCT will be one of:

– ABO-Identical

– Major ABO Incompatible

– Minor ABO Incompatible

– Major and Minor incompatible (Bidirectional)

(more not shown)

Major ABO Blood Group Mismatch Increases the Risk for Graft Failure
after Unrelated Donor Hematopoietic Stem Cell Transplantation

Mats Remberger, E Watz, O Ringdén, J Mattsson, A Shanwell, A Wikman
Biology of Blood and Marrow Transplantation 13:675-682 (2007)
http://dx.doi.org:/10.1016/j.bbmt.2007.01.084

Two hundred twenty-four patients with leukemia transplanted with an unrelated
donor between 1991 and 2003 at the Karolinska University Hospital were
analyzed according to association between graft failure and ABO, RhD, MNSs,
and Kidd blood group antigen compatibility. Median age was 29 years
(range: 0-55). Conditioning consisted of total-body irridiation or busulfan-based myeloablative conditioning. A bone marrow graft was given to 152
patients, and 72 patients received peripheral blood stem cells. Most patients
received graft-versus-host disease prophylaxis with cyclosporine and MTX.
Graft failure (GF) was seen in 6 (2.7%) patients. In the multivariate analysis
major ABO mismatch (odds ratio [OR] 14.9, 95% confidence interval
[CI] 2.01-110, P = .008) and HLA-allele mismatch (6.42, 1.19-34.8, P = .03)
was significantly associated to GF. In patients with and without major ABO
mismatch the incidence of GF was 7.5% and 0.6% (P = .02), respectively.
Using an ABO major mismatched graft increases the risk for GF after
unrelated donor hematopoietic stem cell transplantation.

Perioperative transfusion-related acute lung injury: The Canadian
Blood Services experience

Asim Alam, Mary Huang, Qi-Long Yi, Yulia Lin, Barbara Hannach
Transfusion and Apheresis Science 50 (2014) 392–398
http://dx.doi.org/10.1016/j.transci.2014.04.008

Purpose: Transfusion-related acute lung injury (TRALI) is a devastating transfusion-associated adverse event. There is a paucity of data on the incidence and
characteristics of TRALI cases that occur perioperatively. We classified
suspected perioperative TRALI cases reported to Canadian Blood Services
between 2001 and 2012, and compared them to non-perioperative cases
to elucidate factors that may be associated with an increased risk of developing
TRALI in the perioperative setting. Methods: All suspected TRALI cases
reported to Canadian Blood Services (CBS) since 2001 were reviewed by
two experts or, from 2006 to 2012, the CBS TRALI Medical Review Group
(TMRG). These cases were classified based on the Canadian Consensus
Conference (CCC) definitions and detailed in a database. Two additional
reviewers further categorized them as occurring within 72 h from the onset of
surgery (perioperative) or not in that period (non-perioperative). Various
demographic and characteristic variables of each case were collected and
compared between groups. Results: Between 2001 and 2012, a total of
469 suspected TRALI cases were reported to Canadian Blood Services;
303 were determined to be within the TRALI diagnosis spectrum. Of those,
112 (38%) were identified as occurring during the perioperative period.
Patients who underwent cardiac surgery requiring cardiopulmonary bypass
(25.0%), general surgery (18.0%) and orthopedics patients (12.5%) represented
the three largest surgical groups. Perioperative TRALI cases comprised more
men (53.6% vs. 41.4%, p = 0.04) than non-perioperative patients. Perioperative
TRALI patients more often required supplemental O2 (14.3% vs. 3.1%, p = 0.0003),
mechanical ventilation (18.8% vs. 3.1%), or were in the ICU (14.3% vs. 3.7%,
p = 0.0043) prior to the onset of TRALI compared to non-perioperative TRALI
patients. The surgical patients were transfused on average more components
than non-perioperative patients (6.0 [SD = 8.3] vs. 3.6 [5.2] products per patient,
p = 0.0002).  Perioperative TRALI patients were transfused more plasma (152
vs. 105, p = 0.013) and cryoprecipitate (51 vs. 23, p < 0.01) than nonperioperative
TRALI patients. There was no difference between donor antibody test results
between the groups. Conclusion: CBS data has provided insight into the
nature of TRALI cases that occur perioperatively; this group represents a
large proportion of TRALI cases.

Platelet allo-antibodies identification strategies forpreventing and
managing platelet refractoriness

Basire, C.Picard
Transfusion Clinique et Biologique 21(2014)193–206
http://dx.doi.org/10.1016/j.tracli.2014.08.140

Platelet refractoriness is a serious complication for patients receiving recurrent
platelet transfusions ,which can be explained by non-immune and immune causes.
Human Leukocyte Antigens (HLA) allo-immunization, especially against HLA
class I, is the major cause for immune platelet refractoriness. To a lesser extent,
alloantibodies against specific Human Platelet Antigen (HPA) are also involved.
Pregnancy, transplantation and previous transfusions can lead to allo-immune reaction against platelet antigens. After transfusion, platelet count
is decreased by accelerated platelet destruction related to antibodies
fixation on incompatible platelet antigens. New laboratory tests for allo-antibodies identification were developed to improve sensibility and specificity,
especially with the LUMINEX® technology. The good use and interpretation
of these antibodies assays can improve strategies for platelet refractoriness
prevention and management with a patient adapted response. Compatible
platelets units can be selected according to their identity with recipient
typing or immune compatibility regarding HLA or HPA antibodies or HLA
epitope compatibility. Prospective studies are needed to further confirm the
clinical benefit of new allo-antibodies identification methods and consensus
strategies for immune platelet refractoriness management.

For Anti-HLA-Specific Donor Antibodies Detection By Flow Cytometry
Cytotoxic 
Crossmatches Comparison of Methods

Cervelli, F. Pisani, A. Aureli, R. Azzarone, ..,  A. Famulari, and F. Papola Transplantation Proceedings, 45, 2761e2764 (2013)
http://dx.doi.org/10.1016/j.transproceed.2013.07.023

Anti-HLA-specific donor antibodies induce rapid, irreversible destruction of
the transplant (hyperacute rejection) that today happens rarely due to
immunologic studies prospective crossmatch of patients awaiting the kidney
graft. The usual approach for pretransplant donor/recipient evaluation is
based on 2 methods: (1) the cytotoxic complement crossmatch (CDC) and
(2) the flow cytometric crossmatch  (FCX). The CDC crossmatch is positive
when complement-fixing antibodies are present, an absolute contra-
indication to kidney transplantation. The more sensitive FCX-positive
crossmatch detects low concentrations of unable to fix performed
antibodies complement. It is an  “index” of possible damage due to
accelerated rejection. The target of our study was to develop a cytotoxic
flow cytometry crossmatch (cFCX) that detected cytotoxic antibodies
move sensitively  than the traditional CDC method and also was less
subjective and more standardized for interpretation studying sera from
23 patients; the cFCX showed the requested efficiency characteristics even
in an emergency. In addition, the new method permitted one to calculate a
cutoff for positivity (average value of the negative control at + 2 standard
deviations), assuring an “objective” interpretation of the results that agreed
with the CDC but was more sensitive and accurate allowing solution of
ambiguous results for cases of “doubt”-positive CDC crossmatch.
Furthermore, our aim was to correlate the effect of the strength of the anti-HLA
antibodies determined by mean fluorescence intensity value of LabScreen
Single Antigen beads with results of CDC, cFCX, and FCX methods.

Allogeneic Stem Cell Transplants and Associated Incompatibities

Analysis of Donor and Recipient ABO Incompatibility and Antibody-
Associated Complications after Allogeneic Stem Cell Transplantation
with Reduced-Intensity Conditioning

Emma Watz, Mats Remberger, Olle Ringden, Joachim Lundahl, et al.
Biol Blood Marrow Transplant 20 (2014) 264e271
http://dx.doi.org/10.1016/j.bbmt.2013.11.011

Allogeneic hematopoietic stem cell transplantation (HSCT) can be performed
across the ABO blood group barrier. The impact of ABO incompatibility on
clinical outcome is controversial. A retrospective analysis of 310 patients who
underwent HSCT with reduced-intensity conditioning between 1998 and 2011
was performed to investigate the frequency and clinical implications of anti-RBC
antibodies in passenger lymphocyte syndrome (PLS) after minor ABO mismatch
(mm), persistent or recurring recipient type ABO antibodies (PRABO) after major
ABO mm HSCT, and autoimmune hemolytic anemia (AIHA). Transplantation
characteristics and clinical outcome were analyzed by univariate and multivariate
analysis for groups with or without anti-RBC antibodies. ABO blood group
incompatibility did not affect clinical outcome despite an increased requirement
of blood transfusion. Twelve patients with AIHA, 6 patients with PLS, and 12
patients with PRABO post-HSCT were identified. AIHA did not affect overall
survival (OS) or transplant-related mortality (TRM), but patients with AIHA had
a lower incidence of grades II to IV acute graft-versus-host disease (P < .05).
OS in the PLS group was 0% compared with 61% in the whole group receiving
minor ABO mm transplants (P < .001). Comparing PRABO patients with those
receiving a major ABO mm HSCT, the OS was 17% versus 73% (P <.002) and
TRM was 50% versus 21% (P < .03). At our center, PLS after minor ABO mm
and PRABO antibodies after major ABO mm HSCT are significant risk factors
for decreased OS and TRM. Our results suggest that occurrence of unexpected
ABO antibodies after HSCT warrant a wider investigation individual to find the
underlying cause.

Current Trends in Clinical Studies of Allogeneic Hematopoietic Stem Cell
Transplantation

Sophie Pilon, D Jedrysiak, D Sheppard, CN Bredeson, J Tay, DS Allan
Biol Blood Marrow Transplant 21 (2015) 364e381
http://dx.doi.org/10.1016/j.bbmt.2014.09.014

Allogeneic hematopoietic stem cell transplantation (HSCT) is a specialized
intervention performed at select centers worldwide. The extent to which
specific aspects of care in allogeneic HSCT have been studied and the
types of studies performed for different aspects of care remains incompletely
documented. Studies in allogeneic HSCT were systematically identified from
selected high-profile transplant journals between July 2010 and June 2011
and previously reported in a study addressing the definition of clinical outcomes
in HSCT. All articles were retrieved and assessed for study characteristics and
categorized by specific aspects of care related to allogeneic HSCT. One
hundred sixteen articles were retrieved and reviewed in detail by  investigators.
The most studied aspect of care was conditioning regimens. Transfusion
practices were the most understudied aspect of care. Interestingly, most
studies included both adult and pediatric patients. Studies involving all
hematological malignancies were encountered more often than disease-
specific studies. Geographically, most patients described in the published reports
were treated only in North America or only in Europe. Most studies were
retrospective (78), and 25 reported on multicenter registry data.  Of the 38
prospective studies, 8 were randomized controlled trials (RCTs) and
predominantly focused on prevention and treatment of graft-versus-host disease
(GVHD) and infections. Median follow-up was longer in retrospective registry
studies (54 months) and shortest in RCTs (32 months). The proportion of
positive outcomes in retrospective and prospective studies was remarkably
high (>80% for all categories) and not significantly different across all aspects
of care (P > .05). When comparing RCTs and registry data studies, this proportion
was similar and high (95% and 100%, respectively, P >.05). Our study highlights
the established and important role of retrospective registry studies for many
aspects of care and suggests RCTs may be most relevant for studies on
infectious complications and GVHD.

Efficacy and Long-Term Outcome of Treatment for Pure Red Cell Aplasia
after Allogeneic Stem Cell Transplantation from Major ABO-Incompatible
Donors

Makoto Hirokawa, T Fukuda, K Ohashi, …, H Sakamaki, for The PRCA
Collaborative Study Group
Biol Blood Marrow Transplant 19 (2013) 1026e1032
http://dx.doi.org/10.1016/j.bbmt.2013.04.004

No standard of care for pure red cell aplasia (PRCA) after major ABO-
incompatible hematopoietic stem cell transplantation (HSCT) has been
established. We conducted a retrospective cohort study to learn the
efficacy and outcome of treatment for PRCA. One hundred forty-five
recipients who showed delayed recovery of erythropoiesis and survived
>100 days after transplantation without early disease progression were
selected from 2846 records of major ABO-incompatible transplantation
in the registry database in Japan, and detailed data of 46 recipients
were collected. Treatment of PRCA, such as rapid tapering of calcineurin
inhibitors, corticosteroids, or additional immunosuppressants, was given
to 22 patients but not to the other 24 patients. The overall response rate
of the treatment group was 54.5%. The number of days from diagnosis of
PRCA to recovery of reticulocytes >1% and the cumulative number of red
blood cell transfusions were not significantly different between the 2 groups.
Infections accounted for the death of 7 of 11 patients in the treatment group.
Univariate analysis identified 5 variables influencing survival, including graft-
versus-host disease, disease progression, and treatment of PRCA; disease
progression remained as the only factor negatively affecting survival by
multivariate analysis. The present study could not provide supportive
evidence for the beneficial effects of treatment for PRCA after major
ABO-mismatched HSCT.

Current therapy of myelodysplastic syndromes

Amer M. Zeidan, Yuliya Linhares, Steven D. Gore
Blood Reviews 27 (2013) 243–259
http://dx.doi.org/10.1016/j.blre.2013.07.003

After being a neglected and poorly-understood disorder for many years, there
has been a recent explosion of data regarding the complex pathogenesis of
myelodysplastic syndromes (MDS). On the therapeutic front, the approval of
azacitidine, decitabine, and lenalidomide in the last decade was a major
breakthrough. Nonetheless, the responses to these agents are limited and
most patients progress within 2 years. Allogeneic stem cell transplantation
remains the only potentially curative therapy, but it is associated with significant
toxicity and limited efficacy. Lack or loss of response after standard therapies
is associated with dismal outcomes. Many unanswered questions remain
regarding the optimal use of current therapies including patient selection,
response prediction, therapy sequencing and combinations, and management
of resistance. It is hoped that the improved understanding of the underpinnings
of the complex mechanisms of pathogenesis will be translated into novel
therapeutic approaches and better prognostic/predictive tools that would
facilitate accurate risk-adaptive therapy.

Donor Selection for Killer Immunoglobulin-like Receptors B Haplotype
of the Centromeric Motifs Can Improve the Outcome after HLA-Identical
Sibling Hematopoietic Stem Cell Transplantation

Huifen Zhou, Xiaojing Bao, …, Miao Wang, Depei Wu, Jun He
Biol Blood Marrow Transplant 20 (2014) 98e105
http://dx.doi.org/10.1016/j.bbmt.2013.10.017

After hematopoietic stem cell transplantation (HSCT), natural killer (NK) cell
alloreactivity in HLA cells of recipients is regulated by killer immunoglobulin-like
receptors (KIRs) on donor NK cells. The effect of KIRs on HSCT outcomes
is controversial, particularly in those undergoing HLA-identical sibling HSCT.
In this study, effects of KIR and HLA genotypes on the HSCT outcome were
investigated in a 5-year retrospective study comprising 219 patient-donor pairs
undergoing HLA-identical sibling HSCT for myeloid and lymphoid malignancies.
We found that 39.7% (87 of 219) of these pairs, which were KIR mismatched,
had better overall survival (OS) and reduced grade III to IV acute graft-versus-
host disease (aGVHD), especially in acute myeloid leukemia (AML) patients.
Bx1 donor KIR genotype with haplotype B on a telomeric region was a risk
factor for the OS and relapse-free survival (RFS). Donor centromeric (c) and
telomeric (t) KIR haplotype analysis showed that donor KIR cB-tA/tB was
associated with improved OS and RFS compared with cA-tA or cA-tB.
Furthermore, donor KIR B haplotype of the centromeric motifs (Cen-B) was
an independent beneficial factor in improving OS and RFS and in protecting
from relapse after HSCT. In AML patients, the occurrence of a GVHD was
significantly lower in HLA-C1 group compared with that in HLA-C2 group,
although such effect was not observed in patients with acute lymphoblastic
leukemia or chronic myelogenous leukemia. Our results suggest that KIR
could impact outcome and donor KIR haplotype with Cen-B confer significant
survival benefits to HLA-identical sibling HSCT.

TEL-AML1 Corrupts Hematopoietic Stem Cells to Persist in the Bone
Marrow and Initiate Leukemia

Jeffrey W. Schindler, D Van Buren, A Foudi, O Krejci, J Qin, SH Orkin, and H Hock
Cell Stem Cell 5, 43–53, July 2, 2009
http://dx.doi.org:/10.1016/j.stem.2009.04.019

The initial steps in the pathogenesis of acute leukemia remain incompletely
understood. The TELAML1 gene fusion, the hallmark translocation in Childhood
Acute Lymphoblastic Leukemia and the first hit, occurs years before the clinical
disease, most often in utero. We have generated mice in which TEL-AML1
expression is driven from the endogenous promoter and can be targeted to
specific populations. TEL-AML1 renders mice prone to malignancy after
chemical mutagenesis when expressed in hematopoietic stem cells (HSCs),
but not in early lymphoid progenitors. We reveal that TEL-AML1 markedly
increases the number of HSCs and predominantly maintains them in the
quiescent (G0) stage of the cell cycle. TEL-AML1+ HSCs retain self renewal
properties and contribute to hematopoiesis, but fail to out-compete normal
HSCs. Our work shows that stem cells are susceptible to subversion by weak
oncogenes that can subtly alter their molecular program to provide a latent
reservoir for the accumulation of further mutations.

Factors Affecting the Outcome of Related Allogeneic Hematopoietic
Cell Transplantation in Patients with Fanconi Anemia

Mouhab Ayas, K Siddiqui, A Al-Jefri, , …, A Al-Musa, A Al-Seraihy
Biol Blood Marrow Transplant 20 (2014) 1599e1603
http://dx.doi.org/10.1016/j.bbmt.2014.06.016

Hematopoietic cell transplantation (HCT) can cure bone marrow failure in
patients with Fanconi Anemia (FA), and it is generally accepted that these
patients should receive low-intensity conditioning because of the underlying
DNA repair defect in their cells. Outcomes for recipients of matched related
HCT have generally been favorable, but only a few studies have scrutinized
the factors that may affect the eventual outcome of these patients. This
retrospective analysis of 94 pediatric patients with FA who underwent related
HCT at King Faisal Specialist Hospital & Research Center was carried out to
attempt to identify factors that may affect outcome. Results showed overall
survival (OS) probabilities of 92.5%, 89%, and 86% at 1, 5, and 10 years,
respectively. In univariate analysis, use of higher dose cyclophosphamide
(CY) (60 mg/kg) conditioning was associated with a better 10-year OS than
lower dose CY (20 mg/kg) conditioning (91% versus 82%, respectively;
P < .035), and use of radiation-containing regimens was associated with a
significantly lower 10-year OS than nonradiation regimens (76% versus 91%,
respectively; P < .005). Of the 4 regimens used in this study, the fludarabine-
based regimen was associated with the highest survival (95.2%; P < .034).
The use of the higher dose CY (60 mg/kg) was associated with a
significantly increased incidence of hemorrhagic cystitis (HC) (20% versus 5.6%
respectively; P < .049). Three patients (3%) developed squamous cell carcinoma
(2 oropharyngeal and 1 genitourinary), at 9.4, 5.4, and 13.3 years after HCT;
2 of them had radiation containing conditioning. In conclusion, our data suggest
that although using a higher dose CY (60 mg/kg)
conditioning regimen may be associated with better survival, it is also associated
with a significantly increased risk of HC. The addition of fludarabine to the low-dose
CY (20 mg/kg) is associated with the best survival. On the other hand, radiation-
containing regimens are associated with significantly lower survival.

Donor Cell Leukemia: A Review

Daniel H. Wiseman
Biol Blood Marrow Transplant 17: 771-789 (2011)
http://dx.doi.org:/10.1016/j.bbmt.2010.10.010

Relapse of acute leukemia following hematopoietic stem cell transplantation
(HSCT) usually represents return of an original disease clone, having evaded
eradication by pretransplant chemo-/radiotherapy, conditioning, or posttransplant
graft-versus-leukemia (GVL) effect. Rarely, acute leukemia can develop
de novo in engrafted cells of donor origin. Donor cell leukemia (DCL) was
first recognized in 1971, but for many years, the paucity of reported cases
suggested it to be a rare phenomenon. However, in recent years, an upsurge
in reported cases (in parallel with advances in molecular chimerism monitoring)
suggest that it may be significantly more common than previously appreciated;
emerging evidence suggests that DCL might represent up to 5% of all post-
transplant leukemia ‘‘relapses.’’ Recognition of DCL is important for several
reasons. Donor-derivation of the leukemic clone has implications when selecting
appropriate therapy, because seeking to enhance an allogeneic GVL effect
would intuitively not have the same role as in standard recipient-derived
relapses. There are also broader implications for donor selection and workup,
particularly given the growing popularity of nonmyeloblative HSCTand
corresponding rising age of the potential donor pool. Identification of DCL
raises potential concerns over future health of the donor, posing ethical
dilemmas regarding responsibilities toward donor notification (particularly
in the context of cord blood transplantation). The entity of DCL is also of
research interest, because it might provide a unique human model for studying
the mechanisms of leukemogenesis in vivo. This review presents and collates
all reported cases of DCL, and discusses the various strategies, controversies,
and pitfalls when investigating origin of posttransplant relapse. Putative etiologic
factors and mechanisms are proposed, and attempts made to address the
difficult ethical questions posed by discovery of donor-derived malignancy
within a HSCT recipient.

Feasible Outcomes of T Cell-Replete Haploidentical Stem Cell
Transplantation with Reduced-Intensity Conditioning in Patients
with Myelodysplastic Syndrome

Seung-Hwan Shin, Jung-Ho Kim, Young-Woo Jeon, …,, Woo-Sung Min,
Yoo-Jin Kim, Je-Hwan Lee
Biol Blood Marrow Transplant 21 (2015) 342e349
http://dx.doi.org/10.1016/j.bbmt.2014.10.031

Even with the recent optimization of haploidentical stem cell transplantation
(SCT), its role for patients with myelodysplastic syndrome (MDS) or acute
myeloid leukemia evolving from MDS (sAML) should be validated. We
analyzed the outcomes of consecutive 60 patients with MDS or sAML
who received T cell-replete haploidentical SCT after reduced-intensity
conditioning with fludarabine, busulfan, and rabbit antithymocyte globuline
800 cGy total body irradiation. Patients achieved a rapid neutrophil
engraftment after a median of 12 days (range, 8 to 23) and an early
immune reconstitution without high incidences of acute graft-versus-host
disease (GVHD) II to IV and chronic GVHD (36.7% and 48.3%, respectively).
After a median follow-up of 4 years, incidence of relapse and nonrelapse mortality
and rate of overall survival and disease-free survival was 34.8%, 23.3%, 46.8%,
and 41.9%, respectively. In multivariate analysis, the disease status at peak was
a significant predictor for relapse (lower-risk MDS versus higher-risk MDS or sAML;
hazard ratio [HR], 5.69; 95% confidence interval [CI], 1.45 to 22.29; P <.013)
and disease-free survival (HR, 4.44; 95% CI, 1.14 to 17.34; P <.032). Chronic
GVHD was an additional significant predictor for relapse (no versus yes; HR,
2.87; 95% CI, 1.03 to 7.51; P <.043). Our T cell-replete haploidentical SCT
may be a feasible option for patients with MDS and sAML without conventional
donors.

Extramedullary Relapse of Acute Leukemia after Allogeneic Hematopoietic
Stem Cell Transplantation: Different Characteristics between Acute
Myelogenous Leukemia and Acute Lymphoblastic Leukemia

Ling Ge, Fan Ye, X Mao, …, C Ruan, Depei Wu, Xiaowen Tang
Biol Blood Marrow Transplant 20 (2014) 1040e1047
http://dx.doi.org/10.1016/j.bbmt.2014.03.030

Extramedullary relapse (EMR) of acute leukemia (AL) after allogeneic
hematopoietic stem cell transplantation (allo-HSCT) is a contributor to post-
transplantation mortality and remains poorly understood, especially the
different characteristics of EMR in patients with acute myelogenous
leukemia (AML) and those with acute lymphoblastic leukemia (ALL).
To investigate the incidence, risk factors, and clinical outcomes of EMR
for AML and ALL, we performed a retrospective analysis of 362 patients
with AL who underwent allo-HSCT at the First affiliated Hospital of Soochow
University between January 2001 and March 2012. Compared with patients
with AML, those with ALL had a higher incidence of EMR (12.9% versus
4.6%; P < .009). The most common site of EMR was the central nervous
system, especially in the ALL group. Multivariate analyses identified the
leading risk factors for EMR in the patients with AML as advanced disease
status at HSCT, hyperleukocytosis at diagnosis, history of extramedullary
leukemia before HSCT, and a total body irradiationebased conditioning
regimen, and the top risk factors for EMR in the patients with ALL as
hyperleukocytosis at diagnosis, adverse cytogenetics, and transfusion
of peripheral blood stem cells. The prognosis for EMR of AL is poor,
and treatment options are very limited; however, the estimated 3-year
overall survival (OS) was significantly lower in patients with AML
compared with those with ALL (0 versus 18.5%; P < .000). The
characteristics of post-allo-HSCT EMR differed between the patients
with AML and those with ALL, possibly suggesting different pathogenetic
mechanisms for EMR of AML and EMR of ALL after allo-HSCT; further
investigation is needed.

French Multicenter 22-Year Experience in Stem Cell Transplantation
for Beta-Thalassemia Major: Lessons and Future Directions

Claire Galambrun, C Pondarré, Yves Bertrand, …,C Badens, I Thuret, for the
French Rare Disease Center for Thalassemia and the French Society of Bone
Marrow Transplantation
Biol Blood Marrow Transplant 19 (2013) 62e68
http://dx.doi.org/10.1016/j.bbmt.2012.08.005

Although hematopoietic stem cell transplantation (HSCT) offers curative
potential for beta-thalassemia major (beta-TM), it is associated with a
variable but significant incidence of graft rejection. We studied the French
national experience for improvement over time and the potential benefit
of antithymocyte globulin (ATG). Between December 1985 and December
2007, 108 patients with beta-TM underwent HSCT in 21 different French
transplantation centers. The majority of patients received a matched sibling
transplant (n = 96) and a busulfan- and cyclophosphamide-based conditioning
regimen (n = 95), also with ATG in 57 cases. Ninety five of the 108 patients
survived, with a median follow-up of 12 years. Probabilities of 15-year survival
and thalassemia-free survival after first HSCT were 86.8% and 69.4%, respectively.
Graft failure occurred in 24 patients, 11 of whom underwent a second HSCT.
The use of ATG was associated with a decrease in rejection rate from 35% to 10%.
Thalassemia-free survival improved significantly with time, reaching 83% in the
54 patients undergoing HSCT after 1994 (median time of HSCT). In view of the
increased risk of graft rejection after matched sibling HSCT, current French
national guidelines recommend, for all children at risk for beta-TM, the systematic
addition of ATG to the myeloablative conditioning regimen and special attention
to optimize transfusion and chelation therapy in the pretransplantation period.

Extramedullary Relapse of Acute Myelogenous Leukemia after
Allogeneic Hematopoietic Stem Cell Transplantation: Better
Prognosis Than Systemic Relapse

Melhem Solh, Todd E. DeFor, Daniel J. Weisdorf, Dan S. Kaufman
Biol Blood Marrow Transplant 18: 106-112 (2012)
http://dx.doi.org:/10.1016/j.bbmt.2011.05.023

Allogeneic hematopoietic cell transplantation (HSCT) is considered a curative
treatment for acute myelogenous leukemia (AML). Extramedullary relapse after
HSCT for AML is a rare event and is less well defined than systemic, hematologic
relapse. We retrospectively studied all patients with AML (n = 436) who underwent
HSCT at the University of Minnesota between  1996 and 2008 who developed
either a bone marrow (BM) or extramedullary (EM) relapse, and examined the
incidence and risk factors for BM and EM relapse. Of 128 patients who relapsed
post-HSCT, 25 had relapse in EM sites, either isolated (n = 13) or with  concurrent
BM relapse (n = 12). Relapse sites included bone (n = 1), central nervous system
(n=5 6), gastrointestinal (n=5 4), lymphatic (n = 4), skin (n = 5), genitourinary
(n=5 1), pulmonary (n = 1), and soft tissue (n = 3). The time to relapse was longer
in the EM sites (median, 328 days vs 168 days). Patients with EM relapse were
more likely to have had preceding acute graft-versus-host disease (GVHD) (77%
vs 49%; P = .03) or chronic GVHD (46% vs 15%; P < .02) compared with those
with BM relapse. The 6-month survival post-relapse was significantly better in
patients with isolated EM relapse (69%) compared with those with combined
EM and BM relapse (8%) or those with BM relapse alone (27%) (P <.01).
Compared with local therapy alone, systemic therapy yielded better 6-month
survival in patients with EM relapse. This study suggests differing pathogenesis
of BM relapse versus EM relapse of AML after allogeneic HSCT. GVHD and its
accompanying graft-versus-leukemia effect may better protect BM sites, but
patients with EM relapse have better responses to combined therapy and
improved survival compared with those with BM relapse.

Hematopoietic Cell Transplantation for Thalassemia: A Global
Perspective BMT Tandem Meeting 2013

Parinda A. Mehta, Lawrence B. Faulkner
Biol Blood Marrow Transplant 19 (2013) S70eS73
http://dx.doi.org/10.1016/j.bbmt.2012.10.025

Hematopoietic cell transplantation (HCT) remains the sole available curative
option for patients with β-thalassemia major. Expanded and improved supportive
therapies for thalassemia now routinely extend the life span of affected individuals
well into adulthood. Consequently, in regions of the world where this care is
readily available, HCT has been pursued infrequently, in part owing to concerns
about an expected lack of balance between risks and benefits. More recently,
however, recognition of significant health problems in older patients with
thalassemia, along with recognition of increased risks of graft-versus-host
disease (GVHD), graft rejection, and impaired organ function leading to inferior
HCT outcomes in this particular group, seem to be turning the wheels and tipping
the balance again in the direction of consideration for earlier HCTs. In contrast,
in countries where thalassemia is most prevalent (>100,000 new children born
each year in Middle East and southeast Asia), lack of supportive care standards
together with often insufficient access to dedicated health care facilities, results
in the majority of these children not reaching adulthood, further supporting the
need for expanded access to HCT for these patients. The cost of HCT is equivalent
to that of a few years of noncurative supportive care, such that HCT in low-risk
young children with a compatible sibling is justified not only medically and ethically
but also financially. International cooperation can play a major role in increasing
access to safe and affordable HCT in countries where there is a considerable
shortage of transplantation centers. In this article, we review the current status
of bone marrow transplantation for thalassemia major, with particular emphasis
on a global prospective.

Hematopoietic Stem Cell Transplantation in Autoimmune Diseases: The
Ahmedabad Experience

AV Vanikar, PR Modi, RD Patel, KV Kanodia, VR Shah, VB Trivedi, HL Trivedi
Transplantation Proceedings, 39, 703–708 (2007)
http://dx.doi.org:/10.1016/j.transproceed.2007.01.070

Introduction. Autoimmune disease represents a (AD) breakdown of natural
tolerance against autoreactive antigens leading to a high mortality and morbidity.
The reaction is usually polyclonal; T- and B-cell components of the hematopoietic
system are responsible for disease progression. Allogeneic/ autologous
hematopoietic stem cell transplantation (HSCT) are the current modalities
for treating drug-resistant AD. Patients and Methods. We present a single-
center retrospective evaluation of allogeneic HSCT with nonmyelo-ablative,
low-intensity conditioning in nine patients (five males, four females) with
pemphigus vulgaris (PV) and 27 patients with systemic lupus erythematosus
(SLE; 3 males, 24 females). The mean follow-up period was 4.24 years for PV
and 4.9 years for SLE. Cytokine-mobilized HSC from unmatched related donors,
with mean dose of 21.3108 nucleated cells/kg body weight (BW; mean CD34+
count, 6 x 106/kg BW) was administered in to the thymus as well as the portal and
peripheral circulations of recipients. Cyclosporine (4 + 1 mg/kg BW per day) and
prednisolone (10 mg/kg BW per day) were administered for 6 months to protect
mixed chimerism. A subset of patients with cross-gender donors were analyzed
for peripheral blood chimerism at 1 month post-HSCT and every 3 months
thereafter. Results. Sustained clinical remission with peripheral lymphohemato-
poietic chimerism of 0.7 + 0.3% was observed in PV, whereas SLE relapsed after
mean of 7.35 months of disease-free interval associated with fall in chimerism
from 5 + 3% to 0.08 + 0.03%. Conclusion. HSCT was effective to achieve early
clinical remission of PV; and in SLE relapsed after a 7.35-month disease-free
interval accompanied by a fall in mixed lymphohematopoietic chimerism.

Hematopoietic Stem Cell Transplantation in Children and Young Adults
with Secondary Myelodysplastic Syndrome and Acute Myelogenous
Leukemia after Aplastic Anemia

Ayami Yoshimi, B Strahm, I Baumann, I Furlan, S Schwarz, …, CM Niemeyer
Biol Blood Marrow Transplant 20 (2014) 421-434
http://dx.doi.org/10.1016/j.bbmt.2013.11.031

Secondary myelodysplastic syndrome and acute myelogenous leukemia
(sMDS/sAML) are the most serious secondary events occurring after immuno-
suppressive therapy in patients with aplastic anemia. Here we evaluate the
outcome of hematopoietic stem cell transplantation (HSCT) in 17 children
and young adults with sMDS/sAML after childhood aplastic anemia. The
median interval between the diagnosis of aplastic anemia and the development
of sMDS/sAML was 2.9 years (range, 1.2 to 13.0 years). At a median age of
13.1 years (range, 4.4 to 26.7 years), patients underwent HSCT with bone
marrow (n = 6) or peripheral blood stem cell (n = 11) grafts from HLA-
matched sibling donors (n = 2), mismatched family donors (n = 2), or
unrelated donors (n = 13). Monosomy 7 was detected in 13 patients. The
preparative regimen consisted of busulfan, cyclophosphamide, and melphalan
in 11 patients and other agents in 6 patients. All patients achieved neutrophil
engraftment. The cumulative incidence of grade II-IV acute graft-versus-host
disease (GVHD) was 47%, and that of chronic GVHD was 70%. Relapse
occurred in 1 patient. The major cause of death was transplant-related
complication (n = 9).Overall survival and event-free survival at 5 years after
HSCT were both 41%.In summary, this study indicates that HSCT is a curative
therapy for some patients with sMDS/sAML after aplastic anemia. Future
efforts should focus on reducing transplantation-related mortality.

Hematopoietic stem cells: An overview

Youssef Mohamed Mosaad
Transfusion and Apheresis Science 51 (2014) 68–82
http://dx.doi.org/10.1016/j.transci.2014.10.016

Considerable efforts have been made in recent years in understanding the
mechanisms that govern hematopoietic stem cell (HSC) origin, development,
differentiation, self-renewal, aging, trafficking, plasticity and trans-differentiation.
Hematopoiesis occurs in sequential waves in distinct anatomical locations during
development and these shifts in location are accompanied by changes in the
functional status of the stem cells and reflect the changing needs of the
developing organism. HSCs make a choice of either self-renewal or committing
to differentiation. The balance between self-renewal and differentiation is
considered to be critical to the maintenance of stem cell numbers. It is still
under debate if HSC can rejuvenate infinitely or if they do not possess ‘‘true”
self-renewal and undergo replicative senescence such as any other somatic
cell. Gene therapy applications that target HSCs offer a great potential for the
treatment of hematologic and immunologic diseases. However, the clinical
success has been limited by many factors. This review is intended to
summarize the recent advances made in the human HSC field, and will
review the hematopoietic stem cell from definition through development
to clinical applications.

HLA epitope based matching for transplantation

René J. Duquesnoy
Transplant Immunology 31 (2014) 1–6
http://dx.doi.org/10.1016/j.trim.2014.04.004

As important risk factors for transplant rejection and failure, HLA antibodies
are now recognized as being specific for epitopes which can be defined
structurally with amino acid differences between HLA alleles. Donor–recipient
compatibility should therefore be assessed at the epitope rather than the
antigen level. HLA Matchmaker is a computer algorithm that considers each
HLA antigen as a series of small configurations of polymorphic residues
referred to as eplets as essential components of HLA epitopes. It includes
epitopes on antigens encoded by all HLA-A, B, C, DR, DQ and DP loci as
well as MICA. HLA epitopes have two characteristics namely antigenicity, i.e.
the reactivity with antibody and immunogenicity, i.e. the ability of eliciting
an antibody response. This article addresses the relevance of determining
epitope-specificities of HLA antibodies, the effect of epitope structure on
technique-dependent antibody reactivity and the identification of acceptable
mismatches for sensitized patients considered for transplantation. Permissible
mismatching for non-sensitized patients aimed to prevent or reduce HLA
antibody responses could consider epitope loads of mismatched antigens and
the recently developed nonself-self paradigm of epitope immunogenicity.

Impact of HLA Mismatch Direction on the Outcome of Unrelated Bone
Marrow Transplantation: A Retrospective Analysis from the Japan
Society for Hematopoietic Cell Transplantation

Junya Kanda, T Ichinohe, S Fuji, Y Maeda, K Ohashi, …, Y Atsuta,
Y Kanda, on behalf of the HLA Working Group of the Japan Society
for Hematopoietic Cell Transplantation
Biol Blood Marrow Transplant 21 (2015) 305e311
http://dx.doi.org/10.1016/j.bbmt.2014.10.015

The relative desirability of an unrelated donor with a bidirectional 1-locus
mismatch (1MM-Bi), a 1-locus mismatch only in the graft-versus-host direction
(1MM-GVH), or a 1-locus mismatch only in the host versus-graft direction
(1MM-HVG) is not yet clear. We analyzed adult patients with leukemia or
myelodysplastic syndrome who received a first allogeneic stem cell transplant
from an HLA-A, -B, -C, and -DRB1 matched or 1-allele mismatched unrelated
donor in Japan. The effects of 1MM-Bi (n = 1020), 1MM-GVH (n = 83), and
1MM-HVG (n = 83) compared with a zero mismatch (0MM) (n = 2570)
were analyzed after adjusting for other significant variables. The risk of
grades III to IV acute graft-versus-host disease (GVHD) was higher with
marginal significance in the 1MM-GVH group than in the 0MM group
(hazard ratio, 1.85; P = .014). However, there was no significant difference
in overall or nonrelapse mortality between the 1MM-GVH and 0MM groups.
There was no significant difference in acute GVHD or overall or nonrelapse
mortality between the 1MM-HVG and 0MM groups. The risks of acute
GVHD and overall mortality were significantly higher in the 1MM-Bi group
than in the 0MM group. These findings indicate that unrelated donors with
1MM-GVH and 1MM-HVG are both good candidates for patients without an
HLA-matched unrelated donor in a Japanese cohort.

ABO incompatibility between donor and recipient and clinical
outcomes in allogeneic stem cell transplantation

James Goldman, Jane Liesveld, Diane Nichols, Joanna Heal, Neil Blumberg
Leukemia Research 27 (2003) 489–491 PII: S0145-2126(02)00259-X

We performed a retrospective, cohort study to evaluate the impact on recipient
survival of ABO incompatibility between recipient and donor after allogeneic
stem cell transplantation, primarily involving marrow-derived cells. No
statistically significant difference was noted in survival for 153 patients
with acute or chronic leukemia or myelodysplastic syndrome receiving
ABO identical or ABO mismatched allografts. Five patients who had
allografts that were bidirectionally incompatible (both donor cells and
plasma incompatible) did have significantly poorer survival than the other
recipients, similar to the experience reported in one other cohort study.
However, these patients had other risks for mortality, including being
older and receiving transplants from matched, unrelated donors. Our
data do not support a significant role for ABO donor–recipient matching in
allogeneic stem cell transplantation.

Allogeneic Hematopoietic Cell Transplantation Outcomes in
Acute Myeloid Leukemia: Similar Outcomes Regardless of
Donor Type

Erica D. Warlick, RP de Latour, R Shanley, …, Gerard Socie
Biol Blood Marrow Transplant 21 (2015) 357e363
http://dx.doi.org/10.1016/j.bbmt.2014.10.030

The use of alternative donor transplants is increasing as the transplantation-
eligible population ages and sibling donors are less available. We
evaluated the impact of donor source on transplantation outcomes for
adults with acute myeloid leukemia undergoing myeloablative (MA) or
reduced-intensity conditioning (RIC) transplantation. Between January 2000
and December 2010, 414 consecutive adult patients with acute myeloid
leukemia in remission received MA or RIC allogeneic transplantation from
either a matched related donor (n = 187), unrelated donor (n = 76), or
umbilical cord blood donor (n = 151) at the University of Minnesota or
Hôpital St. Louis in Paris. We noted similar 6-year overall survival
across donor types: matched related donor, 47% (95% confidence interval
[CI], 39% to 54%); umbilical cord blood, 36% (95% CI, 28% to 44%);
matched unrelated donor, 54% (95% CI, 40% to 66%); and mismatched
unrelated donor, 51% (95% CI, 28% to 70%) (P < .11). Survival differed
based on conditioning intensity and age, with 6-year survival of 57% (95% CI,
47% to 65%), 39% (95% CI, 28% to 49%), 23% (95% CI, 6% to 47%), 47%
(95% CI, 36% to 57%), and 28% (95% CI, 17% to 41%) for MA age 18 to 39,
MA age 40þ, or RIC ages 18 to 39, 40 to 56, and 57 to 74, respectively
(P < .01). Relapse was increased with RIC and lowest in younger patients
receiving MA conditioning (hazard ratio, 1.0 versus 2.5 or above for all RIC
age cohorts), P <.01. Transplantation-related mortality was similar across
donor types. In summary, our data support the use of alternative donors as
a graft source with MA or RIC for patients with acute myeloid leukemia
when a sibling donor is unavailable.

A Novel Reduced-Intensity Conditioning Regimen for Unrelated Umbilical
Cord Blood Transplantation in Children with Nonmalignant Diseases

Suhag H. Parikh, A Mendizabal, CL Benjamin, KV Komandur, J Antony, et al.
Biol Blood Marrow Transplant 20 (2014) 326e336
http://dx.doi.org/10.1016/j.bbmt.2013.11.021

Reduced-intensity conditioning (RIC) regimens have the potential to decrease
transplantation-related morbidity and mortality. However, engraftment
failure has been prohibitively high after RIC unrelated umbilical cord blood
transplantation (UCBT) in chemotherapy-naïve children with nonmalignant
diseases (NMD). Twenty-two children with a median age of 2.8 years, many
with severe comorbidities and prior viral infections, were enrolled in a novel RIC
protocol consisting of hydroxyurea, alemtuzumab, fludarabine, melphalan, and
thiotepa followed by single UCBT. Patients underwent transplantation for
inherited metabolic disorders (n = 8), primary immunodeficiencies (n = 9),
hemoglobinopathies (n = 4) and Diamond Blackfan anemia (n = 1). Most
umbilical cord blood (UCB) units were HLA-mismatched with median infused
total nucleated cell dose of 7.9 107/kg. No serious organ toxicities were
attributable to the regimen. The cumulative incidence of neutrophil engraftment
was 86.4% (95% confidence interval [CI], 65% to 100%) in a median of 20
days, with the majority sustaining > 95% donor chimerism at 1 year. Cumulative
incidence of acute graft-versus-host disease (GVHD) grades II to IV and III to IV
by day 180 was 27.3% (95% CI, 8.7% to 45.9%) and 13.6% (95 CI, 0% to 27.6%),
respectively. Cumulative incidence of extensive chronic GVHD was 9.1% (95%
CI, 0% to 20.8%). The primary causes of death were viral infections (n ¼ 3), acute
GVHD (n = 1) and transfusion reaction (n ¼ 1). One-year overall and event-free
survivals were 77.3% (95% CI, 53.7% to 89.8%) and 68.2% (95% CI, 44.6%
to 83.4%) with 31 months median follow-up. This is the first RIC protocol
demonstrating durable UCB engraftment in children with NMD. Future risk-
based modifications of this regimen could decrease the incidence of viral
infections. (www.clinicaltrials.gov/NCT00744692).

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Gastrointestinal Endocrinology

Writer and Curator: Larry H Bernstein, MD, FCAP

The Gut Microbial Endocrine Organ: Bacterially Derived Signals Driving Cardiometabolic DiseasesMark Brown and Stanley L. Hazen

Annual Review of Medicine Jan 2015; 66: 343-359
http://dx.doi.org:/10.1146/annurev-med-060513-093205

The human gastrointestinal tract is home to trillions of bacteria, which vastly outnumber host cells in the body. Although generally overlooked in the field of endocrinology, gut microbial symbionts organize to form a key endocrine organ that converts nutritional cues from the environment into hormone-like signals that impact both normal physiology and chronic disease in the human host. Recent evidence suggests that several gut microbial-derived products are sensed by dedicated host receptor systems to alter cardiovascular disease (CVD) progression. In fact, gut microbial metabolism of dietary components results in the production of proatherogenic circulating factors that act through a meta-organismal endocrine axis to impact CVD risk. Whether pharmacological interventions at the level of the gut microbial endocrine organ will reduce CVD risk is a key new question in the field of cardiovascular medicine. Here we discuss the opportunities and challenges that lie ahead in targeting meta-organismal endocrinology for CVD prevention.

Exogenous glucagon-like peptide 1 reduces contractions in human colon circular muscle

Antonella Amato, Sara Baldassano, Rosa Liotta1, Rosa Serio and Flavia Mulè
J Endocrinol April 1, 2014 221 29-37
http://dx.doi.org:/10.1530/JOE-13-0525

Glucagon-like peptide 1 (GLP1) is a naturally occurring peptide secreted by intestinal L-cells. Though its primary function is to serve as an incretin, GLP1 reduces gastrointestinal motility. However, only a handful of animal studies have specifically evaluated the influence of GLP1 on colonic motility. Consequently, the aims of this study were to investigate the effects induced by exogenous GLP1, to analyze the mechanism of action, and to verify the presence of GLP1 receptors (GLP1Rs) in human colon circular muscular strips. Organ bath technique, RT-PCR, western blotting, and immunofluorescence were used. In human colon, exogenous GLP1 reduced, in a concentration-dependent manner, the amplitude of the spontaneous contractions without affecting the frequency and the resting basal tone. This inhibitory effect was significantly reduced by exendin (9–39), a GLP1R antagonist, which per se significantly increased the spontaneous mechanical activity. Moreover, it was abolished by tetrodotoxin, a neural blocker, or Nω-nitro-L-arginine – a blocker of neuronal nitric oxide synthase (nNOS). The biomolecular analysis revealed a genic and protein expression of the GLP1R in the human colon. The double-labeling experiments with anti-neurofilament or anti-nNOS showed, for the first time, that immunoreactivity for the GLP1R was expressed in nitrergic neurons of the myenteric plexus. In conclusion, the results of this study suggest that GLP1R is expressed in the human colon and, once activated by exogenous GLP1, mediates an inhibitory effect on large intestine motility through NO neural release.

The impact of dipeptidyl peptidase 4 inhibition on incretin effect, glucose tolerance, and gastrointestinal-mediated glucose disposal in healthy subjects

N A Rhee, S H Østoft, J J Holst, C F Deacon, T Vilsbøll and F K Knop
Eur J Endocrinol September 1, 2014 171 353-36
http://dx.doi.org:/10.1530/EJE-14-0314

Objective Inhibition of dipeptidyl peptidase 4 (DPP4) is thought to intensify the physiological effects of the incretin hormones. We investigated the effects of DPP4 inhibition on plasma levels of glucose-dependent insulinotropic polypeptide (GIP), glucagon-like peptide 1 (GLP1), incretin effect, glucose tolerance, gastrointestinal-mediated glucose disposal (GIGD) and gastric emptying in healthy subjects. Design A randomised, controlled and open-labelled study. Methods Ten healthy subjects (six women; age, 40±5 years (mean±S.E.M.); BMI, 24±3 kg/m2; fasting plasma glucose, 5.1±0.2 mmol/l and HbA1c, 34±1 mmol/mol (5.3±0.1%)) were randomised to two-paired study days comprising a 4-h 50 g oral glucose tolerance test (OGTT) with paracetamol (A) and an isoglycaemic intravenous (i.v.) glucose infusion (B), with (A1+B1) and without (A2+B2) preceding administration of the DPP4 inhibitor sitagliptin. Results Isoglycaemia was obtained in all subjects on the paired study days. Significant increases in fasting levels and OGTT-induced responses of active GLP1 and GIP were seen after DPP4 inhibition. No significant impact of DPP4 inhibition on fasting plasma glucose (5.1±0.1 vs 4.9±0.1 mmol/l, P=0.3), glucose tolerance (area under the curve (AUC) for plasma glucose, 151±35 vs 137±26 mmol/l×min, P=0.7) or peak plasma glucose during OGTT (8.5±0.4 vs 8.1±0.3 mmol/l, P=0.3) was observed. Neither incretin effect (40±9% (without DPP4 inhibitor) vs 40±7% (with DPP4 inhibitor), P=1.0), glucagon responses (1395±165 vs 1223±195 pmol/l×min, P=0.41), GIGD (52±4 vs 56±5%, P=0.40) nor gastric emptying (Tmax for plasma paracetamol: 86±9 vs 80±12 min, P=0.60) changed following DPP4 inhibition. Conclusions These results suggest that acute increases in active incretin hormone levels do not affect glucose tolerance, GIGD, incretin effect, glucagon responses or gastric emptying in healthy subjects.

Morphology and Tissue Distribution of Four Kinds of Endocrine Cells in the Digestive Tract of the Chinese Yellow Quail (Coturnix japonica)

He, M., Liang, X., Wang, K., (…), Li, X., Liu, L.
Analytical and Quantitative Cytology and Histology 2014; 36 (4), pp. 199-205

Objective: To describe the tissue distribution, density, and the morphological characteristics of 4 kinds of endocrine cells in the digestive tract of the Chinese yellow quail (Coturnix japonica). Study design: The streptavidin-biotin-peroxidase complex immunohistochemical method was used to identify the distribution of somatostatin (SS), serotonin (5-HT), gastrin and neuropeptide Y (NPY) in digestive tracts including proventriculus, duodenum, jejunum, ileum, and rectum. SPSS 19.0 software was used to perform biological statistical analysis. Results: The results showed that the SS and 5-HT secreting cells were mainly distributed in the proventriculus (19.2±6.9 and 16.1±3.4 cfu/mm2) and duodenum (2.9±2.0 and 1.9±0.6 cfu/mm2). Gastrin and NPY were not detected in each section of the digestive tract. Moreover, there was no significant difference in the quantitative distribution and morphological characteristics of SS and 5-HT secreting cells in the digestive tract between male and female quails. Conclusion: The distribution and morphological characteristics of endocrine cells were closely related to the physiological functions of different parts in the digestive tract. The preferential location of endocrine cells provides additional information for future studies on the physiological roles of gastrointestinal peptides in the gastrointestinal tract of the Chinese yellow quail

GEP-NETS update: Functional localisation and scintigraphy in neuroendocrine tumours of the gastrointestinal tract and pancreas (GEP-NETs)

Wouter W de Herder
Eur J Endocrinol May 1, 2014 170 R173-R183
http://dx.doi.org:/10.1530/EJE-14-0077

For patients with neuroendocrine tumours (NETs) of the gastrointestinal tract and pancreas (GEP) (GEP-NETs), excellent care should ideally be provided by a multidisciplinary team of skilled health care professionals. In these patients, a combination of nuclear medicine imaging and conventional radiological imaging techniques is usually mandatory for primary tumour visualisation, tumour staging and evaluation of treatment. In specific cases, as in patients with occult insulinomas, sampling procedures can provide a clue as to where to localise the insulin-hypersecreting pancreatic NETs. Recent developments in these fields have led to an increase in the detection rate of primary GEP-NETs and their metastatic deposits. Radiopharmaceuticals targeted at specific tumour cell properties and processes can be used to provide sensitive and specific whole-body imaging. Functional imaging also allows for patient selection for receptor-based therapies and prediction of the efficacy of such therapies. Positron emission tomography/computed tomography (CT) and single-photon emission CT/CT are used to map functional images with anatomical localisations. As a result, tumour imaging and tumour follow-up strategies can be optimised for every individual GEP-NET patient. In some cases, functional imaging might give indications with regard to future tumour behaviour and prognosis.

An immunohistochemical study on the distribution of endocrine cells in the digestive tract of gray goose (Anser anser)

Jun YANG1, Lei ZHANG,, Xin LI, , Leii ZHANG, , Xiangjiang LIU, , Kemei PENG

Turk. J. Vet. Anim. Sci. 2012; 36(4): 373-379
http://dx.doi.org:/10.3906/vet-1101-654

The objective of this study was to investigate the morphology and the distribution of 5-hydroxytryptamine (5-HT), somatostatin (SS), gastrin (Gas), glucagon (Glu), and substance P immunoreactive (IR) cells in the digestive tract of gray goose by the immunohistochemical streptavidin-peroxidase method.

The samples were taken from 10 healthy  adult gray geese. Th e results showed that 5 kinds of IR cells were mainly distributed between the mucous epithelium and intestinal gland. The number of 5-HT-IR cells was highest in the rectum and duodenum, but none were observed  in the pylorus. SS-IR cells appeared in great numbers in the pylorus, duodenum, and cecum; however, they were not found in esophagus. Gas-IR cells were mainly distributed in the glandular stomach and jejunum. Glu-IR cells appeared  in small numbers in the glandular stomach, duodenum, and jejunum, but were not detected in other tissues. Substance  P-IR cells were located in the jejunum, cecum, and rectum. Analysis of the present study showed that the distribution and morphological features of these 5 different endocrine cells were related to the feeding habits and metabolism in the digestive tract of the gray goose

Chapter 154 – Somatostatin

Mathias Guggera, Jean-Claude Meunierb

Handbook of Biologically Active Peptides 2006, Pages 1123–1130
http:/dx.doi.org:/10.1016/B978-012369442-3/50157-4

Somatostatin is abundant in the mucosa and in the enteric nervous system of the gastrointestinal tract and in the pancreas. In these tissues, it exerts a broad range of mainly inhibitory physiological actions in multiple targets, including endocrine glands, exocrine glands, smooth muscles, blood vessels, and immune cells, mediated by up to six somatostatin receptor subtypes. Several diseases of the gastrointestinal tract are characterized by disturbances in the somatostatin production or by overexpression of somatostatin receptors. In particular, somatostatin receptors have been found to be overexpressed in neuroendocrine gastroenteropancreatic tumors. These tumors can be diagnostically and therapeutically targeted with somatostatin analogs. In addition, various nonneoplastic diseases, including bleeding in the upper gastrointestinal tract, fistulas, and diarrhea can also be treated with somatostatin analogs.

Immunocytochemical study of the distribution of endocrine cells in the pancreas of the Brazilian sparrow species Zonotrichia Capensis Subtorquata (Swaison, 1837)

Nascimento, AA.*; Sales, A.; Cardoso, TRD.; Pinheiro, NL.; Mendes, RMM.
Braz. J. Biol. Nov. 2007; 67(4):  São Carlos

In the present study, we investigated types of pancreatic endocrine cells and its respective peptides in the Brazilian sparrow species using immunocytochemistry. The use of polyclonal specific antisera for somatostatin, glucagon, avian pancreatic polypeptide (APP), YY polypeptide (PYY) and insulin, revealed a diversified distribution in the pancreas. All these types of immunoreactive cells were observed in the pancreas with different amounts. Insulin- Immunoreactive cells to (B cells) were most numerous, preferably occupying the central place in the pancreatic islets. Somatostatin, PPA, PYY and glucagon immunoreactive cells occurred in a lower frequency in the periphery of pancreatic islets.

Immunolocalisation of the serotonin in the fundus ventriculi and duodenum of the Asia minor ground squirrel: (Spermophilus xanthoprymnus)

Timurkaan, S., Özkan, E., Ilgün, R., Gür, F.M
Veterinarski Arhiv 2009; 79 (1), pp. 69-76

Serotonin immunoreactive cells were located and distributed in the fundus and duodenum with variable frequencies. They were spherical or spindle-shaped and the highest frequency serotonin immunoreactive cells were detected in the whole fundic region. The regional distribution of the endocrine cells in the fundus and duodenum of the citellus resembled other mammalian species.

An Immunohistochemical Study of Gastrointestinal Endocrine Cells in the BALB/c Mouse

Ku, S.K., Lee, H.S., Lee, J.H.
J Vet Med Series C: Anatomia Histologia Embryologia 2004; 33 (1), pp. 42-48

The distributions and frequencies of some endocrine cells in the eight portions of the gastrointestinal tract (GIT) of BALB/c mouse were studied. Endocrine cells were stained using immunohistochemical method with seven types of anti-sera against bovine chromogranin (BCG), serotonin, gastrin, cholecystokinin (CCK)-8, somatostatin, glucagon and human pancreatic polypeptide (HPP), and the regional distributions and their relative frequencies were observed in the eight portions of the GIT of BALB/c mice. All seven types of immunoreactive (IR) cells were identified. Most of the IR cells in the intestinal portion were generally spherical or spindle in shape (open type cell) while round-shaped cells (closed type cell) were found in the intestinal gland and stomach regions occasionally. Their relative frequencies varied according to each portion of the GIT. BCG-IR cells were observed throughout the whole GIT except for the rectum and they were most predominant in the pylorus. Serotonin-IR cells were detected throughout the whole GIT and they showed the highest frequency in the fundus. Gastrin- and CCK-IR cells were restricted to the pylorus and duodenum with a majority in the pylorus and rare or a few frequencies in the duodenum. Compared with other mammals, somatostatin-IR cells were restricted to the fundus and pylorus with a few frequencies, respectively. In addition, glucagon- and HPP-IR cells were restricted to the fundus and duodenum, respectively, with relative low frequencies. Some species-dependent unique distributions and frequencies of endocrine cells were observed in the GIT of BALB/c mouse compared with other rodents.

Immunohistochemical study of the distribution of serotonin in the gastrointestinal tract of the porcupines (Hystrix cristata)

Timurkaan, S., Karan, M., Aydin, A.
Revue de Medecine Veterinaire 2005; 156 (11), pp. 533-536

Serotonin immunoreactive cells were located in the gastric glands and in the intestinal epithelium with variable frequencies. They were spherical or spindle-shaped. Serotonin immuno-reactive cells were detected in almost all regions of the gastrointestinal tract and they showed highest frequency in the stomach and colon.

Effects of carbachol on gastrin and somatostatin release in rat antral tissue culture

Wolfe, M.M., Jain, D.K., Reel, G.M., McGuigan, J.E.
Gastroenterology 1984; 87 (1), pp. 86-93

Recent studies have demonstrated that somatostatin-containing cells are in close anatomic proximity to gastrin-producing cells in antral mucosa, suggesting a potential local regulatory role for somatostatin. The purpose of this study was to examine further the relationships between gastrin and somatostatin and the effects of the cholinergic agonist carbachol on content and release of gastrin and somatostatin using rat antral mucosa in tissue culture. Antral mucosa was cultured at 37 °C in KrebsHenseleit buffer, pH 7.4, gassed with 95% O2-5% CO2. After 1 h, the culture medium was decanted and the tissue was boiled to extract mucosal gastrin and somatostatin. Inclusion of carbachol 2.5 × 10-6 M in the culture medium decreased medium somatostatin from 1.91 ± 0.28 (SEM) ng/mg tissue protein to 0.62 ± 0.12 ng/mg (p < 0.01), extracted mucosal somatostatin from 2.60 ± 0.30 to 1.52 ± 0.16 ng/mg (p < 0.001), and percentage of somatostatin released from 42% ± 2.6% to 27% ± 2.2% (p < 0.01). Carbachol also increased culture media gastrin from 14 ± 2.5 to 27 ± 3.0 ng/mg protein (p < 0.01). Tissue content and release of gastrin and somatostatin were also examined during culture of rat antral mucosa in culture media containing antibodies to somatostatin in the presence and in the absence of carbachol. Incubation with somatostatin antisera, both with and without carbachol, markedly increased culture media concentrations of somatostatin, all of which was effectively bound by antibodies present in the media. Antibody binding of somatostatin was accompanied by significant increases in culture media gastrin concentrations, both in the presence and in the absence of carbachol. Results of these studies support the hypothesis that antral somatostatin exerts a local regulatory effect on gastrin release and that cholinergic stimulation of gastrin release is mediated, at least in part, through inhibition of somatostatin synthesis and release.

Endogenous somatostatin-28 modulates postprandial insulin secretion. Immunoneutralization studies in baboons

J W Ensinck, R E Vogel, E C Laschansky, D J Koerker, et al.
J Clin Invest. 1997; 100(9):2295–2302.
http://dx.doi.org:/10.1172/JCI119767

Somatostatin-28 (S-28), secreted into the circulation from enterocytes after food, and S-14, released mainly from gastric and pancreatic D cells and enteric neurons, inhibit peripheral cellular functions. We hypothesized that S-28 is a humoral regulator of pancreatic B cell function during nutrient absorption. Consistent with this postulate, we observed in baboons a two to threefold increase in portal and peripheral levels of S-28 after meals, with minimal changes in S-14. We attempted to demonstrate a hormonal effect of these peptides by measuring their concentrations before and after infusing a somatostatin-specific monoclonal antibody (mAb) into baboons and comparing glucose, insulin, and glucagon-like peptide-1 levels before and for 4 h after intragastric nutrients during a control study and on 2 d after mAb administration (days 1 and 2). Basal growth hormone (GH) and glucagon levels and parameters of insulin and glucose kinetics were also measured. During immunoneutralization, we found that (a) postprandial insulin levels were elevated on days 1 and 2; (b) GH levels rose immediately and were sustained for 28 h, while glucagon fell; (c) basal insulin levels were unchanged on day 1 but were increased two to threefold on day 2, coincident with decreased insulin sensitivity; and (d) plasma glucose concentrations were similar to control values. We attribute the eventual rise in fasting levels of insulin to its enhanced secretion in compensation for the heightened insulin resistance from increased GH action. Based on the elevated postmeal insulin levels after mAb administration, we conclude that S-28 participates in the enteroinsular axis as a decretin to regulate postprandial insulin secretion.

The Therapeutic Value of Somatostatin and Its Analogues

Sadaf Farooqi, John S. Bevan, Michael C. Shepperd, John A. H. Wass
Pituitary June 1999; 2(1), pp 79-88
http:/dx.doi.org:/10.1023/A:1009978106476

In this review we discuss the physiological effects of somatostatin, which are mediated by specific receptor subtypes on different tissues. These observations have suggested new therapeutic possibilities for the use of the synthetic somatostatin analogues in the treatment of acromegaly as well as a number of other endocrine and non-endocrine disorders.

Somatostatin and Somatostatin Receptors

Ujendra Kumar, Michael Grant
Cellular Peptide Hormone Synthesis and Secretory Pathways
(Results and Problems in Cell Differentiation) 2010; 50: pp 97-120
http://dx.doi.org:/10.1007/400_2009_29

The biological effects of somatostatin (SST) were first encountered unexpectedly in the late 1960s in two unrelated studies, one by Krulich et al. (1968) who reported on a growth hormone (GH)-releasing inhibitory substance from hypothalamic extracts, and the other, by Hellman and Lernmark (1969), on the presence of a potent insulin inhibitory factor from the extracts of pigeon pancreatic islets. However, the inhibitory substance was not officially identified until 1973 by Guillemin’s group (Brazeau et al. 1973). In both synthetic and naturally occurring forms, this tetradecapeptide, originally coined as somatotropin release-inhibitory factor (SRIF, SST-14) was shown by Brazeau et al. to be the substance controlling hypothalamic GH release. This single achievement not only pioneered SST research but was also duly recognized, as Guillemin shared the 1977 Nobel Prize in Medicine. The following years bequeathed an exponential increase in SST-related studies. It soon became clear that SST-synthesis was not restricted to the hypothalamus. Its production is widely distributed throughout the central nervous system (CNS), peripheral neurons, the gastrointestinal tract, and the pancreatic islets of Langerhans (Luft et al. 1974; Arimura et al. 1975; Dubois 1975; Hokfelt et al. 1975; Orci et al. 1975; Pelletier et al. 1975; Polak et al. 1975; Patel and Reichlin 1978). In fact, SST-like immunoreactivity can be found throughout various tissues of vertebrates and invertebrates, including the plant kingdom (Patel 1992; Tostivint et al. 2004). Given its broad anatomical distribution, it is no wonder that SST produces a wide spectrum of biological effects. Generally regarded as an inhibitory factor, SST can function either locally on neighboring cells or distantly through the circulation, to regulate such physiological processes as glandular secretion, neurotransmission, smooth muscle contractility, nutrient absorption, and cell division (Reichlin 1983a, b; Patel 1992, 1999; Patel et al. 2001; Barnett 2003).

Receptor-Mediated Tumor Targeting with Radiopeptides. Part 1. General Concepts and Methods: Applications to Somatostatin Receptor-Expressing Tumors

Alex N. Eberle, Gabriele Mild, and Sylvie Froidevaux
Journal of Receptors and Signal Transduction  2004; 24(4) , Pages 319-455
http://dx.doi.org:/10.1081/RRS-200040939

Radiolabeled peptides have become important tools in nuclear oncology, both as diagnostics and more recently also as therapeutics. They represent a distinct sector of the molecular targeting approach, which in many areas of therapy will implement the old “magic bullet” concept by specifically directing the therapeutic agent to the site of action. In this three-part review, we present a comprehensive overview of the literature on receptor-mediated tumor targeting with the different radiopeptides currently studied. Part I summarizes the general concepts and methods of targeting, the selection of radioisotopes, chelators, and the criteria of peptide ligand development. Then, the >400 studies on the application to somatostatin/somatostatin-release inhibiting factor receptor-mediated tumor localization and treatment will be reviewed, demonstrating that peptide radiopharmaceuticals have gained an important position in clinical medicine.

The somatostatin neuroendocrine system: physiology and clinical relevance in gastrointestinal and pancreatic disorders

Malcolm J. Low
Best Practice & Res Clin Endocr & Metab, 2004; 18(4), pp. 607–622
http://dx.doi.org:/10.1016/j.beem.2004.08.005

The physiologic functions of hypothalamic somatostatin in the regulation of pituitary hormone secretion and the clinical use of somatostatin analogs for the treatment of pituitary adenomas have been reviewed. Similarly, the distribution, normal function and potential pathogenic roles of somatostatin in the central nervous system have been reported in detail. This review will focus exclusively on the physiologic actions of somatostatin and its receptors in the gastrointestinal tract, pancreas and immune system. Diagnostic and therapeutic roles of somatostatin analogs in a diverse catalog of neoplastic, inflammatory and autoimmune conditions affecting peripheral systems are outlined, with an emphasis on both well-established indications and current areas of exploration.

Somatostatin is produced in enteroendocrine D cells and intrinsic neurons of the stomach, intestines and pancreas. Its physiologic actions are mediated primarily by somatostatin receptors type 2 and 5, and include the inhibition of secretion of most endocrine and exocrine factors. Diseases directly attributable to somatostatin excess or deficiency are rare, although there is a complex pathogenic relationship between persistent Helicobacter pylori infection and reduced somatostatin in chronic gastritis. Abundant somatostatin receptors on many neoplastic and inflammatory cells are the basis for sensitive in vivo imaging with radiolabeled somatostatin analogs and provide a therapeutic target. Current indications for somatostatin therapy include hormone-expressing neuroendocrine tumors, intractable diarrhea and variceal bleeding secondary to portal hypertension. Exciting advances are being made in the development of high-affinity nonpeptide analogs with receptor-subtype selectivity and increased bioavailability. Somatostatin analogs coupled to high-energy radionuclides show promise as novel cytotoxic agents for certain metastatic tumors.

Evolution of the somatostatin gene family Both forms of mammalian somatostatin are derived post-translationally from a common pro-hormone by the action of specific pro-protein convertases (PCs). Genetic studies indicate a primary role for PC2 in the generation of SST147, which is the predominant form of somatostatin produced in the brain and most other tissues. SST28 is found in its highest concentrations in the gastrointestinal tract, especially the mucosal epithelial cells of the intestines.
A revised evolutionary concept of the somatostatin gene family is that a primordial gene underwent duplication during or before the advent of chordates and that the two resulting genes subsequently underwent differing rates of mutation to produce the distinct prepro-somatostatin and prepro-cortistatin genes in mammals. A second gene duplication event likely occurred in teleosts to generate PSS1 and PSS-II from the ancestral somatostatin gene.
It is possible that additional related genes have not yet been identified. Recent studies utilizing unique polyclonal antisera and a strain of somatostatin-deficient mouse have demonstrated the existence of a novel gastrointestinal peptide with homology to the amino acid sequence of SST28(1–13) that has been named thrittene.
Somatostatin gene organization and regulation The mammalian PPS1 (or SMST) gene has a relatively simple organization consisting of two coding exons separated by one intron. A single promoter directs transcription of the PPS1 gene in all tissues, and there are no known alternative mRNA splicing events. The molecular mechanisms underlying the developmental and hormonal regulation of somatostatin gene transcription have been most extensively studied in pancreatic islets and islet-derived cell lines. The proximal enhancer elements in the somatostatin gene promoter that bind complexes of homeodomain-containing transcription factors (PAX6, PBX, PREP1) to upregulate transcription in pancreatic islets may actually represent gene silencer elements in neurons (promoter elements TSEII and UE-A). Conversely, another related cis-element in the somatostatin gene (promoter element TSEI) apparently binds a homeodomain transcription factor PDX1 (also called STF1/ IDX1/IPF1) that is common to developing brain, pancreas and foregut, and regulates gene expression in both the CNS and gut.
Enteroendocrine cells of the gut mucosa differentiate from pluripotential stem cells in the crypts, share molecular phenotypes and retain close paracrine interactions among the daughter cells. Similarly, pancreatic islet cells share common precursors. Recent studies have demonstrated that bone marrow contains a stem cell population capable of producing islet-like cell clusters in vitro that contain somatostatin-positive cells together with the other cell types found in normally differentiated islets.
Somatostatin Receptors  There are five somatostatin receptor subtypes (SSTR1–5) encoded by separate genes located on different chromosomes. Alternative mRNA splicing generates SSTR2α and SSTR2β from heteronuclear RNA after transcription from the single SSTR2 gene. SSTRs are members of the rhodopsin-like G protein-coupled receptor superfamily and are most closely related structurally to the opioid receptors. The unique amino acid signature of SSTRs is contained in a seven-element fingerprint of peptide sequences located in conserved regions of the N and C termini, extra- and intra-cellular loops, and transmembrane domains. SSTRs are expressed in discrete or partially overlapping distributions in multiple target organs and differ in their coupling to second messenger signaling molecules, and therefore in their range and mechanism of intracellular actions. The subtypes also differ in their binding affinity to specific somatostatin-like ligands. Some of these differences have important implications for the use of somatostatin analogs in diagnostic imaging and in pharmacotherapy.
All SSTR subtypes are coupled to pertussis toxin-sensitive G proteins and bind SST14 and SST28 with high affinity in the low nanomolar range, although SST28 has a modestly higher affinity for SSTR5. All the subtypes are expressed in brain and pituitary to varying degrees with different distributions, but SSTR2 and SSTR5 are clearly the most abundant in peripheral tissues. These two subtypes are also the most physiologically important in pancreatic islets. SSTR5 is responsible for the inhibition of insulin secretion from b-cells, and SSTR2 is essential for the inhibition of glucagon from a-cells. SSTR1 is expressed at low levels in gastrointestinal structures. The binding of somatostatin to its receptors leads to the activation of one or more inhibitory G proteins (Gi/o), which in turn decrease adenylyl cyclase activity and the concentration of intracellular cAMP. Other G protein-mediated actions common to all The somatostatin neuroendocrine system 609 SSTRs are activation of a vanadate-sensitive phosphotyrosine phosphatase (PTP) and modulation of mitogen-activated protein kinases (MAPKs).
Inhibition of endocrine and exocrine secretion Somatostatin has diverse biologic activities in the gastrointestinal system. It is secreted from D cells into the extracellular space to act as a paracrine factor on nearby endocrine cells and as an autocrine factor to inhibit its own secretion. Most of the circulating hormonal somatostatin originates from the stomach and intestines. Basal plasma levels are in the range of 30–100 pg/ml and increase postprandially by as much as 100% over baseline for a duration up to 2 hours. The release of somatostatin from enteric D cells is regulated by a combination of nutritional, humoral, neural and paracrine signals.

The modulatory role of somatostatin in gastric acid secretion by parietal cells illustrates the typical complexity of hormonal, paracrine and neural integration within the gastrointestinal tract.
Somatostatin secreted from gastric D cells modulates the gastrin-enterochromaffin-like cell—parietal cell axis. Gastrin, secreted from G cells, stimulates the release of histamine from enterochromaffin-like cells (ECL), which is in turn a major secretagog of hydrochloric acid (HCl) from gastric parietal (P) cells. Somatostatin (SST14) inhibits secretion from each of these cell types, although the predominant actions are on the G and ECL cells. Food intake mediates gastric acid secretion by activating both vagal nerves and intrinsic gastric neurons. D cells are stimulated by the autocrine release of amylin, the paracrine release of bombesin and atrial natiuretic peptide (ANP), the enteric neuron release of pituitary adenylate cyclase-activating peptide (PACAP) and cholecystokinin (CCK), and the T lymphocyte release of interleukin-4 (IL-4).D cells are inhibited by histamine acting on H3 receptors in a negative paracrine feedback loop from ECL cells and by other factors, including gamma-aminobutyric acid (GABA) and opioid peptides. The pathways illustrated are not all-inclusive but represent many of the key regulatory steps.

Practice points

† long-acting somatostatin analogs are primary therapeutic tools for the symptomatic treatment of the excessive hormone and monoamine secretion from carcinoids and other neuroendocrine tumors

† somatostatin and long-acting somatostatin analogs are effective first-line
medical treatment for upper gastrointestinal bleeding from esophageal varices associated with hepatic cirrhosis and portal hypertension but are not indicatedfor the treatment of bleeding from gastric varices or duodenal ulcers

† radiolabeled somatostatin analogs provide a sensitive imaging technique for a wide range of neoplastic and inflammatory disorders, including neuroendocrine tumors, meningiomas and sarcoidosis because of their high level expression of somatostatin receptors.

The role(s) of somatostatin, structurally related peptides and somatostatin receptors in the gastrointestinal tract: a review

J Van Op den bosch, D Adriaensen, L Van Nassauw, Jean-Pierre Timmermans
Regulatory Peptides 156 (2009) 1–8
http://dx.doi.org:/10.1016/j.regpep.2009.04.003

Extensive functional and morphological research has demonstrated the pivotal role of somatostatin (SOM) in the regulation of a wide variety of gastrointestinal activities. In addition to its profound inhibitory effects on gastrointestinal motility and exocrine and endocrine secretion processes along the entire gastrointestinal tract, SOM modulates several organ-specific activities. In contrast to these well-known SOM-dependent effects, knowledge on the SOM receptors (SSTR) involved in these effects is much less conclusive. Experimental data on the identities of the SSTRs, although species- and tissue-dependent, point towards the involvement of multiple receptor subtypes in the vast majority of gastrointestinal SOM-mediated effects. Recent evidence demonstrating the role of SOM in intestinal pathologies has extended the interest of gastrointestinal research in this peptide even further. More specifically, SOM is supposed to suppress intestinal inflammatory responses by interfering with the extensive bidirectional communication between mucosal mast cells and neurons. This way, SOM not only acts as a powerful inhibitor of the inflammatory cascade at the site of inflammation, but exerts a profound anti-nociceptive effect through the modulation of extrinsic afferent nerve fibers. The combination of these physiological and pathological activities opens up new opportunities to explore the potential of stable SOM analogues in the treatment of GI inflammatory pathologies.

Schematic overview of the distribution of the SSTRs 1–5

Schematic overview of the distribution of the SSTRs 1–5

Schematic overview of the distribution of the SSTRs 1–5 in the murine small intestine under control conditions (left panel) and during intestinal schistosomiasis (right panel). In non-inflamed conditions, SSTR1, SSTR2A and SSTR4 are expressed in non-neuronal (glial cells, enterocytes…) and neuronal cells, both from intrinsic and extrinsic origin. SSTR3 and SSTR5 are undetectable. In response to intestinal schistosomiasis, profound sprouting of nerve fibres expressing SSTR1, SSTR3 and SSTR4 is observed, in addition to the expression of SSTR1 and SSTR3 in mucosal mast cells (MMC).

Somatostatin and Its Receptor Family

Yogesh C. Patel
Frontiers in Neuroendocrinology 1999; 20, 157–198 Article ID frne.1999.0183

Somatostatin (SST), a regulatory peptide, is produced by neuroendocrine, inflammatory, and immune cells in response to ions, nutrients, neuropeptides, neurotransmitters, thyroid and steroid hormones, growth factors, and cytokines. The peptide is released in large amounts from storage pools of secretory cells, or in small amounts from activated immune and inflammatory cells, and acts as an endogenous inhibitory regulator of the secretory and proliferative responses of target cells that are widely distributed in the brain and periphery. These actions are mediated by a family of seven  transmembrane (TM) domain G-protein-coupled receptors that comprise five distinct subtypes (termed SSTR1–5) that are endoded by separate genes segregated on different chromosomes. The five receptor subtypes bind the natural SST peptides, SST-14 and SST-28, with low nanomolar affinity. Short synthetic octapeptide and hexapeptide analogs bind well to only three of the subtypes, 2, 3, and 5. Selective nonpeptide agonists with nanomolar affinity have been developed for four of the subtypes (SSTR1, 2, 3, and 4) and putative peptide antagonists for SSTR2 and SSTR5 have been identified. The ligand binding domain for SST ligands is made up of residues in TMs III–VII with a potential contribution by the second extracellular loop. SSTRs are widely expressed in many tissues, frequently as multiple subtypes that coexist in the same cell. The five receptors share common signaling pathways such as the inhibition of adenylyl cyclase, activation of phosphotyrosine phosphatase (PTP), and modulation of mitogen-activated protein kinase (MAPK) through G-protein-dependent mechanisms.

Somatostatin receptors

Lars Neisig Møller, Carsten Enggaard Stidsen, Bolette Hartmann, Jens Juul Holst
Biochimica et Biophysica Acta 1616 (2003) 1 – 84
http://dx.doi.org:/10.1016/S0005-2736(03)00235-9

In 1972, Brazeau et al. isolated somatostatin (somatotropin release-inhibiting factor, SRIF), a cyclic polypeptide with two biologically active isoforms (SRIF-14 and SRIF-28). This event prompted the successful quest for SRIF receptors. Then, nearly a quarter of a century later, it was announced that a neuropeptide, to be named cortistatin (CST), had been cloned, bearing strong resemblance to SRIF. Evidence of special CST receptors never emerged, however. CST rather competed with both SRIF isoforms for specific receptor binding. And binding to the known subtypes with affinities in the nanomolar range, it has therefore been acknowledged to be a third endogenous ligand at SRIF receptors. This review goes through mechanisms of signal transduction, pharmacology, and anatomical distribution of SRIF receptors. Structurally, SRIF receptors belong to the superfamily of G protein-coupled (GPC) receptors, sharing the characteristic seven-transmembrane-segment (STMS) topography. Years of intensive research have resulted in cloning of five receptor subtypes (sst1-sst5), one of which is represented by two splice variants (sst2A and sst2B). The individual subtypes, functionally coupled to the effectors of signal transduction, are differentially expressed throughout the mammalian organism, with corresponding differences in physiological impact. It is evident that receptor function, from a physiological point of view, cannot simply be reduced to the accumulated operations of individual receptors. Far from being isolated functional units, receptors co-operate. The total receptor apparatus of individual cell types is composed of different-ligand receptors (e.g. SRIF and non-SRIF receptors) and co-expressed receptor subtypes (e.g. sst2 and sst5 receptors) in characteristic proportions. In other words, levels of individual receptor subtypes are highly cell-specific and vary with the co-expression of different-ligand receptors. However, the question is how to quantify the relative contributions of individual receptor subtypes to the integration of transduced signals, ultimately the result of collective receptor activity. The generation of knock-out (KO) mice, intended as a means to define the contributions made by individual receptor subtypes, necessarily marks but an approximation. Furthermore, we must now take into account the stunning complexity of receptor co-operation indicated by the observation of receptor homo- and heterodimerisation, let alone oligomerisation. Theoretically, this phenomenon adds a novel series of functional megareceptors/super-receptors, with varied pharmacological profiles, to the catalogue of monomeric receptor subtypes isolated and cloned in the past. SRIF analogues include both peptides and non-peptides, receptor agonists and antagonists. Relatively long half lives, as compared to those of the endogenous ligands, have been paramount from the outset. Motivated by theoretical puzzles or the shortcomings of present-day diagnostics and therapy, investigators have also aimed to produce subtype-selective analogues. Several have become available.

Somatostatin And Its Analogues In The Therapy Of Gastrointestinal Disease

Wynick, J. M. Polak And S. R. Bloom
Pharmac. Ther. 1989; 41, pp. 353-370

During the course of efforts to determine the distribution of growth hormone-releasing factor (GHRF) in rat hypothalamus a substance that inhibited growth hormone release was unexpectedly detected by Krulich et aL (1968). Their findings led them to hypothesize that the secretion of growth hormone from the pituitary was regulated by two different interacting neurohumoral factors–one stimulatory, the other inhibitory–each under the control of the nervous system. At about the same time Hellman and Lernmark (1969) found a factor in extracts of pigeon pancreatic islet-cells that inhibited insulin release in vivo from cultured pancreatic islet-cells. These two observations, seemingly unrelated, were ultimately to converge with the chemical identification of somatostatin, as an inhibitory peptide found in both the hypothalamus and pancreas.

Growth hormone-release inhibitory activity was re-discovered in 1972 by Brazeau et al. (1973). A concentrated effort to isolate and sequence the active principal was successful and it proved to be a cyclic peptide, to which the term ‘somatostatin’ (somatotrophin release inhibitory factor) was applied.               Subsequent work (Reichlin, 1982a,b, 1983a,b; Iverson, 1983; Guillemin, 1978a,b) has considerably expanded the initially simple concept of somatostatin as a 14 amino-acid containing peptide (tetradecapeptide), bridged by a sulphur-sulphur bond whose main function was the regulation of growth-hormone secretion (Bonfils, 1985). Somatostatin related peptides are now known to constitute a family that includes the original identified peptide (designated somatostatin 14), an N-terminal extended somatostatin (somatostatin 28), several species specific variants and larger prohormone forms.
The name somatostatin may now be considered to be inappropriate because this compound is distributed widely in cells that have nothing to do with growth-hormone regulation or release. Tissues where somatostatin may be found include the nervous system, the gut and endocrine glands.
Somatostatin is present in every vertebrate class and even in primitive invertebrates (Vale et al., 1976; Falkmer et al., 1978; Jackson, 1978). This would suggest that this molecule and its controlling gene or genes evolved before the appearance on earth of differentiated cell-cell and nerve-cell communication (Roth et al., 1982). The evolutionary paths of mammals and fish are thought to have diverged at least 400 million years ago. The fact that the phenotype of somatostatin 14 is so well conserved (as to a lesser degree is that of somatostatin 28) suggests that throughout evolutionary history the specific configuration of somatostatin 14 has endowed a selective advantage on the animal kingdom, and its absence is not compatible with life.
Though widely distributed in cells throughout the body of vertebrates somatostatin does not in Guillemin’s words (1978a), “inhibit secretion of everything and anything” (since, for example it has no effect on the release of LH and FSH). Despite this it has certainly earned itself the nickname ‘endocrine cyanide’ (Bloom and Polak, 1987). The peptide is found in most but not all organs and displays specific and selective functions depending on its location. Within the nervous system somatostatinergic neurons are found in the cortex, limbic system, anterior pituitary, brain stem and spinal cord.
The various biological effects of somatostatin seem to be mediated through its specific high affinity receptors found in the brain, pituitary, adrenal, pancreas and gastrointestinal tract. Not only normal target tissue, but also tumors from the same endocrine tissues i.e. human pituitary adenomas, human and hamster pancreatic insulinomas, glucagonomas and VIPomas all bear somatostatin receptors (Reubi et al., 1981, 1982a, 1984a, 1985a, 1987a,b). Interestingly, tumors from tissues which are not established targets for somatostatin also seem to bear somatostatin receptors (Goodman et al., 1982; Reubi et al., 1986). Reubi et al. (1987b) demonstrated that many endocrine tumors including meningiomas, breast, pancreatic and pituitary tumors all have somatostatin receptors however, they demonstrated no receptors in prostatic carcinomas, ovarian carcinomas, endometrial carcinomas, primary liver cell carcinomas, pheochromocytomas, aldosterone secreting tumors, medullary carcinoma of the thyroid and a number of pulmonary carcinoids. Somatostatin receptors were also found in benign or malignant tumors originating from tissues not primarily known as somatostatin target organs, the biological function of such receptors is therefore unknown though it may be that they mediate the anti-proliferative effect of somatostatin and may therefore potentially be of therapeutic interest (Blankenstein et al., 1983, 1984).

Review article: somatostatin analogues in the treatment of gastroenteropancreatic neuroendocrine (carcinoid) tumoursModlin,

M. Pavel[1], M. Kidd & B. I. Gustafsson
Aliment Pharmacol Ther 2009; 31, 169–188
http://dx.doi.org:/10.1111/j.1365-2036.2009.04174.x

Background

The discovery of somatostatin (SST) and the synthesis of a variety of analogues constituted a major therapeutic advance in the treatment of gastroenteropancreatic neuroendocrine (carcinoid) tumours (GEP-NETs). They currently provide the most efficient treatment to achieve symptomatic relief and have recently been demonstrated to inhibit tumour growth.

Aim To review 35 years of experience regarding the clinical application and

efficacy of SST analogues. Methods The PubMed database (1972–2009) was searched using somatostatin as a search term with combinations of terms including ‘treatment’; ‘neuroendocrine’; ‘carcinoid’; ‘tumor’; ‘octreotide’; ‘lanreotide’ and ‘pasireotide’. Results In a review of 15 studies including 481 patients, the slow-release formulations Sandostatin LAR and Somatuline SR⁄ Autogel achieved symptomatic relief in 74.2% (61.9–92.8%) and 67.5% (40.0–100%), biochemical response in 51.4% (31.5–100%) and 39.0% (17.9–58%), and tumor response in 69.8% (47.0–87.5%) and 64.4% (48.0–87.0%) respectively. New SST analogues like SOM230 (pasireotide) that exhibit pan SST receptor activity and analogues with high affinity to specific somatostatin receptor (sstr) subtypes show promise. Conclusion As more precise understanding of NET cell biology evolves and molecular biological tools advance, more accurate identification of individual tumours sstr profile will probably facilitate a more precise delineation of SST analogue treatment.

Novel Autonomic Neurotransmitters And Intestinal Function

S. Taylor and R. A. R. Bywater
Pharmac. Ther. 1989; 40, pp. 401 to 438

In this review we will discuss some of the difficulties encountered in ascribing a neurotransmitter function to the more recently discovered peptides and other substances within the intestine. We will also provide a brief (and of necessity incomplete) account of some of the properties of intestinal putative neurotransmitters, and their possible roles in the functions of the small and large intestine.
The Enteric Nervous System The diverse intestinal functions associated with transit, digestion and absorption rely upon an intact enteric nervous system. The enteric nervous system essentially consists of those neurons whose cell bodies lie within the walls of the gastrointestinal tract. In the small and large intestine the cell bodies lie within the myenteric and submucous plexuses; their processes ramify throughout the majority of the intestinal wall and in many areas give rise to additional plexuses (Furness and Costa, 1987; Gabella, 1987). Functionally, these neurons can be divided into sensory neurons, interneurons and motor neurons. Some enteric neurons receive projections from extrinsic neurons and/or send projections centrally; we will not consider these projections further here.
The early observations of the co-existence of peptides in the enteric nervous system (Schultzberg et al., 1980) have now been extended and these studies demonstrate that the co-existence of two or more peptides is the rule rather than the exception (H6kfelt et al., 1987). The mix of peptides within neurons does not appear to be random; rather, there appears to be a systematic grouping of peptides in neurons with particular projections. This has led to the concept of “chemical coding” of enteric neurons. According to this concept, particular combinations of peptides are associated with particular neural pathways and perhaps with particular functions. For example, in the guinea pig small intestine, two chemically coded groups of submucous neurons have projections of different lengths running to the mucosa. Cell bodies with longer projections show immunoreactivity for dynorphin (DYN) and VIP. The other group shows immunoreactivity for choline acetyltransferase (CHAT), cholecystokinin, (CCK), calcitonin gene-related peptide (CGRP), neuropeptide Y (NPY) and somatostatin (SOM) (Costa et al., 1986a; Furness et al., 1987a). More recently it has been demonstrated that both groups of neurons show immunoreactivity for galanin (GAL) (Furness et al., 1987a,b). As for the neurotransmitter roles in the gut, the key question then becomes; “How does the presence of specific combinations of chemical substances (including peptides) relate to neuronal function?” It has been known for several years that “classical” transmitter substances can coexist in combination with various peptides (H6kfelt et al., 1980; Gilbert and Emson, 1983).
The above commentary upon the possible co-existence of several putative transmitter substances highlights the complex neurochemistry of the enteric nervous system. A corresponding degree of complexity appears to exist for the neuronal circuitry that ultimately directs the differing, but highly organized, patterns of motility and the secretory/absorptive functions of the intestinal tract. In vitro electrophysiological studies of the myenteric and submucous plexuses have indicated that several different types of neurons are present, each with their own biophysical characteristics. Furthermore, neurotransmission through, and probably between, the plexuses involves synaptic potentials which have time courses ranging from several milliseconds up to several minutes, depending upon the characteristics (stimulus strength, frequency and train length, etc.) and location of the applied electrical stimulus (see Wood, 1987, for references). Intracellular recordings from smooth muscle cells have also shown that excitatory and inhibitory junction potentials (EJPs and IJPS) of varying time courses can be evoked at various locations along the intestine during transmural electrical stimulation in response to selective stimulus regimens (see, for instance, Bywater and Taylor, 1986).
A number of authors have proposed criteria which should be fulfilled in order that transmitter status can be bestowed upon a particular substance (see Furness and Costa, 1982, for references). These criteria were developed with reference to the classical transmitter substances such as ACh, using the paradigm of a single transmitter per neuron. Regardless of the coexistence of several putative transmitters, status can only be granted to those substances that are found to be released from that nerve terminal. In the enteric nervous system a particular putative transmitter may be contained in several different functional pathways. However, in general, the methods used for eliciting release of putative transmitter substances (e.g. transmural electrical stimulation) are not specific for particular projections. Thus, for any substance, the association of demonstrated release with a given transmitter role is not facile.

New roles of the multidimensional adipokine: Chemerin

Syeda Sadia Fatima, Rehana Rehman, Mukhtiar Baig, Taseer Ahmed Khan
Peptides 62 (2014) 15–20
http://dx.doi.org/10.1016/j.peptides.2014.09.019

The discovery of several adipokines with diverse activities and their involvement in regulation of various pathophysiological functions of human body has challenged the researchers. In the family of adipokine, chemerin is a novel and unique addition. Ever since the first report on chemerin as a chemo-attractant protein, there are numerous studies showing a multitasking capacity of chemerin in the maintenance of homeostasis, for the activation of natural killer cells, macrophages and dendritic cells in both innate and adaptive immunity. Its diversity ranges from generalized inflammatory cascades to being explicitly involved in the manifestation of arthritis, psoriasis and peritonitis. Its association with certain cancerous tissue may render it as a potential tumor marker. In present review, we aim to consolidate recent data of investigations on chemerin in context to functional characteristics with a special reference to its role as a metabolic signal in inflammation and non-metabolic syndromes.

Neuropeptide Y is expressed in subpopulations of insulin- and non-insulin-producing islet cells in the rat after dexamethasone treatment: a combined immunocytochemical and in situ hybridisation study

Myrs6n a, *, B. Ahr6n b, F. Sundler
Regulatory Peptides 1995; 60, 19-31

Neuropeptide Y (NPY) is known to occur in adrenergic and non-adrenergic nerves in rat pancreatic islets. Analysis of islet extracts has revealed local NPY synthesis after glucocorticoid treatment. The cellular localization of NPY expression in rat islets following dexamethasone treatment (2 mg/kg daily, for 12 days), was investigated by a combination of immunocytochemistry (ICC) and in situ hybridization (ISH). NPY-immunoreactive nerve fibers were seen in pancreatic islets of both control and dexamethasone-treated rats. In the controls weak NPY immunoreactivity but no NPY mRNA was observed in occasional i:dets. After dexamethasone treatment, clusters of islet cells distributed both centrally and peripherally displayed intense NPY immunoreactivity and NPY mRNA labelling. Immunocytochemical double staining and ISH combined with ICC for NPY and islet hormones revealed that most NPY expressing cells were identical with insulin cells; a few cells were identical[ with somatostatin or pancreatic polypeptide (PP) cells. In contrast, glucagon cells seemed to be devoid of NPY immunoreactivity and NPY mRNA labelling. Thus, in the rat, glucocorticoids cause a marked upregulation of NPY expression in islet cells, preferentially the insulin cells. The expression of NPY might represent an islet adaptation mechanism to the reduced peripheral insulin sensitivity.

Neuropeptide Y is expressed in islet somatostatin cells of the hamster pancreas: a combined immunocytochemical and in situ hybridization study

Ulrika Myrsrn, Frank Sundler
Regulatory Peptides 1995; 57, 65-76

Neuropeptide Y (NPY) is known to occur in the autonomic nervous system, including the pancreatic islet innervation. We now present evidence that NPY is also expressed in endocrine islet cells in hamster pancreas. Thus, NPY-immunoreactivity and gene expression were detected in peripheral islet cells, using immunocytochemistry (ICC), in situ hybridization (ISH), and a combination of these techniques. Double immunostaining for NPY and somatostatin enabled localization of NPY to the vast majority of the somatostatin cells. However, a few somatostatin cells were devoid of NPY immunoreactivity and an occasional NPY-immunoreactive cell was devoid of somatostatin. ISH with an NPY mRNA specific probe, showed labelling of cells in the islet periphery. Furthermore, combined ISH for NPY mRNA and ICC for somatostatin showed autoradiographic labelling of somatostatin cells to a varying degree. Both somatostatin and NPY are inhibitors of insulin and/or glucagon secretion. Thus, in the islets these two peptides may be coreleased and cooperate in the, regulation of islet hormone secretion. The role for NPY emanating from islet cells is probably paracrine rather than endocrine.

Neuropeptide Y and Peptide YY Immunoreactivities in the Pancreas of Various Vertebrates

Wei-Guang Ding, Hiroshi Kimura, Masaki Fujimura And Mineko Fujimiya
Peptides,  1997; 18(10), pp. 1523–1529   PII S0196-9781(97)00237-4

NPY-like immunoreactivity was observed in nerve fibers and endocrine cells
in pancreas of all species examined except the eel, which showed no NPY innervation. The density of NPY-positive nerve fibers was higher in mammals than in the lower vertebrates. These nerve fibers were distributed throughout the parenchyma, and were particularly associated with the pancreatic duct
and vascular walls. In addition, the density of NPY-positive endocrine cells was found to be higher in lower vertebrates than mammals; in descending order; eel 5 turtle 5 chicken . bullfrog . mouse 5 rat 5 human . guinea pig 5 dog. These NPY-positive cells in the eel and certain mammals tended to be localized throughout the islet region, whereas in the turtle and chicken they were mainly scattered in the exocrine region. PYY-immunoreactivity was only present in the pancreatic endocrine cells of all species studied, and localized similarly to NPY. Thus these two peptides may play endocrine or paracrine roles in the regulation of islet hormone secretion in various vertebrate species.

Inhibitory effect of somatostatin on inflammation and nociception

Erika Pintér, Zsuzsanna Helyes, János Szolcsányi
Pharmacology & Therapeutics 112 (2006) 440–456

Somatostatin is released from capsaicin-sensitive, peptidergic sensory nerve endings in response to noxious heat and chemical stimuli such as vanilloids, protons or lipoxygenase products. It reaches distant parts of the body via the circulation and exerts systemic anti-inflammatory and analgesic effects. Somatostatin binds to G-protein coupled membrane receptors (sst1–sst5) and diminishes neurogenic inflammation by prejunctional action on sensory-efferent nerve terminals, as well as by postjunctional mechanisms on target cells. It decreases the release of pro-inflammatory neuropeptides from sensory nerve endings and also acts on receptors of vascular endothelial, inflammatory and immune cells. Analgesic effect is mediated by an inhibitory action on peripheral terminals of nociceptive neurons, since circulating somatostatin cannot exert central action.
Somatostatin itself is not suitable for drug development because of its broad spectrum and short elimination half-life, stable, receptor-selective agonists have been synthesized and investigated. The present overview is aimed at summarizing the physiological importance of somatostatin and sst receptors, pharmacological significance of synthetic agonists and their potential in the development of novel anti-inflammatory and analgesic drugs. These compounds might provide novel perspectives in the pharmacotherapy of acute and chronic painful inflammatory diseases, as well as neuropathic conditions.

the sources, target cells and effects of somatostatin (SST) involved in inflammatory and nociceptive processes

the sources, target cells and effects of somatostatin (SST) involved in inflammatory and nociceptive processes

This schematic drawing demonstrates the sources, target cells and effects of somatostatin (SST) involved in inflammatory and nociceptive processes

Characterization, detection and regulation of somatostatin receptors

The physiological actions of SST are initiated by its binding to membrane receptors. Five human somatostatin receptors (sst), have been cloned and characterized and referred to as sst1-5 receptors using the nomenclature suggested by Hoyer et al. (1995). Structurally, sst receptors are 7 transmembrane domain glycoproteins, comprised of 7 membrane spanning α helical domains connected by short loops, an N-terminal extracellular domain and a C-terminal intracellular domain. On the basis of binding studies using synthetic somatostatin analogs, sst receptors can be divided into 2 different subgroups: SRIF1 group comprising sst2, sst3 and sst5 are able to bind octapeptide analogs, whereas SRIF2 group comprising sst1 and sst4 have negligible affinity for these compounds. Within sst2 receptors, sst2A and sst2B are encoded on the same chromosome 17 and generated through alternative splicing of sst2 mRNA (Patel et al., 1993). None of the peptide analogs bind exclusively to only one of the sst subtypes, although new approaches might yield subtype-selective agonists and antagonists (Hofland et al., 1995; Hoyer et al., 1995; Patel et al., 1995; Reisine & Bell, 1995; Florio & Schettini, 1996; Patel, 1997; Meyerhof, 1998; Janecka et al., 2001). Somatostatin receptors are linked to multiple cellular effector systems via G-proteins. They mediate the inhibition of adenylate cyclase activity (Jakobs et al., 1983; Patel et al., 1995), reduce the conductance of voltage-dependent Ca2+ channels (Schally, 1988; Patel et al., 1995) and activate K+ channels (Mihara et al., 1987; Moore et al., 1988; Wang et al., 1989). Somatostatin receptors also mediate the stimulation of tyrosine phosphatase activity, induce a reduction of cell proliferation and inhibit a Na+/H+ exchanger (NHE1) (Barber et al., 1989; Buscail et al., 1994; Patel et al., 1995). Sst receptors represent a major class of inhibitory receptors which play an important role in modulating higher brain functions, secretory processes, cell proliferation and apoptosis.
Endogenous Somatostatin-28 Modulates Postprandial Insulin Secretion Immunoneutralization Studies in Baboons

John W. Ensinck, Robin E. Vogel, Ellen C. Laschansky, Donna J. Koerker, et al.
J Clin Invest 1997. 100: 2295–2302.).  http://dx.doi.org/10.1172/JCI119767

Somatostatin-28 (S-28), secreted into the circulation from enterocytes after food, and S-14, released mainly from gastric and pancreatic δ cells and enteric neurons, inhibit peripheral cellular functions. We hypothesized that S-28 is a humoral regulator of pancreatic β cell function during nutrient absorption. Consistent with this postulate, we observed in baboons a two to threefold increase in portal and peripheral levels of S-28 after meals, with minimal changes in S-14. We attempted to demonstrate a hormonal effect of these peptides by measuring their concentrations before and after infusing a somatostatin-specific monoclonal antibody (mAb) into baboons and comparing glucose, insulin, and glucagon-like peptide-1 levels before and for 4 h after intragastric nutrients during a control study and on 2 d after mAb administration (days 1 and 2). Basal growth hormone (GH) and glucagon levels and parameters of insulin and glucose kinetics were also measured. During immunoneutralization, we found that
(a) postprandial insulin levels were elevated on days 1 and 2;
(b) GH levels rose immediately and were sustained for 28 h, while glucagon fell; (c) basal insulin levels were unchanged on day 1 but were increased two to threefold on day 2, coincident with decreased insulin sensitivity; and
(d) plasma glucose concentrations were similar to control values.
We attribute the eventual rise in fasting levels of insulin to its enhanced secretion in compensation for the heightened insulin resistance from increased GH action. Based on the elevated postmeal insulin levels after mAb administration, we conclude that S-28 participates in the enteroinsular axis as a decretin to regulate postprandial insulin secretion.

Effects of glucagon-like peptide 1 on appetite and body weight: focus on the CNS

L van Bloemendaal, J S ten Kulve, S E la Fleur, R G Ijzerman and M Diamant
Journal of Endocrinology 2014; 221, T1–T16
http://dx.doi.org:/10.1530/JOE-13-0414

The delivery of nutrients to the gastrointestinal tract after food ingestion activates the secretion of several gut-derived mediators, including the incretin hormone glucagon-like peptide 1 (GLP-1). GLP-1 receptor agonists (GLP-1RA), such as exenatide and liraglutide, are currently employed successfully in the treatment of patients with type 2 diabetes mellitus. GLP-1RA improve glycaemic control and stimulate satiety, leading to reductions in food intake and body weight. Besides gastric distension and peripheral vagal nerve activation, GLP-1RA induce satiety by influencing brain regions involved in the regulation of feeding, and several routes of action have been proposed. This review summarises the evidence for a physiological role of GLP-1 in the central regulation of feeding behavior and the different routes of action involved. Also, we provide an overview of presently available data on pharmacological stimulation of GLP-1 pathways leading to alterations in CNS activity, reductions in food intake and weight loss.

Critical role for peptide YY in protein-mediated satiation and body-weight regulation

Rachel L. Batterham, Helen Heffron, Saloni Kapoor, Joanna E. Chivers, et al.
Cell Metab 2006; 4, 223–233 http://dx.doi.org:/10.1016/j.cmet.2006.08.001

Dietary protein enhances satiety and promotes weight loss, but the mechanisms by which appetite is affected remain unclear. We investigated the role of gut hormones, key regulators of ingestive behavior, in mediating the satiating effects of different macronutrients. In normal-weight and obese human subjects, high-protein intake induced the greatest release of the anorectic hormone peptide YY (PYY) and the most pronounced satiety. Long-term augmentation of dietary protein in mice increased plasma PYY levels, decreased food intake, and reduced adiposity. To directly determine the role of PYY in mediating the satiating effects of protein, we generated PYY null mice, which were selectively resistant to the satiating and weight-reducing effects of protein and developed marked obesity that was reversed by exogenous PYY treatment. Our findings suggest that modulating the release of endogenous satiety factors, such as PYY, through alteration of specific diet constituents could provide a rational therapy for obesity.

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Genomics and Metabolomics Advances in Cancer

Writer and Curator: Larry H. Bernstein, MD, FCAP

UPDATED 6/01/2019 

UPDATED 9/26/2021

Genomics

Unraveling the clonal hierarchy of somatic genomic aberrations

D Prandi, SC Baca, A Romanel, CE Barbieri, Juan-Miguel Mosquera, et al.
Genome Biology 2014, 15:439
http://genomebiology.com/2014/15/8/439

Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations. Comparative analysis across 100 sequenced genomes from prostate, melanoma, and lung cancers established diverse evolutionary hierarchies, demonstrating the early disruption of tumor-specific pathways. The analyses highlight the diversity of clonal evolution within and across tumor types that might be informative for risk stratification and patient selection for targeted therapies. CLONET addresses heterogeneous clinical samples seen in the setting of precision medicine.

The Transcription Factor Titration Effect Dictates Level of Gene Expression

RC Brewster, FM Weinert, HG Garcia, D Song, M Rydenfelt, and R Phillips
Cell,  Mar 13, 2014;156: 1312–1323
http://dx.doi.org/10.1016/j.cell.2014.02.022

Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number—in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle.

Telomere dynamics in human mesenchymal stem cells after exposure to acute oxidative stress

M Harbo, S Koelvraa, N Serakinci, L Bendixa
DNA Repair 2012.  http://dx.doi.org/10.1016/j.dnarep.2012.06.003

A gradual shortening of telomeres due to replication can be measured using the standard telomere restriction fragments (TRF) assay and other methods by measuring the mean length of all the telomeres in a cell. In contrast, stress-induced telomere shortening, which is believed to be just as important for causing cellular senescence, cannot be measured properly using these methods. Stress-induced telomere shortening caused by, e.g. oxidative damage happens in a stochastic manner leaving just a few single telomeres critically short. It is now possible to visualize these few ultra-short telomeres due to the advantages of the newly developed Universal single telomere length assay (STELA), and we therefore believe that this method should be considered the method of choice when measuring the length of telomeres after exposure to oxidative stress. In order to test our hypothesis, cultured human mesenchymal stem cells, either primary or hTERT immortalized, were exposed to sub-lethal doses of hydrogen peroxide, and the short term effect on telomere dynamics was monitored by Universal STELA and TRF measurements. Both telomere measures were then correlated with the percentage of senescent cells estimated by senescence-associated β-galactosidase staining. The exposure to acute oxidative stress resulted in an increased number of ultra-short telomeres, which correlated strongly with the percentage of senescent cells, whereas a correlation between mean telomere length and the percentage of senescent cells was absent. Based on the findings in the present study, it seems reasonable to conclude that Universal STELA is superior to TRF in detecting telomere damage caused by exposure to oxidative stress. The choice of method should therefore be considered carefully in studies examining stress-related telomere shortening as well as in the emerging field of lifestyle studies involving telomere length measurements.

tDNA insulators and the emerging role of TFIIIC in genome organization

Kevin Van Bortle and Victor G. Corces
Transcription Dec 12, 2012; 3(6): 1-8. www.landesbioscience.com

Recent findings provide evidence that tDNAs function as chromatin insulators from yeast to humans. TFIIIC, a transcription factor that interacts with the B-box in tDNAs as well as thousands of ETC sites in the genome, is responsible for insulator function. Though tDNAs are capable of enhancer-blocking and barrier activities for which insulators are defined, new insights into the relationship between insulators and chromatin structure suggest that TFIIIC serves a complex role in genome organization. We review the role of tRNA genes and TFIIIC as chromatin insulators, and highlight recent findings that have broadened our understanding of insulators in genome biology.

Structure and organization of insulators in eukaryotes. (A) From yeast to mammals, in organisms in which it has been studied, the TFIIIC protein interacts with the B-box sequence in tRNA genes or sites in the genome named ETC sites.

Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

E Wachter, T Quante, C Merusi, A Arczewska, F Stewart, S Webb, A Bird
eLife 2014;3:e03397. http://dx.doi.org:/10.7554/eLife.03397.001

The mammalian genome is punctuated by CpG islands (CGIs), which differ sharply from the bulk genome by being rich in G + C and the dinucleotide CpG. CGIs often include transcription initiation sites and display ‘active’ histone marks, notably histone H3 lysine 4 methylation. In embryonic stem cells (ESCs) some CGIs adopt a ‘bivalent’ chromatin state bearing simultaneous ‘active’ and ‘inactive’ chromatin marks. To determine whether CGI chromatin is developmentally programmed at specific genes or is imposed by shared features of CGI DNA, we integrated artificial CGI-like DNA sequences into the ESC genome. We found that bivalency is the default chromatin structure for CpG-rich, G + C-rich DNA. A high CpG density alone is not sufficient for this effect, as A + T-rich sequence settings invariably provoke de novo DNA methylation leading to loss of CGI signature chromatin. We conclude that both CpG-richness and G + C-richness are required for induction of signature chromatin structures at CGIs.

Locus-specific mutation databases: pitfalls and good practice based on the p53 experience

Thierry Soussi, Chikashi Ishioka, Mireille Claustres and Christophe Béroud
NATURE REVIEWS | CANCER JAN 2006; 6: 83-90.

Between 50,000 and 60,000 mutations have been described in various genes that are associated with a wide variety of diseases. Reporting, storing and analysing these data is an important challenge as such data provide invaluable information for both clinical medicine and basic science.

The practical value of mutation analysis All studies performed to date show that mutations are, in general, not randomly distributed. Hot-spot regions have been demonstrated, corresponding to a region of DNA that is susceptible to mutations (such as CpG dinucleotides), a codon encoding a key residue in the biological function of the protein, or both (BOX 1). Identification of these hot-spot regions and natural mutants is essential to define crucial regions in an unknown protein.

Locus-specific databases have been developed to exploit this huge volume of data. The p53 mutation database is a paradigm, as it constitutes the largest collection of somatic mutations (22,000). However, there are several biases in this database that can lead to serious erroneous interpretations. We describe several rules for mutation database management that could benefit the entire scientific community.

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

A Subramaniana, P Tamayo, VK  Mootha, S Mukherjee, BL Ebert, et al.
PNAS  Oct 25, 2005; 102(43): 15545–15550
http://pnas.org/cgi/doi/10.1073/pnas.0506580102

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

Mutational landscape and significance across 12 major cancer types

C Kandoth, MD McLellan, F Vandin, Kai Ye, B Niu, C Lu, et al.
NATURE  OCT 2013; 502: 333-337. http://dx.doi.org:/10.1038/nature12634

The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis methods to identify somatic variants across thousands of tumours. Here we present data and analytical results for point mutations and small insertions/deletions from 3,281 tumours across 12 tumour types as part of the TCGA Pan-Cancer effort. We illustrate the distributions of mutation frequencies, types and contexts across tumour types, and establish their links to tissues of origin, environmental/ carcinogen influences, and DNA repair defects. Using the integrated data sets, we identified 127 significantly mutated genes from well-known(for example, mitogen-activated protein kinase, phosphatidylinositol-3-OH kinase,Wnt/b-catenin and receptor tyrosine kinase signalling pathways, and cell cycle control) and emerging (for example, histone, histone modification, splicing, metabolism and proteolysis) cellular processes in cancer. The average number of mutations in these significantly mutated genes varies across tumour types; most tumours have two to six, indicating that the numberof driver mutations required during oncogenesis is relatively small. Mutations in transcriptional factors/regulators show tissue specificity, whereas histone modifiers are often mutated across several cancer types. Clinical association analysis identifies genes having a significant effect on survival, and investigations of mutations with respect to clonal/subclonal architecture delineate their temporal orders during tumorigenesis. Taken together, these results lay the groundwork for developing new diagnostics and individualizing cancer treatment.

Molecular insights into RNA and DNA helicase evolution from the determinants of  specificity for a DEAD-box RNA helicase

Anna L. Mallam, David J. Sidote and Alan M. Lambowitz
eLife 2014; http://dx.doi.org:/10.7554/eLife.04630

How different helicase families with a conserved catalytic ‘helicase core’ evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. Here, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the ‘closed-state’ helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day  helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.

Identification of human TERT elements necessary for telomerase recruitment to telomeres

Jens C Schmidt, Andrew B Dalby, Thomas R Cech
eLife 2014; http://dx.doi.org/10.7554/eLife.03563

Human chromosomes terminate in telomeres, repetitive DNA sequences bound by the shelterin complex. Shelterin protects chromosome ends, prevents recognition by the DNA damage machinery, and recruits telomerase. A patch of  amino acids, termed the TEL-patch, on the OB-fold domain of the shelterin  component TPP1 is essential to recruit telomerase to telomeres. In contrast, the site on telomerase that interacts with the TPP1 OB-fold is not well defined. Here we identify separation-of-function mutations in the TEN-domain of human telomerase reverse transcriptase (hTERT) that disrupt the interaction of telomerase with TPP1 in vivo and in vitro but have very little effect on the catalytic activity of telomerase. Suppression of a TEN-domain mutation with a compensatory charge-swap mutation in the TEL-patch indicates that their association is direct. Our findings define the interaction interface required for telomerase recruitment to telomeres, an important step towards developing modulators of this interaction as therapeutics for human disease.

Metabolomics

Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines

MN Mindrinos, G Bhanot, SH Dairkee, RW Davis, SS Jeffrey
PLoS ONE 7(5): e33788. http://dx.doi.org:/doi:10.1371/journal.pone.0033788

Background: To improve cancer therapy, it is critical to target metastasizing cells. Circulating tumor cells (CTCs) are rare cells found in the blood of patients with solid tumors and may play a key role in cancer dissemination. Uncovering CTC phenotypes offers a potential avenue to inform treatment. However, CTC transcriptional profiling is limited by leukocyte contamination; an approach to surmount this problem is single cell analysis. Here we demonstrate feasibility of performing high dimensional single CTC profiling, providing early insight into CTC heterogeneity and allowing comparisons to breast cancer cell lines widely used for drug discovery.
Methodology/Principal Findings: We purified CTCs using the MagSweeper, an immunomagnetic enrichment device that isolates live tumor cells from unfractionated blood. CTCs that met stringent criteria for further analysis were obtained from 70% (14/20) of primary and 70% (21/30) of metastatic breast cancer patients; none were captured from patients with nonepithelial cancer (n = 20) or healthy subjects (n = 25). Microfluidic-based single cell transcriptional profiling of 87 cancer associated and reference genes showed heterogeneity among individual CTCs, separating them into two major subgroups, based on 31 highly expressed genes. In contrast, single cells from seven breast cancer cell lines were tightly clustered together by sample ID and ER status. CTC profiles were distinct from those of cancer cell lines, questioning the suitability of such lines for drug discovery efforts for late stage cancer therapy.
Conclusions/Significance: For the first time, we directly measured high dimensional gene expression in individual CTCs without the common practice of pooling such cells. Elevated transcript levels of genes associated with metastasis NPTN, S100A4, S100A9, and with epithelial mesenchymal transition: VIM, TGFß1, ZEB2, FOXC1, CXCR4, were striking compared to cell lines. Our findings demonstrate that profiling CTCs on a cell-by-cell basis is possible and may facilitate the application of ‘liquid biopsies’ to better model drug discovery

Simplifying Disease Complexity part 6 – Bringing Metabolomics into Practice
Dr. Kirk Beebe, Director of Application Science, Metabolon, Inc.

n the previous editions of this 6-part series, we’ve explored numerous example of how metabolomics is bringing success to areas such as cancer, metabolic disease, cardiovascular, and rare disease research. Although we did not devote attention to every area of biology or therapeutic area, the intent of this broad series was not only to convey how metabolomics can be used in a specific area of research (e.g. cancer), but actually, how metabolomics is a central science for interrogating any biological question. So, although it may seem like an oversimplification, to understand whether metabolomics could be used in a research setting one need only ask themselves, “Do I have a biological question that would benefit from a hypothesis-free approach?, am I interested in exploring my system for potential new discoveries? Or do I need a biomarker/better biomarker?

As described in our first part, metabolites have been and continue to be a staple for clinical and in vivo decision making (e.g. cholesterol, glucose, bilirubin, creatinine, thyroid hormone, newborn screening for inborn errors of metabolism (IEMs)). In short, this utility is fundamental to the foundations of biology since metabolism is central to all kingdoms of life and contemporary biology is driven to maintain metabolic homeostasis to maintain the phenotype. An unappreciated point that we leave this series with is that this fundamental nature (the connection of metabolism to the phenotype) confers an important advantage of metabolism for deriving biomarkers and understanding the underlying physiology.

Metabolites are a diagnostic data stream.

Whether a phenotype is driven by a single mutation or a combination of genetic differences, environmental influences or the microbiota, metabolism provides a systems-level diagnostic.

That is, no matter the source of the physiological or phenotypic change (i.e. genes, microbiota, environmental), the change will almost invariably register within metabolism. Thus, modern metabolomic approaches offer the opportunity to more deeply interrogate the “metabolome” to discover more sensitive and specific biomarkers and understand the basis of disease and drug response.

As such, metabolomics has the potential to be able to integrate systems on a number of levels. It is useful through its ability to enrich genomics, transcriptomics and proteomics, thus integrating a number of data streams that provide knowledge and contribute to informed decision-making and patient management1. Using metabolomics, individual tissues can be queried but less invasive sample types (e.g., blood, urine, feces, and/or saliva) can also yield biomarkers and mechanistic insight. The integration of the individual tissues at the level of these more accessible samples can offer an overview of the entire system and inform on important biological pathways. Finally, although the focus of this series was on what metabolomics can bring to biomarker and other related research areas, it should be noted that a combination of metabolomics with other scientific approaches will undoubtedly broaden insight and produce verifiable, validatable biomarkers that track with efficacy and therapy.

As we close this series, we hope that we have conveyed 4 critical points – 1) metabolism is central to biology and hence, key in research and biomarker discovery, 2) the reason for this is due to the fundamental nature of metabolism being central to the development of all life and being the focal point of contemporary biology’s drive to maintain homeostasis, 3) metabolomic is the most powerful way to survey metabolism by offering a simultaneous read-out if hundreds of reactions and pathways, and 4) metabolomics as a practical tool has only recently emerged.

And it is on this last point that we leave the reader with some final considerations. We imagine that, after careful review of the information outlined in this series, many readers will be motivated to explore the use of metabolomics in their research. However, as outlined throughout this series, mature technologies have only recently arisen. Nevertheless, there are many laboratories that perform some version of “metabolomics”. Although the experimental goal often dictates the precise approach, there are 5 critical features  that a metabolomic technology must harbor in order for it to achieve a similar purpose as mature omic technologies (e.g. DNA sequencers) in terms of depth of coverage and data quality. These minimally include:

  1. Must be based on an authenticated chemical library
    2. Must have procedures for eliminated noise from the data
    5. Must have a mechanism to identify novel metabolites
    6. Must have robust QC process from sample preparation through statistical analysis
    4. Must provide a mechanism to abstract information/interpret the data

References

  1. Eckhart, A.D., Beebe, K. & Milburn, M. Metabolomics as a key integrator for “omic” advancement of personalized medicine and future therapies. Clin Transl Sci 5, 285-288

(2012).

  1. Evans, A., Mitchell, M., Dai, H. & DeHaven, C.D. Categorizing Ion –Features in Liquid Chromatography/Mass Spectrometry Metobolomics Data. Metabolomics 2 (2012).
  2. DeHaven, C.D., Evans, A., Dai, H. & Lawton, K.A. in Metabolomics. (ed. U. Roessner) (InTech, 2012).
  3. Dehaven, C.D., Evans, A.M., Dai, H. & Lawton, K.A. Organization of GC/MS and LC/MS metabolomics data into chemical libraries. J Cheminform 2, 9 (2010).
  4. Evans, A.M., DeHaven, C.D., Barrett, T., Mitchell, M. & Milgram, E. Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. Anal Chem 81, 6656-6667 (2009).

Prediction of intracellular metabolic states from extracellular metabolomic data

MK Aurich, G Paglia, Ottar Rolfsson, S Hrafnsdottir, M  Magnusdottir, MM, et al.

Metabolomics Aug 14, 2014;  http://dx.doi.org:/10.1007/s11306-014-0721-3
http://link.springer.com/article/10.1007/s11306-014-0721-3/fulltext.html#Sec1

intra- extracellular metabolites

intra- extracellular metabolites

http://link.springer.com/static-content/images/404/
art%253A10.1007%252Fs11306-014-0721-3/MediaObjects/11306_2014_721_Fig1_HTML.gif

Metabolic models can provide a mechanistic framework to analyze information-rich omics data sets, and are increasingly being used to investigate metabolic alternations in human diseases. An expression of the altered metabolic pathway utilization is the selection of metabolites consumed and released by cells. However, methods for the inference of intracellular metabolic states from extracellular measurements in the context of metabolic models remain underdeveloped compared to methods for other omics data. Herein, we describe a workflow for such an integrative analysis emphasizing on extracellular metabolomics data. We demonstrate, using the lymphoblastic leukemia cell lines Molt-4 and CCRF-CEM, how our methods can reveal differences in cell metabolism. Our models explain metabolite uptake and secretion by predicting a more glycolytic phenotype for the CCRF-CEM model and a more oxidative phenotype for the Molt-4 model, which was supported by our experimental data. Gene expression analysis revealed altered expression of gene products at key regulatory steps in those central metabolic pathways, and literature query emphasized the role of these genes in cancer metabolism. Moreover, in silico gene knock-outs identified unique control points for each cell line model, e.g., phosphoglycerate dehydrogenase for the Molt-4 model. Thus, our workflow is well suited to the characterization of cellular metabolic traits based on extracellular metabolomic data, and it allows the integration of multiple omics data sets into a cohesive picture based on a defined model context.

Metabolome Informatics Research

Metabolome Informatics Research

Identification of Metabolites in the Normal Ovary and Their Transformation in Primary and Metastatic Ovarian Cancer MOC vs EOC

Identification of Metabolites in the Normal Ovary and Their Transformation in Primary and Metastatic Ovarian Cancer MOC vs EOC

Genomics and Cancer

Identification of Gene Networks Associated with Acute Myeloid Leukemia by Comparative Molecular Methylation and Expression Profiling

M Dellett, KA O’Hagan, HA Alexandra Colyer and KI Mills
Biomarkers in Cancer 2010:2 43–55  http://www.la-press.com.

Around 80% of acute myeloid leukemia (AML) patients achieve a complete remission, however many will relapse and ultimately die of their disease. The association between karyotype and prognosis has been studied extensively and identified patient cohorts as having favourable [e.g. t(8; 21), inv (16)/t(16; 16), t(15; 17)], intermediate [e.g. cytogenetically normal (NK-AML)] or adverse risk [e.g. complex karyotypes]. Previous studies have shown that gene expression profiling signatures can classify the sub-types of AML, although few reports have shown a similar feature by using methylation markers. The global methylation patterns in 19 diagnostic AML samples were investigated using the Methylated CpG Island Amplification Microarray (MCAM) method and CpG island microarrays containing 12,000 CpG sites. The first analysis, comparing favourable and intermediate cytogenetic risk groups, revealed significantly differentially methylated CpG sites (594 CpG islands) between the two subgroups. Mutations in the NPM1 gene occur at a high frequency (40%) within the NK-AML subgroup and are associated with a more favourable prognosis in these patients. A second analysis comparing the NPM1 mutant and wild-type research study subjects again identified distinct methylation profiles between these two subgroups. Network and pathway analysis revealed possible molecular mechanisms associated with the different risk and/or mutation sub-groups. This may result in a better classification of the risk groups, improved monitoring targets, or the identification of novel molecular therapies.

Molecular Imaging of Proteases in Cancer

Yunan Yang, Hao Hong, Yin Zhang and Weibo Cai
Cancer Growth and Metastasis 2009:2 13–27. http://www.la-press.com

Proteases play important roles during tumor angiogenesis, invasion, and metastasis. Various molecular imaging techniques have been employed for protease imaging: optical (both fluorescence and bioluminescence), magnetic resonance imaging (MRI), single-photon emission computed tomography (SPECT), and positron emission tomography (PET). In this review, we will summarize the current status of imaging proteases in cancer with these techniques. Optical imaging of proteases, in particular with fluorescence, is the most intensively validated and many of the imaging probes are already commercially available. It is generally agreed that the use of activatable probes is the most accurate and appropriate means for measuring protease activity. Molecular imaging of proteases with other techniques (i.e. MRI, SPECT, and PET) has not been well-documented in the literature which certainly deserves much future effort. Optical imaging and molecular MRI of protease activity has very limited potential for clinical investigation. PET/SPECT imaging is suitable for clinical investigation; however the optimal probes for PET/SPECT imaging of proteases in cancer have yet to be developed. Successful development of protease imaging probes with optimal in vivo stability, tumor targeting efficacy, and desirable pharmacokinetics for clinical translation will eventually improve cancer patient management. Not limited to cancer, these protease-targeted imaging probes will also have broad applications in other diseases such as arthritis, atherosclerosis, and myocardial infarction.

Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells

E Tosti, JA Katakowski, S Schaetzlein, Hyun-Soo Kim, CJ Ryan, M Shales, et al.
Genome Medicine 2014, 6:68. http://genomemedicine.com/content/6/9/68

Background: The evolutionarily conserved DNA mismatch repair (MMR) system corrects base-substitution and insertion-deletion mutations generated during erroneous replication. The mutation or inactivation of many MMR factors strongly predisposes to cancer, where the resulting tumors often display resistance to standard chemotherapeutics. A new direction to develop targeted therapies is the harnessing of synthetic genetic interactions, where the simultaneous loss of two otherwise non-essential factors leads to reduced cell fitness or death. High-throughput screening in human cells to directly identify such interactors for disease-relevant genes is now widespread, but often requires extensive case-by-case optimization. Here we asked if conserved genetic interactors (CGIs) with MMR genes from two evolutionary distant yeast species (Saccharomyces cerevisiae and Schizosaccharomyzes pombe) can predict orthologous genetic relationships in higher eukaryotes.
Methods: High-throughput screening was used to identify genetic interaction profiles for the MutSα and MutSβ heterodimer subunits (msh2Δ, msh3Δ, msh6Δ) of fission yeast. Selected negative interactors with MutSβ (msh2Δ/msh3Δ) were directly analyzed in budding yeast, and the CGI with SUMO-protease Ulp2 further examined after RNA interference/drug treatment in MSH2-deficient and -proficient human cells.
Results: This study identified distinct genetic profiles for MutSα and MutSβ, and supports a role for the latter in recombinatorial DNA repair. Approximately 28% of orthologous genetic interactions with msh2Δ/msh3Δ are conserved in both yeasts, a degree consistent with global trends across these species. Further, the CGI between budding/fission yeast msh2 and SUMO-protease Ulp2 is maintained in human cells (MSH2/SENP6), and enhanced by Olaparib, a PARP inhibitor that induces the accumulation of single-strand DNA breaks. This identifies SENP6 as a promising new target for the treatment of MMR-deficient cancers.
Conclusion: Our findings demonstrate the utility of employing evolutionary distance in tractable lower eukaryotes to predict orthologous genetic relationships in higher eukaryotes. Moreover, we provide novel insights into the genome maintenance functions of a critical DNA repair complex and propose a promising targeted treatment for MMR deficient tumors.

Cancer Genome Landscapes

B Vogelstein, N Papadopoulos, VE Velculescu, S Zhou, LA Diaz Jr., KW Kinzler, et al.
Science 339, 1546 (2013); http://dx.doi.org:/10.1126/science.1235122

Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.

Approaches for establishing the function of regulatory genetic variants involved in disease

Julian Charles Knight
Genome Medicine 2014, 6:92.  http://genomemedicine.com/content/6/10/92

The diversity of regulatory genetic variants and their mechanisms of action reflect the complexity and context-specificity of gene regulation. Regulatory variants are important in human disease and defining such variants and establishing mechanism is crucial to the interpretation of disease-association studies. This review describes approaches for identifying and functionally characterizing regulatory variants, illustrated using examples from common diseases. Insights from recent advances in resolving the functional epigenomic regulatory landscape in which variants act are highlighted, showing how this has enabled functional annotation of variants and the generation of hypotheses about mechanism of action. The utility of quantitative trait mapping at the transcript, protein and metabolite level to define association of specific genes with particular variants and further inform disease associations are reviewed. Establishing mechanism of action is an essential step in resolving functional regulatory variants, and this review describes how this is being facilitated by new methods for analyzing allele-specific expression, mapping chromatin interactions and advances in genome editing. Finally, integrative approaches are discussed together with examples highlighting how defining the mechanism of action of regulatory variants and identifying specific modulated genes can maximize the translational utility of genome-wide association studies to understand the pathogenesis of diseases and discover new drug targets or opportunities to repurpose existing drugs to treat them.

Biomarkers

TRIM29 as a Novel Biomarker in Pancreatic Adenocarcinoma

Hongli Sun, Xianwei Dai, and Bing Han
Disease Markers 2014, Article ID 317817, 7 pages
http://dx.doi.org/10.1155/2014/317817

Background and Aim. Tripartite motif-containing 29 (TRIM29) is structurally a member of the tripartite motif family of proteins and is involved in diverse human cancers. However, its role in pancreatic cancer remains unclear.
Methods. The expression pattern of TRIM29 in pancreatic ductal adenocarcinoma was assessed by immunocytochemistry. Multivariate logistic regression analysis was used to investigate the association between TRIM29 and clinical characteristics. In vitro analyses by scratch wound healing assay and invasion assays were performed using the pancreatic cancer cell lines.
Results. Immunohistochemical analysis showed TRIM29 expression in pancreatic cancer tissues was significantly higher (𝑛 = 186) than that in matched adjacent nontumor tissues. TRIM29 protein expression was significantly correlated with lymph node metastasis (𝑃 = 0.019). Patients with positive TRIM29 expression showed both shorter overall survival and shorter recurrence-free survival than those with negative TRIM29 expression. Multivariate analysis revealed that TRIM29 was an independent factor for pancreatic cancer over survival (HR = 2.180, 95% CI: 1.324–4.198, 𝑃 = 0.011). In vitro, TRIM29 knockdown resulted in inhibition of pancreatic cancer cell proliferation, migration, and invasion.
Conclusions. Our results indicate that TRIM29 promotes tumor progression and may be a novel prognostic marker for pancreatic ductal adenocarcinoma.

Bioinformatic identification of proteins with tissue-specific expression for biomarker discovery

I Prassas, CC Chrystoja, S Makawita1, and EP Diamandis
BMC Medicine 2012, 10:39. http://www.biomedcentral.com/1741-7015/10/39

Background: There is an important need for the identification of novel serological biomarkers for the early detection of cancer. Current biomarkers suffer from a lack of tissue specificity, rendering them vulnerable to nondisease-specific increases. The present study details a strategy to rapidly identify tissue-specific proteins using bioinformatics.
Methods: Previous studies have focused on either gene or protein expression databases for the identification of candidates. We developed a strategy that mines six publicly available gene and protein databases for tissue-specific proteins, selects proteins likely to enter the circulation, and integrates proteomic datasets enriched for the cancer secretome to prioritize candidates for further verification and validation studies.
Results: Using colon, lung, pancreatic and prostate cancer as case examples, we identified 48 candidate tissuespecific biomarkers, of which 14 have been previously studied as biomarkers of cancer or benign disease. Twenty six candidate biomarkers for these four cancer types are proposed.
Conclusions: We present a novel strategy using bioinformatics to identify tissue-specific proteins that are potential cancer serum biomarkers. Investigation of the 26 candidates in disease states of the organs is warranted

The Serum Glycome to Discriminate between Early-Stage Epithelial Ovarian Cancer and Benign Ovarian Diseases

K Biskup, E Iona Braicu, J Sehouli, R Tauber, and V Blanchard
Disease Markers 2014, Article ID 238197, 10 pages
http://dx.doi.org/10.1155/2014/238197

Epithelial ovarian cancer (EOC) is the sixth most common cause of cancer deaths in women because the diagnosis occurs mostly when the disease is in its late-stage. Current diagnostic methods of EOC show only a moderate sensitivity, especially at an early-stage of the disease; hence, novel biomarkers are needed to improve the diagnosis. We recently reported that serum glycome modifications observed in late-stage EOC patients by MALDI-TOF-MS could be combined as a glycan score named GLYCOV that was calculated from the relative areas of the 11 N-glycan structures that were significantly modulated. Here, we evaluated the ability of GLYCOV to recognize early-stage EOC in a cohort of 73 individuals comprised of 20 early-stage primary serous EOC, 20 benign ovarian diseases (BOD), and 33 age-matched healthy controls. GLYCOV was able to recognize stage I EOC whereas CA125 values were statistically significant only for stage II EOC patients. In addition, GLYCOV was more sensitive and specific compared to CA125 in distinguishing early-stage EOC from BOD patients, which is of high relevance to clinicians as it is difficult for them to diagnose malignancy prior to operation.

The Clinicopathological Significance of miR-133a in Colorectal Cancer

Timothy Ming-Hun Wan, Colin Siu-Chi Lam, Lui Ng, Ariel Ka-Man Chow, et al.
Disease Markers  2014, Article ID 919283, 8 pages http://dx.doi.org/10.1155/2014/919283

This study determined the expression of microRNA-133a (MiR-133a) in colorectal cancer (CRC) and adjacent normal mucosa samples and evaluated its clinicopathological role in CRC. The expression of miR-133a in 125 pairs of tissue samples was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) and correlated with patient’s clinicopathological data by statistical analysis. Endogenous expression levels of several potential target genes were determined by qRT-PCR and correlated using Pearson’s method. MiR-133a was downregulated in 83.2% of tumors compared to normal mucosal tissue. Higher miR-133a expression in tumor tissues was associated with development of distant metastasis, advanced Dukes and TNM staging, and poor survival. The unfavorable prognosis of higher miR-133a expression was accompanied by dysregulation of potential miR-133a target genes, LIM and SH3 domain protein 1 (LASP1), Caveolin-1 (CAV1), and Fascin-1 (FSCN1). LASP1 was found to possess a negative correlation (𝛾 = −0.23), whereas CAV1 exhibited a significant positive correlation (𝛾 = 0.27), and a stronger correlation was found in patients who developed distant metastases (𝛾 = 0.42). In addition, a negative correlation of FSCN1 was only found in nonmetastatic patients. In conclusion, miR-133a was downregulated in CRC tissues, but its higher expression correlated with adverse clinical characteristics and poor prognosis.

The Clinical Significance of PR, ER, NF-𝜅B, and TNF-𝛼 in Breast Cancer

Xian-Long Zhou, Wei Fan, Gui Yang, and Ming-Xia Yu
Disease Markers 2014, Article ID 494581, 7 pages http://dx.doi.org/10.1155/2014/494581

Objectives. To investigate the expression of estrogen (ER), progesterone receptors (PR), nuclear factor-𝜅B (NF-𝜅B), and tumor necrosis factor-𝛼 (TNF-𝛼) in human breast cancer (BC), and the correlation of these four parameters with clinicopathological features of BC.
Methods and Results. We performed an immunohistochemical SABC method for the identification of ER, PR, NF-𝜅B, and TNF-𝛼 expression in 112 patients with primary BC.The total positive expression rate of ER, PR, NF-𝜅B, and TNF-𝛼 was 67%, 76%, 84%, and 94%, respectively. The expressions of ER and PR were correlated with tumor grade, TNM stage, and lymph node metastasis (𝑃 < 0.01, resp.), but not with age, tumor size, histological subtype, age at menarche, menopause status, number of pregnancies, number of deliveries, and family history of cancer. Expressions of ER and PR were both correlated with NF-𝜅B and TNF-𝛼 expression (𝑃 < 0.05, resp.). Moreover, there was significant correlation between ER and PR (𝑃 < 0.0001) as well as between NF-𝜅B and TNF-𝛼 expression (𝑃 < 0.05).
Conclusion. PR and ER are highly expressed, with significant correlation with NF-𝜅B and TNF-𝛼 expression in breast cancer. The important roles of ER and PR in invasion and metastasis of breast cancer are probably associated with NF-𝜅B and TNF-𝛼 expression.

Serum Protein Profile at Remission Can Accurately Assess Therapeutic Outcomes and Survival for Serous Ovarian Cancer

J Wang, A Sharma, SA Ghamande, S Bush, D Ferris, W Zhi, et la.
PLoS ONE 8(11): e78393. http://dx.doi.org:/10.1371/journal.pone.0078393

Background: Biomarkers play critical roles in early detection, diagnosis and monitoring of therapeutic outcome and recurrence of cancer. Previous biomarker research on ovarian cancer (OC) has mostly focused on the discovery and validation of diagnostic biomarkers. The primary purpose of this study is to identify serum biomarkers for prognosis and therapeutic outcomes of ovarian cancer. Experimental Design: Forty serum proteins were analyzed in 70 serum samples from healthy controls (HC) and 101 serum samples from serous OC patients at three different disease phases: post diagnosis (PD), remission (RM) and recurrence (RC). The utility of serum proteins as OC biomarkers was evaluated using a variety of statistical methods including survival analysis.
Results: Ten serum proteins (PDGF-AB/BB, PDGF-AA, CRP, sFas, CA125, SAA, sTNFRII, sIL-6R, IGFBP6 and MDC) have individually good area-under-the-curve (AUC) values (AUC = 0.69–0.86) and more than 10 three-marker combinations have excellent AUC values (0.91–0.93) in distinguishing active cancer samples (PD & RC) from HC. The mean serum protein levels for RM samples are usually intermediate between HC and OC patients with active cancer (PD & RC). Most importantly, five proteins (sICAM1, RANTES, sgp130, sTNFR-II and sVCAM1) measured at remission  can classify, individually and in combination, serous OC patients into two subsets with significantly different overall survival (best HR = 17, p,1023).
Conclusion: We identified five serum proteins which, when measured at remission, can accurately predict the overall survival of serous OC patients, suggesting that they may be useful for monitoring the therapeutic outcomes for ovarian cancer.

Serum Clusterin as a Tumor Marker and Prognostic Factor for Patients with Esophageal Cancer

Wei Guo, Xiao Ma, Christine Xue, Jianfeng Luo, Xiaoli Zhu, et al.
Disease Markers 2014, Article ID 168960, 7 pages http://dx.doi.org/10.1155/2014/168960

Background. Recent studies have revealed that clusterin is implicated in many physiological and pathological processes, including tumorigenesis. However, the relationship between serum clusterin expression and esophageal squamous cell carcinoma (ESCC) is unclear.
Methods. The serum clusterin concentrations of 87 ESCC patients and 136 healthy individuals were examined. An independent-samples Mann-Whitney 𝑈 test was used to compare serum clusterin concentrations of ESCC patients to those of healthy controls. Univariate analysis was conducted using the log-rank test and multivariate analyses were performed using the Cox proportional hazards model. Results. In healthy controls, the mean clusterin concentration was 288.8 ± 75.1 𝜇g/mL, while in the ESCC patients, the mean clusterin concentration was higher at 412.3±159.4 𝜇g/mL (𝑃 < 0.0001). The 1-, 2-, and 4-year survival rates for the 87 ESCC patients were 89.70%, 80.00%, and 54.50%. Serum clusterin had an optimal diagnostic cut-off point (serum clusterin concentration = 335.5 𝜇g/mL) for esophageal squamous cell carcinoma with sensitivity of 71.26% and specificity of 77.94%. And higher serum clusterin concentration (>500 𝜇g/mL) indicated better prognosis (𝑃 = 0.030).
Conclusions. Clusterin may play a key role during tumorigenesis and tumor progression of ESCC and it could be applied in clinical work as a tumor marker and prognostic factor.

Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer

JD Warren, Wei Xiong, AM Bunker, CP Vaughn, LV Furtado, et al.
BMC Medicine 2011, 9:133. http://www.biomedcentral.com/1741-7015/9/133

Background: About half of Americans 50 to 75 years old do not follow recommended colorectal cancer (CRC) screening guidelines, leaving 40 million individuals unscreened. A simple blood test would increase screening compliance, promoting early detection and better patient outcomes. The objective of this study is to demonstrate the performance of an improved sensitivity blood-based Septin 9 (SEPT9) methylated DNA test for colorectal cancer. Study variables include clinical stage, tumor location and histologic grade.
Methods: Plasma samples were collected from 50 untreated CRC patients at 3 institutions; 94 control samples were collected at 4 US institutions; samples were collected from 300 colonoscopy patients at 1 US clinic prior to endoscopy. SEPT9 methylated DNA concentration was tested in analytical specimens, plasma of known CRC cases, healthy control subjects, and plasma collected from colonoscopy patients.
Results: The improved SEPT9 methylated DNA test was more sensitive than previously described methods; the test had an overall sensitivity for CRC of 90% (95% CI, 77.4% to 96.3%) and specificity of 88% (95% CI, 79.6% to 93.7%), detecting CRC in patients of all stages. For early stage cancer (I and II) the test was 87% (95% CI, 71.1% to 95.1%) sensitive. The test identified CRC from all regions, including proximal colon (for example, the cecum) and had a 12% false-positive rate. In a small prospective study, the SEPT9 test detected 12% of adenomas with a false-positive rate of 3%.
Conclusions: A sensitive blood-based CRC screening test using the SEPT9 biomarker specifically detects a majority of CRCs of all stages and colorectal locations. The test could be offered to individuals of average risk for CRC who are unwilling or unable to undergo colonoscopy.

Matrix Metalloproteinases in Cancer: Prognostic Markers and Therapeutic Targets

Pia Vihinen And Veli-Matti K¨Ah¨Ari
Int. J. Cancer 2002; 99: 157–166 http://dx.doi.org:/10.1002/ijc.10329

Degradation of extracellular matrix is crucial for malignant tumour growth, invasion, metastasis and angiogenesis. Matrix metalloproteinases (MMPs) are a family of zinc-dependent neutral endopeptidases collectively capable of degrading essentially all matrix components. Elevated levels of distinct MMPs can be detected in tumour tissue or serumof patients with advanced cancer and their role as prognostic indicators in cancer is studied. In addition, therapeutic intervention of tumour growth and invasion based on inhibition of MMP activity is under intensive investigation and several MMP inhibitors are in clinical trials in cancer. In this review, we discuss the current view on the feasibility of MMPs as prognostic markers and as targets for therapeutic intervention in cancer.

Mass Spectrometric Screening of Ovarian Cancer with Serum Glycans

Jae-Han Kim, Chang Won Park, Dalho Um, Ki Hwang Baek, Yohahn Jo, et al.
Disease Markers  2014, Article ID 634289, 9 pages
http://dx.doi.org/10.1155/2014/634289

development of novel biomarkers based on the glycomic analysis. In this study, N-linked glycans from human serum were quantitatively profiled by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and compared between healthy controls and ovarian cancer patients. A training set consisting of 40 healthy controls and 40 ovarian cancer cases demonstrated an inverse correlation between 𝑃 value of ANOVA and area under the curve (AUC) of each candidate biomarker peak from MALDI-TOF MS, providing standards for the classification. A multi-biomarker panel composed of 15 MALDI-TOF MS peaks resulted in AUC of 0.89, 80∼90% sensitivity, and 70∼83% specificity in the training set. The performance of the biomarker panel was validated in a separate blind test set composed of 23 healthy controls and 37 ovarian cancer patients, leading to 81∼84% sensitivity and 83% specificity with cut-off values determined by the training set. Sensitivity of CA-125, the most widely used ovarian cancer marker, was 74%in the training set and 78% in the test set, respectively. These results indicate that MALDI-TOF MS-mediated serum N-glycan analysis could provide critical information for the screening of ovarian cancer.

Large, Collaborative Lung Cancer Trial Goes for Precision Medicine Goal

News | June 30, 2014 | Lung Cancer Targets

By Anna Azvolinsky, PhD

In a new biomarker-focused clinical trial, five therapies will be tested to develop new, precision medicine approaches to treat squamous cell lung cancer. The Lung Cancer Master Protocol (Lung-MAP)/SWOG S1400 phase 2/3 clinical trial, brings together the National Cancer Institute (NCI), the Foundation for the National Institutes of Health (FNIH), SWOG Cancer Research, five pharmaceutical companies (Amgen, AstraZeneca, Genentech, MedImmune, and Pfizer), Foundation Medicine (a molecular informatics company), and Friends of Cancer Research, a non-profit foundation.

The trial aims to enroll about 10,000 patients total and will cost about $160 million, of which the NCI is contributing $25 million.

Lung-MAP is unique as this is the first public-private partnership in drug development that includes the NCI, the Food and Drug Administration (FDA), U.S. oncology cooperative groups, and a number of patient advocacy groups according to one of the study investigators, David Gandara, MD, chair of the SWOG lung committee, and thoracic oncologist at the UC Davis Cancer Center. “Funds are made available for every aspect of the trial,” said Gandara. “There is nothing in the history of oncology or drug development like it.”

The clinical trial seeks to identify molecular aberrations in patients with advanced squamous cell lung cancer that can be targeted either by existing therapies or through the development of new ones. The innovation of this trial is a master protocol that will rely on the strength of numbers—up to 1000 patients per year at more than 200 sites throughout the U.S. for more than 200 cancer-related genetic alterations. Testing results will then dictate which experimental trial arm is most appropriate for which patient. Unlike a trial that seeks to enroll patients harboring just one mutation, which limits the access for many patients, the Lung-MAP design better ensures that a patient who is screened will be eligible for a targeted therapy trial arm.

This type of umbrella trial design is particularly suitable for squamous cell lung cancer. Thus far, has not been defined by one or several driver mutations. Instead, these tumors are made of a spectrum of genetic aberrations that are each relatively rare within the squamous lung cancer patient population, making enrollment into targeted therapy clinical trials difficult. According to the NCI, Lung-MAP “aims to establish a model of clinical testing that more efficiently meets the needs of both patients and drug developers,” facilitating more efficient matching of a patient to an investigational targeted therapy trial.

Lung-MAP was specifically designed for squamous cell lung cancer because this lung cancer subtype represents the greatest unmet need for new treatment, Gandara told OncoTherapy Network:

“All of the dramatic advances that have been made in the treatment of lung cancer over the last ten years have occurred in adenocarcinoma, a lung cancer subtype with several recently recognized and ‘druggable oncogenes’ such as EGFR mutations or ALK translocations. However, there have been essentially no advances in squamous cell lung cancer.”

But, recent genome-wide studies have identified several gene alterations in squamous cell lung cancer that are also druggable, including PI3K, FGFR, and CDK mutations, said Gandara. The trial is initially testing four targeted therapies: Genentech’s GDC-0032 (a PI3 kinase inhibitor), Pfizer’s palbociclib (an oral cyclin-dependent-kinase 4/6 inhibitor, AZD4547), an oral fibroblast growth factor receptor inhibitor from AstraZeneca, and rilotumumab, Amgen’s antibody against the human hepatocyte growth factor.

The fifth agent is, MEDI4736, an immune checkpoint inhibitor antibody targeting PD-L1. Patients whose tumors do not harbor a mutation suitable for targeting with one of the four targeted therapies will be enrolled in the MED4736 sub-study.

Once a patient is matched to a specific trial sub-study, randomization will determine whether the patient receives the experimental therapy or standard of care chemotherapy. The planned trial endpoints for each sub-study are overall survival and progression-free survival.

“I cannot overemphasize the importance of the FDA’s participation in this project, since each of these sub-studies is designed to result in approval of a paired biomarker and new drug if that sub-study meets the requirements for improved effectiveness,” said Gandara.

– See more at: http://www.oncotherapynetwork.com/lung-cancer-targets/large-collaborative-lung-cancer-trial-goes-precision-medicine-goal

The BATTLE Trial: Personalizing Therapy for Lung Cancer

Kim, RS. Herbst, II. Wistuba, JJ Lee, GR. Blumenschein Jr., A Tsao, DJ. Stewart, et al.

Authors’ Affiliations: 1Departments of Thoracic/Head and Neck Medical Oncology, 2Pathology, 3Biostatistics, and 4Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas; 5Winship Cancer Center, Emory University, Atlanta, Georgia; 6Dana-Farber Cancer Institute, Boston, Massachusetts; and 7University of Maryland, Baltimore, Maryland.

Corresponding Author:

Waun K. Hong, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030. Phone: 713-794-1441; Fax: 1-713-792-4654; E-mail:whong@mdanderson.org

The Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) trial represents the first completed prospective, biopsy-mandated, biomarker-based, adaptively randomized study in 255 pretreated lung cancer patients. Following an initial equal randomization period, chemorefractory non–small cell lung cancer (NSCLC) patients were adaptively randomized to erlotinib, vandetanib, erlotinib plus bexarotene, or sorafenib, based on relevant molecular biomarkers analyzed in fresh core needle biopsy specimens. Overall results include a 46% 8-week disease control rate (primary end point), confirm prespecified hypotheses, and show an impressive benefit from sorafenib among mutant-KRAS patients. BATTLE establishes the feasibility of a new paradigm for a personalized approach to lung cancer clinical trials.

(ClinicalTrials.gov numbers:NCT00409968, NCT00411671, NCT00411632, NCT00410059, and   NCT00410189.

Significance: The BATTLE study is the first completed prospective, adaptively randomized study in heavily pretreated NSCLC patients that mandated tumor profiling with “real-time” biopsies, taking a substantial step toward realizing personalized lung cancer therapy by integrating real-time molecular laboratory findings in delineating specific patient populations for individualized treatment. Cancer Discovery; 1(1); 44–53. © 2011 AACR.

Read the Commentary on this article by Sequist et al., p. 14
Read the Commentary on this article by Rubin et al., p. 17
This article is highlighted in the In This Issue feature, p. 4

Pharmacometabolomics in Drug Discovery & Development: Applications and Challenges

Yang and F. Marotta
Metabolomics 2012, 2:5 http://dx.doi.org/10.4172/2153-0769.1000e122

Recently, the concept of pharmaco-metabolomics is mentioned more frequently as an emerging discipline to study the effect of drugs on the whole pattern of small endogenous molecules and in applying the profiles of metabolomics for drug development. For the latter part, metabolomics is majorly used to differentiate patients into responder or non-responder groups in an effort to decrease large inter-individual variation in clinical trials. It is a novel approach that combines metabolite profile and chemo-metrics to model and predict drug targets, efficacy, pharmacokinetics and toxicity on both individual and population basis. It attracts many scientists’ attention because of its intrinsic advantages and promising potentials in drug discovery and development. Considering personalized drug treatment is the desired goal for current drug development, pharmaco-metabolomics provide an effective and inexpensive strategy to evaluate drug efficacy and toxicology, which may make personalized medicine realistic both from scientific and financial perspectives. Furthermore, the FDA also realized that metabolomics coupling with other “Omics” approaches could be a valuable tool in evaluating general toxicology and could eventually replace the use of animals after addressing certain challenges.

Networking metabolites and diseases

Pascal Braun, Edward Rietman, and Marc Vidal
PNAS  July 22, 2008; 105(29): 9849–9850

Diseasome and Drug-Target Network

Recently, Goh et al. constructed a ‘‘diseasome’’ network in which two diseases are linked to each other if they share at least one gene, in which mutations are associated with both diseases. In the resulting network, related disease families cluster tightly together, thus phenotypically defining functional modules. Importantly, for the first time this study applied concepts from network biology to human diseases, thus opening the door for discovering causal relationships between  disregulated networks and resulting ailments.

Subsequently Yilderim et al. linked drugs to protein targets in a drug–target network, which could then be overlaid with the diseasome network. One notable finding was the recent trend toward the development of new compounds directly targeted at disease gene products, whereas previous drugs, often found by trial and error, appear to target proteins only indirectly related to the actual disease molecular mechanisms. An important question that remains in this emerging field of network analysis consists of investigating the extent to which directly targeting the product of mutated genes is an efficient approach or whether targeting network properties instead, and thereby accounting for indirect nonlinear effects of system perturbations by drugs, may prove more fruitful. However, to answer such questions it is important to have a good understanding of the various influences that can lead to diseases.

UPDATED 6/01/2019

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers

from  2015 Mar;47(3):257-62. doi: 10.1038/ng.3202. Epub 2015 Feb 2.

Shlien A1, Campbell BB2, de Borja R3, Alexandrov LB4, Merico D5, Wedge D4, Van Loo P6, Tarpey PS4, Coupland P7, Behjati S4, Pollett A8, Lipman T9, Heidari A9, Deshmukh S9, Avitzur N9, Meier B10, Gerstung M4, Hong Y10, Merino DM3, Ramakrishna M4, Remke M11, Arnold R3, Panigrahi GB3, Thakkar NP12, Hodel KP13, Henninger EE13, Göksenin AY13, Bakry D14, Charames GS15, Druker H16, Lerner-Ellis J17, Mistry M2, Dvir R18, Grant R14, Elhasid R18, Farah R19, Taylor GP20, Nathan PC14, Alexander S14, Ben-Shachar S21, Ling SC22, Gallinger S23, Constantini S24, Dirks P25, Huang A26, Scherer SW27, Grundy RG28, Durno C29, Aronson M30, Gartner A10, Meyn MS31, Taylor MD25, Pursell ZF13, Pearson CE12, Malkin D32, Futreal PA4, Stratton MR4, Bouffet E26, Hawkins C33, Campbell PJ34, Tabori U35; Biallelic Mismatch Repair Deficiency Consortium.

Abstract: DNA replication-associated mutations are repaired by two components: polymerase proofreading and mismatch repair. The mutation/consequences of disruption to both repair components in humans are not well studied. We sequenced cancer genomes from children with inherited biallelic mismatch repair deficiency (bMMRD). High-grade bMMRD brain tumors exhibited massive numbers of substitution mutations (>250/Mb), which was greater than all childhood and most cancers (>7,000 analyzed). All ultra-hypermutated bMMRD cancers acquired early somatic driver mutations in DNA polymerase ɛ or δ. The ensuing mutation signatures and numbers are unique and diagnostic of childhood germ-line bMMRD (P < 10(-13)). Sequential tumor biopsy analysis revealed that bMMRD/polymerase-mutant cancers rapidly amass an excess of simultaneous mutations (∼600 mutations/cell division), reaching but not exceeding ∼20,000 exonic mutations in <6 months. This implies a threshold compatible with cancer-cell survival. We suggest a new mechanism of cancer progression in which mutations develop in a rapid burst after ablation of replication repair.

Genetic changes which occur in spontaneous arising somatic cancers include point mutations, copy number alterations and rearrangements and in general result from a defective DNA repair mechanisms during proliferation/replication over many years however as most somatic cancers are heterogeneous it is difficult to pinpoint the exact repair defects which may be ultimately responsible for such genetic aberrations.

However, early-onset cancers (e.g. pediatric cancers) in patients with hereditary DNA repair defects offer a good view of the mutation types and secondary pathways that drive oncogenesis. bMMRD is a childhood cancer syndrome characterized by early-onset cancers in various organs and caused by biallelic mutations.  In this study, genomes from 17 inherited cancers, by exomic sequencing and microarrays, were analyzed and compared to non-neoplastic tissue genomes from matched patients.  Brain cancers from these patients had an extremely high number of point mutations compared to other childhood cancers and adult cancers.

Mismatch repair was defective in all these cancers therefore it appeared that secondary mutations are required to cause the ultrahypermutated state.  The most frequently mutated gene was POLE (polymerase epsilon), affecting the proofreading ability of this DNA polymerase.  The genomes of tumors with mutant POLE had signature mutational spectrum and the signature occurred early but these signatures had been found in endometrial and colorectal cancers.  The authors concluded, based on serial analysis of other brain cancers with bMMRD and the observation that recurrent brain cancers accumulated mutations over a relatively short period, once the proofreading capability of pol epsilon is compromised in MMR deficient cells there is no defense against rapid and catastrophic accumulations of mutations.  This rapid accumulation of mutations apparently do not lead to apoptosis but rather rapid tumor initiation, and generating multiple subclones of tumor cells.

UPDATED 9/26/2021

Metabolic Profiling Reveals a Dependency of Human Metastatic Breast Cancer on Mitochondrial Serine and One-Carbon Unit Metabolism

Source: https://pubmed.ncbi.nlm.nih.gov/31941752/

Abstract

Breast cancer is the most common cancer among American women and a major cause of mortality. To identify metabolic pathways as potential targets to treat metastatic breast cancer, we performed metabolomics profiling on the breast cancer cell line MDA-MB-231 and its tissue-tropic metastatic subclones. Here, we report that these subclones with increased metastatic potential display an altered metabolic profile compared with the parental population. In particular, the mitochondrial serine and one-carbon (1C) unit pathway is upregulated in metastatic subclones. Mechanistically, the mitochondrial serine and 1C unit pathway drives the faster proliferation of subclones through enhanced de novo purine biosynthesis. Inhibition of the first rate-limiting enzyme of the mitochondrial serine and 1C unit pathway, serine hydroxymethyltransferase (SHMT2), potently suppresses proliferation of metastatic subclones in culture and impairs growth of lung metastatic subclones at both primary and metastatic sites in mice. Some human breast cancers exhibit a significant association between the expression of genes in the mitochondrial serine and 1C unit pathway with disease outcome and higher expression of SHMT2 in metastatic tumor tissue compared with primary tumors. In addition to breast cancer, a few other cancer types, such as adrenocortical carcinoma and kidney chromophobe cell carcinoma, also display increased SHMT2 expression during disease progression. Together, these results suggest that mitochondrial serine and 1C unit metabolism plays an important role in promoting cancer progression, particularly in late-stage cancer. IMPLICATIONS: This study identifies mitochondrial serine and 1C unit metabolism as an important pathway during the progression of a subset of human breast cancers.

ntroduction

The majority of breast cancer patients die from metastatic disease. The process of cancer metastasis involves local invasion into surrounding tissue, dissemination into the bloodstream, extravasation, and eventual colonization of a new tissue. Following a period of dormancy, small numbers of micrometastases eventually proliferate into large macrometastases, or secondary tumors.

Previous studies have illuminated several themes of metabolic reprogramming that occur during metastasis (–). However, the majority of these reported site-specific metabolic features of metastatic cancer cells. We reason that breast cancer cells that leave the primary tumor and successfully establish new lesions at distal sites would encounter similar metabolic stresses during metastasis. By performing comparative metabolomics on the MDA-MB-231 human breast cancer cell line and its tissue-tropic metastatic subclones, we uncovered that the catabolism of the non-essential amino acid serine through the mitochondrial one-carbon (1C) unit pathway is an important driver of proliferation in a subset of metastatic breast cancers that closely resembles the molecular features of MDA-MB-231 cells. Emerging evidence shows that the non-essential amino acid serine is essential for cancer cell survival and proliferation. The genomic regions containing PHGDH are amplified in breast cancer and melanoma, diverting 3PG to serine synthesis (,). We also reported that PHGDH is upregulated upon amino acid starvation by the transcription factor ATF4 (). On one hand, serine serves as a precursor for the synthesis of protein, lipids, nucleotides and other amino acids, which are necessary for cell division and growth. On the other hand, serine catabolism through the mitochondrial 1C unit pathway is critical for maintaining cellular redox control under stress conditions (,). In mitochondria, serine catabolism is initiated by serine hydroxymethyltransferase 2 (SHMT2). SHMT2 catalyzes a reversible reaction converting serine to glycine, with concurrent generation of the 1C unit donor methylene-THF, which is further oxidized by downstream enzymes MTHFD2 and MTHFD1L to produce NAD(P)H and formate. Subsequent export of formate from the mitochondria can then be re-assimilated into the cytosolic folate pool to support anabolic reactions. All three mitochondrial serine and 1C unit pathway enzymes (SHMT2, MTHFD2 and MTHFD1L) are upregulated in breast tumor samples compared to normal tissues (,). However, due to lack of functional investigations targeting this pathway in in vitro and in vivo breast cancer models, it remains unclear whether the mitochondrial 1C unit pathway represents a good target for treating metastatic breast cancer.

In this study, we report that enzymes in the mitochondrial serine and 1C unit pathway are even further upregulated specifically in subclones of the aggressive breast cancer cell line MDA-MB-231 that have been selected in vivo for the ability to preferentially metastasize to specific organs. We demonstrate that SHMT2 inhibition suppresses proliferation more strongly in these highly metastatic subclones compared to the parental population in vitro. Knockdown of SHMT2 also impairs breast cancer growth in vivo at both the primary and metastatic sites. In addition, we find that the expression of mitochondrial 1C unit pathway enzymes significantly associates with poor disease outcome in a subset of human breast cancer patients, potentiating its role as a therapeutic target or biomarker in advanced cancer. Finally, SHMT2 expression increases in breast invasive carcinoma, adrenocortical carcinoma, chromophobe renal cell carcinoma and papillary renal cell carcinoma during tumor progression, particularly in late stage tumors, suggesting that inhibitors targeting SHMT2 may hold promise for treating these late stage cancers when other therapeutic options become limited.

Materials and Methods

Cell lines

All of the paired parental and metastatic subclones were generated in Dr. Joan Massagué’s laboratory (Memorial Sloan-Kettering Cancer Center) (–). Cells were cultured in DMEM/F12 with 10% fetal bovine serum (Sigma) with 1% penicillin/streptomycin. All cells lines were tested every three to six months and found negative for mycoplasma (MycoAlert Mycoplasma Detection Kit; Lonza). These cell lines were not authenticated by the authors. All cell lines used in experiments were passaged no more than ten times from time of thawing.

RNAi

Stable 831-BrM,1833-BoM, and 4175-LM cell lines expressing shRNA against SHMT2, MTHFD2, and c-Myc were generated through infection with lentivirus and 1 μg/mL puromycin selection. shRNA-expressing virus was obtained using a previously published method (). Pooled populations were tested for on-target knockdown by immunoblot.

Immunoblot

The following antibodies were used: SHMT1, SHMT2 (Sigma), MTHFD2, MTHFD1L, c-Myc, Actin (Cell Signaling Technologies).

RNA Isolation, Reverse Transcription, and Real-Time PCR

Total RNA was isolated from tissue culture plates according to the TRIzol Reagant (Invitrogen) protocol. 3 μg of total RNA was used in the reverse transcription reaction using the SuperScript III (Invitrogen) protocol. Quantitative PCR amplification was performed on the Prism 7900 Sequence Detection System (Applied Biosystems) using Taqman Gene Expression Assays (Applied Biosystems). Gene expression data were normalized to 18S rRNA.

In vivo Tumor Growth Assays

All procedures involving animals and their care were approved by the Institutional Animal Care and Use Committee of Stanford University in accordance with institutional and National Institutes of Health guidelines. For orthotopic growth studies, 4175-LM shNT and 4175-LM shSHMT2 cells (1 × 106 cells in 0.1 mL of PBS, n = 8 per group) were injected into the flanks of NU/J 10-week-old female mice (The Jackson Laboratory). Tumors were measured with calipers over a 50-day time course. Volumes were calculated using the formula width2 × length × 0.5.

For lung metastasis assays, 4175-LM shNT and 4175-LM shSHMT2 cells (0.2 × 105 cells, n = 8 per group) were injected via tail vein into 6–8 week-old female NOD SCID mice. Mice were imaged weekly using the Xenogen IVIS 200 (PerkinElmer, Waltham, MA). Briefly, mice were injected intraperitoneally with 100 μg/g of D-luciferin (potassium salt; PerkinElmer) on the day of imaging. 8 min later, mice were anesthetized in an anesthesia-induction chamber using a mixture of 3% isoflurane (Fluriso, VetOne) in O2. Anesthesia was maintained with a mixture of 2% isoflurane in O2 inside the imaging chamber. Using Living Image (PerkinElmer, Waltham, MA), images were acquired (Exposure time, auto; F stop. 1.2; Binning, medium) from both dorsal and ventral sides of mice and a total photon flux (p/sec/cm2/sr) per animal was calculated by averaging the signal acquired from the dorsal and ventral side. After 4 weeks, surviving mice were sacrificed and lungs snap frozen in liquid N2 prior to homogenization in TRIzol for RNA extraction.

Metabolite Profiling and Mass Spectrometry

For total metabolite analysis, parental and metastatic cell lines were seeded in 60mm culture dishes in DMEM/F12 supplemented with 10% dialyzed fetal bovine serum. Media was refreshed 2 hours prior to harvesting by washing 3x with PBS before quenching with 800mL of −80 C 80:20 methanol:water. Extracts were spun down, supernatants collected, dried and resuspended in water before LC-MS analysis. Samples were analyzed by reversed-phase ion-pairing chromatography coupled with negative-mode electrospray-ionization high-resolution MS on a stand-alone ThermoElectron Exactive orbitrap mass spectrometer (). Peak picking and quantification were conducted using MAVEN analysis software. Heatmap was generated in R. Multiple testing correction and q-value generation were performed in PRISM software (GraphPad).

For [2,3,3-2H]serine labeling experiments, parental and metastatic cells were cultured in RPMI medium lacking glucose, serine, and glycine (TEKnova) supplemented with 2 g/L glucose and 0.03 g/L [2,3,3-2H]serine (Cambridge Isotope Laboratories) for up to 24 hours before harvesting. Cells were washed twice with ice-cold PBS prior to extraction with 400 μL of 80:20 acetonitrile:water over ice for 15 min. Cells were scraped off plates to be collected with supernatants, sonicated for 30s, then spun down at 1.5 × 104 RPM for 10 min. 200 μL of supernatant was taken out for LC-MS/MS analysis immediately.

Quantitative LC-ESI-MS/MS analysis of [2,3,3-2H]serine-labeled cell extracts was performed using an Agilent 1290 UHPLC system equipped with an Agilent 6545 Q-TOF mass spectrometer (Santa Clara, CA, US). A hydrophilic interaction chromatography method (HILIC) with an BEH amide column (100 × 2.1 mm i.d., 1.7 μm; Waters) was used for compound separation at 35 °C with a flow rate of 0.3ml/min. The mobile phase A consisted of 25 mM ammonium acetate and 25mM ammonium hydroxide in water and mobile phase B was acetonitrile. The gradient elution was 0–1 min, 85 % B; 1–12 min, 85 % B → 65 % B; 12– 12.2 min, 65 % B-40%B; 12.2–15 min, 40%B. After the gradient, the column was re-equilibrated at 85%B for 5min. The overall runtime was 20 min and the injection volume was 5 μL. Agilent Q-TOF was operated in negative mode and the relevant parameters were as listed: ion spray voltage, 3500 V; nozzle voltage, 1000 V; fragmentor voltage, 125 V; drying gas flow, 11 L/min; capillary temperature, 325 °C, drying gas temperature, 350 °C; and nebulizer pressure, 40 psi. A full scan range was set at 50 to 1600 (m/z). The reference masses were 119.0363 and 980.0164. The acquisition rate was 2 spectra/s. Isotopologues extraction was performed in Agilent Profinder B.08.00 (Agilent Technologies). Retention time (RT) of each metabolite was determined by authentic standards (Supplementary Table S1). The mass tolerance was set to +/−15 ppm and RT tolerance was +/− 0.2 min. Natural isotope abundance was corrected using Agilent Profinder software (Agilent Technologies).

Cell Line Classification

Cell line expression and copy number data were downloaded from the COSMIC cell line dataset (https://cancer.sanger.ac.uk/cell_lines), and all cell lines were classified using different cell line classifiers, including PAM50 and scmod2 using the package genefu from Bioconductor; and iC10 using package iC10 (–). The MDA-MB-231 parental and metastatic subclones were classified as Basal (posterior probability of 0.516), ER-Her2- (posterior probability of 0.997), IC4 (posterior probability of 0.999).

Outcome Analysis

METABRIC clinical and expression data was downloaded from EGA (EGAS00000000083) (). Outcome analysis was performed in IC4 samples only (N=342) in order to mimic the phenotype of the MDA-MB-231 breast cancer cell line. Survival analysis was performed over disease specific survival (DSS) censored to 20 years. Gene high/low categorization was performed using the maxstat algorithm, which determines the optimal threshold for separating high and low expression (from the surv cutpoint function of package survminer). Cox Proportional Hazard multivariate models use continuous expression adjusted by age, grade, size, number of lymph nodes, ER, PR and Her2 status. Kaplan-Meier plots were generated using the package survcomp, and Cox Proportional Hazards were generated using the package rms.

Immunohistochemical Staining and Quantification for SHMT2

Human primary breast cancer tissue and paired lymph node metastases were obtained from Biomax.us. Tumors were graded by Biomax.us pathologists according to the Nottingham grading system with respect to degree of glandular duct formation, nuclear pleomorphism, and nuclear fission counting. Each feature was scored from 1–3, and the total score was used to determine the following grades: Grade 1 (total score 3–5; low grade or well differentiated), Grade 2 (total score 6–7; intermediate grade or moderately differentiated), Grade 3 (total score 8–9; high grade or poorly differentiated). Standard immunohistochemical methods were performed as previously described (). The primary anti-human SHMT2 antibody (Sigma) was used at a concentration of 1:3000. Images were acquired on a Leica DMi8 system (Leica Microsystems) and quantified for positive SHMT2 signal intensity by ImageJ software.

SHMT2 Expression Analysis by Individual Cancer Stage

SHMT2 expression data across every annotated TCGA cancer data set was queried and downloaded from the UALCAN database (http://ualcan.path.uab.edu/index.html) ().

Statistical Analyses

All statistical tests were performed using the paired or unpaired Student’s t test by PRISM software. Values with a p value of < 0.05 were considered significant.

Results

Metastatic breast cancer cells exhibit altered metabolic profiles

To identify common metabolic pathways reprogrammed in metastatic breast cancer cells during cancer progression, we performed metabolomic profiling of the human triple negative breast cancer cell line MDA-MB-231 and its metastatic subpopulations (Fig. 1A and ​andB).B). This cell line was derived from the pleural effusion of a patient with widespread metastatic disease years after primary tumor removal (), and the subclones of this cell line with higher metastasis rate and preference to the bone, lung, or brain were previously isolated by in vivo selection (–) (831-BrM: brain metastasis. 1833-BoM: bone metastasis. 4175-LM: lung metastasis).

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Metastatic breast cancer subclones display an altered metabolic profile. (A) Schematic of targeted metabolomics workflow. Brain (831-BrM), bone (1833-BoM), and lung (4175-LM) metastatic subclones from tissue-tropic subpopulations were generated following IV injection of a parental population of MDA-MB-231 (231-Parental) cells into the tail vein or heart. Stable cell lines were passaged in culture prior to metabolite extraction for LC-MS/MS. (B) LC-MS profile of the 231-Parental, 831-BrM, and 1833-BoM cell lines. Cell lines were plated in biological triplicates prior to metabolite extraction. Signals were normalized to the mean signal of each metabolite across all samples, log2 transformed, and clustered.

At the time of initial metabolomics comparison, the lung metastatic subclone 4175-LM did not recover well in culture, so we profiled the 831-BrM and 1833-BoM metastatic subclones along with the parental population. We observed multiple metabolites involved in a plethora of metabolic pathways that were differentially enriched or depleted in the metastatic 831-BrM and 1833-BoM subclones compared to the parental population of MDA-MB-231 (231-Parental) cells (Fig. 1B). Following correction for false discovery rate, the levels of twenty-four metabolites were significantly altered in both 831-BrM and 1833-BoM cells compared to 231-Parental cells (Supplementary Table S2). Metabolites significantly enriched in metastatic subclones included the glycolytic intermediate dihydroxyacetone-phosphate (which is reversibly isomerized to glyceraldehyde-3-phosphate), the tricarboxylic acid (TCA) cycle intermediate succinate, amino acids such as proline and asparagine, and the pentose-phosphate pathway product 5-phosphoribosyl-1-pyrophosphate. These observations are consistent with prior observations of perturbations in lower glycolysis and the TCA cycle observed in other cell line models (notably murine 4T1 cells), suggesting common metabolic developments during metastasis of breast cancers in both mice and humans (–,,). Additionally, enrichment of asparagine has been reported to promote metastatic cancer cell phenotypes by epithelial-to-mesenchymal transition (). Nonetheless, the most significantly depleted class of metabolites in 831-BrM and 1833-BoM cells compared to 231-Parental cells were free purine nucleotides, suggesting alterations in purine metabolism in metastatic cells (Fig. 1B).

c-Myc is important for breast cancer cell proliferation

We wondered whether reduced levels of purines reflected decreased synthesis or higher consumption in the metastatic subclones. Because it was previously reported that the oncogenic transcription factor c-Myc induces the expression of nucleotide biosynthesis genes and that c-Myc amplification and overexpression is a common event in triple-negative breast cancer (–), we wondered if the relative differences in purine abundance could be explained by altered c-Myc protein levels in our cell line system. Indeed, 831-BrM, 1833-BoM, and 4175-LM cells overexpressed c-Myc compared to 231-Parental cells (Fig. 2A). Since sufficiency of free nucleotides can act as an important checkpoint for cell division (), we then compared the proliferation rates of parental and metastatic subclones. Accordingly, 831-BrM, 1833-BoM, and 4175-LM cells proliferated faster than 231-Parental cells in vitro (Fig. 2B), suggesting that the higher consumption rate is the cause of lower purine levels in the metastatic subclones.

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c-Myc drives proliferation in metastatic breast cancer cell subclones. (A) IB for c-Myc from whole-cell extracts of parental and metastatic subclones. (B) Proliferation of parental cells and metastatic subclones over 3 days (mean ± SD, n = 3). (C) 3 day proliferation of 231-Parental, 831-BrM, 1833-BoM, and 4175-LM cells expressing either a nontargeting (shNT) or c-Myc targeting (shMyc) vectors. (mean ± SD, n = 3).

Because the role of c-Myc in metastasis is still unclear, with evidence suggesting it plays both pro-metastatic and anti-metastatic functions in breast cancer depending on the genetic context (,), we tested the sensitivity of parental and metastatic subclones to c-Myc inhibition. Small hairpin RNA (shRNA)–mediated knockdown of c-Myc reduced cell proliferation in all four cell lines, although the degree of inhibition was stronger in 831-BrM and 1833-BoM cells (Fig. 2C, Supplementary Fig. S1). Parental cells expressing a non-targeting shRNA showed elevated c-Myc expression, possibly due to puromycin selection. These data suggest that c-Myc is an important mediator of cell proliferation, and c-Myc overexpression provided a proliferative advantage at least in brain and bone-metastatic subclones.

Identification of serine and one-carbon unit pathway elevation in metastatic subclones

The products of several metabolic pathways feed into nucleotide synthesis, including ribulose-5-phosphate from the pentose phosphate pathway, and one-carbon (1C) units and glycine from the serine and 1C unit pathway. It is also known that c-Myc can promote the expression of serine and glycine metabolism genes in cancer cells (,). We performed expression analyses of the metastatic subclones and found elevated levels of the key mitochondrial enzymes serine hydroxymethyltransferase 2 (SHMT2), methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), and methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L), in contrast to the downregulated expression of the cytosolic isoenzyme serine hydroxymethyltransferase 1 (SHMT1) (Fig. 3A–C). Consistent with previous reports in other cell types, knockdown of c-Myc in parental and metastatic breast cancer subclones diminished MTHFD2 and MTHFD1L protein expression, suggesting these enzymes are c-Myc-regulated (Supplementary Fig. S1). SHMT2 expression did not reduce upon c-Myc knockdown, suggesting that SHMT2 expression was regulated by other transcription factors. To determine whether c-Myc and mitochondrial 1C unit pathway enzyme overexpression was a common co-occurrence in other cancer metastasis models, we checked protein expression levels in the parental and metastatic subpopulations of other human cell line systems derived from lung adenocarcinoma or ER+ breast carcinoma patients (,). There was a clear correlation of SHMT2, MTHFD2, and MTHFD1L expression with c-Myc expression among all the cell lines tested. The brain metastatic subclones of lung adnocacinoma cell lines PC9 and H2030 had increased MTHFD2 expression, though we could not find another system that also displayed overexpression of c-Myc and all the three mitochondrial 1C unit pathway enzymes in metastatic subclones relative to their corresponding parental cells (Supplementary Fig. S2). Taken together with the observations of higher serine and glycine levels in 831-BrM and 1833-BoM cells compared to 231-Parental cells (Fig. 1B), these data suggest that the role of c-Myc in regulating mitochondrial serine and 1C unit metabolism in metastatic cancer may be tissue-specific.

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The mitochondrial serine and one-carbon unit pathway is upregulated in metastatic breast cancer subclones. (A) Schematic of the cytosolic and mitochondrial serine and one-carbon unit pathway. (B) qPCR for serine and one-carbon unit pathway genes (mean ± SD, n = 3, *P < 0.05 **P < 0.01 ***P < 0.001 ****P < 0.0001 by two-tailed Student’s t test, compared to expression in parental cells). (C) IB for serine and one-carbon unit pathway enzymes from whole-cell extracts of parental cells and metastatic subclones. (D) Schematic diagram of incorporation of 2H (D) from [2,3,3-2H]serine onto glycine, one-carbon units, and purines. (E) SHMT flux estimated by relative abundance of labeled glycine from serine (mean ± SD, n = 3, **P < 0.01 by two-tailed Student’s t test). (F) Fractional labeling of [2,3,3-2H]serine onto GTP and ATP (mean ± SD, n = 3, *P < 0.05 **P < 0.01 ***P < 0.001 by two-tailed Student’s t test).

Metastatic subclones display increased mitochondrial serine and one-carbon unit pathway activity

We next asked if higher expression of mitochondrial serine and 1C unit pathway enzymes might indeed reflect higher pathway activity. Serine can be catabolized in both the mitochondrial and cytosolic branch of the 1C unit pathway. Since cancer cells predominately express the mitochondrial serine catabolic enzymes over the cytosolic enzymes, serine is generally catabolized in the mitochondria in cancer cells (,,). Serine hydroxyl-methyltransferase 2 (SHMT2) initiates this reaction by converting serine to glycine while donating a carbon group to tetrahydrafolate (THF) to generate methylene-THF. Subsequent oxidation of methylene-THF by MTHFD2 and MTHFD1L generates NAD(P)H and formate. Formate can cross the mitochondrial membrane to provide 1C units for anabolic reactions such as nucleotide synthesis ().

We hypothesized that the reason metastatic cells upregulate the serine and 1C unit pathway is to enhance nucleotide synthesis to fuel cell proliferation. Indeed, most cancer cells have been reported to utilize serine as the predominant source of 1C units for biosynthesis (). We performed [2,3,3-2H]serine tracing to examine 1C unit pathway flux to glycine and purine nucleotides. In cells grown in media containing [2,3,3-2H]serine, the cytosolic pathway generates methylene-THF (me-THF) mass heavy by 2 (M+2) and 10-formyl-THF mass heavy by 1 (M+1), while 10-formyl-THF derived from mitochondrial formate exchange to the cytosol is strictly M+1. [2,3,3-2H]serine labeling onto the metabolites glycine and purine nucleotide triphosphates produced from the mitochondrial pathway thereby produces glycine M+1 and purines either M+1 or M+2 (Fig. 3D). Time course experiments were performed in 4175-LM cells to determine the optimal steady state labeling conditions for glycine and ATP from serine: 2 hours and 24 hours respectively (Supplementary Fig. S3). We observed higher SHMT flux in metastatic subclones, as the relative abundance of M+1 glycine was approximately 1.5-fold higher in 4175-LM cells compared to 231-Parental cells, indicating that higher purine turnover in metastatic cells was fueled by higher SHMT flux (Fig. 3E). Importantly, while robust fractions of ATP and GTP were labeled in parental cells, the metastatic subclones displayed even higher labeling fractions from serine (Fig. 3F). These results demonstrate that upregulation of serine catabolism through the mitochondrial 1C unit pathway promotes de novo purine synthesis in metastatic breast cancer cells.

Serine catabolism is necessary for metastatic cancer cell proliferation in vitro

To address the extent to which mitochondrial serine catabolism is necessary for cell proliferation, 231-Parental, 831-BrM, 1833-BoM, and 4175-LM cells were infected with lentivirus expressing shRNAs against SHMT2 (shSHMT2) or a nontargeting control (shNT). Intriguingly, knockdown of SHMT2 protein expression with two different shRNAs drastically suppressed proliferation of the metastatic subclones significantly, with a reduced effect in 231-Parental cells (Fig. 4A and ​andB).B). In contrast, knockdown of the downstream enzyme of the mitochondrial serine and 1C unit pathway, MTHFD2, suppressed proliferation to a lesser extent (Supplementary Fig. S4A and B). To evaluate the therapeutic potential of targeting 1C unit metabolism to block metastatic growth, we treated cells with a small-molecule inhibitor of SHMT called SHIN1 (). In vitro, metastatic subclones were sensitive to SHIN1 with an EC50 in the 100–500 nM range (Supplementary Fig. S5). There was no obvious enhancement of SHIN1 sensitivity in 831-BrM, 1833-BoM, and 4175-LM cells compared to 231-Parental cells, possibly because SHIN1 inhibits both SHMT2 and SHMT1 (Fig. 4C). Importantly, inhibition of cell proliferation in the presence of SHIN1 could be rescued by the supplementation of formate (2 mM), a source of cellular 1C units (Fig. 4C). These results indicate that the major role of elevated mitochondrial serine catabolism is to generate 1C units for cytosolic purine biosynthesis in the metastatic subclones. Thus, targeting SHMT activity may be a promising way to restrict nucleotide availability to block metastatic breast cancer cell proliferation.

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Metastatic subclones are particularly sensitive to SHMT2 inhibition. (A) 3 day proliferation of 231-Parental, 831-BrM,1833-BoM, and 4175-LM cells expressing either a nontargeting (shNT) or SHMT2 targeting (shSHMT2) vectors. Relative proliferation was calculated relative to average proliferation of shNT cells (mean ± SD, n = 3). (B) IB for SHMT2 in parental and metastatic subclones. (C) 3 day proliferation of parental and metastatic cells with 2 μM SHIN1, in RPMI with or without 2 mM formate and dialyzed FBS (mean ± SD, n = 3, ***P < 0.001 ****P < 0.0001 by two-tailed Student’s t test). Counts were normalized to the proliferation of 231-Parental cells in media without SHIN1 and formate treatment. (D) Growth of 4175-LM shNT and shSHMT2 tumors in the mammary fat pad of nude mice (mean ± SEM, n = 8, **P < 0.01 by two-tailed Student’s t test). (E) Quantification of luminescence signal in the lungs of mice 3 weeks post injection of either 4175-LM shNT or shSHMT2 cells (mean ± SEM, **P < 0.01 by two-tailed Student’s t test, shNT;n = 8 shSHMT2;n = 7). (F) qPCR analysis of hGAPDH expression in the lungs of mice 4 weeks post injection of either 4175-LM shNT or shSHMT2 cells (mean ± SEM, *P < 0.05 by two-tailed Student’s t test, shNT;n = 6 shSHMT2;n = 7).

SHMT2 knockdown impairs primary and metastatic growth in vivo

We then interrogated the effect of reducing mitochondrial 1C unit pathway activity in two different models of cancer growth in vivo. 4175-LM cells were chosen due to the relative ease of monitoring, measuring, and collecting tissue from lung metastasis compared to brain and bone metastasis. For the first model, we monitored breast cancer growth at the primary tumor site. SHMT2 knockdown significantly impaired the growth of 4175-LM cells in the mammary fat pads of immunodeficient mice (Fig. 4D, Supplementary Fig. S6). For the second model, we induced breast cancer metastasis to the lung by intravenous tail vein injection. Because 4175-LM cells express firefly luciferase (), we tracked tumor growth in the lung by bioluminescence imaging (BLI). Both BLI and quantification of human GAPDH (hGAPDH) expression from resected mouse lungs revealed a roughly two-fold reduction of lung tumor burden in mice injected with shSHMT2 cells compared to shNT cells (Fig. 4E and ​andF,F, Supplementary Fig. S7A). While on average, shSHMT2 tumors had reduced human SHMT2 (hSHMT2) expression compared to shNT tumors, some shSHMT2 tumors appeared to have reacquired hSHMT2 expression (Supplementary Fig. S7B and C). These data suggest that SHMT2 is necessary for metastatic growth in vivo.

Mitochondrial serine and 1C unit pathway genes are associated with more aggressive metastatic disease in some human breast cancer patients

To further explore the relevancy of mitochondrial one-carbon unit metabolism in human breast cancer metastasis, we examined the expression of SHMT1, SHMT2, MTHFD2, and MTHFD1L in the METABRIC dataset of human breast cancer patients (). We retrospectively inferred metastatic recurrence in patients by examining the frequency of disease-specific survival (DSS) up to 20 years. Patients were separated into two groups based on the maxstat algorithm (see Materials and Methods). Patients with high SHMT2 expression were significantly more likely to succumb to metastatic recurrent disease, while patients with high expression of the cytosolic isozyme SHMT1 were significantly protected from metastatic relapse (Fig. 5A, Supplementary Fig. S8). Using three different breast cancer subtype clustering analyses based on gene expression (PAM50, IC10, SCMOD2), we classified the MDA-MB-231 cell line as basal, IC4 (copy number flat), and ER−Her2− (,). We have previously described IC4 as consisting of a mixture of ER− tumors with lymphocytic infiltration and ER+ tumors with abundant stroma. Accordingly, further analysis of the IC4 patient subgroup following adjustment for covariates of age, grade, size, number of lymph nodes, ER, PR and Her2 status revealed a significant association of MTHFD1, MTHFD1L, MTHFD2, and SHMT2 expression with worse survival and SHMT1 expression with better survival (Fig. 5B). Finally, we stained a tissue microarray panel of human breast invasive ductal carcinoma and matched lymph node metastases and found significantly higher expression of SHMT2 in metastatic cancer cells comparing to the primary tumors (Fig. 5C and ​andD).D). Together, these data suggest that SHMT2 and other mitochondrial 1C unit pathway enzymes may be used as prognostic markers that indicate worse patient outcome, while cytosolic SHMT1 expression may indicate better survival rate in the IC4 patient subgroup.

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Mitochondrial serine and one-carbon unit pathway enzyme expression correlates with poor survival in human breast cancer. (A) Kaplan-Meier plot for SHMT1 (left) and SHMT2 (right) expression associated with disease-specific survival (DSS) in the human IC4 patient subgroup (METABRIC). (B) Forest plot for the hazard of individual 1C unit pathway genes adjusted for covariates (age, grade, size, number of lymph nodes, ER, PR and Her2 status) in the IC4 subgroup (n=343). (C) Representative SHMT2 staining (at 40x) of human breast invasive ductal carcinoma and matched metastatic carcinoma tissue samples (LN = lymph node). (D) Quantification of SHMT2 intensity by IHC in metastatic lesions compared to primary tumors (mean ± SD, n = 33 per group, *P < 0.05 by two-tailed Student’s t test).

Relevance of SHMT2 expression in the progression and aggressiveness of other cancer types

To evaluate the contribution of mitochondrial 1C unit metabolism to the progression of other cancer types, we queried SHMT2 expression in TCGA datasets through the UALCAN portal (). In addition to breast invasive carcinoma (BRCA), we identified adrenocortical carcinoma (ACC), head and neck squamous cell carcinoma (HNSC), kidney chromophobe cell carcinoma (KICH), and kidney renal papillary cell carcinoma (KIRP) as cancer types in which SHMT2 expression progressively increased as a function of stage (Fig. 6). Notably, gain of SHMT2 expression in BRCA and HNSC tended to occur early on in cancer progression, whereas in KICH, SHMT2 upregulation may occur only during the very late stage. A few cancer types such as mesothelioma (MESO) and ovarian serous cystadenocarcinoma (OV) showed the opposite trend: a progressive loss of SHMT2 expression with increasing cancer stage (Supplementary Fig. 9). Collectively, these data present the possibility that there exist additional cancer types in which mitochondrial 1C unit metabolism promotes progression and aggressiveness.

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SHMT2 expression increases with stage in various cancers.

Box plots depicting the average expression level (transcripts per million) of SHMT2 in normal tissue (N) and as a function of cancer stage (stage 1 = S1; stage 2 = S2; stage 3 = S4; stage 4 = S4). Statistically significant differences between pairwise comparisons are highlighted in red. Abbreviations for cancer types are explained as follows: ACC (adrenocortical carcinoma), BRCA (breast invasive carcinoma), HNSCC (head and neck squamous cell carcinoma), KICH (kidney chromophobe carcinoma), KIRP (kidney renal papillary cell carcinoma).

Discussion

For breast cancer, common metastatic sites include the brain, bone, liver, and lung. At the cellular level, the original heterogeneous population of cancer cells from the primary tumor undergo a selection process whereby those clones with alterations (carrying both genetic lesions and epigenetic modifications) favoring fitness and plasticity are enriched. These adaptations, in turn, equip cells with the ability to withstand standard treatments such as chemotherapy and radiation therapy, ultimately leading to cancer progression and metastatic recurrence (). While many previous studies have elucidated a role for molecular processes such as epithelial to mesenchymal transition and invasion and migration of cancer cells, our understanding of how metabolic pathway alterations shape metastatic growth is still limited. It is important to note that the MDA-MB-231 cells we studied were isolated from a pleural population that already metastasizes well in vivo. Our metabolomics profiling of the even more highly metastatic triple-negative breast cancer subclones suggested alterations in both glycolysis and the TCA cycle during the late stages of cancer progression, consistent with findings from other groups of heightened mitochondrial metabolism in metastatic cells (,,,). We further discovered elevated catabolism of serine in the mitochondria of our metastatic subclones. A previous study in isogenic murine 4T1 breast cancer cell lines found that transformed cells showed higher levels of nucleotides than nontransformed cells, and that “more metastatic” lines had even more nucleotides than “less metastatic” ones (). In contrast, we found lower levels of free purines in metastatic variants of human MDA-MB-231 cell lines compared to the parental population (Fig. 1B). This discrepancy may be attributed to different oncogenic contexts in 4T1 cells versus MDA-MB-231 cells or inherent differences in purine metabolism between murine and human cells. Due to the difficulty of obtaining pure metastatic tumor tissue from in vivo studies, the metabolomic analysis were performed using established cell lines in vitro. Microenvironmental factors from metastatic niche, such as hypoxia and nutrient starvation, also regulate cancer cell metabolism. Since mitochondrial 1C unit metabolism can utilize both NAD+ and NADP+, cancer cells with upregulation of mitochondrial 1C unit metabolism may gain metabolic flexibility to sustain proliferation under stress conditions. When cells engage active respiration, the mitochondrial 1C unit pathway can utilize NAD+ to generate 1C units; under hypoxia or starvation conditions, when the NAD+/NADH ratio decreases, elevated mitochondrial ROS leads to an increased NADP+/NADPH ratio, which can also drive the 1C unit pathway and purine synthesis. Further investigations comparing the metabolic profile changes under these stress conditions may provide more insight into potential links between metabolic stresses and the evolution of metastatic cancer cells.

The role of serine in cancer growth has drawn increasing interest over the years ever since the identification of PHGDH amplifications in melanoma and breast cancer (,). A variety of mechanisms have been proposed to explain why increased serine synthesis and serine catabolism could promote tumorigenesis, including rerouting glucose carbon flux, maintenance of compartment-specific NAD(P)+/NAD(P)H ratios, and the control of metabolites such as acetyl-coA, α-ketoglutarate, or 2-hydroxyglutarate (,,). Moreover, a previous study had implicated SHMT2 and a neutral amino acid importer of serine and glycine (ASCT2) as prognostic biomarkers for breast cancer (). Our study is the first to directly evaluate the therapeutic potential of targeting SHMT2 in metastatic breast cancer using both genetic and pharmaceutical approaches. Intriguingly, genetic knockdown of SHMT2 strongly inhibited the proliferation of metastatic cells, while treatment with a dual SHMT1/SHMT2 inhibitor suppressed proliferation of both parental and metastatic subclones. This discrepancy may be explained by prior observations that while MDA-MB-231 cells preferentially utilize the mitochondrial pathway for 1C unit production, inhibition of individual mitochondrial enzymes can lead to a switch to the cytosolic pathway (). We thus speculate that 231-Parental cells may be more adept at switching to cytosolic serine catabolism, and for reasons still unclear, the metastatic subclones are less flexible. Consistent with observations in colon cancer xenografts (), SHMT2 knockdown in the lung metastatic subclone slowed, but not completely suppressed, tumor growth in the mammary fat pad and lung. In addition, we found that in the IC4 subset of human breast cancer patients, the expression of mitochondrial one-carbon unit enzymes is positively associated with more aggressive disease. Thus, interrogating the expression status of mitochondrial one-carbon unit enzymes through transcriptional or proteomic methods holds prognostic value in the metastatic setting, and warrants the need for further development of drugs that selectively inhibit serine catabolism for treating the metastasis of triple-negative breast cancer.

What causes the upregulation of mitochondrial serine catabolic flux in highly metastatic cancer cells? We provide evidence that a crucial oncogenic event promotes the ability of metastatic breast cancer subclones to catabolize serine faster than parental cells: c-Myc activation. c-Myc overexpression is known to be associated with up to 40% of breast cancers, with hyperactive c-Myc enriched particularly in the basal-like subtype (,). These observations are consistent with our findings of the MDA-MB-231 cell line as basal-like and its metastatic subclones expressing even higher levels of c-Myc than the parental population (Fig. 2A). We found that c-Myc was required for the maintenance of the mitochondrial serine and 1C unit pathway genes MTHFD2 and MTHFD1L, consistent with previous reports that c-Myc supports serine/glycine metabolism at the transcriptional level in other cell types (,). These results suggest a model for breast cancer metastasis in which a small fraction of c-Mychigh expressing cells from the primary tumor acquire the ability to upregulate serine catabolism to fuel growth in metastatic tissue sites. Alternatively, high c-Myc expression and the linked ability to upregulate serine catabolism may be intrinsic properties of stem-like metastasis-initiating cells that are enriched in breast cancer cell populations selected for high metastatic activity in mice. As one of the key oncogenic transcription factors, there is increasing evidence that c-Myc plays multiple roles during the metastatic process. c-Myc knockdown reduces invasion and migration of MDA-MB-231 cells (). Moreover, a recent study corroborated our findings of elevated c-Myc levels in brain-metastatic derivatives of human breast cancer cells and demonstrated its necessity for the invasive growth of brain metastases (). Our study highlights the role of c-Myc in enhancing 1C unit pathway activity and proliferation, which is also important for metastatic growth. Since SHMT2 expression was not reduced by c-Myc shRNA, it is likely that other tumor-promoting factors, such as ATF4 and NRF2, also play important roles in late stage cancer progression by modulating 1C unit metabolism. Intriguingly, a recent report showed that TGF-β signaling induces the expression of SHMT2 (). Given the critical role of TGF-β in promoting metastasis (,), it may be interesting to further investigate whether serine and 1C unit pathway metabolic reprogramming is controlled by TGF-ß signaling in metastatic subpopulations of human breast cancer cells.

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The Challenge of Antimicrobial Resistance

Writer and Curator: Larry H. Bernstein, MD, FCAP

 

Antibiotic resistance has become a major challenge of our time.  Common microorganisms that inhabit the skin, mouth and nares, and fecal organisms are transmitted in the hospital setting. Handwashing procedures have had limited benefit. Operating rooms are ventilated and environmentally engineered to minimize transmission intraoperatively. The patient may be immune-compromized. The organisms that are encountered have genetically adapted to the most effective antibiotics at our disposal. even with some risk of secondary toxicity in some cases.

What is Drug Resistance?

Antimicrobial resistance is the ability of microbes, such as bacteria, viruses,
parasites, or fungi, to grow in the presence of a chemical (drug) that would
normally kill it or limit its growth.

Diagram showing the difference between non-resistant bacteria and drug
resistant bacteria.

Drug Resistance difference between non-resistant bacteria and drug resistant bacteria

Drug Resistance difference between non-resistant bacteria and drug resistant bacteria

Credit: NIAID

http://www.niaid.nih.gov/SiteCollectionImages/topics/
antimicrobialresistance/1whatIsDrugResistance.gif

Diagram showing the difference between non-resistant bacteria and drug
resistant bacteria. Non-resistant bacteria multiply, and upon drug treatment,
the bacteria die. Drug resistant bacteria multiply as well, but upon drug
treatment, the bacteria continue to spread.

Many infectious diseases are increasingly difficult to treat because of
antimicrobial-resistant organisms, including HIV infection, staphylococcal
infection, tuberculosis, influenza, gonorrhea, candida infection, and malaria.

Between 5 and 10 percent of all hospital patients develop an infection. About
90,000 of these patients die each year as a result of their infection, up from
13,300 patient deaths in 1992.

According to the Centers for Disease Control and Prevention (April 2011),
antibiotic resistance in the United States costs an estimated $20 billion a year
in excess health care costs, $35 million in other societal costs and more than 8
million additional days that people spend in the hospital.

World Health Organization – 2014 Report
WHO/HSE/PED/AIP/2014.2
http://www.who.int.org/

Antimicrobial resistance (AMR) is an increasingly serious threat to
global public health. AMR develops when a microorganism (bacteria,
fungus, virus or parasite) no longer responds to a drug to which it
was originally sensitive. This means that standard treatments no
longer work; infections are harder or impossible to control; the risk
of the spread of infection to others is increased; illness and hospital
stays are prolonged, with added economic and social costs; and the
risk of death is greater—in some cases, twice that of patients who
have infections caused by non-resistant bacteria. The problem is so
serious that it threatens the achievements of modern medicine. A
post-antibiotic era—in which common infections and minor
injuries can kill—is a very real possibility for the 21st century.

WHO is developing a global action plan for AMR that
will include:
• development of tools and standards for harmonized
surveillance of ABR in humans, and for integrated
surveillance in food-producing animals and the
food chain;
• elaboration of strategies for population-based
surveillance of AMR and its health and economic
impact; and
• collaboration between AMR surveillance networks
and centres to create or strengthen coordinated
regional and global surveillance.
AMR is a global health security threat that requires
action across government sectors and society as a
whole. Surveillance that generates reliable data is the
essential foundation of global strategies and public
health actions to contain AMR.

Resistance to Antibiotics: Are We in the Post-Antibiotic Era?
Alfonso J. Alanis
Archives of Medical Research 36 (2005) 697–705
http://dx.doi.org:/10.1016/j.arcmed.2005.06.009

Serious infections caused by bacteria that have become resistant
to commonly used antibiotics have become a major global healthcare
problem in the 21st century. They not only are more severe and
require longer and more complex treatments, but they are also
significantly more expensive to diagnose and to treat. Antibiotic
resistance, initially a problem of the hospital setting associated
with an increased number of hospital acquired infections usually
in critically ill and immunosuppressed patients, has now extended
into the community causing severe infections difficult to diagnose
and treat. The molecular mechanisms by which bacteria have
become resistant to antibiotics are diverse and complex. Bacteria
have developed resistance to all different classes of antibiotics
discovered to date. The most frequent type of resistance is
acquired and transmitted horizontally via the conjugation
of a plasmid. In recent times new mechanisms of resistance
have resulted in the simultaneous development of resistance
to several antibiotic classes creating very dangerous multidrug
-resistant (MDR) bacterial strains, some also known as
‘‘superbugs’’. The indiscriminate and inappropriate use of
antibiotics in outpatient clinics, hospitalized patients and
in the food industry is the single largest factor leading to
antibiotic resistance. In recent years, the number of new
antibiotics licensed for human use in different parts of the
world has been lower than in the recent past. In addition,
there has been less innovation in the field of antimicrobial
discovery research and development. The pharmaceutical
industry, large academic institutions or the government are
not investing the necessary resources to produce the next
generation of newer safe and effective antimicrobial drugs.
In many cases, large pharmaceutical companies have terminated
their anti-infective research programs altogether due to economic
reasons. The potential negative consequences of all these events
are relevant because they put society at risk for the spread of
potentially serious MDR bacterial infections.

Structural and biological studies on bacterial nitric oxide synthase
inhibitors
JK Holden,  H Li, Q Jing, S Kang, J Richo, RB Silverman, TL Poulos

Significance: Nitric oxide (NO) produced by bacterial nitric oxide
synthase has recently been shown to protect the Gram-positive
pathogens Bacillus anthracis and Staphylococcus aureus from
antibiotics and oxidative stress. Using Bacillus subtilis as a model
system, we identified two NOS inhibitors that work in conjunction
with an antibiotic to kill B. subtilis. Moreover, comparison of inhibitor-bound crystal structures between the bacterial NOS and mammalian
NOS revealed an unprecedented mode of binding to the bacterial NOS
that can be further exploited for future structure-based drug design.
Overall, this work is an important advance in developing inhibitors
against gram-positive pathogens.

Summary: Nitric oxide (NO) produced by bacterial NOS functions as a
cytoprotective agent against oxidative stress in Staphylococcus aureus,
Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors with potential antimicrobial
properties. These two compounds impede the growth of B. subtilis under
oxidative stress, and crystal structures show that each compound exhibits
a unique binding mode. Both compounds serve as excellent leads for the
future development of antimicrobials against bacterial NOS-containing
bacteria.  http://dx.doi.org/10.1073/pnas.1314080110

Speciation of clinically significant coagulase negative Staphylococci
and their antibiotic resistant patterns in a tertiary care hospital
PR Vysakh, S Kandasamy and RM Prabhavathi
Int.J.Curr.Microbiol.App.Sci (2015) 4(1): 704-709
http://www.ijcmas.com

Human skin and mucus membrane has Coagulase Negative Staphylococci
(CoNS) as the indigenous flora. CoNS had become an important agent for
nosocomial infections accounting for about 9%. These infections are
difficult to treat because of the risk factors and the multiple drug resistance
nature of these organisms. The study was undertaken to identify the
prevalence of clinical isolates of CoNS, their speciation and to determine
the antibiotic sensitivity/resistant patterns of CoNS. A total of 490 isolates
were collected from different samples and subjected to biochemical
characterization and antimicrobial screening using conventional
microbiological methods. 165 isolates were identified as CoNS. 23% of
CoNS were isolated from blood, 30% from post-operative wound infections,
23% from pus, 18% from urine, 3% from body fluids (CSF, ascitic fluid etc)
and 3% from CVP tips. The antibiotic sensitivity revealed 81% resistance
to Penicillin,32% resistance to Cefoxitin, 27% resistance to Cefazolin,
55% resistance to Erythromycin, 22% to Clindamycin and 35% to
Cotrimoxazole and with no resistance to Vancomycin, Linezolid and
Ciprofloxacin. The increased recognition of CoNS and emergence of
drug resistance among them demonstrates the need to consider them
as a potent pathogen and to devise laboratory procedure to identify
and to determine the prevalence and antibiotic resistant patterns of CoNS.

Resistance to rifampicin: a review
Beth P Goldstein
The Journal of Antibiotics (2014) 67, 625–630
http:://dx.doi.org:/10.1038/ja.2014.107

Resistance to rifampicin (RIF) is a broad subject covering not just the
mechanism of clinical resistance, nearly always due to a genetic change
in the b subunit of bacterial RNA polymerase (RNAP), but also how
studies of resistant polymerases have helped us understand the structure
of the enzyme, the intricacies of the transcription process and its role
in complex physiological pathways. This review can only scratch the
surface of these phenomena. The identification, in strains of
Escherichia coli, of the positions within b of the mutations determining
resistance is discussed in some detail, as are mutations in organisms
that are therapeutic targets of RIF, in particular Mycobacterium
tuberculosis. Interestingly, changes in the same three codons of
the consensus sequence occur repeatedly in unrelated RIF-resistant
(RIFr) clinical isolates of several different single mutation
predominates in mycobacteria. The utilization of our knowledge of
these mutations to develop rapid screening tests for detecting resistance
is briefly discussed. Cross-resistance among rifamycins has been a topic
of controversy; current thinking is that there is no difference in the
susceptibility of RNAP mutants to RIF, rifapentine and rifabutin.
Also summarized are intrinsic RIF resistance and other resistance
mechanisms.

Multi-drug resistance, inappropriate initial antibiotic therapy and
mortality in Gram negative severe sepsis and septic shock: A
retrospective cohort study
MD Zilberberg, AF Shorr, ST Micek, C Vazquez-Guillamet, MH Kollef
Critical Care 2014, 18:596 http://dx.doi.org:/10.1186/s13054-014-0596-8
http://ccforum.com/content/18/6/596

Introduction
The impact of in vitro resistance on initially appropriate antibiotic therapy
(IAAT) remains unclear. We elucidated the relationship between non-IAAT
and mortality, and between IAAT and multi-drug resistance (MDR) in
sepsis due to Gram-negative bacteremia (GNS).
Methods
We conducted a single-center retrospective cohort study of adult intensive
care unit patients with bacteremia and severe sepsis/septic shock caused by
a gram-negative (GN) organism. We identified the following MDR pathogens:
MDR P. aeruginosa, extended spectrum beta lactamase and carbapenemase-
producing organisms. IAAT was defined as exposure within 24 hours of
infection onset to antibiotics active against identified pathogens based on
in vitro susceptibility testing. We derived logistic regression models to
examine a) predictors of hospital mortality and b) impact of MDR on
non-IAAT. Proportions are presented for categorical variables, and
median values with interquartile ranges (IQR) for continuous
variables.

Results
Out of 1,064 patients with GNS, 351 (29.2%) did not survive
hospitalization. Non-survivors were older (66.5 (55, 73.5)
versus 63 (53, 72) years, P =0.036), sicker (Acute Physiology and
Chronic Health Evaluation II (19 (15, 25) versus 16 (12, 19),
P <0.001), and more likely to be on pressors (odds ratio (OR) 2.79,
95% confidence interval (CI) 2.12 to 3.68), mechanically ventilated
(OR 3.06, 95% CI 2.29 to 4.10) have MDR (10.0% versus 4.0%,
P <0.001) and receive non-IAAT (43.4% versus 14.6%, P <0.001).
In a logistic regression model, non-IAAT was an independent
predictor of hospital mortality (adjusted OR 3.87, 95% CI 2.77 to
5.41). In a separate model, MDR was strongly associated with
the receipt of non-IAAT (adjusted OR 13.05, 95% CI 7.00 to 24.31).
Conclusions
MDR, an important determinant of non-IAAT, is associated with
a three-fold increase in the risk of hospital mortality. Given the
paucity of therapies to cover GN MDRs, prevention and
development of new agents are critical.

Phenotypic and molecular characteristics of methicillin-resistant
Staphylococcus aureus isolates from Ekiti State, Nigeria
OA Olowe, OO Kukoyi, SS Taiwo, O Ojurongbe, OO Opaleye, et al.
Infection and Drug Resistance 2013:6 87–92
http://dx.doi.org/10.2147/IDR.S48809

Introduction: The characteristics and antimicrobial resistance profiles
of Staphylococcus aureus differs according to geographical regions and
in relation to antibiotic usage. The aim of this study was to determine
the biochemical characteristics of the prevalent S. aureus from Ekiti State,
Nigeria, and to evaluate three commonly used disk diffusion methods
(cefoxitin, oxacillin, and methicillin) for the detection of methicillin
resistance in comparison with mecA gene detection by polymerase chain
reaction.
Materials and methods: A total of 208 isolates of S. aureus recovered
from clinical specimens were included in this study. Standard
microbiological procedures were employed in isolating the strains.
Susceptibility of each isolate to methicillin (5 μg), oxacillin (1 μg),
and cefoxitin (30 μg) was carried out using the modified Kirby–Bauer/
Clinical and Laboratory Standard Institute disk diffusion technique.
They were also tested against panels of antibiotics including vancomycin.
The conventional polymerase chain reaction method was used to detect
the presence of the mecA gene.
Results: Phenotypic resistance to methicillin, oxacillin, and cefoxitin
were 32.7%, 40.3%, and 46.5%, respectively. The mecA gene was detected
in 40 isolates, giving a methicillin-resistant S. aureus (MRSA) prevalence
of 19.2%. The S. aureus isolates were resistant to penicillin (82.7%) and
tetracycline (65.4%), but largely susceptible to erythromycin (78.8%
sensitive), pefloxacin (82.7%), and gentamicin (88.5%). When compared
to the mecA gene as the gold standard for MRSA detection, methicillin,
oxacillin, and cefoxitin gave sensitivity rates of 70%, 80%, and 100%,
and specificity rates of 76.2%, 69.1%, and 78.5% respectively.
Conclusion: When compared with previous studies employing mecA
polymerase chain reaction for MRSA detection, the prevalence of 19.2%
reported in Ekiti State, Nigeria in this study is an indication of gradual rise
in the prevalence of MRSA in Nigeria. A cefoxitin (30 μg) disk diffusion test
is recommended above methicillin and oxacillin for the phenotypic detection
of MRSA in clinical laboratories.

Direct sequencing for rapid detection of multidrug resistant Mycobacterium
tuberculosis strains in Morocco
F Zakham, I Chaoui, AH Echchaoui, F Chetioui, M Driss Elmessaoudi, et al.
Infection and Drug Resistance 2013:6 207–213
http://dx.doi.org/10.2147/IDR.S47724

Background: Tuberculosis (TB) is a major public health problem with high
mortality and morbidity rates, especially in low-income countries.
Disturbingly, the emergence of multidrug resistant (MDR) and extensively
drug resistant (XDR) TB cases has worsened the situation, raising concerns
of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis
of MDR TB is a critical issue for TB management. This study is an attempt to
establish a rapid diagnosis of MDR TB by sequencing the target fragments of
the rpoB gene which linked to resistance against rifampicin and the katG gene
and inhA promoter region, which are associated with resistance to isoniazid.
Methods: For this purpose, 133 sputum samples of TB patients from Morocco
were enrolled in this study. One hundred samples were collected from new
cases, and the remaining 33 were from previously treated patients (drug
relapse or failure, chronic cases) and did not respond to anti-TB drugs after
a sufficient duration of treatment. All samples were subjected to rpoB, katG
and pinhA mutation analysis by polymerase chain reaction and DNA sequencing.
Results: Molecular analysis showed that seven strains were isoniazid-
monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were
identified in nine cases (6.8%). Among them, eight were traditionally
diagnosed as critical cases, comprising four chronic and four drug-relapse
cases. The last strain was isolated from a new case. The most recorded
mutation in the rpoB gene was the substitution TCG . TTG at codon 531
(Ser531 Leu), accounting for 46.15%. Significantly, the only mutation found
in the katG gene was at codon 315 (AGC to ACC) with a Ser315Thr amino acid
change. Only one sample harbored mutation in the inhA promoter region
and was a point mutation at the −15p position (C . T). Conclusion: The
polymerase chain reaction sequencing approach is an accurate and rapid
method for detection of drug-resistant TB in clinical specimens, and could
be of great interest in the management of TB in critical cases to adjust the
treatment regimen and limit the emergence of MDR and XDR strains.

Limiting and controlling carbapenem-resistant Klebsiella pneumoniae
L Saidel-Odes, A Borer.
Infection and Drug Resistance 2014:7 9–14
http://dx.doi.org/10.2147/IDR.S44358

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is resistant to
almost all antimicrobial agents, is associated with substantial morbidity
and mortality, and poses a serious threat to public health. The ongoing
worldwide spread of this pathogen emphasizes the need for immediate
intervention. This article reviews the global spread and risk factors for
CRKP colonization/infection, and provides an overview of the strategy
to combat CRKP dissemination.

Staphylococcus aureus – antimicrobial resistance and the immuno-
compromised child
J Chase McNeil
Infection and Drug Resistance 2014:7 117–127
http://dx.doi.org/10.2147/IDR.S39639

Children with immunocompromising conditions represent a unique
group for the acquisition of antimicrobial resistant infections due to
their frequent encounters with the health care system, need for empiric
antimicrobials, and immune dysfunction. These infections are further
complicated in that there is a relative paucity of literature on the clinical
features and management of Staphylococcus aureus infections in
immunocompromised children. The available literature on the clinical
features, antimicrobial susceptibility, and management of S. aureus
infections in immunocompromised children is reviewed. S. aureus
infections in children with human immunodeficiency virus (HIV) are
associated with higher HIV viral loads and a greater degree of CD4 T-cell
suppression. In addition, staphylococcal infections in children with HIV
often exhibit a multidrug resistant phenotype. Children with cancer have
a high rate of S. aureus bacteremia and associated complications. Increased
tolerance to antiseptics among staphylococcal isolates from pediatric
oncology patients is an emerging area of research. The incidence of S. aureus
infections among pediatric solid organ transplant recipients varies
considerably by the organ transplanted; in general however, staphylococci
figure prominently among infections in the early post-transplant period.
Staphylococcal infections are also prominent pathogens among children
with a number of immunodeficiencies, notably chronic granulomatous
disease. Significant gaps in knowledge exist regarding the epidemiology
and management of S. aureus infection in these vulnerable children.

selected Staphylococcus aureus mechanisms for immune evasion.

selected Staphylococcus aureus mechanisms for immune evasion.

Figure 1 A schematic depiction of selected Staphylococcus aureus
mechanisms for immune evasion.
Notes: Cna interacts with C1q preventing formation of the C1qrs complex.
ClfA and SdrE each promote Factor I mediated conversion of C3b to iC3b.
Protein A is depicted binding to the Fc region of IgG preventing immunoglobulin
opsonization.
Abbreviations: ClfA, staphylococcal clumping factor A; Cna, collagen adhesin;
IgG, immunoglobulin G; PVL, Panton–Valentine leukocidin; SdrE, S. aureus
surface protein.

The Future of Antibiotics and Resistance
B Spellberg, JG Bartlett, and DN Gilbert
N Engl J Med Jan 24, 2013; 368(4): 299-302
http://dx.doi.org:/ 10.1056/NEJMp1215093

In its recent annual report on global risks, the World Economic
Forum (WEF) concluded that “arguably the greatest
risk . . . to human health comes in the form of antibiotic-resistant
bacteria. We live in a bacterial world where we will never be able
to stay ahead of the mutation curve. A test of our resilience is
how far behind the curve we allow ourselves to fall.”

The WEF report underscores the facts that antibiotic resistance
and the collapse of the antibiotic research and-development
pipeline continue to worsen despite our ongoing efforts on
current fronts. If we’re to develop countermeasures that
have lasting effects, new ideas that complement traditional
approaches will be needed.

Resistance is primarily the result of bacterial adaptation to eons
of antibiotic exposure. What are the fundamental implications of
this reality? First, in addition to antibiotics’ curative power, their
use naturally selects for preexisting resistant populations of bacteria
in nature. Second, it is not just “inappropriate” antibiotic use
that selects for resistance. Rather, the speed with which resistance
spreads is driven by microbial exposure to all antibiotics, whether
appropriately prescribed or not. Thus, even if all inappropriate
antibiotic use were eliminated, antibiotic-resistant infections
would still occur (albeit at lower frequency). Third, after billions
of years of evolution, microbes have most likely invented
antibiotics against every biochemical target that can be attacked
— and, of necessity, developed resistance mechanisms
to protect all those biochemical targets.

Remarkably, resistance was found even to synthetic antibiotics
that did not exist on earth until the 20th century. These results
underscore a critical reality: antibiotic resistance already exists,
widely disseminated in nature, to drugs we have not yet invented.

Table **

Interventions to Address the Antibiotic-Resistance Crisis.*

Intervention Status                                                   Preventing infection
and resistance

“Self-cleaning” hospital rooms;                                Some commercially available
automated disinfectant application                         but require clinical validation;
through misting, vapor, radiation, etc.                    more needed

Novel drug-delivery systems to replace                  Basic science and
IV catheters; regenerative-tissue technology        conceptual stages
to replace prosthetics; superior, noninvasive
ventilation strategies

Improvement of population health and                 Implementation
health care systems to reduce admissions             research stage
to hospitals and skilled nursing facilities

Niche vaccines to prevent resistant                        Basic and clinical
bacterial infections                                                    development stage

Refilling antibiotic pipeline by aligning
economic and regulatory approaches

Models in place, expansion needed in number    Government or nonprofit grants
and scope; new nonprofit corporations                 and contracts to defray R&D costs
needed                                                                          and establish nonprofits
to develop antibiotics

Institution of novel approval pathways                 Proposed, legislative
(e.g., Limited Population Antibiotic                        and regulatory
Drug proposal)                                                            action needed

Preserving available antibiotics,
slowing resistance

Public reporting of antibiotic-use data as a         Policy action needed to
basis for benchmarking and reimbursement      develop and implement

Development of and reimbursement for            Basic and applied research
rapid diagnostic and biomarker tests to              and policy action and
enable appropriate use of antibiotics                   policy action needed

Elimination of use of antibiotics to                       Legislation proposed
promote livestock growth

New waste-treatment strategies;                       One strategy approaching
targeted chemical or biologic                              clinical trials
degradation of antibiotics in waste

Studies to define shortest effective                    Some trials completed
courses of antibiotics for infections

Developing microbe-attacking                            Preclinical, proof-of-
treatments with diminished                                principle stage
potential to drive resistance

Immune-based therapies, such
as infusion of monoclonal antibodies
and white cells that kill microbes

Antibiotics or biologic agents that
don’t kill bacteria but alter their ability
to trigger inflammation or cause disease

Developing treatments attacking host             Preclinical, proof-of-principle stage
targets rather than microbial targets to
avoid selective pressure driving resistance

Direct moderation of host inflammation
in response to infection (e.g., cytokine
agonists or antagonists, PAMP receptor
agonists)

Sequestration of host nutrients to
prevent microbial access to nutrients

Probiotics that compete with microbial
growth

* IV denotes intravenous, PAMP pathogen-associated molecular
pattern, and R&D research and development

Antibiotic-Resistant Bugs Appear to Use Universal Ribosome-Stalling Mechanism

GEN News  Jan 26, 2015
http://www.genengnews.com/gen-news-highlights/antibiotic-resistant-bugs-
appear-to-use-universal-ribosome-stalling-mechanism/81250847/

Researchers at St. Louis University say they have discovered new information
about how antibiotics like azithromycin stop staph infections, and why staph
sometimes becomes resistant to drugs. The team, led by Mee-Ngan F. Yap, Ph.D.,
believe their evidence suggests a universal, evolutionary mechanism by which
the bacteria elude this kind of drug, offering scientists a way to improve the
effectiveness of antibiotics to which bacteria have become resistant.  Their
study (“Sequence selectivity of macrolide-induced translational attenuation”)
was published in PNAS.

Staphylococcus aureus  is a strain of bacteria that frequently has become
resistant to antibiotics, a development that has been challenging for doctors
and dangerous for patients with severe infections. Dr. Yap and her research
team studied staph that had been treated with the antibiotic azithromycin and
learned two things: One, it turns out that the antibiotic isn’t as effective as was
previously thought. And two, the process that the bacteria use to evade the
antibiotic appears to be an evolutionary mechanism that the bacteria developed
in order to delay genetic replication when beneficial.

Genomic epidemiology of a protracted hospital outbreak caused by multidrug-
resistant Acinetobacter baumannii in Birmingham, England
MR Halachev, J Z-M Chan, CI Constantinidou, N Cumley, C Bradley, et al.
Genome Medicine 2014, 6:70 http://genomemedicine.com/content/6/11/70

Background: Multidrug-resistant Acinetobacter baumannii commonly causes
hospital outbreaks. However, within an outbreak, it can be difficult to identify
the routes of cross-infection rapidly and accurately enough to inform infection
control. Here, we describe a protracted hospital outbreak of multidrug-resistant
A. baumannii, in which whole-genome sequencing (WGS) was used to obtain
a high-resolution view of the relationships between isolates.
Methods: To delineate and investigate the outbreak, we attempted to genome-
sequence 114 isolates that had been assigned to the A. baumannii complex
by the Vitek2 system and obtained informative draft genome sequences from
102 of them. Genomes were mapped against an outbreak reference sequence
to identify single nucleotide variants (SNVs).
Results: We found that the pulsotype 27 outbreak strain was distinct from all
other genome-sequenced strains. Seventy-four isolates from 49 patients
could be assigned to the pulsotype 27 outbreak on the basis of genomic
similarity, while WGS allowed 18 isolates to be ruled out of the outbreak.
Among the pulsotype 27 outbreak isolates, we identified 31 SNVs and seven
major genotypic clusters. In two patients, we documented within-host diversity,
including mixtures of unrelated strains and within-strain clouds of SNV diversity.
By combining WGS and epidemiological data, we reconstructed potential
transmission events that linked all but 10 of the patients and confirmed links
between clinical and environmental isolates. Identification of a contaminated
bed and a burns theatre as sources of transmission led to enhanced
environmental decontamination procedures.
Conclusions: WGS is now poised to make an impact on hospital infection
prevention and control, delivering cost-effective identification of routes of
infection within a clinically relevant timeframe and allowing infection control
teams to track, and even prevent, the spread of drug-resistant hospital pathogens.

Discovery of β-lactam-resistant variants in diverse pneumococcal populations
Regine Hakenbeck
Genome Medicine 2014, 6:72  http://genomemedicine.com/content/6/9/72

Understanding of antibiotic resistance in Streptococcus pneumoniae has been
hindered by the low frequency of recombination events in bacteria and thus the
presence of large linked haplotype blocks, which preclude identification of
causative variants. A recent study combining a large number of genomes of
resistant phenotypes has given an insight into the evolving resistance to
β-lactams, providing the first large-scale identification of candidate variants
underlying resistance.

Additional sources:

A Simple Method for Assessment of MDR Bacteria for Over-Expressed
Efflux Pumps
M Martins, MP McCusker, M Viveiros, I Couto, S Fanning, .., L Amaral
The Open Microbiology Journal, 2013, 7, 1-5

Identification of Efflux Pump-mediated Multidrug-resistant
Bacteria by the Ethidium Bromide-agar Cartwheel Method
M MARTINS, M VIVEIROS, I COUTO,, SS COSTA, .., L AMARAL
in vivo 25: 171-178 (2011)

Efflux Pumps that Bestow Multi-Drug Resistance of Pathogenic
Gram negative Bacteria
Amaral L, Spengler G, Martins A and Molnar J
Biochem Pharmacol 2013; 2(3):119
http://dx.doi.org/10.4172/2167-0501.1000119

graphical abstract

graphical abstract

An Instrument-free Method for the Demonstration
of Efflux Pump Activity of Bacteria
M MARTINS, B SANTOS, A MARTINS, M VIVEIROS, I COUTO,
A CRUZ, THE MANAGEMENT COMMITTEE MEMBERS
OF COST B16 OF THE EUROPEAN COMMISSION/
EUROPEAN SCIENCE FOUNDATION,…, J MOLNAR, S FANNING
and LEONARD AMARAL
in vivo 20: 657-664 (2006)

Potential Therapy of Multidrug-resistant and Extremely
Drug-resistant Tuberculosis with Thioridazine
LEONARD AMARAL and JOSEPH MOLNAR
in vivo 26: 231-236 (2012)

Inhibitors of efflux pumps of Gram-negative bacteria
inhibit Quorum Sensing
Leonard Amaral, Joseph Molnar
Open Journal of Pharmacology, 2012, 2-2

An Overview of Clinical Microbiology, Classification,
and Antimicrobial Resistance
Larry H. Bernstein
http://pharmaceuticalintelligence.com/2015/01/17/an-overview-
of-clinical-microbiology-classification-and-antimicrobial-resistance/

New protein detonates bacteria from within

By Tim Sandle     in Science

Tel Aviv – By sequencing the DNA of bacteria resistant to viral toxins, scientists have identified novel proteins capable of stymieing growth in pathogenic, antibiotic-resistant bacteria.

Today’s arsenal of antibiotics is ineffective against some emerging strains of antibiotic-resistant pathogens. Novel inhibitors of bacterial growth therefore need to be found. One way is looking into the viruses that infect bacteria.

Key to the new initiative is the concept of fighting bacteria from within, rather than using an external chemical to batter through the bacterial cell wall. the basis of the new weapon is viral. In order to select an appropriate viral protein, researchers undertook a comprehensive screening exercise in order to identify proteins in viruses that are known to infect bacteria (bacteriophages). Bacteriophages occur abundantly in the biosphere, with different virions, genomes and lifestyles. The review was so comprehensive that it took almost three years to complete.

The screening was achieved through the use of high-throughput DNA sequencing. This is the process of determining the precise order of nucleotides within a DNA molecule. By using this advanced genetic method, the scientists identified mutations in bacterial genes that resisted the toxicity of growth inhibitors produced by bacterial viruses. Through this, a new, tiny protein was found. The protein is termed “growth inhibitor gene product (Gp) 0.6”.

Later testing found that the protein specifically targets and inhibits the activity of a protein essential to bacterial cells. The bacterial protein affected has the function of holding the microbe’s cell wall together. Without this protein functioning correctly, the cell bursts open from within and the bacterium dies.

For the next wave of research, the Israeli science group are looking further at bacterial viruses with the aim of finding compounds that facilitate improved treatment of antibiotic-resistant bacteria.
Read more: http://www.digitaljournal.com/science/new-protein-detonates-bacteria-from-within/article/424747#ixzz3QJN0uo1d

Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7

Shahar Molshanski-Mora, Ido Yosefa, Ruth Kiroa, Rotem Edgara, Miriam Manora, Michael Gershovitsb, Mia Lasersonb, Tal Pupkob, and Udi Qimrona,1

Author Affiliations

Edited* by Sankar Adhya, National Institutes of Health, National Cancer Institute, Bethesda, MD, and approved November 24, 2014 (received for review July 13, 2014)

Significance

Antibiotic resistance of pathogens is a growing threat to human health, requiring immediate action. Identifying new gene products of bacterial viruses and their bacterial targets may provide potent tools for fighting antibiotic-resistant strains. We show that a significant number of phage proteins are inhibitory to their bacterial host. DNA sequencing was used to map the targets of these proteins. One particular target was a key cytoskeleton protein whose function is impaired following the phage protein’s expression, resulting in bacterial death. Strikingly, in over 70 y of extensive research into the tested bacteriophage, this inhibition had never been characterized. We believe that the presented approach may be broadened to identify novel, clinically relevant bacteriophage growth inhibitors and to characterize their targets.

Abstract

Today’s arsenal of antibiotics is ineffective against some emerging strains of antibiotic-resistant pathogens. Novel inhibitors of bacterial growth therefore need to be found. The target of such bacterial-growth inhibitors must be identified, and one way to achieve this is by locating mutations that suppress their inhibitory effect. Here, we identified five growth inhibitors encoded by T7 bacteriophage. High-throughput sequencing of genomic DNA of resistant bacterial mutants evolving against three of these inhibitors revealed unique mutations in three specific genes. We found that a nonessential host gene, ppiB, is required for growth inhibition by one bacteriophage inhibitor and another nonessential gene, pcnB, is required for growth inhibition by a different inhibitor. Notably, we found a previously unidentified growth inhibitor, gene product (Gp) 0.6, that interacts with the essential cytoskeleton protein MreB and inhibits its function. We further identified mutations in two distinct regions in the mreB gene that overcome this inhibition. Bacterial two-hybrid assay and accumulation of Gp0.6 only in MreB-expressing bacteria confirmed interaction of MreB and Gp0.6. Expression of Gp0.6 resulted in lemon-shaped bacteria followed by cell lysis, as previously reported for MreB inhibitors. The described approach may be extended for the identification of new growth inhibitors and their targets across bacterial species and in higher organisms.

New funding to fight antibiotic resistance SPECIAL

By Tim Sandle

This week the White House stated that it will double the amount of federal funding put aside to combat and preventing antibiotic resistance. The sum stands at greater than $1.2 billion.

Read more: http://www.digitaljournal.com/life/health/new-funding-to-fight-antibiotic-resistance/article/424745#ixzz3QJSBRxLU

U.S. Senator Sherrod Brown has been campaigning across the U.S. about the risks related to antibiotic-resistant infections for several years. Such infections affect more than two million U.S. citizens each year. The issue is not only of importance in one country for the growing menace of antibiotic resistance is, arguably, the single biggest threat faced by the world’s population. Moreover, emerging antimicrobial resistance and the growing shortage of effective antibiotic drugs is widely regarded as a crisis that jeopardizes patient safety and public health.

Senator Brown has welcomed the increased spending, although he also feels that more action is required. “To combat antibiotic resistance, it’s important that we leverage the best in medical expertise, stewardship, and technological innovation,” Brown has told Digital Journal.

He went on to add: “This unprecedented proposal underscores the importance of taking a comprehensive, wide-ranging approach to tackle this issue. I look forward to continuing to work with federal agencies, research institutions, and health care providers to combat this threat to America’s health.”

In 2014, Brown proposed the Strategies to Address Antimicrobial Resistance (STAAR) Act. The aim of this legislation was to boost the federal response to antibiotic resistance through promoting prevention and control. Other measures included: tracking drug-resistant bacteria; supporting enhanced research efforts; and improving the development, use, and stewardship of antibiotics. The Act would have provided an opportunity to bring multiple federal and non-governmental partners together to protect the public health from these drug-resistant bugs.

The Act, reported by Digital Journal, did not get through, despite the recent announcement of increased federal spending. Senator Brown argues that more preventative measures are needed. For this reason he plans to reintroduce similar legislation this year.

The STAAR Act would:

Promote prevention through public health partnerships at the U.S. Centers for Disease Control and Prevention (CDC) and local health departments;

Track resistant bacteria by making data collection better and requiring better reporting;

Improve the use of antibiotics by educating health care facilities on appropriate antibiotic use;

Enhance leadership and accountability in antibiotic resistance by reauthorizing a task force and coordinating agency efforts;

Support research by directing the National Institutes of Health (NIH) to work with other agencies and experts to create a strategic plan to address the problem.

Read more: http://www.digitaljournal.com/life/health/new-funding-to-fight-antibiotic-resistance/article/424745#ixzz3QJSliTXy

Senator takes on antibiotic resistant organisms SPECIAL

By Tim Sandle     Apr 16, 2014 in Science

Washington – With so-called “super bugs” on the rise, U.S. Sen. Sherrod Brown (D-OH) has introduced a bill aimed at slowing down the rate of antibiotic resistant microorganisms.

Read more: http://www.digitaljournal.com/science/senator-takes-on-antibiotic-resistant-organisms/article/381328#ixzz3QJT1jbOk

Senator Brown has introduced the Strategies to Address Antimicrobial Resistance (STAAR) Act. This is legislation aimed at combating antimicrobial resistance. In presenting the Act, Brown called for greater Federal attention to the growth of antibiotic-resistant infections, which affect more than two million Americans each year.

Brown is aiming for the STAAR Act to provide an opportunity to bring multiple federal and non-governmental partners together to protect the public health from these drug-resistant bugs.

Senator Brown contacted Digital Journal to explain more. In explaining the basis to the Act, Brown said: “Each year more than 23,000 Americans die from bacterial infections that are resistant to antibiotics.”

Antimicrobial resistance describes the ability of a microorganism to resist the action of antimicrobial drugs. In some instances some microorganisms are naturally resistant to particular antimicrobial agents; in other instances, the genes of non-disease-causing bacteria can be transferred to pathogenic bacteria, leading to patterns of clinically significant antibiotic resistance. Since the 1990s antibiotic resistance has been of concern for scientists and health policy makers.

Looking at the reasons for this, Brown explained that: “Antibiotics and other antimicrobial drugs have been a victim of their own success. We have used these drugs so widely and for so long that the microbes they are designed to kill have adapted to them, making the drugs less effective.”

Considering this in the context of his Act, Brown added: “We need a comprehensive strategy to address antimicrobial resistance. That is why I am introducing the STAAR Act, which would revitalize efforts to combat super bugs.”

Emerging antimicrobial resistance and the growing shortage of effective antibiotic drugs is widely regarded as a crisis that jeopardizes patient safety and public health. Once confined to hospitals, drug-resistant microbes, such as multi-drug-resistant Staphylococcus aureus (MRSA), are now striking down healthy, non-hospitalized citizens. This includes both the young and old, adults and children. These infections are painful, difficult to treat, and have become a silent epidemic in communities and hospitals across the U.S. (according to CDC).

Brown hopes that the STAAR Act will help strengthen the federal response to antimicrobial resistance by placing more of an emphasis on federal antimicrobial resistance surveillance, prevention and control, and research efforts.

In addition the Senator hopes that the Act will strengthen coordination within both Department of Health and Human Services (HHS) agencies as well as across other federal departments that are important to addressing antimicrobial resistance and enable opportunities to address this issue globally.

By providing for a more comprehensive and coordinated approach to the antimicrobial resistance crisis, it would seem that the STAAR Act represents a critical first step toward resolving what has become a major public health crisis.

Read more: http://www.digitaljournal.com/science/senator-takes-on-antibiotic-resistant-organisms/article/381328#ixzz3QJTWUxTB

H.R. 2285 (113th): Strategies to Address Antimicrobial Resistance Act

Introduced:
Jun 6, 2013 (113th Congress, 2013–2015)

Status:
Died (Referred to Committee) in a previous session of Congress

See Instead:
S. 2236 (same title)

Referred to Committee — Apr 10, 2014

  • Vaccination -how is vaccination important in preventing resistance?
  • Bioterrorism – what are the risks of resistance associated with bioterrorism
  • Antibacterials – do they cause resistance?
  • Food & Farming – why are antimicrobials used in farming?

Read Full Post »

Classification of Microbiota –

An Overview of Clinical Microbiology, Classification, and Antimicrobial Resistance

Author and Curator: Larry H. Bernstein, MD, FCAP

Classification of Microbiota

Introduction to Overview of Microbiology

This is a contribution to a series of pieces on the history of biochemistry, molecular biology, physiology and medicine in the 20th century.  Here I describe the common microbial organisms encountered in the clinical laboratory, the method of their collection, plating, culture and identification, and antibiotic sensitivity testing and resistant strains.

I may begin with the recognition that there are common strains in the environment that are not pathogenic, and there are pathogenic bacteria.
In addition, there are bacteria that coexist in the body habitat under specific conditions so that we are able to map the types expected to location, such as, skin, mouth and nasal cavities, the colon, the vagina and urinary system.  Meningitides occur as a result of extension from the nasal cavity to the brain.  When bacteria invade the circulation, it is referred to as septicemia, and the bacteria can cause valvular heart damage.

Bacteriology can be traced to origins in the 19th century.  The clinical features of localized infection are classically referred to as redness, heat, a raised lesion (pustule), and exudate (serous or purulent – watery or cellular).  This not only holds for a focal lesion (as skin), but also for pneumonia, urinary infection, and genital. It may be accompanied by cough, or bloody cough and wheezing, or by an unclear urine. In the case of septicemia, there is fever, and there may be seizures or delirium.

Collection and handling of specimens

Specimens are collected by sterile technique by a nurse or physician and sent to a lab as a swab, or as a blood specimen.  In the case of a febrile illness, blood cultures may be obtained from opposite arms, and another an hour later.  This is related to the possible cyclical seeding of bacteria into the circulation.  If the specimen is collected from a site of infection, a swab may be put onto a glass slide for gram staining.  The specimen collected is sent to the laboratory.

We may consider syphilis and tuberculosis special cases that I’ll set aside.  I shall not go into virology either, although I may referred to smallpox, influenza, polio, HIV under epidemic.  The first step in identification is the Gram stain, developed in the 19th century.  Organisms of the skin are Gram positive and appear blue on staining.  They are cocci, or circular, organized in characteristic clusters (staphylococcus, streptococcus) or in pairs (diplococci, eg. Pneumococcus), and if from the intestine (enterococcus).  If they are elongated rods, they might be coliform.  If they stain red, they are Gram negative.  Gram negative rods are coliform, and are enterobacteriaceae. Meningococci are Gram negative cocci.  So we have certain information about these organisms before we plate them for growth.

Laboratory growth characteristics

The specimen is applied to an agar plate with a metal rod applicator, or perhaps onto more than one agar plate.  The agar plate contains a growth media or a growth inhibitor that is more favorable to certain species than to others.  The bacteria are grown at 37o C in an incubator and colonies develop that are white or nonwhite, and they are smooth or wrinkled.  The appearance of the colonies is characteristic for certain strains.  If there is no contamination, all of the colonies look the same.  The next step is to:

  • Gram stain from a colony
  • Transfer samples from the colony to a series of growth media that identify presence or absence of specific nutrient requirements for growth (which is presumed from the prior findings).

In addition, the colony samples are grown on an agar to which is applied antibiotic tabs.  The tabs either allow or repress growth.  It wa some 50 years ago that the infectious disease physician and microbiologist Abraham Braude would culture the bacteria on agar plates that had a gradient of antibiotic to check for concentration that would inhibit growth.

Principles of Diagnosis (Extracts)

By John A. Washington

The clinical presentation of an infectious disease reflects the interaction between the host and the microorganism. This interaction is affected by the host immune status and microbial virulence factors. Signs and symptoms vary according to the site and severity of infection. Diagnosis requires a composite of information, including history, physical examination, radiographic findings, and laboratory data.

Microbiologic Examination

Direct Examination and Techniques: Direct examination of specimens reveals gross pathology. Microscopy may identify microorganisms. Immunofluorescence, immuno-peroxidase staining, and other immunoassays may detect specific microbial antigens. Genetic probes identify genus- or species-specific DNA or RNA sequences.

Culture: Isolation of infectious agents frequently requires specialized media. Nonselective (noninhibitory) media permit the growth of many microorganisms. Selective media contain inhibitory substances that permit the isolation of specific types of microorganisms.

Microbial Identification: Colony and cellular morphology may permit preliminary identification. Growth characteristics under various conditions, utilization of carbohydrates and other substrates, enzymatic activity, immunoassays, and genetic probes are also used.

Serodiagnosis: A high or rising titer of specific IgG antibodies or the presence of specific IgM antibodies may suggest or confirm a diagnosis.

Antimicrobial Susceptibility: Microorganisms, particularly bacteria, are tested in vitro to determine whether they are susceptible to antimicrobial agents.

Diagnostic medical microbiology is the discipline that identifies etiologic agents of disease. The job of the clinical microbiology laboratory is to test specimens from patients for microorganisms that are, or may be, a cause of the illness and to provide information (when appropriate) about the in vitro activity of antimicrobial drugs against the microorganisms identified (Fig. 1).

Laboratory procedures used in confirming a clinical diagnosis of infectious disease with a bacterial etiology

http://www.ncbi.nlm.nih.gov/books/NBK8014/bin/ch10f1.jpg

A variety of microscopic, immunologic, and hybridization techniques have been developed for rapid diagnosis

techniques have been developed for rapid diagnosis

techniques have been developed for rapid diagnosis

From: Chapter 10, Principles of Diagnosis
Medical Microbiology. 4th edition.
Baron S, editor.
Galveston (TX): University of Texas Medical Branch at Galveston; 1996.

For immunologic detection of microbial antigens, latex particle agglutination, coagglutination, and enzyme-linked immunosorbent assay (ELISA) are the most frequently used techniques in the clinical laboratory. Antibody to a specific antigen is bound to latex particles or to a heat-killed and treated protein A-rich strain of Staphylococcus aureus to produce agglutination (Fig. 10-2). There are several approaches to ELISA; the one most frequently used for the detection of microbial antigens uses an antigen-specific antibody that is fixed to a solid phase, which may be a latex or metal bead or the inside surface of a well in a plastic tray. Antigen present in the specimen binds to the antibody as inFig. 10-2. The test is then completed by adding a second antigen-specific antibody bound to an enzyme that can react with a substrate to produce a colored product. The initial antigen antibody complex forms in a manner similar to that shown inFigure 10-2. When the enzyme-conjugated antibody is added, it binds to previously unbound antigenic sites, and the antigen is, in effect, sandwiched between the solid phase and the enzyme-conjugated antibody. The reaction is completed by adding the enzyme substrate.

agglutination test ch10f2

agglutination test ch10f2

Figure 2 Agglutination test in which inert particles (latex beads or heat-killed S aureus Cowan 1 strain with protein A) are coated with antibody to any of a variety of antigens and then used to detect the antigen in specimens or in isolated bacteria

http://www.ncbi.nlm.nih.gov/books/NBK8014/bin/ch10f2.jpg

Genetic probes are based on the detection of unique nucleotide sequences with the DNA or RNA of a microorganism. Once such a unique nucleotide sequence, which may represent a portion of a virulence gene or of chromosomal DNA, is found, it is isolated and inserted into a cloning vector (plasmid), which is then transformed into Escherichia coli to produce multiple copies of the probe. The sequence is then reisolated from plasmids and labeled with an isotope or substrate for diagnostic use. Hybridization of the sequence with a complementary sequence of DNA or RNA follows cleavage of the double-stranded DNA of the microorganism in the specimen.

The use of molecular technology in the diagnoses of infectious diseases has been further enhanced by the introduction of gene amplication techniques, such as the polymerase chain reaction (PCR) in which DNA polymerase is able to copy a strand of DNA by elongating complementary strands of DNA that have been initiated from a pair of closely spaced oligonucleotide primers. This approach has had major applications in the detection of infections due to microorganisms that are difficult to culture (e.g. the human immunodeficiency virus) or that have not as yet been successfully cultured (e.g. the Whipple’s disease bacillus).

Solid media, although somewhat less sensitive than liquid media, provide isolated colonies that can be quantified if necessary and identified. Some genera and species can be recognized on the basis of their colony morphologies.

In some instances one can take advantage of differential carbohydrate fermentation capabilities of microorganisms by incorporating one or more carbohydrates in the medium along with a suitable pH indicator. Such media are called differential media (e.g., eosin methylene blue or MacConkey agar) and are commonly used to isolate enteric bacilli. Different genera of the Enterobacteriaceae can then be presumptively identified by the color as well as the morphology of colonies.

Culture media can also be made selective by incorporating compounds such as antimicrobial agents that inhibit the indigenous flora while permitting growth of specific microorganisms resistant to these inhibitors. One such example is Thayer-Martin medium, which is used to isolate Neisseria gonorrhoeae. This medium contains vancomycin to inhibit Gram-positive bacteria, colistin to inhibit most Gram-negative bacilli, trimethoprim-sulfamethoxazole to inhibit Proteus species and other species that are not inhibited by colistin and anisomycin to inhibit fungi. The pathogenic Neisseria species, N gonorrhoeae and N meningitidis, are ordinarily resistant to the concentrations of these antimicrobial agents in the medium.

Infection of the bladder (cystitis) or kidney (pyelone-phritis) is usually accompanied by bacteriuria of about ≥ 104 CFU/ml. For this reason, quantitative cultures (Fig. 10-3) of urine must always be performed. For most other specimens a semiquantitative streak method (Fig. 10-3) over the agar surface is sufficient. For quantitative cultures, a specific volume of specimen is spread over the agar surface and the number of colonies per milliliter is estimated.

Identification of bacteria (including mycobacteria) is based on growth characteristics (such as the time required for growth to appear or the atmosphere in which growth occurs), colony and microscopic morphology, and biochemical, physiologic, and, in some instances, antigenic or nucleotide sequence characteristics. The selection and number of tests for bacterial identification depend upon the category of bacteria present (aerobic versus anaerobic, Gram-positive versus Gram-negative, cocci versus bacilli) and the expertise of the microbiologist examining the culture. Gram-positive cocci that grow in air with or without added CO2 may be identified by a relatively small number of tests. The identification of most Gram-negative bacilli is far more complex and often requires panels of 20 tests for determining biochemical and physiologic characteristics.

Antimicrobial susceptibility tests are performed by either disk diffusion or a dilution method. In the former, a standardized suspension of a particular microorganism is inoculated onto an agar surface to which paper disks containing various antimicrobial agents are applied. Following overnight incubation, any zone diameters of inhibition about the disks are measured. An alternative method is to dilute on a log2 scale each antimicrobial agent in broth to provide a range of concentrations and to inoculate each tube or, if a microplate is used, each well containing the antimicrobial agent in broth with a standardized suspension of the microorganism to be tested. The lowest concentration of antimicrobial agent that inhibits the growth of the microorganism is the minimal inhibitory concentration.

Classification Principles

This Week’s Citation Classic®_______ Sneath P H A & Sokal R R.
Numerical taxonomy: the principles and practice of
numerical classification. San Francisco: Freeman, 1973. 573 p.
[Medical Research Council Microbial Systematics Unit, Univ. Leicester, England
and Dept. Ecology and Evolution, State Univ. New York, Stony Brook, NY]
Numerical taxonomy establishes classification
of organisms based on their similarities. It utilizes
many equally weighted characters and employs
clustering and similar algorithms to yield
objective groupings. It can beextended to give
phylogenetic or diagnostic systems and can be
applied to many other fields of endeavour.

Mathematical Foundations of Computer Science 1998
Lecture Notes in Computer Science Volume 1450, 1998, pp 474-482
Date: 28 May 2006
Positive Turing and truth-table completeness for NEXP are incomparable 1998
Levke Bentzien

The truth-table method [matrix method] is one of the decision procedures for sentence logic (q.v., §3.2). The method is based on the fact that the truth value of a compound formula of sentence logic, construed as a truth-function, is determined by the truth values of its arguments (cf. “Sentence logic” §2.2). To decide whether a formula A is a tautology or not, we list all possible combinations of truth values to the variables in A: A is a tautology if it takes the value truth under each assignment.

Using ideas introduced by Buhrman et al. ([2], [3]) to separate various completeness notions for NEXP = NTIME (2poly), positive Turing complete sets for NEXP are studied. In contrast to many-one completeness and bounded truth-table completeness with norm 1 which are known to coincide on NEXP ([3]), whence any such set for NEXP is positive Turing complete, we give sets A and B such that

A is ≤ bT(2) P -complete but not ≤ posT P -complete for NEXP

B is ≤ posT P -complete but not ≤ tt P -complete for NEXP. These results come close to optimality since a further strengthening of (1), as was done by Buhrman in [1] for EXP = DTIME(2poly), seems to require the assumption NEXP = co-NEXP.

Computability and Models
The University Series in Mathematics 2003, pp 1-10
Truth-Table Complete Computably Enumerable Sets
Marat M. Arslanov

We prove a truth-table completeness criterion for computably enumerable sets.
The authors research was partially supported by Russian Foundation of Basic Research, Project 99-01-00830, and RFBR-INTAS, Project 97-91-71991.

TRUTH TABLE CLASSIFICATION AND IDENTIFICATION*
EUGENE W. RYPKA
Department of Microbiology, Lovelace Foundation for Medical Education and Research,
Albuquerque, N.M. 87108, U.S.A.
Space life sciences 1971-12-1; 3(2): pp 135-156
http://dx.doi.org:/10.1007/BF00927988
(Received 15 July, 1971)
Abstract. A logical basis for classification is that elements grouped together and higher categories of elements should have a high degree of similarity with the provision that all groups and categories be disjoint to some degree. A methodology has been developed for constructing classifications automatically that gives
nearly instantaneous correlations of character patterns of organisms with time and clusters with apparent similarity. This means that automatic numerical identification will always construct schemes from which disjoint answers can be obtained if test sensitivities for characters are correct. Unidentified organisms are recycled through continuous classification with reconstruction of identification schemes. This process is
cyclic and self-correcting. The method also accumulates and analyzes data which updates and presents a more accurate biological picture.

Syndromic classification: A process for amplifying information using S-clustering

Eugene W. Rypka, PHD

http://dx.doi.org:/10.1016/S0899-9007(96)00315-2

Optimal classification/Rypka < Optimal classification>

Contents

1 Rypka’s Method

1.1 Equations

1.2 Examples

2 Notes and References

Rypka’s Method

Rypka’s[1] method[2] utilizes the theoretical and empirical separatory equations shown below to perform the task of optimal classification. The method finds the optimal order of the fewest attributes, which in combination define a bounded class of elements.

Application of the method begins with construction of an attribute-valued system in truth table[3] or spreadsheet form with elements listed in the left most column beginning in the second row. Characteristics[4] are listed in the first row beginning in the second column with the code name of the data in the upper left most cell. The values which connect each characteristic with each element are placed in the intersecting cells. Selecting appropriate characteristics to universally define the class of elements may be the most difficult part for the classifier of utilizing this method.

The elements are first sorted in descending order according to their truth table value, which is calculated from the existing sequence and value of characteristics for each element. Duplicate truth table values or multisets for the entire bounded class reveal either the need to eliminate duplicate elements or the need to include additional characteristics.

An empirical separatory value is calculated for each characteristic in the set and the characteristic with the greatest empirical separatory value is exchanged with the characteristic which occupies the most significant attribute position.

Next the second most significant characteristic is found by calculating an empirical separatory value for each remaining characteristic in combination with the first characteristic. The characteristic which produces the greatest separatory value is then exchanged with the characteristic which occupies the second most significant attribute position.

Next the third most significant characteristic is found by calculating an empirical separatory value for each remaining characteristic in combination with the first and second characteristics. The characteristic which produces the greatest empirical separatory value is then exchanged with the characteristic which occupies the third most significant attribute position. This procedure may continue until all characteristics have been processed or until one hundred percent separation of the elements has been achieved.

A larger radix will allow faster identification by excluding a greater percentage of elements per characteristic. A binary radix for instance excludes only fifty percent of the elements per characteristic whereas a five-valued radix excludes eighty percent of the elements per characteristic.[5] What follows is an elucidation of the matrix and separatory equations.[6]

Computational Example
Bounded Class Data

bounded class data

Bounded Class Dimensions

G = 28 – 28 elements – i = 0…G-1[1]

C = 10 – 10 characteristics or attributes – j = 0…C-1

V = 5 – 5 valued logic – l = 0…V-1

Order of Elements

order of elements

Count multisets

count multisets

Squared multiset Counts

squared multiset counts

Separatory Values

separatory values

T=

max(T) = 309 = S8 = highest initial separatory value

Notes

Mathcad’s ORIGIN function applies to all arrays such that if more than one array is being used and one array requires a zero origin then the other arrays must use a zero origin with all variables being adapted as well.

Rypka’s Method Edit

Rypka’s[1] method[2] utilizes the theoretical and empirical separatory equations shown below to perform the task of optimal classification. The method finds the optimal order of the fewest attributes, which in combination define a bounded class of elements.

Application of the method begins with construction of an attribute-valued system in truth table[3] or spreadsheet form with elements listed in the left most column beginning in the second row. Characteristics[4] are listed in the first row beginning in the second column with the title of the attributes in the upper left most cell. Normally the file name of the data is given the title of the element class. The values which connect each characteristic with each element are placed in the intersecting cells. Selecting characteristics which all elements share may be the most difficult part of creating a database which can utilizing this method.

The elements are first sorted in descending order according to their truth table value, which is calculated from the existing sequence and value of characteristics for each element. Duplicate truth table values or multisets for the entire bounded class reveal either the need to eliminate duplicate elements or the need to include additional characteristics.

An empirical separatory value is calculated for each characteristic in the set and the characteristic with the greatest empirical separatory value is exchanged with the characteristic which occupies the most significant attribute position.

Next the second most significant characteristic is found by calculating an empirical separatory value for each remaining characteristic in combination with the first characteristic. The characteristic which produces the greatest separatory value is then exchanged with the characteristic which occupies the second most significant attribute position.

Next the third most significant characteristic is found by calculating an empirical separatory value for each remaining characteristic in combination with the first and second characteristics. The characteristic which produces the greatest empirical separatory value is then exchanged with the characteristic which occupies the third most significant attribute position. This procedure may continue until all characteristics have been processed or until one hundred percent separation of the elements has been achieved.

A larger radix will allow faster identification by excluding a greater percentage of elements per characteristic. A binary radix for instance excludes only fifty percent of the elements per characteristic whereas a five-valued radix excludes eighty percent of the elements per characteristic.[5] What follows is an elucidation of the matrix and separatory equations.[6]

Syndromic Classification: A Process for Amplifying Information Using S-Clustering

Eugene W. Rypka, PhD
University of New Mexico, Albuquerque, New Mexico, USA
Statistics Editor: Marcello Pagano, PhD
Harvard School of Public Health, Boston, Massachusetts, USA
Nutrition 1996; 12(11/12): 827-829

In a previous issue of Nutrition, Drs. Bernstein and Pleban’ use the method of S-clustering to aid in nutritional classification of patients directly on-line. Classification of this type is called primary or syndromic classification.* It is created by a process called separatory (S-) clustering (E. Rypka, unpublished observations). The authors use S-clustering in Table I.  S-clustering extracts features (analytes, variables) from endogenous data that amplify or maximize structural information to create classes of patients (pathophysiologic events) which are the most disjointed or separable. S-clustering differs from other classificatory methods because it finds in a database a theoretic- or more- number of variables with the required variety that map closest to an ideal, theoretic, or structural information standard. In Table I of their article, Bernstein and Pleban’ indicate there would have to be 3 ’ = 243 rows to show all possible patterns. In Table II of this article, I have used a 33 = 27 row truth table to convey the notion of mapping amplified information to an ideal, theoretic standard using just the first three columns. Variables are scaled for use in S-clustering.

A Survey of Binary Similarity and Distance Measures
Seung-Seok Choi, Sung-Hyuk Cha, Charles C. Tappert
SYSTEMICS, CYBERNETICS AND INFORMATICS 2010; 8(1): 43-48
The binary feature vector is one of the most common
representations of patterns and measuring similarity and
distance measures play a critical role in many problems
such as clustering, classification, etc. Ever since Jaccard
proposed a similarity measure to classify ecological
species in 1901, numerous binary similarity and distance
measures have been proposed in various fields. Applying
appropriate measures results in more accurate data
analysis. Notwithstanding, few comprehensive surveys
on binary measures have been conducted. Hence we
collected 76 binary similarity and distance measures used
over the last century and reveal their correlations through
the hierarchical clustering technique.

This paper is organized as follows. Section 2 describes
the definitions of 76 binary similarity and dissimilarity
measures. Section 3 discusses the grouping of those
measures using hierarchical clustering. Section 4
concludes this work.

Historically, all the binary measures observed above have
had a meaningful performance in their respective fields.
The binary similarity coefficients proposed by Peirce,
Yule, and Pearson in 1900s contributes to the evolution
of the various correlation based binary similarity
measures. The Jaccard coefficient proposed at 1901 is
still widely used in the various fields such as ecology and
biology. The discussion of inclusion or exclusion of
negative matches was actively arisen by Sokal & Sneath
in during 1960s and by Goodman & Kruskal in 1970s.

Polyphasic Taxonomy of the Genus Vibrio: Numerical Taxonomy of Vibrio cholerae, Vibrio
parahaemolyticus, and Related Vibrio Species
R. R. COLWELL
JOURNAL OF BACTERIOLOGY, Oct. 1970;  104(1): 410-433
A set of 86 bacterial cultures, including 30 strains of Vibrio cholerae, 35 strains of
V. parahaemolyticus, and 21 representative strains of Pseudomonas, Spirillum,
Achromobacter, Arthrobacter, and marine Vibrio species were tested for a total of 200
characteristics. Morphological, physiological, and biochemical characteristics were
included in the analysis. Overall deoxyribonucleic acid (DNA) base compositions
and ultrastructure, under the electron microscope, were also examined. The taxonomic
data were analyzed by computer by using numerical taxonomy programs
designed to sort and cluster strains related phenetically. The V. cholerae strains
formed an homogeneous cluster, sharing overall S values of >75%. Two strains,
V. cholerae NCTC 30 and NCTC 8042, did not fall into the V. cholerae species
group when tested by the hypothetical median organism calculation. No separation
of “classic” V. cholerae, El Tor vibrios, and nonagglutinable vibrios was observed.
These all fell into a single, relatively homogeneous, V. cholerae species cluster.
PJ. parahaemolyticus strains, excepting 5144, 5146, and 5162, designated members
of the species V. alginolyticus, clustered at S >80%. Characteristics uniformly
present in all the Vibrio species examined are given, as are also characteristics and
frequency of occurrence for V. cholerae and V. parahaemolyticus. The clusters formed
in the numerical taxonomy analyses revealed similar overall DNA base compositions,
with the range for the Vibrio species of 40 to 48% guanine plus cytosine. Generic
level of relationship of V. cholerae and V. parahaemolyticus is considered
dubious. Intra- and intergroup relationships obtained from the numerical taxonomy
studies showed highly significant correlation with DNA/DNA reassociation data.

A Numerical Classification of the Genus Bacillus
By FERGUS G . PRIEST, MICHAEL GOODFELLOW AND CAROLE TODD
Journal of General Microbiology (1988), 134, 1847-1882.

Three hundred and sixty-eight strains of aerobic, endospore-forming bacteria which included type and reference cultures of Bacillus and environmental isolates were studied. Overall similarities of these strains for 118 unit characters were determined by the SSMS,, and Dp coefficients and clustering achieved using the UPGMA algorithm. Test error was within acceptable limits. Six cluster-groups were defined at 70% SSM which corresponded to 69% Sp and 48-57% SJ.G roupings obtained with the three coefficients were generally similar but there were some changes in the definition and membership of cluster-groups and clusters, particularly with the SJ coefficient. The Bacillus strains were distributed among 31 major (4 or more strains), 18 minor (2 or 3 strains) and 30 single-member clusters at the 83% SsMle vel. Most of these clusters can be regarded as taxospecies. The heterogeneity of several species, including Bacillus breuis, B. circulans, B. coagulans, B. megateriun, B . sphaericus and B . stearothermophilus, has been indicated  and the species status of several taxa of hitherto uncertain validity confirmed. Thus on the basis of the numerical phenetic and appropriate (published) molecular genetic data, it is proposed
that the following names be recognized; BacillusJlexus (Batchelor) nom. rev., Bacillus fusiformis (Smith et al.) comb. nov., Bacillus kaustophilus (Prickett) nom. rev., Bacilluspsychrosaccharolyticus (Larkin & Stokes) nom. rev. and Bacillus simplex (Gottheil) nom. rev. Other phenetically well-defined taxospecies included ‘ B. aneurinolyticus’, ‘B. apiarius’, ‘B. cascainensis’, ‘B. thiaminolyticus’ and three clusters of environmental isolates related to B . firmus and previously described as ‘B. firmus-B. lentus intermediates’. Future developments in the light of the numerical phenetic data are discussed.

Numerical Classification of Bacteria
Part II. * Computer Analysis of Coryneform Bacteria (2)
Comparison of Group-Formations Obtained on Two
Different Methods of Scoring Data
By Eitaro MASUOan d Toshio NAKAGAWA
[Agr. Biol. Chem., 1969; 33(8): 1124-1133.
Sixty three organisms selected from 12 genera of bacteria were subjected to numerical analysis. The purpose of this work is to examine the relationships among 38 coryneform bacteria included in the test organisms by two coding methods-Sneath’s and Lockhart’s systems-, and to compare the results with conventional classification. In both cases of codification, five groups and one or two single item(s) were found in the resultant classifications. Different codings brought, however, a few distinct differences in some groups , especially in a group of sporogenic bacilli or lactic-acid bacteria. So far as the present work concerns, the result obtained on Lockhart’s coding rather than that obtained on Sneath’s coding resembled the conventional classification. The taxonomic positions of corynebacteria were quite different from those of the conventional classification, regardless
of which coding method was applied.
Though animal corynebacteria have conventionally been considered to occupy the
taxonomic position neighboring to genera Arthrobacter and Cellulornonas and regarded to be the nucleus of so-called “coryneform bacteria,’ the present work showed that many of the corynebacteria are akin to certain mycobacteria rather than to the organisms belonging to the above two genera.

Numerical Classification of Bacteria
Part III. Computer Analysis of “Coryneform Bacteria” (3)
Classification Based on DNA Base Compositions
By EitaroM ASUaOnd ToshioN AKAGAWA
Agr. Biol. Chem., 1969; 33(11): 1570-1576
It has been known that the base compositions of deoxyribonucleic acids (DNA) are
quite different from organism to organism. A pertinent example of this diversity is
found in bacterial species. The base compositions of DNA isolated from a wide variety
of bacteria are distributed in a range from 25 to 75 GC mole-percent (100x(G+C)/
(A+T+G+C)).1) The usefulness of the information of DNA base composition for
the taxonomy of bacteria has been emphasized by several authors. Lee et al.,” Sueoka,” and Freese) have speculated on the evolutionary significance of microbial DNA base composition. They pointed out that closely related microorganisms generally showed similar base compositions of DNA, and suggested that phylogenetic relationship should be reflected in the GC content.
In the present paper are compared the results of numerical classifications of 45
bacteria based on the two different similarity matrices: One representing the overall
similarities of phenotypic properties, the other representing the similarities of GC contents.

Advanced computational algorithms for microbial community analysis using massive 16S rRNA
sequence data
Y Sun, Y Cai, V Mai, W Farmerie, F Yu, J Li and S Goodison
Nucleic Acids Research, 2010; 38(22): e205
http://dx.doi.org:/10.1093/nar/gkq872

With the aid of next-generation sequencing technology, researchers can now obtain millions of microbial signature sequences for diverse applications ranging from human epidemiological studies to global ocean surveys. The development of advanced computational strategies to maximally extract pertinent information from massive nucleotide data has become a major focus of the bioinformatics community. Here, we describe a novel analytical strategy including discriminant and topology analyses that enables researchers to deeply investigate the hidden world of microbial communities, far beyond basic microbial diversity estimation. We demonstrate the utility of our
approach through a computational study performed on a previously published massive human gut 16S rRNA data set. The application of discriminant and
topology analyses enabled us to derive quantitative disease-associated microbial signatures and describe microbial community structure in far more detail than previously achievable. Our approach provides rigorous statistical tools for sequence based studies aimed at elucidating associations between known or unknown organisms and a variety of physiological or environmental conditions.

What is Drug Resistance?

Antimicrobial resistance is the ability of microbes, such as bacteria, viruses, parasites, or fungi, to grow in the presence of a chemical (drug) that would normally kill it or limit its growth.

Diagram showing the difference between non-resistant bacteria and drug resistant bacteria.

Credit: NIAID

DrugResistance difference between non-resistant bacteria and drug resistant bacteria

DrugResistance difference between non-resistant bacteria and drug resistant bacteria

http://www.niaid.nih.gov/SiteCollectionImages/topics/antimicrobialresistance/1whatIsDrugResistance.gif

Diagram showing the difference between non-resistant bacteria and drug resistant bacteria. Non-resistant bacteria multiply, and upon drug treatment, the bacteria die. Drug resistant bacteria multiply as well, but upon drug treatment, the bacteria continue to spread.

Between 5 and 10 percent of all hospital patients develop an infection. About 90,000 of these patients die each year as a result of their infection, up from 13,300 patient deaths in 1992.

According to the Centers for Disease Control and Prevention (April 2011), antibiotic resistance in the United States costs an estimated $20 billion a year in excess health care costs, $35 million in other societal costs and more than 8 million additional days that people spend in the hospital.

Resistance to Antibiotics: Are We in the Post-Antibiotic Era?

Alfonso J. Alanis
Archives of Medical Research 36 (2005) 697–705
http://dx.doi.org:/10.1016/j.arcmed.2005.06.009

Serious infections caused by bacteria that have become resistant to commonly used antibiotics have become a major global healthcare problem in the 21st century. They not only are more severe and require longer and more complex treatments, but they are also significantly more expensive to diagnose and to treat. Antibiotic resistance, initially a problem of the hospital setting associated with an increased number of hospital acquired infections usually in critically ill and immunosuppressed patients, has now extended into the community causing severe infections difficult to diagnose and treat. The molecular mechanisms by which bacteria have become resistant to antibiotics are diverse and complex. Bacteria have developed resistance to all different classes of antibiotics discovered to date. The most frequent type of resistance is acquired and transmitted horizontally via the conjugation of a plasmid. In recent times new mechanisms of resistance have resulted in the simultaneous development of resistance to several antibiotic classes creating very dangerous multidrug-resistant (MDR) bacterial strains, some also known as ‘‘superbugs’’. The indiscriminate and inappropriate use of antibiotics in outpatient clinics, hospitalized patients and in the food industry is the single largest factor leading to antibiotic resistance. The pharmaceutical industry, large academic institutions or the government are not investing the necessary resources to produce the next generation of newer safe and effective antimicrobial drugs. In many cases, large pharmaceutical companies have terminated their anti-infective research programs altogether due to economic reasons. The potential negative consequences of all these events are relevant because they put society at risk for the spread of potentially serious MDR bacterial infections.

Targeting the Human Macrophage with Combinations of Drugs and Inhibitors of Ca2+ and K+ Transport to Enhance the Killing of Intracellular Multi-Drug Resistant M. tuberculosis (MDR-TB) – a Novel, Patentable Approach to Limit the Emergence of XDR-TB

Marta Martins
Recent Patents on Anti-Infective Drug Discovery, 2011, 6, 000-000

The emergence of resistance in Tuberculosis has become a serious problem for the control of this disease. For that reason, new therapeutic strategies that can be implemented in the clinical setting are urgently needed. The design of new compounds active against mycobacteria must take into account that Tuberculosis is mainly an intracellular infection of the alveolar macrophage and therefore must maintain activity within the host cells. An alternative therapeutic approach will be described in this review, focusing on the activation of the phagocytic cell and the subsequent killing of the internalized bacteria. This approach explores the combined use of antibiotics and phenothiazines, or Ca2+ and K+ flux inhibitors, in the infected macrophage. Targeting the infected macrophage and not the internalized bacteria could overcome the problem of bacterial multi-drug resistance. This will potentially eliminate the appearance of new multi-drug resistant tuberculosis (MDR-TB) cases and subsequently prevent the emergence of extensively-drug resistant tuberculosis (XDR-TB). Patents resulting from this novel and innovative approach could be extremely valuable if they can be implemented in the clinical setting. Other patents will also be discussed such as the treatment of TB using immunomodulator compounds (for example: betaglycans).

Six Epigenetic Faces of Streptococcus

Kevin Mayer
http://www.genengnews.com/gen-news-highlights/six-epigenetic-faces-of-streptococcus/81250430/

Medical illustration of Streptococcus pneumonia. [CDC]

Streptococcus pneumonia

Streptococcus pneumonia

It appears that S. pneumoniae has even more personalities, each associated with a different proclivity toward invasive, life-threatening disease. In fact, any of six personalities may emerge depending on the action of a single genetic switch.

To uncover the switch, an international team of scientists conducted a study in genomics, but they looked beyond nucleotide polymorphisms or accessory regions as possible phenotype-shifting mechanisms. Instead, they focused on the potential of restriction-modification (RM) systems to mediate gene regulation via epigenetic changes.

Scientists representing the University of Leicester, Griffith University’s Institute for Glycomics, theUniversity of Adelaide, and Pacific Biosciences realized that the S. pneumoniae genome contains two Type I, three Type II, and one Type IV RM systems. Of these, only the DpnI Type II RM system had been described in detail. Switchable Type I systems had been described previously, but these reports did not provide evidence for differential methylation or for phenotypic impact.

As it turned out, the Type I system embodied a mechanism capable of randomly changing the bacterium’s characteristics into six alternative states. The mechanism’s details were presented September 30 in Nature Communications, in an article entitled, “A random six-phase switch regulates pneumococcal virulence via global epigenetic changes.”

“The underlying mechanism for such phase variation consists of genetic rearrangements in a Type I restriction-modification system (SpnD39III),” wrote the authors. “The rearrangements generate six alternative specificities with distinct methylation patterns, as defined by single-molecule, real-time (SMRT) methylomics.”

Eradication of multidrug-resistant A. baumanniii in burn wounds by antiseptic pulsed electric field.

A Golberg, GF Broelsch, D Vecchio,S Khan, MR Hamblin, WG Austen, Jr, RL Sheridan,  ML Yarmush.

Emerging bacterial resistance to multiple drugs is an increasing problem in burn wound management. New non-pharmacologic interventions are needed for wound disinfection. Here we report on a novel physical method for disinfection: antiseptic pulsed electric field (PEF) applied externally to the infected wounds.  In an animal model, we show that PEF can reduce the load of multidrug resistant Acinetobacter baumannii present in a full thickness burn wound by more than four orders of magnitude, as detected by bioluminescence imaging. Furthermore, using a finite element numerical model, we demonstrate that PEF provides non-thermal, homogeneous, full thickness treatment for the burn wound, thus, overcoming the limitation of treatment depth for many topical antimicrobials. These modeling tools and our in vivo results will be extremely useful for further translation of the PEF technology to the clinical setting. We believe that PEF, in combination with systemic antibiotics, will synergistically eradicate multidrug-resistant burn wound infections, prevent biofilm formation and restore natural skin microbiome. PEF provides a new platform for infection combat in patients, therefore it has a potential to significantly decreasing morbidity and mortality.

Golberg, A. & Yarmush, M. L. Nonthermal irreversible electroporation: fundamentals, applications, and challenges. IEEE Trans Biomed Eng 60, 707-14 (2013).

Mechanisms Of Antibiotic Resistance In Salmonella: Efflux Pumps, Genetics, Quorum Sensing And Biofilm Formation.

Martins M, McCusker M, Amaral L, Fanning S
Perspectives in Drug Discovery and Design 02/2011; 8:114-123.

In Salmonella the main mechanisms of antibiotic resistance are mutations in target genes (such as DNA gyrase and topoisomerase IV) and the over-expression of efflux pumps. However, other mechanisms such as changes in the cell envelope; down regulation of membrane porins; increased lipopolysaccharide (LPS) component of the outer cell membrane; quorum sensing and biofilm formation can also contribute to the resistance seen in this microorganism. To overcome this problem new therapeutic approaches are urgently needed. In the case of efflux-mediated multidrug resistant isolates, one of the treatment options could be the use of efflux pump inhibitors (EPIs) in combination with the antibiotics to which the bacteria is resistant. By blocking the efflux pumps resistance is partly or wholly reversed, allowing antibiotics showing no activity against the MDR strains to be used to treat these infections. Compounds that show potential as an EPI are therefore of interest, as well as new strategies to target the efflux systems. Quorum sensing (QS) and biofilm formation are systems also known to be involved in antibiotic resistance. Consequently, compounds that can disrupt or inhibit these bacterial “communication systems” will be of use in the treatment of these infections.

Role of Phenothiazines and Structurally Similar Compounds of Plant Origin in the Fight against Infections by Drug Resistant Bacteria

SG Dastidar, JE Kristiansen, J Molnar and L Amaral
Antibiotics 2013, 2, 58-71;
http://dx.doi.org:/10.3390/antibiotics2010058

Phenothiazines have their primary effects on the plasma membranes of prokaryotes and eukaryotes. Among the components of the prokaryotic plasma membrane affected are efflux pumps, their energy sources and energy providing enzymes, such as ATPase, and genes that regulate and code for the permeability aspect of a bacterium. The response of multidrug and extensively drug resistant tuberculosis to phenothiazines shows an alternative therapy for its treatment. Many phenothiazines have shown synergistic activity with several antibiotics thereby lowering the doses of antibiotics administered for specific bacterial infections. Trimeprazine is synergistic with trimethoprim. Flupenthixol (Fp) has been found to be synergistic with penicillin and chlorpromazine (CPZ); in addition, some antibiotics are also synergistic. Along with the antibacterial action described in this review, many phenothiazines possess plasmid curing activities, which render the bacterial carrier of the plasmid sensitive to antibiotics. Thus, simultaneous applications of a phenothiazine like TZ would not only act as an additional antibacterial agent but also would help to eliminate drug resistant plasmid from the infectious bacterial cells.

Multidrug Efflux Pumps Described for Staphylococcus aureus

Efflux Pump  Familya  Regulator(s)b  Substrate Specificity  References 
Chromosomally-encoded Efflux Systems 
NorA MFS MgrA, NorG(?) Hydrophilic fluoroquinolones (ciprofloxacin, norfloxacin)QACs (tetraphenylphosphonium, benzalkonium chloride)

Dyes (e.g. ethidium bromide, rhodamine)

[16,18,19]
NorB MFS MgrA, NorG Fluoroquinolones (e.g. hydrophilic: ciprofloxacin, norfloxacin and hydrophobic: moxifloxacin,
sparfloxacin)TetracyclineQACs (e.g. tetraphenylphosphonium, cetrimide)Dyes (e.g. ethidium bromide)
[31]
NorC MFS MgrA(?), NorG Fluoroquinolones (e.g. hydrophilic: ciprofloxacin and hydrophobic: moxifloxacin)Dyes (e.g. rhodamine) [35,36]
MepA MATE MepR Fluoroquinolones (e.g. hydrophilic: ciprofloxacin, norfloxacin and hydrophobic: moxifloxacin,
sparfloxacin)Glycylcyclines (e.g. tigecycline)QACs (e.g. tetraphenylphosphonium, cetrimide, benzalkonium chloride)Dyes (e.g. ethidium bromide)
[37,38]
MdeA MFS n.i. Hydrophilic fluoroquinolones (e.g. ciprofloxacin, norfloxacin)Virginiamycin, novobiocin, mupirocin, fusidic acid

QACs (e.g. tetraphenylphosphonium, benzalkonium chloride, dequalinium)

Dyes (e.g. ethidium bromide)

[39,40]
SepA n.d. n.i. QACs (e.g. benzalkonium chloride)Biguanidines (e.g. chlorhexidine)

Dyes (e.g. acriflavine)

[41]
SdrM MFS n.i. Hydrophilic fluoroquinolones (e.g. norfloxacin)Dyes (e.g. ethidium bromide, acriflavine) [42]
LmrS MFS n.i. Oxazolidinone (linezolid)Phenicols (e.g. choramphenicol, florfenicol)

Trimethoprim, erythromycin, kanamycin, fusidic acid

QACs (e.g. tetraphenylphosphonium)

Detergents (e.g. sodium docecyl sulphate)

Dyes (e.g. ethidium bromide)

[43]

Plasmid-encoded Efflux Systems

QacA MFS QacR QACs (e.g. tetraphenylphosphonium, benzalkonium chloride, dequalinium)Biguanidines (e.g. chlorhexidine)

Diamidines (e.g. pentamidine)

Dyes (e.g. ethidium bromide, rhodamine, acriflavine)

[45,49]
QacB MFS QacR QACs (e.g. tetraphenylphosphonium, benzalkonium chloride)Dyes (e.g. ethidium bromide, rhodamine, acriflavine) [53]
Smr SMR n.i. QACs (e.g. benzalkonium chloride, cetrimide)Dyes (e.g. ethidium bromide) [58,61]
QacG SMR n.i. QACs (e.g. benzalkonium chloride, cetyltrymethylammonium)Dyes (e.g. ethidium bromide) [67]
QacH SMR n.i. QACs (e.g. benzalkonium chloride, cetyltrymethylammonium)Dyes (e.g. ethidium bromide) [68]
QacJ SMR n.i. QACs (e.g. benzalkonium chloride, cetyltrymethylammonium)Dyes (e.g. ethidium bromide) [69]

a n.d.: The family of transporters to which SepA belongs is not elucidated to date.
b n.i.: The transporter has no regulator identified to date.
QACs: quaternary ammonium compounds
The importance of efflux pumps in bacterial antibiotic resistance

  1. A. Webber and L. J. V. Piddock
    Journal of Antimicrobial Chemotherapy (2003) 51, 9–11
    http://dx.doi.org:/10.1093/jac/dkg050Efflux pumps are transport proteins involved in the extrusion of toxic substrates (including virtually all classes of clinically relevant antibiotics) from within cells into the external environment. These proteins are found in both Gram-positive and -negative bacteria as well as in eukaryotic organisms. Pumps may be specific for one substrate or may transport a range of structurally dissimilar compounds (including antibiotics of multiple classes); such pumps can be associated with multiple drug resistance (MDR). In the prokaryotic kingdom there are five major families of efflux transporter: MF (major facilitator), MATE (multidrug and toxic efflux), RND (resistance-nodulation-division), SMR (small multidrug resistance) and ABC (ATP binding cassette). All these systems utilize the proton motive force as an energy source. Advances in DNA technology have led to the identification of members of the above families. Transporters that efflux multiple substrates, including antibiotics, have not evolved in response to the stresses of the antibiotic era. All bacterial genomes studied contain efflux pumps that indicate their ancestral origins. It has been estimated that ∼5–10% of all bacterial genes are involved in transport and a large proportion of these encode efflux pumps.
The efflux pump

The efflux pump

Multidrug-resistance efflux pumps — not just for resistance

Laura J. V. Piddock
Nature Reviews | Microbiology | Aug 2006; 4: 629

It is well established that multidrug-resistance efflux pumps encoded by bacteria can confer clinically relevant resistance to antibiotics. It is now understood that these efflux pumps also have a physiological role(s). They can confer resistance to natural substances produced by the host, including bile, hormones and host defense molecules. In addition, some efflux pumps of the resistance nodulation division (RND) family have been shown to have a role in the colonization and the persistence of bacteria in the host. Here, I present the accumulating evidence that multidrug-resistance efflux pumps have roles in bacterial pathogenicity and propose that these pumps therefore have greater clinical relevance than is usually attributed to them.

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Highlights in the History of Physiology

Larry H. Bernstein, MD, FCAP, Curator

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William Harvey can be credited with founding modern physiology, then Claude Bernard, and then the great anatomist John Hunter, all before the twentieth century.

In the 19th century, curiosity, medical necessity, and economic interest stimulated research concerning the physiology of all living organisms. Discoveries of unity of structure and functions common to all living things resulted in the development of the concept of general physiology, in which general principles and concepts applicable to all living things are sought. Since the mid-19th century, therefore, the word physiology has implied the utilization of experimental methods, as well as techniques and concepts of the physical sciences, to investigate causes and mechanisms of the activities of all living things.
One view of the history of physiology is that it was shortened from a macro-
to a microstructural view with the developments of biochemistry and then molecular biology.  Though that view is attractive, it is not really compliant with a holistic view
of human and mammalian development.  But form and function are the concern of anatomy and physiology, even with the emergence of a subcellular domain.

William Harvey

William Harvey, discoverer of blood circulation and heart function, was born in 1578 in England. He graduated in Padua in 1602, returned to England, and practiced medicine for a long time. Among his patients were two kings of England (James I and Charles I), and Francis Bacon. He published the work “Exercitatio Anatomica de Motu Cordis et Sanguinis in Animalibus (An Anatomical Dissertation Upon the Movement of the Heart and Blood in Animals)  in 1682. It is identified as the beginning of modern experimental physiology. Harvey’s study was based only on anatomical experiments; despite increased knowledge in physics and chemistry during the 17th century, physiology remained closely tied to anatomy and medicine.

The seminal work  lays a basic foundation accurately explaining the circulation. In 1609 Harvey was appointed to the staff of St. Bartholomew’s Hospital. He was elected a fellow of the Royal College of Physicians in 1607. His ideas about circulation of the blood were first publicly expressed in lectures he gave in 1616. The work of Aristotle was the basis for Galen’s De usu partium (“On the Use of Parts”) and a source for many early misconceptions in physiology. Galen, the leading physician in ancient times, never thought that the blood circulates.

Harvey first formulated an opinion about the blood circulation by making a simple calculation. Harvey first studied the heartbeat, establishing the existence of the pulmonary (heart-lung-heart) circulation process and noting the one-way flow of blood. When he also realized how much blood was pumped by the heart, he realized there must be a constant amount of blood flowing through the arteries and returning through the veins of the heart, a continuing circular flow. He estimated that the amount of blood that is emitted by each heartbeat about 2 ounces. Because the heart beats 72 times per minute, the sum is about 540 pounds per hour of emitted blood into the aorta. After formulating this hypothesis, he performed experiments and conducted thorough investigation to determine the details of the circulation of the blood.

Harvey stated that arteries carry blood away from the heart while veins carry blood back to the heart. Although Harvey could not visualize the capillaries, the smallest blood vessels that connect the arterioles to small veins, he concluded that there must be capillaries. Harvey pointed out that the function of the heart is to pump blood into the arteries. His theory of the circulation was not readily accepted, Harvey’s work got recognition at the end of his life. The discovery of capillaries by Marcello Malpighi in 1661 provided factual evidence to confirm Harvey’s theory of blood circulation.

Harvey was also involved in the field of Embryology, although less important than the investigation in terms of the circulation of the blood, not something that should be underestimated. He was a careful observer, and his book On the Generation of Animals (On-generation animal world), published in 1651 showed the beginning of the actual field of Embryology. Harvey rejected the theory that the overall structure of the animal body are the same as young and adult animals, the only difference being size. He rightly declared that an embryo grows to its final structure step by step.

http://www.discoveriesinmedicine.com/General-Information-and-Biographies/Harvey-William.html

Herman Boerhaave is sometimes referred to as the father of physiology due to his exemplary teaching in Leiden and his textbook Institutiones medicae (1708).

In the United States, the first physiology professorship was founded in 1789 at the College of Philadelphia, and in 1832, Robert Dunglison published the first comprehensive work on the subject, Human Physiology (Encyclopedia of American History, 2007). In 1833, William Beaumont published a classic work on digestive function.

In the 19th century, physiological knowledge began to accumulate at a rapid rate, in particular with the 1838 appearance of the Cell theory of Matthias Schleiden and Theodor Schwann. It radically stated that organisms are made up of units called cells. Claude Bernard’s (1813–1878) further discoveries ultimately led to his concept of milieu interieur (internal environment), which would later be taken up and championed as “homeostasis” by American physiologist Walter Cannon.

Claude Bernard

Claude Bernard’s first important work was on the functions of the exocrine pancreas; this achievement won him the prize for experimental physiology from the French Academy of Sciences. His most famous work was on the glycogenic function of the liver; in the course of his study he was led to the conclusion that the liver is the seat of an internal secretion, by which it prepares sugar from the elements of the blood passing through it.

In 1851, while examining the effects produced in the temperature of various parts of the body by section of the nerve or nerves belonging to them, he noticed that division of the cervical sympathetic nerve gave rise to more active circulation and more forcible pulsation of the arteries in certain parts of the head, and a few months afterwards he observed that electrical excitation of the upper portion of the divided nerve had the contrary effect. In this way he established the existence of vasomotor nerves, both
vasodilator and vasoconstrictor.

Milieu intérieur is the key process with which Bernard is associated. He wrote, “The stability of the internal environment [the milieu intérieur] is the condition for the free and independent life.”

The living body, though it has need of the surrounding environment, is nevertheless relatively independent of it. This independence which the organism has of its external environment, derives from the fact that in the living being, the tissues are withdrawn from external influences and are protected by a veritable internal environment. The constancy of the internal environment is the condition for free and independent life: the mechanism that makes it possible is that which assures the maintenance, within the internal environment, of all the conditions necessary for the life of the elements.

The constancy of the environment presupposes a perfection of the organism such that external variations are at every instant compensated and brought into balance. In consequence, the higher animal is in a close relation with its environment so that its equilibrium results from a continuous and delicate compensation established as if the most sensitive of balances.

In his major discourse on the scientific method, An Introduction to the Study of Experimental Medicine (1865), Bernard described what makes a scientific theory good and what makes a scientist important, a true discoverer. Unlike many scientific writers of his time, Bernard wrote about his own experiments and thoughts, and used the first person.
http://en.wikipedia.org/wiki/Claude_Bernard

Physiology as a distinct discipline utilizing chemical, physical, and anatomical methods began to develop in the 19th century. Claude Bernard in France; Johannes Müller, Justus von Liebig, and Carl Ludwig in Germany; and Sir Michael Foster in England may be numbered among the founders of physiology as it now is known. At the beginning of the 19th century, German physiology was under the influence of the romantic school of Naturphilosophie. In France, on the other hand, romantic elements were opposed by rational and skeptical viewpoints. Bernard’s teacher, François Magendie, the pioneer of experimental physiology, was one of the first men to perform experiments on living animals. Both Müller and Bernard, however, recognized that the results of observations and experiments must be incorporated into a body of scientific knowledge, and that the theories of natural philosophers must be tested by experimentation. Many important ideas in physiology were investigated experimentally by Bernard, who also wrote books on the subject. He recognized cells as functional units of life and developed the concept of blood and body fluids as the internal environment (milieu intérieur) in which cells carry out their activities. This concept of physiological regulation of the internal environment occupies an important position in physiology and medicine; Bernard’s work had a profound influence on succeeding generations of physiologists in France, Russia, Italy, England, and the United States.

Müller’s interests were anatomical and zoological, whereas Bernard’s were chemical and medical, but both men sought a broad biological viewpoint in physiology rather than one limited to human functions. Although Müller did not perform many experiments, his textbook Handbuch der Physiologie des Menschen für Vorlesungen and his personal influence determined the course of animal biology in Germany during the 19th century.

It has been said that, if Müller provided the enthusiasm and Bernard the ideas for modern physiology, Carl Ludwig provided the methods. During his medical studies at the University of Marburg in Germany, Ludwig applied new ideas and methods of the physical sciences to physiology. In 1847 he invented the kymograph, a cylindrical drum that still is used to record muscular motion, changes in blood pressure, and other physiological phenomena. He also made significant contributions to the physiology of circulation and urine secretion. His textbook of physiology, published in two volumes in 1852 and 1856, was the first to stress physical instead of anatomical orientation in physiology. In 1869 at Leipzig, Ludwig founded the Physiological Institute (neue physiologische Anstalt), which served as a model for research institutes in medical schools all over the world. The chemical approach to physiological problems, developed first in France by Lavoisier, was expanded in Germany by Justus von Liebig, whose books on Organic Chemistry and its Applications to Agriculture and Physiology (1840) and Animal Chemistry (1842) created new areas of study both in medical physiology and agriculture. German schools devoted to the study of physiological chemistry evolved from Liebig’s laboratory at Giessen.

The British tradition of physiology is distinct from that of the continental schools. In 1869 Sir Michael Foster became Professor of Practical Physiology at University College in London, where he taught the first laboratory course ever offered as a regular part of instruction in medicine. The pattern Foster established still is followed in medical schools in Great Britain and the United States. In 1870 Foster transferred his activities to Trinity College at Cambridge, England, and a postgraduate medical school emerged from his physiology laboratory there. Although Foster did not distinguish himself in research, his laboratory produced many of the leading physiologists of the late 19th century in Great Britain and the United States. In 1877 Foster wrote a major book (Textbook of Physiology), which passed through seven editions and was translated into German, Italian, and Russian. He also published Lectures on the History of Physiology (1901). In 1876, partly in response to increased opposition in England to experimentation with animals, Foster was instrumental in founding the Physiological Society, the first organization of professional physiologists. In 1878, again due largely to Foster’s activities, the Journal of Physiology, which was the first journal devoted exclusively to the publication of research results in physiology, was initiated.

Foster’s teaching methods in physiology and a new evolutionary approach to zoology were transferred to the United States. in 1876 by Henry Newell Martin, a professor of biology at Johns Hopkins University in Baltimore, Md. The American tradition drew also on the continental schools. S. Weir Mitchell, who studied under Claude Bernard, and Henry P. Bowditch, who worked with Carl Ludwig, joined Martin to organize the American Physiological Society in 1887, and in 1898 the society sponsored publication of the American Journal of Physiology. In 1868 Eduard Pflüger, professor at the Institute of Physiology at Bonn, founded the Archiv für die gesammte Physiologie, which became the most important journal of physiology in Germany.

Physiological chemistry followed a course partly independent of physiology. Müller and Liebig provided a stronger relationship between physical and chemical approaches to physiology in Germany than prevailed elsewhere. Felix Hoppe-Seyler, who founded his Zeitschrift für physiologische Chemie in 1877, gave identity to the chemical approach to physiology. The American tradition in physiological chemistry initially followed that in Germany; in England, however, it developed from a Cambridge laboratory founded in 1898 to complement the physical approach started earlier by Foster.

Physiology in the 20th century is a mature science; during a century of growth, physiology became the parent of a number of related disciplines, of which of comparative physiology and ecophysiology, biochemistry, biophysics, and molecular biology are examples. Major figures in these fields include Knut Schmidt-Nielsen and George Bartholomew. Most recently, evolutionary physiology has become a distinct subdiscipline.

Physiology, however, retains an important position among the functional sciences that are closely related to the field of medicine. Although many research areas, especially in mammalian physiology, have been fully exploited from a classical-organ and organ-system point of view, comparative studies in physiology may be expected to continue. The solution of the major unsolved problems of physiology will require technical and expensive research by teams of specialized investigators. Unsolved problems include the unravelling of the ultimate bases of the phenomena of life. Research in physiology also is aimed at the integration of the varied activities of cells, tissues, and organs at the level of the intact organism. Both analytical and integrative approaches uncover new problems that also must be solved. In many instances, the solution is of practical value in medicine or helps to improve the understanding of both human beings and other animals.

Among areas that have shown significant growth in the twentieth century are endocrinology (study of function of hormones) and neurobiology (study of function of nerve cells and the nervous system).

Fye, B. W. 1987. The Development of American Physiology: Scientific Medicine in the Nineteenth Century. Baltimore: Johns Hopkins University Press.

Rothschuh, K. E. 1973. History of Physiology. Huntington, N.Y.: Krieger.

The Nobel Prize in Physiology or Medicine

Year Laureate[A] Country[B] Rationale[C]
1901 Emil Adolf von Behring Germany “for his work on serum therapy, especially its application against diphtheria, by which he has opened a new road in the domain of medical science and thereby placed in the hands of the physician a victorious weapon against illness and deaths”[10]
1902 Sir Ronald Ross United Kingdom “for his work on malaria, by which he has shown how it enters the organism and thereby has laid the foundation for successful research on this disease and methods of combating it”[11]
1903 Niels Ryberg Finsen Denmark
(Faroe Islands)
“[for] his contribution to the treatment of diseases, especially lupus vulgaris, with concentrated light radiation, whereby he has opened a new avenue for medical science”[12]
1904 Ivan Petrovich Pavlov Russia “in recognition of his work on the physiology of digestion, through which knowledge on vital aspects of the subject has been transformed and enlarged”[13]
1905 Robert Koch Germany “for his investigations and discoveries in relation to tuberculosis“[14]
1906 Camillo Golgi Italy “in recognition of their work on the structure of the nervous system“[15]
Santiago Ramón y Cajal Spain
1907 Charles Louis Alphonse Laveran France “in recognition of his work on the role played by protozoa in causing diseases”[16]
1908 Ilya Ilyich Mechnikov Russia “in recognition of their work on immunity“[17]
Paul Ehrlich Germany
1909 Emil Theodor Kocher Switzerland “for his work on the physiology, pathology and surgery of the thyroid gland“[18]
1910 Albrecht Kossel Germany “in recognition of the contributions to our knowledge of cell chemistry made through his work on proteins, including the nucleic substances“[19]
1911 Allvar Gullstrand Sweden “for his work on the dioptrics of the eye“[20]
1912 Alexis Carrel France “[for] his work on vascular suture and the transplantation of blood vessels and organs“[21]
1913 Charles Richet France “[for] his work on anaphylaxis“[22]
1914 Robert Bárány Austria “for his work on the physiology and pathology of the vestibular apparatus“[23]
1919 Jules Bordet Belgium “for his discoveries relating to immunity“[24]
1920 Schack August Steenberg Krogh Denmark “for his discovery of the capillary motor regulating mechanism”[25]
1921 Not awarded
1922 Archibald Vivian Hill United Kingdom “for his discovery relating to the production of heat in the muscle“[26]
Otto Fritz Meyerhof Germany “for his discovery of the fixed relationship between the consumption of oxygen and the metabolism of lactic acid in the muscle”[26]
1923 Sir Frederick Grant Banting Canada “for the discovery of insulin“[27]
John James Rickard Macleod Canada
1924 Willem Einthoven The Netherlands “for the discovery of the mechanism of the electrocardiogram“[28]
1925 Not awarded
1926 Johannes Andreas Grib Fibiger Denmark “for his discovery of the Spiroptera carcinoma“[29]
1927 Julius Wagner-Jauregg Austria “for his discovery of the therapeutic value of malaria inoculation in the treatment of dementia paralytica“[30]
1928 Charles Jules Henri Nicolle France “for his work on typhus“[31]
1929 Christiaan Eijkman The Netherlands “for his discovery of the antineuritic vitamin“[32]
Sir Frederick Gowland Hopkins United Kingdom “for his discovery of the growth-stimulating vitamins“[32]
1930 Karl Landsteiner Austria “for his discovery of human blood groups“[33]
1931 Otto Heinrich Warburg Germany “for his discovery of the nature and mode of action of the respiratory enzyme“[34]
1932 Sir Charles Scott Sherrington United Kingdom “for their discoveries regarding the functions of neurons“[35]
Edgar Douglas Adrian United Kingdom
1933 Thomas Hunt Morgan United States “for his discoveries concerning the role played by the chromosome in heredity“[36]
1934 George Hoyt Whipple United States “for their discoveries concerning liver therapy in cases of anaemia“[37]
George Richards Minot United States
William Parry Murphy United States
1935 Hans Spemann Germany “for his discovery of the organizer effect in embryonic development“[38]
1936 Sir Henry Hallett Dale United Kingdom “for their discoveries relating to chemical transmission of nerve impulses“[39]
Otto Loewi Austria
1937 Albert Szent-Györgyi von Nagyrapolt Hungary “for his discoveries in connection with the biological combustion processes, with special reference to vitamin C and the catalysis of fumaric acid“[40]
1938 Corneille Jean François Heymans Belgium “for the discovery of the role played by the sinus and aortic mechanisms in the regulation of respiration“[41]
1939 Gerhard Domagk Germany “for the discovery of the antibacterial effects of prontosil“[42]
1943 Carl Peter Henrik Dam Denmark “for his discovery of vitamin K“[43]
Edward Adelbert Doisy United States “for his discovery of the chemical nature of vitamin K“[43]
1944 Joseph Erlanger United States “for their discoveries relating to the highly differentiated functions of single nerve fibres“[44]
Herbert Spencer Gasser United States
1945 Sir Alexander Fleming United Kingdom “for the discovery of penicillin and its curative effect in various infectious diseases“[45]
Sir Ernst Boris Chain United Kingdom
Howard Walter Florey Australia
1946 Hermann Joseph Muller United States “for the discovery of the production of mutations by means of X-ray irradiation“[46]
1947 Carl Ferdinand Cori United States “for their discovery of the course of the catalytic conversion of glycogen“[47]
Gerty Theresa Cori, née Radnitz United States
Bernardo Alberto Houssay Argentina “for his discovery of the part played by the hormone of the anterior pituitary lobe in the metabolism of sugar“[47]
1948 Paul Hermann Müller Switzerland “for his discovery of the high efficiency of DDT as a contact poison against several arthropods“[48]
1949 Walter Rudolf Hess Switzerland “for his discovery of the functional organization of the interbrain as a coordinator of the activities of the internal organs”[49]
António Caetano Egas Moniz Portugal “for his discovery of the therapeutic value of leucotomy (lobotomy) in certain psychoses”[49]
1950 Philip Showalter Hench United States “for their discoveries relating to the hormones of the adrenal cortex, their structure and biological effects”[50]
Edward Calvin Kendall United States
Tadeusz Reichstein Switzerland
Poland
Year Laureate[A] Country[B] Rationale[C]
1951 Max Theiler South Africa “for his discoveries concerning yellow fever and how to combat it”[51]
1952 Selman Abraham Waksman United States “for his discovery of streptomycin, the first antibiotic effective against tuberculosis“[52]
1953 Sir Hans Adolf Krebs United Kingdom “for his discovery of the citric acid cycle“[53]
Fritz Albert Lipmann United States “for his discovery of co-enzyme A and its importance for intermediary metabolism”[53]
1954 John Franklin Enders United States “for their discovery of the ability of poliomyelitis viruses to grow in cultures of various types of tissue”[54]
Frederick Chapman Robbins United States
Thomas Huckle Weller United States
1955 Axel Hugo Theodor Theorell Sweden “for his discoveries concerning the nature and mode of action of oxidation enzymes”[55]
1956 André Frédéric Cournand United States “for their discoveries concerning heart catheterization and pathological changes in the circulatory system“[56]
Werner Forssmann Federal Republic of Germany
Dickinson W. Richards United States
1957 Daniel Bovet Italy “for his discoveries relating to synthetic compounds that inhibit the action of certain body substances, and especially their action on the vascular system and the skeletal muscles”[57]
1958 George Wells Beadle United States “for their discovery that genes act by regulating definite chemical events”[58]
Edward Lawrie Tatum United States
Joshua Lederberg United States “for his discoveries concerning genetic recombination and the organization of the genetic material of bacteria“[58]
1959 Arthur Kornberg United States “for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid“[59]
Severo Ochoa Spain
United States
1960 Sir Frank Macfarlane Burnet Australia “for discovery of acquired immunological tolerance“[60]
Sir Peter Brian Medawar Brazil
United Kingdom
1961 Georg von Békésy United States “for his discoveries of the physical mechanism of stimulation within the cochlea“[61]
1962 Francis Harry Compton Crick United Kingdom “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material”[62]
James Dewey Watson United States
Maurice Hugh Frederick Wilkins New Zealand
United Kingdom
1963 Sir John Carew Eccles Australia “for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in the peripheral and central portions of the nerve cell membrane“[63]
Sir Alan Lloyd Hodgkin United Kingdom
Sir Andrew Fielding Huxley United Kingdom
1964 Konrad Bloch United States “for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism“[64]
Feodor Lynen Federal Republic of Germany
1965 François Jacob France “for their discoveries concerning genetic control of enzyme and virus synthesis“[65]
André Lwoff France
Jacques Monod France
1966 Peyton Rous United States “for his discovery of tumour-inducing viruses“[66]
Charles Brenton Huggins United States “for his discoveries concerning hormonal treatment of prostatic cancer“[66]
1967 Ragnar Granit Finland/Sweden “for their discoveries concerning the primary physiological and chemical visual processes in the eye“[67]
Haldan Keffer Hartline United States
George Wald United States
1968 Robert W. Holley United States “for their interpretation of the genetic code and its function in protein synthesis“[68]
Har Gobind Khorana India
Marshall W. Nirenberg United States
1969 Max Delbrück United States “for their discoveries concerning the replication mechanism and the genetic structure of viruses“[69]
Alfred D. Hershey United States
Salvador E. Luria Italy
United States
1970 Julius Axelrod United States “for their discoveries concerning the humoral transmittors in the nerve terminals and the mechanism for their storage, release and inactivation”[70]
Ulf von Euler Sweden
Sir Bernard Katz United Kingdom
1971 Earl W. Sutherland, Jr. United States “for his discoveries concerning the mechanisms of the action of hormones“[71]
1972 Gerald M. Edelman United States “for their discoveries concerning the chemical structure of antibodies“[72]
Rodney R. Porter United Kingdom
1973 Karl von Frisch Federal Republic of Germany “for their discoveries concerning organization and elicitation of individual and social behaviour patterns”[73]
Konrad Lorenz Austria
Nikolaas Tinbergen United Kingdom
1974 Albert Claude Belgium “for their discoveries concerning the structural and functional organization of the cell“[74]
Christian de Duve Belgium
George E. Palade Romania
1975 David Baltimore United States “for their discoveries concerning the interaction between tumour viruses and the genetic material of the cell”[75]
Renato Dulbecco Italy
United States
Howard Martin Temin United States
1976 Baruch S. Blumberg United States “for their discoveries concerning new mechanisms for the origin and dissemination of infectious diseases“[76]
D. Carleton Gajdusek United States
1977 Roger Guillemin United States “for their discoveries concerning the peptide hormone production of the brain“[77]
Andrew V. Schally United States
Rosalyn Yalow United States “for the development of radioimmunoassays of peptide hormones“[77]
1978 Werner Arber Switzerland “for the discovery of restriction enzymes and their application to problems of molecular genetics“[78]
Daniel Nathans United States
Hamilton O. Smith United States
1979 Allan M. Cormack South Africa “for the development of computer assisted tomography“[79]
Sir Godfrey N. Hounsfield United Kingdom
1980 Baruj Benacerraf Venezuela “for their discoveries concerning genetically determined structures on the cell surface that regulate immunological reactions“[80]
Jean Dausset France
George D. Snell United States
1981 Roger W. Sperry United States “for his discoveries concerning the functional specialization of the cerebral hemispheres“[81]
David H. Hubel Canada “for their discoveries concerning information processing in the visual system“[81]
Torsten N. Wiesel Sweden
1982 Sune K. Bergström Sweden “for their discoveries concerning prostaglandins and related biologically active substances”[82]
Bengt I. Samuelsson Sweden
Sir John R. Vane United Kingdom
1983 Barbara McClintock United States “for her discovery of mobile genetic elements“[83]
1984 Niels K. Jerne Denmark “for theories concerning the specificity in development and control of the immune system and the discovery of the principle for production of monoclonal antibodies“[84]
Georges J.F. Köhler Federal Republic of Germany
César Milstein Argentina
United Kingdom
1985 Michael S. Brown United States “for their discoveries concerning the regulation of cholesterol metabolism“[85]
Joseph L. Goldstein United States
1986 Stanley Cohen United States “for their discoveries of growth factors“[86]
Rita Levi-Montalcini Italy
1987 Susumu Tonegawa Japan “for his discovery of the genetic principle for generation of antibody diversity”[87]
1988 Sir James W. Black United Kingdom “for their discoveries of important principles for drug treatment“[88]
Gertrude B. Elion United States
George H. Hitchings United States
1989 J. Michael Bishop United States “for their discovery of the cellular origin of retroviral oncogenes“[89]
Harold E. Varmus United States
1990 Joseph E. Murray United States “for their discoveries concerning organ and cell transplantation in the treatment of human disease”[90]
E. Donnall Thomas United States
1991 Erwin Neher Federal Republic of Germany “for their discoveries concerning the function of single ion channels in cells”[91]
Bert Sakmann Federal Republic of Germany
1992 Edmond H. Fischer Switzerland
United States
“for their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism”[92]
Edwin G. Krebs United States
1993 Sir Richard J. Roberts United Kingdom “for their discoveries of split genes“[93]
Phillip A. Sharp United States
1994 Alfred G. Gilman United States “for their discovery of G-proteins and the role of these proteins in signal transduction in cells”[94]
Martin Rodbell United States
1995 Edward B. Lewis United States “for their discoveries concerning the genetic control of early embryonic development“[95]
Christiane Nüsslein-Volhard Federal Republic of Germany
Eric F. Wieschaus United States
1996 Peter C. Doherty Australia “for their discoveries concerning the specificity of the cell mediated immune defence“[96]
Rolf M. Zinkernagel Switzerland
1997 Stanley B. Prusiner United States “for his discovery of Prions – a new biological principle of infection”[97]
1998 Robert F. Furchgott United States “for their discoveries concerning nitric oxide as a signalling molecule in the cardiovascular system”[98]
Louis J. Ignarro United States
Ferid Murad United States
1999 Günter Blobel Germany/United States “for the discovery that proteins have intrinsic signals that govern their transport and localization in the cell”[99]
2000 Arvid Carlsson Sweden “for their discoveries concerning signal transduction in the nervous system“[100]
Paul Greengard United States
Eric R. Kandel United States
Year Laureate[A] Country[B] Rationale[C]
2001 Leland H. Hartwell United States “for their discoveries of key regulators of the cell cycle“[101]
Sir Tim Hunt United Kingdom
Sir Paul M. Nurse United Kingdom
2002 Sydney Brenner South Africa “for their discoveries concerning ‘genetic regulation of organ development and programmed cell death‘”[102]
H. Robert Horvitz United States
Sir John E. Sulston United Kingdom
2003 Paul Lauterbur United States “for their discoveries concerning magnetic resonance imaging“[103]
Sir Peter Mansfield United Kingdom
2004 Richard Axel United States “for their discoveries of odorant receptors and the organization of the olfactory system“[104]
Linda B. Buck United States
2005 Barry J. Marshall Australia “for their discovery of the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease“[105]
J. Robin Warren Australia
2006 Andrew Z. Fire United States “for their discovery of RNA interference – gene silencing by double-stranded RNA”[106]
Craig C. Mello United States
2007 Mario R. Capecchi United States “for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells.”[107]
Sir Martin J. Evans United Kingdom
Oliver Smithies United States
2008 Harald zur Hausen Germany “for his discovery of human papilloma viruses causing cervical cancer“[108]
Françoise Barré-Sinoussi France “for their discovery of human immunodeficiency virus“[108]
Luc Montagnier France
2009 Elizabeth H. Blackburn United States
Australia
“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase“[109]
Carol W. Greider United States
Jack W. Szostak United States
2010 Sir Robert G. Edwards United Kingdom “for the development of in vitro fertilization“[110]
2011
Bruce A. Beutler United States “for their discoveries concerning the activation of innate immunity“[111]
Jules A. Hoffmann France
Ralph M. Steinman United States
Canada
“for his discovery of the dendritic cell and its role in adaptive immunity“[111]
(awarded posthumously)[112][113]
2012 Sir John B. Gurdon United Kingdom “for the discovery that mature cells can be reprogrammed to become pluripotent“[114]
Shinya Yamanaka Japan
2013 James E. Rothman United States “for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells“[5]
Randy W. Schekman United States
Thomas C. Südhof United States
2014 John O’Keefe United States
United Kingdom
“for their discoveries of cells that constitute a positioning system in the brain”
May-Britt Moser Norway
Edvard I. Moser Norway

Footnotes:

  1. In chronological order with prizes not given during war years.
  2. There are distinct categories to observe: infectious disease; vitamins; neurophysiology; biochemistry and molecular biology; immunology and pharmacology; cancer; endocrinology.
  3. There were deserving scientists who did not receive the Nobel Prize:  Most notable – were…
    Rosalind Franklin, Britton Chance, Bernard Horacker, Allan Wilson, perhaps others..

Excerpt from “Sound and Hearing”, Stevens, S. S., & Warshofsky, Fred,eds., Time-Life Books, NY, 1965. p54  “The molder of the modern theory of basilar-membrane “resonance” is Georg von Bekesy. In 1928 Bekesy was a communications engineer in Budapest, studying the mechanical and electrical adaptation of telephone equipment to the demands of the human hearing mechanism. One day, in the course of a casual conversation, an acquantance asked him whether a major improvement would soon be forthcoming in the quality of telephone systems. The idle remark strarted a chain of thought that eventually posed to Bekesy a more fundamental question: “How much better is the quality of the human ear than that of any telephone system?” His search for the answer has added volumes to our present-day knowledge of hearing.”

a sound impulse sends a wave sweeping along the basilar membrane. As the wave moves along the membrane, its amplitude increases until it reaches a maximum, then falls off sharply until the wave dies out. That point at which the wave reaches its greatest amplitude is the point at which the frequency of the sound is detected by the ear. And as Helmholtz had postulated, Bekesy found that the high-frequency tones were perceived near the base of the cochlea and the lower frequencies toward the apex.”
For his studines of the traveling wave, Georg von Bekesy received the Nobel Prize in 1961. His incredible delicate and elegant experiments had traced sound to the very threshold of sensation. …”
http://hyperphysics.phy-astr.gsu.edu/hbase/sound/bekesy.html

In the 1950s, Wald and his colleagues used chemical methods to extract pigments from the retina. Then, using a spectrophotometer, they were able to measure the light absorbance of the pigments. Since the absorbance of light by retina pigments corresponds to thewavelengths that best activate photoreceptor cells, this experiment showed the wavelengths that the eye could best detect. However, since rod cells make up most of the retina, what Wald and his colleagues were specifically measuring was the absorbance of rhodopsin, the main photopigment in rods. Later, with a technique called microspectrophotometry, he was able to measure the absorbance directly from cells, rather than from an extract of the pigments. This allowed Wald to determine the absorbance of pigments in the cone cells (Goldstein, 2001).

Schack August Steenberg Krogh ForMemRS (November 15, 1874 – September 13, 1949) was a Danish professor at the department of zoophysiology at the University of Copenhagen from 1916-1945.[3][4][5] He contributed a number of fundamental discoveries within several fields of physiology, and is famous for developing the Krogh Principle. In 1920 August Krogh was awarded the Nobel Prize in Physiology or Medicine for the discovery of the mechanism of regulation of the capillaries in skeletal muscle. Krogh was first to describe the adaptation of blood perfusion in muscle and other organs according to demands through opening and closing the arterioles and capillaries.

Although neurobiology (as it is now called) has always been subsumed under physiology, its rapid growth in the twentieth century, along with its institutionalization in separate university departments and separate funding programs, has made it an almost completely autonomous discipline. Neurobiology can be divided into two major areas: neurophysiology, or the study of the process by which nerve cells transmit a message; and neurology, the study of the structure and organization of the nervous system. A general work is The Neurosciences: Paths of Discovery, edited by Frederic G. Worden, Judith P. Swazey, and George Adelman (Cambridge, Mass.: MIT Press, 1975). Two articles in this collection stand out as particularly interesting: Richard Jung’s “Some European Neuroscientists: A Personal Tribute” (pp. 477-511), and Judith P. Swazey and Frederic G. Worden’s “On the Nature of Research in Neuroscience” (pp. 569-587). Swazey and Worden look at the development of twentieth-century neurobiology in terms of Thomas Kuhn’s concept of scientific revolution.

Two major questions confronted neurologists at the end of the nineteenth and beginning of the twentieth centuries: What was the basic anatomical element of the nervous system (individual cells, or a continuous nerve network)? How were parts of the nervous system (e.g., peripheral nerves and spinal cord) integrated to produce an overall functioning system? The first question involved considerable debate in the period of the 1870s through the 1890s, though it was resolved ultimately in favor of the neuron theory (individual nerve cells as the basic structural and functional unit of the nervous system) by the early 1909.

Central to that debate was the work of the Spanish cytologist Santiago Ramón y Cajal (1852-1934), whose autobiography Recollections of My Life, translated by E. Horne Craigie with the assistance of Juan Cano (Philadelphia: American Philosophical Society, 1937), contains considerable information about the debate, the clash of paradigms, and Ramón y Cajal’s exquisite techniques for bringing about the resolution. A more recent and historically oriented account is Susan Billings’s “Concepts of Nerve Fiber Development 1839- 1930,” Journal of the History of Biology, 1971, 4:275-306, which shows how study of the embryological development of the nervous system (which Ramón y Cajal wisely exploited) helped to demonstrate that the nervous system arises from many discrete individual cells.

The structural and functional organization of the nervous system has been an area of great advancement during the twentieth century. Much work on the mode of action of the reflex response (as well as on how reflexes are learned) and on the relation between inhibition and excitation of nerve tracks was done by Russian neurologists in the latter part of the nineteenth and especially the early part of the twentieth century. The chief figures there were Ivan Michailovich Sechenov (1829-1905) and Ivan P. Pavlov (1849-1936). Pavlov’s inerest in digestion led him, under Sechenov’s infuence, to study the now-classic conditioned reflex involved in salivation. Pavlov’s life and work is the subject of one English-language volume: B.P. Babkin’s Pavlov, A Biography (Chicago: Univ. Chicago Press, 1949). This source provides valuable insight into a whole school of neurological work that has had as much influence on psychology as on neurobiology in this century.

While the general features and functions of the reflex were understood by the turn of the century, its manner of organization (especially in terms of connections with the brain) was not. A towering figure in elucidating the relationship between central and peripheral nervous systems, and especially the integrative function of the spinal cord, was the British physiologist Charles Scott Sherrington (1857-1952). Regnar Granit’s biography, Charles Scott Sherrington, An Appraisal (London: Nelson, 1967), and  Judith Swayze’s Reflexes and Motor Integration: Sharington’s Concept of Integrative Action (Cambridge, Mass.: Harvard Univ. Press, 1969) are significant sources. Swayze concentrates on a detailed but clear and insightful analysis of Sherrington’s scientific background, his experimental methods, and the development of his hypotheses about integrative action.

Concerning the development of the neurotransmitter hypothesis (conduction across the synapse between adjacent neurons occurs by a chemical process), its antagonists and protagonists, see Michael V. L. Bennett’s “Nicked by Occam’s Razor: Unitarianism in the Investigation of Synaptic Transmission,” Biological Bulletin, Suppl., June 1985, 168:159-167.

http://depts.washington.edu/hssexec/newsletter/1997/allen.html

Sir John Carew Eccles (27 January 1903 – 2 May 1997) was an Australian neurophysiologist who won the 1963 Nobel Prize in Physiology or Medicine for his work on the synapse. He shared the prize with Andrew Huxley and Alan Lloyd Hodgkin. Eccles and colleagues used the stretch reflex as a model. When Eccles passed a current into the sensory neuron in the quadriceps, the motor neuron innervating the quadriceps produced a small excitatory postsynaptic potential (EPSP). When he passed the same current through the hamstring, the opposing muscle to the quadriceps, he saw an inhibitory postsynaptic potential (IPSP) in the quadriceps motor neuron. Although a single EPSP was not enough to fire an action potential in the motor neuron, the sum of several EPSPs from multiple sensory neurons synapsing onto the motor neuron could cause the motor neuron to fire, thus contracting the quadriceps. On the other hand, IPSPs could subtract from this sum of EPSPs, preventing the motor neuron from firing.

However, neuroscience has been repositioned in the 21st century. Arvid Carlsson, 77, of the University of Gothenburg in Sweden, as well as Paul Greengard of Rockefeller University in New York City, and Eric Kandel of New York’s Columbia University, shared the 2000 Nobel Prize in Physiology or Medicine.

Carlsson overturned conventional wisdom in 1950 by proving that dopamine–once thought to be a mere building block in the synthesis of the neurotransmitter norepinephrine–was an important nervous system messenger in its own right. He and others later discovered that Parkinson’s disease, which causes rigidity and tremors, results from a lack of dopamine in the brain.

Greengard, 74, took Carlsson’s insights several steps further in the 1960s by exploring how dopamine, norepinephrine, and serotonin control transmission of nerve signals at the synapse, the junction between communicating nerve cells. Greengard showed that the three neurotransmitters trigger the addition or removal of phosphate groups to proteins involved in nerve signaling, prompting them to interact with other proteins in a cascade of phosphorylation in and around the synapse.

The discovery that protein phosphorylation is key to nerve cell signaling helped inspire the research of Kandel, 70, who found that the ease with which ions such as calcium pass through a cell membrane– depends on whether the proteins forming the membrane’s pore are phosphorylated. Based on these findings, Kandel showed that short-term and long-term memory are related to the strength and duration of nerve impulses, and that new proteins are synthesized to maintain long-term memory.

Neuroscientist Thomas Südhof, MD, professor of molecular and cellular physiology at the Stanford University School of Medicine, shared the 2013 Nobel Prize in Physiology or Medicine with James Rothman, PhD, a former Stanford professor of biochemistry, and Randy Schekman, PhD, who earned his doctorate at Stanford under the late Arthur Kornberg, MD, another winner of the Nobel Prize in Physiology or Medicine. They were awarded the prize “for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells.” Rothman is now a professor at Yale University, and Schekman is a professor at UC-Berkeley.

“Tom Südhof has done brilliant work that lays a molecular basis for neuroscience and brain chemistry,” said Roger Kornberg, PhD, Stanford’s Mrs. George A. Winzer Professor in Medicine. Kornberg was awarded the Nobel Prize in Chemistry in 2006. He is the son of Arthur Kornberg, in whose lab Schekman received his doctorate.

“The brain works by neurons communicating via synapses,” Südhof said in a phone conversation this morning shortly after the announcement. “We’d like to understand how synapse communication leads to learning on a larger scale. How are the specific connections established? How do they form? And what happens in schizophrenia and autism when these connections are compromised?” In 2009, he published research describing how a gene implicated in autism and schizophrenia alters mice’s synapses and produces behavioral changes in the mice, such as excessive grooming and impaired nest building, that are reminiscent of these human neuropsychiatric disorders.

Südhof, along with other researchers worldwide, has identified integral protein components critical to the membrane fusion process. Südhof purified key protein constituents sticking out of the surfaces of neurotransmitter-containing vesicles, protruding from nearby presynaptic-terminal membranes, or bridging them. Then, using biochemical, genetic and physiological techniques, he elucidated the ways in which the interactions among these proteins contribute to carefully orchestrated membrane fusion.

The Nobel Prize in Physiology or Medicine 2014 was divided, one half awarded to John O’Keefe, the other half jointly to May-Britt Moser and Edvard I. Moser “for their discoveries of cells that constitute a positioning system in the brain.”

In 1971, John O’Keefe discovered the first component of this positioning system. He found that a type of nerve cell in an area of the brain called the hippocampus that was always activated when a rat was at a certain place in a room. Other nerve cells were activated when the rat was at other places. O’Keefe concluded that these “place cells” formed a map of the room.

More than three decades later, in 2005, May-Britt and Edvard Moser discovered another key component of the brain’s positioning system. They identified another type of nerve cell, which they called “grid cells”, that generate a coordinate system and allow for precise positioning and pathfinding. Their subsequent research showed how place and grid cells make it possible to determine position and to navigate.

http://www.nobelprize.org/nobel_prizes/medicine/laureates/

History of Physiology
Lois N Magner,
Purdue University, West Lafayette, USA
Published online: April 2001
http://dx.doi.org:/10.1038/npg.els.0003083

Major developments in the history of physiology include William Harvey’s demonstration of the circulation of the blood in the seventeenth century and Claude Bernard’s discovery of internal secretions in the nineteenth century.

For a neglected side of the story, see Seymour S. Cohen’s “The Biochemical Origins of Molecular Biology (Introduction),” Trends in Biochemical Sciences, 1984, 9:334-336, which argues that many of the histories of molecular biology have ignored the contributions of biochemistry to molecular genetics in general and to the discovery of DNA in particular.

Rather than covering the vast array of subjects that rightfully fall under the history of physiology (such as plant physiology and pathology, etc.), I focus on three areas that have been major concerns in the twentieth century: general physiology, neurobiology and endocrinology. For a brief introduction and overview of twentieth-century physiology, it is worthwhile to consult Karl E. Rothschuh’s History of Physiology (Huntington, N.Y.: Krieger, 1973). Chapter 7 (pp. 264-361) deals with the twentieth century; while it does not provide in-depth coverage, the broad outline establishes the framework within which more specialized topics can be placed.

The Prussian-born American physiologist Jacques Loeb (1859-1924), a long-time investigator at the Rockefeller Institute and a close professional friend of such figures as T. H. Morgan, Boss Harrison, J. McKeen Cattell, and W.J. V. Osterhout, set the style of experimental and quantitative biology that influenced a whole generation of biologists, especially in the United States. Loeb championed what he called “the mechanistic conception of life”–the title of a major address he gave in 1911 and of a book of essays collected in 1912 (Cambridge, Mass.: Harvard Univ. Press, 1964). The reprint edition benefits from a superb introduction by Donald Fleming. The Mechanistic Conception of Life was a celebration of the mechanistic materialist viewpoint in twentieth-century biology. A new biography of Loeb is Philip J. Pauly’s Controlling Life: Jacques Loeb and the Engineering Ideal in Biology (New York: Oxford Univ. Press, 1987). As the title suggests, Pauly emphasizes that Loeb’s guiding ideal was the scientific control of life.

Opposition to the “mechanistic conception of life” came from a number of sources–principally embryology and areas of general physiology–from the 1920s onward. Prominent among those who advanced a more holistic approach were the physiologist Walter Bradford Cannon (1871-1942) and the physiological chemist Lawrence J. Henderson (1878-1942). Cannon’s work, is summarized in his popular book The Wisdom of the Body (1932; New York: Norton, 1960). Henderson’s work is summarized, along with a number of other chemical topics, in his “The Fitness of the Environment” (1913; Boston: Beacon Press, 1958). The development of the idea of homeostasis is the subject of a superb essay by Donald Fleming, “Walter B. Cannon and homeostasis,” Social Research, 1984, 51:609-640.

Henderson’s work has been the subject of several studies. John Parascandola’s “Organismic and Holistic Concepts in the Thought of L. J. Henderson,” Journal of the Histoty of Biology, 1971, 4:63-113, relates Henderson’s scientific to his philosophical work. Henderson and Cannon were strongly interested in social regulation and equilibrium, as was fitting for products of the “Progressive Era,” and sought in physiological processes analogies for the notion of social and economic balance. A specific discussion of Henderson’s view of the interrelationship between social and physiological equilibrium theory can be found in Cynthia Eagle Russett’s The Concept of Equilibrium in American Social Thought (New Haven, Conn.: Yale Univ. Press, 1968). See also Stephen J. Cross and William R. Albury, “Walter B. Cannon, L.J. Henderson, and the Organic Analogy,” Osiris, 1987, N.S. 3:165-192.

Endocrinology (the study of the nature and effect of hormones, or “chemical messengers,” produced by the endocrine glands) is an area of general physiology that has shown enormous growth in the twentieth century. It has also been the subject of numerous historical studies. Arthur F. Hughes has prepared a brief but useful introduction titled “A History of Endocrinology,” Journal of the History of Medcine and Allied Sciences, 1977, 32(3): 292-313. While it is largely descriptive and chronological, Hughes’s study demonstrates the close link between clinical pathology and the gradual discovery of the role of hormones in maintaining physiological balance.

The history of endocrinology is the subject of a special issue of the Journal of the History of Biology, 1976, 9. A general introduction to the historiography of endocrinology is provided for the volume by Diana Long Hall and Thomas F. Click (pp. 229-233). Hall has explored some social and technical aspects of the history of sex-hormone research in “Biology, Sex Hormones, and Sexism in the 1920s,” Philosophical Forum 1974, 5:81-96. She suggests that sexist biases about the importance of male over female hormones proved to be a barrier to the technical solution of problems associated with extracting, isolating, and characterizing the chemical nature of sex hormones (principally testosterone and estrogen) in the 1920s.

On a somewhat more specific aspect of endocrinology, Michael Bliss’s The Discovery of Insulin (Chicago: Univ. Chicago Press, 1982) provides a close picture of the technical problems that investigators in any field of endocrinology had to surmount in order to identify, isolate, and purify a given hormone. The insulin story also provides a fascinating picture of the role of drug companies in encouraging and financing hormone research in the period (1920s) before government subsidy of basic scientific research.

http://depts.washington.edu/hssexec/newsletter/1997/allen.html
Cardiovascular Physiology
The Frank–Starling law of the heart (also known as Starling’s law or the Frank–Starling mechanism or Maestrini heart’s law) states that the stroke volume of the heart increases in response to an increase in the volume of blood filling the heart (the end diastolic volume) when all other factors remain constant.  It is based on the late19th century studies by Otto Frank, who found using isolated frog hearts that the strength of ventricular contraction was increased when the ventricle was stretched prior to contraction. This observation was extended by the elegant studies of Ernest Starling and colleagues in the early 20th century who found that increasing venous return, and therefore the filling pressure of the ventricle, led to increased stroke volume in dogs.

The increased volume of blood stretches the ventricular wall, causing cardiac muscle to contract more forcefully. The stroke volume – contractile force model of  Ernest Starling was also based on the earlier observations of Maestrini in 1914.  The hypothesis states that “the mechanical energy set free in the passage from the resting to the active state is a function of the length of the fiber.”  This allows the cardiac output to be synchronized with the venous return without depending upon external regulation to make alterations. Initial length of myocardial fibers determines the initial work done during the cardiac cycle.

The stroke volume may also increase as a result of greater contractility of the cardiac muscle during exercise, independent of the end-diastolic volume. The Frank–Starling mechanism appears to make its greatest contribution to increasing stroke volume at lower work rates, and contractility has its greatest influence at higher work rates.

The first formulation of the law was theorized by the Italian physiologist Dario Maestrini, who on December 13, 1914, started the first of 19 experiments that led him to formulate the “legge del cuore”. Starling, the holder of the Physiology chair at London University, traced Maestrini’s work in 1918. While Starling was identified for the proposed award of the Nobel Prize, Maestrini never received his recognition, and today the “law of the heart” is known worldwide as “Starling’s Law,” though, among the Italian doctors, it is known by the nickname “Legge di Maestrini”.

One mechanism to explain how preload influences contractile force is that increasing the sarcomere length increases troponin C calcium sensitivity, which increases the rate of cross-bridge attachment and detachment, and the amount of tension developed by the muscle fiber (see Excitation-Contraction Coupling).  The effect of increased sarcomere length on the contractile proteins is termed length-dependent activation

It has traditionally been taught that the Frank-Starling mechanism is due to changes in the number of overlapping actin and myosin units within the sarcomere as in skeletal muscle. According to this view, changes in the force of contraction do not result from a change in inotropy. Because we now know that changes in preload are associated with altered calcium handling and troponin C affinity for calcium, a sharp distinction cannot be made mechanistically between length-dependent (Frank-Starling mechanism) and length-independent changes (inotropic mechanisms) in contractile function.

There is no single Frank-Starling curve on which the ventricle operates. There is actually a family of curves, each of which is defined by the afterload and inotropic state of the heart (Figure 2). For example, increasing afterload or decreasing inotropy shifts the curve down and to the right. Decreasing afterload and increasing inotropy shifts the curve up and to the left. To summarize, changes in venous return cause the ventricle to move along a single Frank-Starling curve that is defined by the existing conditions of afterload and inotropy.

Frank-Starling curves show how changes in ventricular preload lead to changes in stroke volume. This graphical representation, however, does not show how changes in venous return affect end-diastolic and end-systolic volume. In order to do this, it is necessary to describe ventricular function in terms of pressure-volume diagrams. When venous return is increased, there is increased filling of the ventricle along its passive pressure curve leading to an increase in end-diastolic volume (Figure 3). If the ventricle now contracts at this increased preload, and the afterload is held constant, the ventricle will empty to the same end-systolic volume, thereby increasing its stroke volume. The increased stroke volume is manifested by an increase in the width of the pressure-volume loop. The normal ventricle, therefore, is capable of increasing its stroke volume to match physiological increases in venous return.

Starling_

Starling_

Starling's Law of the heart

Starling’s Law of the heart

Starling's Law of the heart

Starling’s Law of the heart

Skeletal Muscle Contraction

Muscle Contraction and Relaxation

Step 1

A nerve impulse travels down and axon and causes the release of acetylcholine.

Step 2

Acetylecholine causes the impulse to spread across the surface of the sarcolemma.

Step 3

The nerve impulse enters the T Tubules and Sarcoplasmic Reticulum, stimulating the release of calcium ions.

Step 4

Calcium ions combine with Troponin, shifting troponin and exposing the myosin binding sites on the actin.

Step 5

ATP breaks down ADP + P. The released energy activates the myosin cross bridges and results in the sliding of thin actin myofilament past the thick myosin myofilaments.

Step 6

The sliding of the myofilaments draws the Z lines towards each other, the sarcomere shortens, the muscle fibers contract and therefore muscle contracts.

Step 7

ACh is inactivated by Acetylcholinesterase, inhibiting the nerve impulse conduction across the sarcolemma.

Step 8

Nerve impulse is inhibited, calcium ions are actively transported back into the Sarcoplasmic Reticulum, using the energy from the earlier ATP breakdown.

Step 9

The low calcium concentration causes the myosin cross bridges to separate from the think actin myofilaments and the actin myofilaments return to their relaxed position.

Step 10

Sarcomeres return to their resting lengths, muscle fibers relax and the muscle relaxes.

muscle contraction

muscle contraction

sarcomere structure

sarcomere structure

Contraction

Contraction

Pulmonary Gas Exchange

Inhalation (breathing in) is usually an active movement. The contraction of the diaphragm muscles causes the thoracic cavity to increase in volume, thus decreasing the pressures within the lung (Intrapleural and Alveolar Pressures). This negative pressure within the lungs acts as a Pressure Gradient, thus pulling air into the lungs. As air fills the lungs, the negative alveolar pressure moves back towards atmospheric pressure, and air flow into the lungs slows down. In contrast, expiration (breathing out) is usually a passive process.

Where Pel equals the product of elastance E (inverse of compliance) and volume of the system V, Pre equals the product of flow resistance R and time derivate of volume V (which is equivalent to the flow), Pin equals the product of inertance I and second time derivate of V. R and I are sometimes referred to as Rohrer’s constants.

Alveoli.

Alveoli.

Alveoli_diagram

Alveoli_diagram

Pulmonary circulation

Gas exchange/transport (primarily oxygen and carbon dioxide)

 

Oxyhaemoglobin_dissociation_curve

Oxyhaemoglobin_dissociation_curve

Oxygen-hemoglobin dissociation curve
(Bohr effect, Haldane effect)

The Young–Laplace equation (/ˈjʌŋ ləˈplɑːs/) is a nonlinear partial differential equation that describes the capillary pressure difference sustained across the interface between two static fluids, such as water and air, due to the phenomenon of surface tension or wall tension, although usage on the latter is only applicable if assuming that the wall is very thin. The Young–Laplace equation relates the pressure difference to the shape of the surface or wall and it is fundamentally important in the study of static capillary surfaces. It is a statement of normal stress balance for static fluids meeting at an interface, where the interface is treated as a surface (zero thickness).

The equation is named after Thomas Young, who developed the qualitative theory of surface tension in 1805, and Pierre-Simon Laplace who completed the mathematical description in the following year. It is sometimes also called the Young–Laplace–Gauss equation, as Gauss unified the work of Young and Laplace in 1830, deriving both the differential equation and boundary conditions using Johann Bernoulli‘s virtual work principles.

Dalton’s law (also called Dalton’s law of partial pressures) states that in a mixture of non-reacting gases, the total pressure exerted is equal to the sum of the partial pressures of the individual gases. This empirical law was observed by John Dalton in 1801 and is related to the ideal gas laws. Dalton’s law is not strictly followed by real gases with deviations being considerably large at high pressures.
http://en.wikipedia.org/wiki/

Histidine residues in hemoglobin can accept protons and act as buffers. Deoxygenated hemoglobin is a better proton acceptor than the oxygenated form.

In red blood cells, the enzyme carbonic anhydrase catalyzes the conversion of dissolved carbon dioxide to carbonic acid, which rapidly dissociates to bicarbonate and a free proton:
CO2 + H2O → H2CO3 → H+ + HCO3–
By Le Chatelier’s principle, anything that stabilizes the proton produced will cause the reaction to shift to the right, thus the enhanced affinity of deoxyhemoglobin for protons enhances synthesis of bicarbonate and accordingly increases capacity of deoxygenated blood for carbon dioxide. The majority of carbon dioxide in the blood is in the form of bicarbonate. Only a very small amount is actually dissolved as carbon dioxide, and the remaining amount of carbon dioxide is bound to hemoglobin.

In addition to enhancing removal of carbon dioxide from oxygen-consuming tissues, the Haldane effect promotes dissociation of carbon dioxide from hemoglobin in the presence of oxygen. In the oxygen-rich capillaries of the lung, this property causes the displacement of carbon dioxide to plasma as low-oxygen blood enters the alveolus and is vital for alveolar gas exchange.

The general equation for the Haldane Effect is: H+ + HbO2 ←→ H+Hb + O2; however, this equation is confusing as it reflects primarily the Bohr effect. The significance of this equation lies in realizing that oxygenation of Hb promotes dissociation of H+ from Hb, which shifts the bicarbonate buffer equilibrium towards CO2 formation; therefore, CO2 is released from RBCs, so it can diffuse out into the lungs (vs the Bohr effect being most relevant at non high O2 environment tissues; useful comparison to not confuse the 2 concepts of Haldane vs Bohr- Haldane@lung and Bohr@tissues for their physiological relevance).

http://en.wikipedia.org/wiki/Haldane_effect

Liver

In 1957, the french surgeon Claude Couinaud described 8 liver segments. Since then, radiographic studies describe an average of twenty segments based on distribution of blood supply. Each segment has its own independent vascular and biliary branches. Surgeons utilize these independent segments when performing liver resection for tumor or transplantation.

There are at least three reasons why segmental resection is superior to simple wedge resection. First, segmental resection minimizes blood loss because vascular density is reduced at the borders between segments. Second, it results in improved tumor removal for those cancers which are disseminated via intrasegmental branches of the portal vein. Third, segmental resection spares normal liver allowing for repeat partial hepatectomy.

liver triad

liver triad

Each segment of the liver is further divided into lobules. Lobules are usually represented as discrete hexagonal aggregations of hepatocytes. The hepatocytes assemble as plates which radiate from a central vein. Lobules are served by arterial, venous and biliary vessels at their periphery. Human lobules have little connective tissue separating one lobule from another. The paucity of connective tissue makes it more difficult to identify the portal triads and the boundaries of individual lobules. Central veins are easier to identify due to their large lumen and because they lack connective tissue that invests the portal triad vessels.

Lobules consist of hepatocytes and the spaces between them. Sinusoids are the spaces between the plates of hepatocytes. Sinusoids receive blood from the portal triads. About 25% of total cardiac output enters the sinusoids via terminal portal and arterial vessels. Seventy-five percent of the blood flowing into the liver comes through the portal vein; the remaining 25% is oxygenated blood that is carried by the hepatic artery. The blood mixes, passes through the sinusoids, bathes the hepatocytes and drains into the central vein. About 1.5 liters of blood exit the liver every minute.

The liver is central to a multitude of physiologic functions, including:

Clearance of damaged red blood cells & bacteria by phagocytosis

Nutrient management

Synthesis of plasma proteins such as albumin, globulin, protein C, insulin-like growth factor, clotting factors etc.

Biotransformation of toxins, hormones, and drugs

Vitamin & mineral storage

Kidney

Renal physiology (Latin rēnēs, “kidneys”) is the study of the physiology of the kidney. This encompasses all functions of the kidney, including reabsorption of glucose, amino acids, and other small molecules; regulation of sodium, potassium, and other electrolytes; regulation of fluid balance and blood pressure; maintenance of acid-base balance; the production of various hormones including erythropoietin, and the activation of vitamin D.

Much of renal physiology is studied at the level of the nephron, the smallest functional unit of the kidney. Each nephron begins with a filtration component that filters blood entering the kidney. This filtrate then flows along the length of the nephron, which is a tubular structure lined by a single layer of specialized cells and surrounded by capillaries. The major functions of these lining cells are the reabsorption of water and small molecules from the filtrate into the blood, and the secretion of wastes from the blood into the urine.

Proper function of the kidney requires that it receives and adequately filters blood. This is performed at the microscopic level by many hundreds of thousands of filtration units called renal corpuscles, each of which is composed of a glomerulus and a Bowman’s capsule. A global assessment of renal function is often ascertained by estimating the rate of filtration, called the glomerular filtration rate (GFR).

Renal

Renal

vit D and receptor complex

vit D and receptor complex

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The Union of Biomarkers and Drug Development

The Union of Biomarkers and Drug Development

Author and Curator: Larry H. Bernstein, MD, FCAP

There has been consolidation going on for over a decade in both thr pharmaceutical and in the diagnostics industry, and at the same time the page is being rewritten for health care delivery.  I shall try to work through a clear picture of these not coincidental events.

Key notables:

  1. A growing segment of the US population is reaching Medicare age
  2. There is also a large underserved population in both metropolitan and nonurban areas and a fragmentation of the middle class after a growth slowdown in the economy since the 2008 deep recession.
  3. The deep recession affecting worldwide economies was only buffered by availability of oil or natural gas.
  4. In addition, there was a self-destructive strategy to cut spending on national scales that withdrew the support that would bolster support for infrastrucrue renewl.
  5. There has been a dramatic success in the clinical diagnostics industry, with a long history of being viewed as a loss leader, and this has been recently followed by the pharmaceutical industry faced with inability to introduce new products, leading to more competition in off-patent medications.
  6. The introduction of the Accountable Care Act has opened the opportunities for improved care, despite political opposition, and has probably sustained opportunity in the healthcare market.

Let’s take a look at this three headed serpent. – Pharma, Diagnostics, New Entity
?  The patient  ?
?  Insurance    ?
?  Physician    ?

Part I.   The Concept

When Illumina Buys Roche: The Dawning Of The Era Of Diagnostics Dominance

Robert J. Easton, Alain J. Gilbert, Olivier Lesueur, Rachel Laing, and Mark Ratner
http://PharmaMedtechBI.com    | IN VIVO: The Business & Medicine Report Jul/Aug 2014; 32(7).

  • With current technology and resources, a well-funded IVD company can create and pursue a strategy of information gathering and informatics application to create medical knowledge, enabling it to assume the risk and manage certain segments of patients
  • We see the first step in the process as the emergence of new specialty therapy companies coming from an IVD legacy, most likely focused in cancer, infection, or critical care

When Illumina Inc. acquired the regulatory consulting firm Myraqa, a specialist in in vitro diagnostics (IVD), in July, the press release announcement characterized the deal as one that would bolster illumina’s in-house capabilities for clinical readiness and help prepare for its next growth phase in regulated markets. That’s not surprising given the US Food and Drug Administration’s (FDA) approval a year and a half ago of its MiSeq next-generation sequencer for clinical use. But the deal could also suggest illumina is beginning to move along the path toward taking on clinical risk – that is, eventually

  • advising physicians and patients, which would mean facing regulators directly

Such a move – by illumina, another life sciences tools firm, or an information specialist from the high-tech universe – is inevitable given

  • the emerging power of diagnostics and traditional health care players’ reluctance to themselves take on such risk.

Alternatively, we believe that a well-funded diagnostics company could establish this position. either way, such a champion would establish dominion over and earn higher valuation than less-aggressive players who

  • only supply compartmentalized drug and device solutions.

Diagnostics companies have long been dogged by a fundamental issue:

  1. they are viewed and valued more along the lines of a commodity business than as firms that deliver a unique product or service
  2. diagnostics companies are in position to do just that today because they are now advantaged by having access to more data points.
  3. if they were to cobble together the right capabilities, diagnostics companies would have the ability to turn information into true medical knowledge

Example: PathGEN PathChip

nucleic-acid-based platform detects 296 viruses, bacteria, fungi & parasites

http://ow.ly/d/2GvQhttp://ow.ly/DSORV

This puts the diagnostics player in an unfamiliar realm where it can ask the question of what value they offer compared with a therapeutic. The key is that diagnostics can now offer unique information and potentially unique tools to capture that information. In order to do so, it has to create information from the data it generates, and then to supply that knowledge to users who will value and act on that knowledge. Complex genomic tests, as much as physical examination, may be the first meaningful touch point for physicians’ classification of disease.

Even if lab tests are more expensive, it is a cheaper means for deciding what to do first for a patient than the trial and error of prescribing medication without adequate information. Information is gaining in value as the amount of treatment data available on genomically characterizable subpopulations increases. In such a circumstance
it is the ability to perform that advisory function that will add tremendous value above what any test provides, the leverage of being able to apply a proprietary diagnostics platform – and importantly, the data it generates. It is the ability to perform that advisory function that will add tremendous value above what any test provides.

Integrated Diagnostics Inc. and Biodesix Inc. with mass spectrometry has the tools for unraveling disease processes, and numerous players are quite visibly in or are getting into the business of providing medical knowledge and clinical decision support in pursuit of a huge payout for those who actually solve important disease mysteries. Of course one has to ask whether MS/MS is sufficient for the assigned task, and also whether the technology is ready for the kind of workload experienced in a clinical service compared to a research vehicle.  My impression (as a reviewer) is that it is not now the time to take this seriously.

Roche has not realized its intent with Ventana: failing to deliver on the promise of boosting Roche’s pipeline, which was a significant factor in the high price Roche paid. The combined company was to be “uniquely positioned to further expand Ventana’s business globally and together develop more cost-efficient, differentiated, and targeted medicines.  On the other hand,  Biodesix decided to use Veristrat to look back and analyze important trial data to try to ascertain which patients would benefit from ficlatuzumab (subset). The predictive effect for the otherwise unimpressive trial results was observed in both progression-free survival and overall survival endpoints, and encouraged the companies to conduct a proof-of-concept study of ficlatuzumab in combination with Tarceva in advanced Non Small Cell Lung Cancer Patients (NSCLC) selected using the Veristrat test.

A second phase of IVD evolution will be far more challenging to pharma, when the most accomplished companies begin to assemble and integrate much broader data
sets, thereby gaining knowledge sufficient to actually manage patients and dictate therapy, including drug selection. No individual physician has or will have access to all of this information on thousands of patients, combined with the informatics to tease out from trillions of data points the optimal personalized medical approach. When the IVD-origin knowledge integrator amasses enough data and understanding to guide therapy decisions in large categories, particularly drug choices, it will become more valuable than any of the drug suppliers.

This is an apparent reversal of fortune. The pharmaceutical industry has been considered the valued provider, while the IVD manufacturer has been the low valued cousin. Now, it is by an ability to make kore accurate the drug administration that the IVD company can control the drug bill, to the detriment of drug developers, by finding algorithms that generate equal-to-innovative-drug outcomes using generics for most of the patients, thereby limiting the margins of drug suppliers and the upsides for new drug discovery/development.

It is here that there appears to be a misunderstanding of the whole picture of the development of the healthcare industry.  The pharmaceutical industry had a high value added only insofar it could replace market leaders for treatment before or at the time of patent expiration, which largely depended either introducing a new class of drug, or by relieving the current drug in its class of undesired toxicities or “side effects”.  Otherwise, the drug armamentarium was time limited to the expiration date. In other words, the value was dependent on a window of no competition.  In addition, as the regulation of healthcare costs were tightening under managed care, the introduction of new products that were deemed to be only marginally better, could be substitued by “off-patent” drug products.

The other misunderstanding is related to the IVD sector.  Laboratory tests in the 1950’s were manual, and they could be done by “technicians” who might not have completed a specialized training in clinical laboratory sciences.  The first sign of progress was the introduction of continuous flow chemistry, with a sampling probe, tubing to bring the reacting reagents into a photocell, and the timing of the reaction controlled by a coiled glass tubing before introducing the colored product into a uv-visible photometer.  In perhaps a decade, the Technicon SMA 12 and 6 instruments were introduced that could do up to 18 tests from a single sample.

Part 2. Emergence of an IVD Clinical Automated Diagnostics Industry

Why tests are ordered

  1. Screening
  2. Diagnosis
  3. Monitoring

Historical Perspective

Case in Point 1:  Outstanding Contributions in Clinical Chemistry. 1991. Arthur Karmen.

Dr. Karmen was born in New York City in 1930. He graduated from the Bronx High School of Science in 1946 and earned an A.B. and M.D. in 1950 and 1954, respectively, from New York University. In 1952, while a medical student working on a summer project at Memorial-Sloan Kettering, he used paper chromatography of amino acids to demonstrate the presence of glutamic-oxaloacetic and glutaniic-pyruvic ransaminases (aspartate and alanine aminotransferases) in serum and blood. In 1954, he devised the spectrophotometric method for measuring aspartate aminotransferase in serum, which, with minor modifications, is still used for diagnostic testing today. When developing this assay, he studied the reaction of NADH with serum and demonstrated the presence of lactate and malate dehydrogenases, both of which were also later used in diagnosis. Using the spectrophotometric method, he found that aspartate aminotransferase increased in the period immediately after an acute myocardial infarction and did the pilot studies that showed its diagnostic utility in heart and liver diseases.  This became as important as the EKG. It was replaced in cardiology usage by the MB isoenzyme of creatine kinase, which was driven by Burton Sobel’s work on infarct size, and later by the troponins.

Case in point 2: Arterial Blood Gases.  Van Slyke. National Academy of Sciences.

The test is used to determine the pH of the blood, the partial pressure of carbon dioxide and oxygen, and the bicarbonate level. Many blood gas analyzers will also report concentrations of lactate, hemoglobin, several electrolytes, oxyhemoglobin, carboxyhemoglobin and methemoglobin. ABG testing is mainly used in pulmonology and critical care medicine to determine gas exchange which reflect gas exchange across the alveolar-capillary membrane.

DONALD DEXTER VAN SLYKE died on May 4, 1971, after a long and productive career that spanned three generations of biochemists and physicians. He left behind not only a bibliography of 317 journal publications and 5 books, but also more than 100 persons who had worked with him and distinguished themselves in biochemistry and academic medicine. His doctoral thesis, with Gomberg at University of Michigan was published in the Journal of the American Chemical Society in 1907.  Van Slyke received an invitation from Dr. Simon Flexner, Director of the Rockefeller Institute, to come to New York for an interview. In 1911 he spent a year in Berlin with Emil Fischer, who was then the leading chemist of the scientific world. He was particularly impressed by Fischer’s performing all laboratory operations quantitatively —a procedure Van followed throughout his life. Prior to going to Berlin, he published the  classic nitrous acid method for the quantitative determination of primary aliphatic amino groups,  the first of the many gasometric procedures devised by Van Slyke, and made possible the determination of amino acids. It was the primary method used to study amino acid

composition of proteins for years before chromatography. Thus, his first seven postdoctoral years were centered around the development of better methodology for protein composition and amino acid metabolism.

With his colleague G. M. Meyer, he first demonstrated that amino acids, liberated during digestion in the intestine, are absorbed into the bloodstream, that they are removed by the tissues, and that the liver alone possesses the ability to convert the amino acid nitrogen into urea.  From the study of the kinetics of urease action, Van Slyke and Cullen developed equations that depended upon two reactions: (1) the combination of enzyme and substrate in stoichiometric proportions and (2) the reaction of the combination into the end products. Published in 1914, this formulation, involving two velocity constants, was similar to that arrived at contemporaneously by Michaelis and Menten in Germany in 1913.

He transferred to the Rockefeller Institute’s Hospital in 2013, under Dr. Rufus Cole, where “Men who were studying disease clinically had the right to go as deeply into its fundamental nature as their training allowed, and in the Rockefeller Institute’s Hospital every man who was caring for patients should also be engaged in more fundamental study”.  The study of diabetes was already under way by Dr. F. M. Allen, but patients inevitably died of acidosis.  Van Slyke reasoned that if incomplete oxidation of fatty acids in the body led to the accumulation of acetoacetic and beta-hydroxybutyric acids in the blood, then a reaction would result between these acids and the bicarbonate ions that would lead to a lower than-normal bicarbonate concentration in blood plasma. The problem thus became one of devising an analytical method that would permit the quantitative determination of bicarbonate concentration in small amounts of blood plasma.  He ingeniously devised a volumetric glass apparatus that was easy to use and required less than ten minutes for the determination of the total carbon dioxide in one cubic centimeter of plasma.  It also was soon found to be an excellent apparatus by which to determine blood oxygen concentrations, thus leading to measurements of the percentage saturation of blood hemoglobin with oxygen. This found extensive application in the study of respiratory diseases, such as pneumonia and tuberculosis. It also led to the quantitative study of cyanosis and a monograph on the subject by C. Lundsgaard and Van Slyke.

In all, Van Slyke and his colleagues published twenty-one papers under the general title “Studies of Acidosis,” beginning in 1917 and ending in 1934. They included not only chemical manifestations of acidosis, but Van Slyke, in No. 17 of the series (1921), elaborated and expanded the subject to describe in chemical terms the normal and abnormal variations in the acid-base balance of the blood. This was a landmark in understanding acid-base balance pathology.  Within seven years after Van moved to the Hospital, he had published a total of fifty-three papers, thirty-three of them coauthored with clinical colleagues.

In 1920, Van Slyke and his colleagues undertook a comprehensive investigation of gas and electrolyte equilibria in blood. McLean and Henderson at Harvard had made preliminary studies of blood as a physico-chemical system, but realized that Van Slyke and his colleagues at the Rockefeller Hospital had superior techniques and the facilities necessary for such an undertaking. A collaboration thereupon began between the two laboratories, which resulted in rapid progress toward an exact physico-chemical description of the role of hemoglobin in the transport of oxygen and carbon dioxide, of the distribution of diffusible ions and water between erythrocytes and plasma,
and of factors such as degree of oxygenation of hemoglobin and hydrogen ion concentration that modified these distributions. In this Van Slyke revised his volumetric gas analysis apparatus into a manometric method.  The manometric apparatus proved to give results that were from five to ten times more accurate.

A series of papers on the CO2 titration curves of oxy- and deoxyhemoglobin, of oxygenated and reduced whole blood, and of blood subjected to different degrees of oxygenation and on the distribution of diffusible ions in blood resulted.  These developed equations that predicted the change in distribution of water and diffusible ions between blood plasma and blood cells when there was a change in pH of the oxygenated blood. A significant contribution of Van Slyke and his colleagues was the application of the Gibbs-Donnan Law to the blood—regarded as a two-phase system, in which one phase (the erythrocytes) contained a high concentration of nondiffusible negative ions, i.e., those associated with hemoglobin, and cations, which were not freely exchaThe importance of Vanngeable between cells and plasma. By changing the pH through varying the CO2 tension, the concentration of negative hemoglobin charges changed in a predictable amount. This, in turn, changed the distribution of diffusible anions such as Cl” and HCO3″ in order to restore the Gibbs-Donnan equilibrium. Redistribution of water occurred to restore osmotic equilibrium. The experimental results confirmed the predictions of the equations.

As a spin-off from the physico-chemical study of the blood, Van undertook, in 1922, to put the concept of buffer value of weak electrolytes on a mathematically exact basis.
This proved to be useful in determining buffer values of mixed, polyvalent, and amphoteric electrolytes, and put the understanding of buffering on a quantitative basis. A
monograph in Medicine entitled “Observation on the Courses of Different Types of Bright’s Disease, and on the Resultant Changes in Renal Anatomy,” was a landmark that
related the changes occurring at different stages of renal deterioration to the quantitative changes taking place in kidney function. During this period, Van Slyke and R. M. Archibald identified glutamine as the source of urinary ammonia. During World War II, Van and his colleagues documented the effect of shock on renal function and, with R. A. Phillips, developed a simple method, based on specific gravity, suitable for use in the field.

Over 100 of Van’s 300 publications were devoted to methodology. The importance of Van Slyke’s contribution to clinical chemical methodology cannot be overestimated.
These included the blood organic constituents (carbohydrates, fats, proteins, amino acids, urea, nonprotein nitrogen, and phospholipids) and the inorganic constituents (total cations, calcium, chlorides, phosphate, and the gases carbon dioxide, carbon monoxide, and nitrogen). It was said that a Van Slyke manometric apparatus was almost all the special equipment needed to perform most of the clinical chemical analyses customarily performed prior to the introduction of photocolorimeters and spectrophotometers for such determinations.

The progress made in the medical sciences in genetics, immunology, endocrinology, and antibiotics during the second half of the twentieth century obscures at times the progress that was made in basic and necessary biochemical knowledge during the first half. Methods capable of giving accurate quantitative chemical information on biological material had to be painstakingly devised; basic questions on chemical behavior and metabolism had to be answered; and, finally, those factors that adversely modified the normal chemical reactions in the body so that abnormal conditions arise that we characterize as disease states had to be identified.

Viewed in retrospect, he combined in one scientific lifetime (1) basic contributions to the chemistry of body constituents and their chemical behavior in the body, (2) a chemical understanding of physiological functions of certain organ systems (notably the respiratory and renal), and (3) how such information could be exploited in the
understanding and treatment of disease. That outstanding additions to knowledge in all three categories were possible was in large measure due to his sound and broadly based chemical preparation, his ingenuity in devising means of accurate measurements of chemical constituents, and the opportunity given him at the Hospital of the Rockefeller Institute to study disease in company with physicians.

In addition, he found time to work collaboratively with Dr. John P. Peters of Yale on the classic, two-volume Quantitative Clinical Chemistry. In 1922, John P. Peters, who had just gone to Yale from Van Slyke’s laboratory as an Associate Professor of Medicine, was asked by a publisher to write a modest handbook for clinicians describing useful chemical methods and discussing their application to clinical problems. It was originally to be called “Quantitative Chemistry in Clinical Medicine.” He soon found that it was going to be a bigger job than he could handle alone and asked Van Slyke to join him in writing it. Van agreed, and the two men proceeded to draw up an outline and divide up the writing of the first drafts of the chapters between them. They also agreed to exchange each chapter until it met the satisfaction of both.At the time it was published in 1931, it contained practically all that could be stated with confidence about those aspects of disease that could be and had been studied by chemical means. It was widely accepted throughout the medical world as the “Bible” of quantitative clinical chemistry, and to this day some of the chapters have not become outdated.

History of Laboratory Medicine at Yale University.

The roots of the Department of Laboratory Medicine at Yale can be traced back to John Peters, the head of what he called the “Chemical Division” of the Department of Internal Medicine, subsequently known as the Section of Metabolism, who co-authored with Donald Van Slyke the landmark 1931 textbook Quantitative Clinical Chemistry (2.3); and to Pauline Hald, research collaborator of Dr. Peters who subsequently served as Director of Clinical Chemistry at Yale-New Haven Hospital for many years. In 1947, Miss Hald reported the very first flame photometric measurements of sodium and potassium in serum (4). This study helped to lay the foundation for modern studies of metabolism and their application to clinical care.

The Laboratory Medicine program at Yale had its inception in 1958 as a section of Internal Medicine under the leadership of David Seligson. In 1965, Laboratory Medicine achieved autonomous section status and in 1971, became a full-fledged academic department. Dr. Seligson, who served as the first Chair, pioneered modern automation and computerized data processing in the clinical laboratory. In particular, he demonstrated the feasibility of discrete sample handling for automation that is now the basis of virtually all automated chemistry analyzers. In addition, Seligson and Zetner demonstrated the first clinical use of atomic absorption spectrophotometry. He was one of the founding members of the major Laboratory Medicine academic society, the Academy of Clinical Laboratory Physicians and Scientists.

Davenport fig 10.jpg

Case in Point 3.  Nathan Gochman.  Developer of Automated Chemistries.

Nathan Gochman, PhD, has over 40 years of experience in the clinical diagnostics industry. This includes academic teaching and research, and 30 years in the pharmaceutical and in vitro diagnostics industry. He has managed R & D, technical marketing and technical support departments. As a leader in the industry he was President of the American Association for Clinical Chemistry (AACC) and the National Committee for Clinical Laboratory Standards (NCCLS, now CLSI). He is currently a Consultant to investment firms and IVD companies.

Nathan Gochman

Nathan Gochman

The clinical laboratory has become so productive, particularly in chemistry and immunology, and the labor, instrument and reagent costs are well determined, that today a physician’s medical decisions are 80% determined by the clinical laboratory.  Medical information systems have lagged far behind.  Why is that?  Because the decision for a MIS has historical been based on billing capture.  Moreover, the historical use of chemical profiles were quite good at validating healthy dtatus in an outpatient population, but the profiles became restricted under Diagnostic Related Groups.    Thus, it came to be that the diagnostics was considered a “commodity”.  In order to be competitive, a laboratory had to provide “high complexity” tests that were drawn in by a large volume of “moderate complexity”tests.

Part 3. Biomarkers in Medical Practice

Case in Point 1.

A Solid Prognostic Biomarker

HDL-C: Target of Therapy or Fuggedaboutit?

Steven E. Nissen, MD, MACC, Peter Libby, MD

DisclosuresNovember 06, 2014

Steven E. Nissen, MD, MACC: I am Steve Nissen, chairman of the Department of Cardiovascular Medicine at the Cleveland Clinic. I am here with Dr Peter Libby, chief of cardiology at the Brigham and Women’s Hospital and professor of medicine at Harvard Medical School. We are going to discuss high-density lipoprotein cholesterol (HDL-C), a topic that has been very controversial recently. Peter, HDL-C has been a pretty good biomarker. The question is whether it is a good target.

Peter Libby, MD: Since the early days in Berkley, when they were doing ultracentrifugation, and when it was reinforced and put on the map by the Framingham Study,[1] we have known that HDL-C is an extremely good biomarker of prospective cardiovascular risk with an inverse relationship with all kinds of cardiovascular events. That is as solid a finding as you can get in observational epidemiology. It is a very reliable prospective marker. It’s natural that the pharmaceutical industry and those of us who are interested in risk reduction would focus on HDL-C as a target. That is where the controversies come in.

Dr Nissen: It has been difficult. My view is that the trials that have attempted to modulate HDL-C or the drugs they used have been flawed. Although the results have not been promising, the jury is yet out. Torcetrapib, the cholesteryl ester transfer protein (CETP) inhibitor developed by Pfizer, had anoff-target toxicity.[2] Niacin is not very effective, and there are a lot of downsides to the drug. That has been an issue, but people are still working on this. We have done some studies. We did our ApoA-1 Milano infusion study[3]about a decade ago, which showed very promising results with respect to shrinking plaques in coronary arteries. I remain open to the possibility that the right drug in the right trial will work.

Dr Libby: What do you do with the genetic data that have come out in the past couple of years? Sekar Kathiresan masterminded and organized an enormous collaboration[4] in which they looked, with contemporary genetics, at whether HDL had the genetic markers of being a causal risk factor. They came up empty-handed.

Dr Nissen: I am cautious about interpreting those data, like I am cautious about interpreting animal studies of atherosclerosis. We have both lived through this problem in which something works extremely well in animals but doesn’t work in humans, or it doesn’t work in animals but it works in humans. The genetic studies don’t seal the fate of HDL. I have an open mind about this. Drugs are complex. They work by complex mechanisms. It is my belief that what we have to do is test these hypotheses in well-designed clinical trials, which are rigorously performed with drugs that are clean—unlike torcetrapib—and don’t have off-target toxicities.

An Unmet Need: High Lp(a) Levels

Dr Nissen: I’m going to push back on that and make a couple of points. The HPS2-THRIVE study was flawed. They studied the wrong people. It was not a good study, and AIM-HIGH[8] was underpowered. I am not putting people on niacin. What do you do with a patient whose Lp(a) is 200 mg/dL?

Dr Libby: I’m waiting for the results of the PCSK9 and anacetrapib studies. You can tell me about evacetrapib.[9]Reducing Lp(a) is an unmet medical need. We both care for kindreds with high Lp(a) levels and premature coronary artery disease. We have no idea what to do with them other than to treat them with statins and lower their LDL-C levels.

Dr Nissen: I have taken a more cautious approach with respect to taking people off of niacin. If I have patients who are doing well and tolerating it (depending on why it was started), I am discontinuing niacin in some people. I am starting very few people on the drug, but I worry about the quality of the trial.

Dr Libby: So you are of the “don’t start don’t stop” school?

Dr Nissen: Yes. It’s difficult when the trial is fatally flawed. There were 11,000 patients from China in this study. I have known for years that if you give niacin to people of Asiatic ethnic descent, they have terrible flushing and they won’t continue the drug. One question is, what was the adherence? The adverse events would have been tolerable had there been efficacy. The concern here is that this study was destined to fail because they studied a low LDL/high HDL population, a group of people for whom niacin just isn’t used.

Triglycerides and HDL: Do We Have It Backwards?

Dr Libby: What about the recent genetic[10] and epidemiologic data that support triglycerides, and apolipoprotein C3 in particular as a causal risk factor? Have we been misled through all of the generations in whom we have been adjusting triglycerides for HDL-C and saying that triglycerides are not a causal risk factor because once we adjust for HDL, the risk goes away? Do you think we got it backwards?

Dr Nissen: The tricky factor here is that because of this intimate inverse relationship between triglycerides and HDL, we may be talking about the same phenomenon. That is one of the reasons that I am not certain we are not going to be able to find a therapy. What if you had a therapy that lowered triglycerides and raised HDL-C? Could that work? Could that combination be favorable? I want answers from rigorous, well-designed clinical trials that ask the right questions in the right populations. I am disappointed, just as I have been disappointed by the fibrate trials.[11,12] There is a class of drugs that raises HDL-C a little and lowers triglycerides a lot.

Dr Nissen: But the gemfibrozil studies (VA-HIT[13] and Helsinki Heart[14]) showed benefit.

The Dyslipidemia Bar Has Been Raised

Dr Libby: Those studies were from the pre-statin era. We both were involved in trials in which patients were on high-dose statins at baseline. Do you think that this is too high a bar?

Dr Nissen: The bar has been raised, and for the pharmaceutical industry, the studies that we need to find out whether lowering triglycerides or raising HDL is beneficial are going to be large. We are doing a study with evacetrapib. It has 12,000 patients. It’s fully enrolled. Evacetrapib is a very clean-looking drug. It doesn’t have such a long biological half-life as anacetrapib, so I am very encouraged that it won’t have that baggage of being around for 2-4 years. We’ve got a couple of shots on goal here. Don’t forget that we have multiple ongoing studies of HDL-C infusion therapies that are still under development. Those have some promise too. The jury is still out.

Dr Libby: We agree on the need to do rigorous, large-scale endpoint trials. Do the biomarker studies, but don’t wait to start the endpoint trial because that’s the proof in the pudding.

Dr Nissen: Exactly. We have had a little controversy about HDL-C. We often agree, but not always, and we may have a different perspective. Thanks for joining me in this interesting discussion of what will continue to be a controversial topic for the next several years until we get the results of the current ongoing trials.

Case in Point 2.

NSTEMI? Honesty in Coding and Communication?

Melissa Walton-Shirley

November 07, 2014

The complaint at ER triage: Weakness, fatigue, near syncope of several days’ duration, vomiting, and decreased sensorium.

The findings: O2sat: 88% on room air. BP: 88 systolic. Telemetry: Sinus tachycardia 120 bpm. Blood sugar: 500 mg/dL. Chest X ray: atelectasis. Urinalysis: pyuria. ECG: T-wave-inversion anterior leads. Echocardiography: normal left ventricular ejection fraction (LVEF) and wall motion. Troponin I: 0.3 ng/mL. CT angiography: negative for pulmonary embolism (PE). White blood cell count: 20K with left shift. Blood cultures: positive for Gram-negative rods.

The treatment: Intravenous fluids and IV levofloxacin—changed to ciprofloxacin.

The communication at discharge: “You had a severe urinary-tract infection and grew bacteria in your bloodstream. Also, you’ve had a slight heart attack. See your cardiologist immediately upon discharge-no more than 5 days from now.”

The diagnoses coded at discharge: Urosepsis and non-ST segment elevation MI (NSTEMI) 410.1.

One year earlier: This moderately obese patient was referred to our practice for a preoperative risk assessment. The surgery planned was a technically simple procedure, but due to the need for precise instrumentation, general endotracheal anesthesia (GETA) was being considered. The patient was diabetic, overweight, and short of air. A stress exam was equivocal for CAD due to poor exercise tolerance and suboptimal imaging. Upon further discussion, symptoms were progressive; therefore, cardiac cath was recommended, revealing angiographically normal coronaries and a predictably elevated left ventricular end diastolic pressure (LVEDP) in the mid-20s range. The patient was given a diagnosis of diastolic dysfunction, a prescription for better hypertension control, and in-depth discussion on exercise and the Mediterranean and DASH diets for weight loss. Symptoms improved with a low dose of diuretic. The surgery was completed without difficulty. Upon follow-up visit, the patient felt well, had lost a few pounds, and blood pressure was well controlled.

Five days after ER workup: While out of town, the patient developed profound weakness and went to the ER as described above. Fast forward to our office visit in the designated time frame of “no longer than 5 days’ postdischarge,” where the patient and family asked me about the “slight heart attack” that literally came on the heels of a normal coronary angiogram.

But the patient really didn’t have a “heart attack,” did they? The cardiologist aptly stated that it was likely nonspecific troponin I leak in his progress notes. Yet the hospitalist framed the diagnosis of NSTEMI as item number 2 in the final diagnoses.

The motivations on behalf of personnel who code charts are largely innocent and likely a direct result of the lack of understanding of the coding system on behalf of us as healthcare providers. I have a feeling, though, that hospitals aren’t anxious to correct this misperception, due to an opportunity for increased reimbursement. I contacted a director of a coding department for a large hospital who prefers to remain anonymous. She explained that NSTEMI ICD9 code 410.1 falls in DRG 282 with a weight of .7562. The diagnosis of “demand ischemia,” code 411.89, a slightly less inappropriate code for a nonspecific troponin I leak, falls in DRG 311 with a weight of .5662. To determine reimbursement, one must multiply the weight by the average hospital Medicare base rate of $5370. Keep in mind that each hospital’s base rate and corresponding payment will vary. The difference in reimbursement for a large hospital bill between these two choices for coding is substantial, at over $1000 difference ($4060 vs $3040).

Although hospitals that are already reeling from shrinking revenues will make more money on the front end by coding the troponin leak incorrectly as an NSTEMI, when multiple unnecessary tests are generated to follow up on a nondiagnostic troponin leak, the amount of available Centers for Medicare & Medicaid Services (CMS) reimbursement pie shrinks in the long run. Furthermore, this inappropriate categorization generates extreme concern on behalf of patients and family members that is often never laid to rest. The emotional toll of a “heart-attack” diagnosis has an impact on work fitness, quality of life, cost of medication, and the cost of future testing. If the patient lived for another 100 years, they will likely still list a “heart attack” in their medical history.

As a cardiologist, I resent the loose utilization of one of “my” heart-attack codes when it wasn’t that at all. At discharge, we need to develop a better way of communicating what exactly did happen. Equally important, we need to communicate what exactly didn’t happen as well.

Case in Point 3.

Blood Markers Predict CKD Heart Failure 

Published: Oct 3, 2014 | Updated: Oct 3, 2014

Elevated levels of high-sensitivity troponin T (hsTnT) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) strongly predicted heart failure in patients with chronic kidney disease followed for a median of close to 6 years, researchers reported.

Compared with patients with the lowest blood levels of hsTnT, those with the highest had a nearly five-fold higher risk for developing heart failure and the risk was 10-fold higher in patients with the highest NT-proBNP levels compared with those with the lowest levels of the protein, researcher Nisha Bansal, MD, of the University of Washington in Seattle, and colleagues wrote online in the Journal of the American Society of Nephrology.

A separate study, published online in theJournal of the American Medical Association earlier in the week, also examined the comorbid conditions of heart and kidney disease, finding no benefit to the practice of treating cardiac surgery patients who developed acute kidney injury with infusions of the antihypertensive drug fenoldopam.

The study, reported by researcher Giovanni Landoni, MD, of the IRCCS San Raffaele Scientific Institute, Milan, Italy, and colleagues, was stopped early “for futility,” according to the authors, and the incidence of hypotension during drug infusion was significantly higher in patients infused with fenoldopam than placebo (26% vs. 15%; P=0.001).

Blood Markers Predict CKD Heart Failure

The study in patients with mild to moderate chronic kidney disease (CKD) was conducted to determine if blood markers could help identify patients at high risk for developing heart failure.

Heart failure is the most common cardiovascular complication among people with renal disease, occurring in about a quarter of CKD patients.

The two markers, hsTnT and NT-proBNP, are associated with overworked cardiac myocytes and have been shown to predict heart failure in the general population.

However, Bansal and colleagues noted, the markers have not been widely used in diagnosing heart failure among patients with CKD due to concerns that reduced renal excretion may raise levels of these markers, and therefore do not reflect an actual increase in heart muscle strain.

To better understand the importance of elevated concentrations of hsTnT and NT-proBNP in CKD patients, the researchers examined their association with incident heart failure events in 3,483 participants in the ongoing observational Chronic Renal Insufficiency Cohort (CRIC) study.

All participants were recruited from June 2003 to August 2008, and all were free of heart failure at baseline. The researchers used Cox regression to examine the association of baseline levels of hsTnT and NT-proBNP with incident heart failure after adjustment for demographic influences, traditional cardiovascular risk factors, makers of kidney disease, pertinent medication use, and mineral metabolism markers.

At baseline, hsTnT levels ranged from ≤5.0 to 378.7 pg/mL and NT-proBNP levels ranged from ≤5 to 35,000 pg/mL. Compared with patients who had undetectable hsTnT, those in the highest quartile (>26.5 ng/mL) had a significantly higher rate of heart failure (hazard ratio 4.77; 95% CI 2.49-9.14).

Compared with those in the lowest NT-proBNP quintile (<47.6 ng/mL), patients in the highest quintile (>433.0 ng/mL) experienced an almost 10-fold increase in heart failure risk (HR 9.57; 95% CI 4.40-20.83).

The researchers noted that these associations remained robust after adjustment for potential confounders and for the other biomarker, suggesting that while hsTnT and NT-proBNP are complementary, they may be indicative of distinct biological pathways for heart failure.

Even Modest Increases in NP-proBNP Linked to Heart Failure

The findings are consistent with an earlier analysis that included 8,000 patients with albuminuria in the Prevention of REnal and Vascular ENd-stage Disease (PREVEND) study, which showed that hsTnT was associated with incident cardiovascular events, even after adjustment for eGFR and severity of albuminuria.

“Among participants in the CRIC study, those with the highest quartile of detectable hsTnT had a twofold higher odds of left ventricular hypertrophy compared with those in the lowest quartile,” Bansal and colleagues wrote, adding that the findings were similar after excluding participants with any cardiovascular disease at baseline.

Even modest elevations in NT-proBNP were associated with significantly increased rates of heart failure, including in subgroups stratified by eGFR, proteinuria, and diabetic status.

“NT-proBNP regulates blood pressure and body fluid volume by its natriuretic and diuretic actions, arterial dilation, and inhibition of the renin-aldosterone-angiotensin system and increased levels of this marker likely reflect myocardial stress induced by subclinical changes in volume or pressure, even in persons without clinical disease,” the researchers wrote.

The researchers concluded that further studies are needed to develop and validate risk prediction tools for clinical heart failure in patients with CKD, and to determine the potential role of these two biomarkers in a heart failure risk prediction and prevention strategy.

Fenoldopam ‘Widely Promoted’ in AKI Cardiac Surgery Setting

The JAMA study examined whether the selective dopamine receptor D agonist fenoldopam mesylate can reduce the need for dialysis in cardiac surgery patients who develop acute kidney injury (AKI).

Fenoldopam induces vasodilation of the renal, mesenteric, peripheral, and coronary arteries, and, unlike dopamine, it has no significant affinity for D2 receptors, meaning that it theoretically induces greater vasodilation in the renal medulla than in the cortex, the researchers wrote.

“Because of these hemodynamic effects, fenoldopam has been widely promoted for the prevention and therapy of AKI in the United States and many other countries with apparent favorable results in cardiac surgery and other settings,” Landoni and colleagues wrote.

The drug was approved in 1997 by the FDA for the indication of in-hospital, short-term management of severe hypertension. It has not been approved for renal indications, but is commonly used off-label in cardiac surgery patients who develop AKI.

Although a meta analysis of randomized trials, conducted by the researchers, indicated a reduction in the incidence and progression of AKI associated with the treatment, Landoni and colleagues wrote that the absence of a definitive trial “leaves clinicians uncertain as to whether fenoldopam should be prescribed after cardiac surgery to prevent deterioration in renal function.”

To address this uncertainty, the researchers conducted a prospective, randomized, parallel-group trial in 667 patients treated at 19 hospitals in Italy from March 2008 to April 2013.

All patients had been admitted to ICUs after cardiac surgery with early acute kidney injury (≥50% increase of serum creatinine level from baseline or low output of urine for ≥6 hours). A total of 338 received fenoldopam by continuous intravenous infusion for a total of 96 hours or until ICU discharge, while 329 patients received saline infusions.

The primary end point was the rate of renal replacement therapy, and secondary end points included mortality (intensive care unit and 30-day mortality) and the rate of hypotension during study drug infusion.

Study Showed No Benefit, Was Stopped Early

Yale Lampoon – AA Liebow.   1954

Not As a Doctor
[Fourth Year]

These lyrics, sung by John Cole, Jack Gariepy and Ed Ransenhofer to music borrowed from Gilbert and Sullivan’s The Mikado, lampooned Averill Liebow, M.D., a pathologist noted for his demands on students. (CPC stands for clinical pathology conference.)

If you want to know what this is,
it’s a medical CPC
Where we give the house staff
the biz, for there’s no one so
wise as we!
We pathologists show them how,
Although it is too late now.
Our art is a sacred cow!

American physician, born 1911, Stryj in Galicia, Austria (now in Ukraine); died 1978.

Averill Abraham Liebow, born in Austria, was the “founding father” of pulmonary pathology in the United States. He started his career as a pathologist at Yale, where he remained for many years. In 1968 he moved to the University of California School of Medicine, San Diego, where he taught for 7 years as Professor and Chairman, Department of Pathology.

His studies include many classic studies of lung diseases. Best known of these is his famous classification of interstitial lung disease. He also published papers on sclerosing pneumocytoma, pulmonary alveolar proteinosis, meningothelial-like nodules, pulmonary hypertension, pulmonary veno-occlusive disease, lymphomatoid granulomatosis, pulmonary Langerhans cell histiocytosis, pulmonary epithelioid hemangioendothelioma and pulmonary hyalinizing granuloma .

As a Lieutenant Colonel in the US Army Medical Corps, He was a member of the Atomic Bomb Casualty Commission who studied the effects of the atomic bomb in Hiroshima and Nagasaki.

We thank Sanjay Mukhopadhyay, M.D., for information submitted.

As a resident at UCSD, Dr. Liebow held “Organ Recitals” every morning, including Mother’s day.  The organs had to be presented in specified order… heart, lung, and so forth.  On one occasion, we needed a heart for purification of human lactate dehydrogenase for a medical student project, so I presented the lung out of order.  Dr. Liebow asked where the heart was, and I told the group it was noprmal and I froze it for enzyme purification (smiles).  In the future show it to me first. He was generous to those who showed interest.  As I was also doing research in Nathan Kaplan’s laboratory, he made special arrangements for me to mentor Deborah Peters, the daughter of a pulmonary physician, and granddaughter of the Peters who collaborated with Van Slyke.  I mentored many students with great reward since then.  He could look at a slide and tell you what the x-ray looked like.  I didn’t encounter that again until he sent me to the Armed Forces Institute of Pathology, Washington, DC during the Vietnam War and Watergate, and I worked in Orthopedic Pathology with Lent C. Johnson.  He would not review a case without the x-ray, and he taught the radiologists.

Part 3

My Cancer Genome from Vanderbilt University: Matching Tumor Mutations to Therapies & Clinical Trials

Reporter: Aviva Lev-Ari, PhD, RN

My Cancer Genome from Vanderbilt University: Matching Tumor Mutations to Therapies & Clinical Trials


GenomOncology and Vanderbilt-Ingram Cancer Center (VICC) today announced a partnership for the exclusive commercial development of a decision support tool based on My Cancer Genome™, an online precision cancer medicine knowledge resource for physicians, patients, caregivers and researchers.

Through this collaboration, GenomOncology and VICC will enhance My Cancer Genome through the development of a new genomics content management tool. The MyCancerGenome.org website will remain free and open to the public. In addition, GenomOncology will develop a decision support tool based on My Cancer Genome™ data that will enable automated interpretation of mutations in the genome of a patient’s tumor, providing actionable results in hours versus days.

Vanderbilt-Ingram Cancer Center (VICC) launched My Cancer Genome™ in January 2011 as an integral part of their Personalized Cancer Medicine Initiative that helps physicians and researchers track the latest developments in precision cancer medicine and connect with clinical research trials. This web-based information tool is designed to quickly educate clinicians on the rapidly expanding list of genetic mutations that impact cancers and enable the research of treatment options based on specific mutations. For more information on My Cancer Genome™visit www.mycancergenome.org/about/what-is-my-cancer-genome.

Therapies based on the specific genetic alterations that underlie a patient’s cancer not only result in better outcomes but often have less adverse reactions

Up front fee

Nominal fee covers installation support, configuring the Workbench to your specification, designing and developing custom report(s) and training your team.

Per sample fee

GenomOncology is paid on signed-out clinical reports. This philosophy aligns GenomOncology with your Laboratory as we are incentivized to offer world-class support and solutions to differentiate your clinical NGS program. There is no annual license fee.

Part 4

Clinical Trial Services: Foundation Medicine & EmergingMed to Partner

Reporter: Aviva Lev-Ari, PhD, RN

Clinical Trial Services: Foundation Medicine & EmergingMed to Partner


Foundation Medicine and EmergingMed said today that they will partner to offer clinical trial navigation services for health care providers and their patients who have received one of Foundation Medicine’s tumor genomic profiling tests.

The firms will provide concierge services to help physicians

  • identify appropriate clinical trials for patients
  • based on the results of FoundationOne or FoundationOne Heme.

“By providing clinical trial navigation services, we aim to facilitate

  • timely and accurate clinical trial information and enrollment support services for physicians and patients,
  • enabling greater access to treatment options based on the unique genomic profile of a patient’s cancer

Currently, there are over 800 candidate therapies that target genomic alterations in clinical trials,

  • but “patients and physicians must identify and act on relevant options
  • when the patient’s clinical profile is aligned with the often short enrollment window for each trial.

These investigational therapies are an opportunity to engage patients with cancer whose cancer has progressed or returned following standard treatment in a most favorable second option after relapse.  The new service is unique in notifying when new clinical trials emerge that match a patient’s genomic and clinical profile.

Google signs on to Foundation Medicine cancer Dx by offering tests to employees

By Emily Wasserman

Diagnostics luminary Foundation Medicine ($FMI) is generating some upward momentum, fueled by growing revenues and the success of its clinical tests. Tech giant Google ($GOOG) has taken note and is signing onto the company’s cancer diagnostics by offering them to employees.

Foundation Medicine CEO Michael Pellini said during the company’s Q3 earnings call that Google will start covering its DNA tests for employees and their family members suffering from cancer as part of its health benefits portfolio, Reuters reports.

Both sides stand to benefit from the deal, as Google looks to keep a leg up on Silicon Valley competitors and Foundation Medicine expands its cancer diagnostics platform. Last month, Apple ($AAPL) and Facebook ($FB) announced that they would begin covering the cost of egg freezing for female employees. A diagnostics partnership and attractive health benefits could work wonders for Google’s employee retention rates and bottom line.

In the meantime, Cambridge, MA-based Foundation Medicine is charging full speed ahead with its cancer diagnostics platform after filing for an IPO in September 2013. The company chalked up 6,428 clinical tests during Q3 2014, an eye-popping 149% increase year over year, and brought in total revenue for the quarter of $16.4 million–a 100% leap from last year. Foundation Medicine credits the promising numbers in part to new diagnostic partnerships and extended coverage for its tests.

In January, the company teamed up with Novartis ($NVS) to help the drugmaker evaluate potential candidates for its cancer therapies. In April, Foundation Medicine announced that it would develop a companion diagnostic test for a Clovis Oncology ($CLVS) drug under development to treat patients with ovarian cancer, building on an ongoing collaboration between the two companies.

Foundation Medicine also has its sights set on China’s growing diagnostics market, inking a deal in October with WuXi PharmaTech ($WX) that allows the company to perform lab testing for its FoundationOne assay at WuXi’s Shanghai-based Genome Center.

a nod to the deal with Google during a corporate earnings call on Wednesday, according to a person who listened in. Pellini said Google employees were made aware of this new benefit last week.

Foundation Medicine teams with MD Anderson for new trial of cancer Dx

Second study to see if targeted therapy can change patient outcomes

August 15, 2014 | By   FierceDiagnostics

Foundation Medicine ($FMI) is teaming up with the MD Anderson Cancer Center in Texas for a new trial of the the Cambridge, MA-based company’s molecular diagnostic cancer test that targets therapies matched to individual patients.

The study is called IMPACT2 (Initiative for Molecular Profiling and Advanced Cancer Therapy) and is designed to build on results from the the first IMPACT study that found

  • 40% of the 1,144 patients enrolled had an identifiable genomic alteration.

The company said that

  • by matching specific gene alterations to therapies,
  • 27% of patients in the first study responded versus
  • 5% with an unmatched treatment, and
  • “progression-free survival” was longer in the matched group.

The FoundationOne molecular diagnostic test

  • combines genetic sequencing and data gathering
  • to help oncologists choose the best treatment for individual patients.

Costing $5,800 per test, FoundationOne’s technology can uncover a large number of genetic alterations for 200 cancer-related genes,

  • blending genomic sequencing, information and clinical practice.

“Based on the IMPACT1 data, a validated, comprehensive profiling approach has already been adopted by many academic and community-based oncology practices,” Vincent Miller, chief medical officer of Foundation Medicine, said in a release. “This study has the potential to yield sufficient evidence necessary to support broader adoption across most newly diagnosed metastatic tumors.”

The company got a boost last month when the New York State Department of Health approved Foundation Medicine’s two initial cancer tests: the FoundationOne test and FoundationOne Heme, which creates a genetic profile for blood cancers. Typically,

  • diagnostics companies struggle to win insurance approval for their tests
  • even after they gain a regulatory approval, leaving revenue growth relatively flat.

However, Foundation Medicine reported earlier this week its Q2 revenue reached $14.5 million compared to $5.9 million for the same period a year ago. Still,

  1. net losses continue to soar as the company ramps up
  2. its commercial and business development operation,
  • hitting $13.7 million versus a $10.1 million deficit in the second quarter of 2013.

Oncology

There has been a remarkable transformation in our understanding of

  • the molecular genetic basis of cancer and its treatment during the past decade or so.

In depth genetic and genomic analysis of cancers has revealed that

  • each cancer type can be sub-classified into many groups based on the genetic profiles and
  • this information can be used to develop new targeted therapies and treatment options for cancer patients.

This panel will explore the technologies that are facilitating our understanding of cancer, and

  • how this information is being used in novel approaches for clinical development and treatment.
Oncology _ Reprted by Dr. Aviva Lev-Ari, Founder, Leaders in Pharmaceutical Intelligence

Opening Speaker & Moderator:

Lynda Chin, M.D.
Department Chair, Department of Genomic Medicine
MD Anderson Cancer Center

  • Who pays for PM?
  • potential of Big data, analytics, Expert systems, so not each MD needs to see all cases, Profile disease to get same treatment
  • business model: IP, Discovery, sharing, ownership — yet accelerate therapy
  • security of healthcare data
  • segmentation of patient population
  • management of data and tracking innovations
  • platforms to be shared for innovations
  • study to be longitudinal,
  • How do we reconcile course of disease with PM
  • phinotyping the disease vs a Patient in wait for cure/treatment

Panelists:

Roy Herbst, M.D., Ph.D.
Ensign Professor of Medicine and Professor of Pharmacology;
Chief of Medical Oncology, Yale Cancer Center and Smilow Cancer Hospital

Development new drugs to match patient, disease and drug – finding the right patient for the right Clinical Trial

  • match patient to drugs
  • partnerships: out of 100 screened patients, 10 had the gene, 5 were able to attend the trial — without the biomarker — all 100 patients would participate for the WRONG drug for them (except the 5)
  • patients wants to participate in trials next to home NOT to have to travel — now it is in the protocol
  • Annotated Databases – clinical Trial informed consent – adaptive design of Clinical Trial vs protocol
  • even Academic MD can’t read the reports on Genomics
  • patients are treated in the community — more training to MDs
  • Five companies collaborating – comparison og 6 drugs in the same class
  • if drug exist and you have the patient — you must apply PM

Summary and Perspective:

The current changes in Biotechnology have been reviewed with an open question about the relationship of In Vitro Diagnostics to Biopharmaceuticals switching, with the potential, particularly in cancer and infectious diseases, to added value in targeted therapy by matching patients to the best potential treatment for a favorable outcome.

This reviewer does not see the movement of the major diagnostics leaders entering into the domain of direct patient care, even though there are signals in that direction.  The Roche example is perhaps the most interesting because Roche already became the elephant in the room after the introduction of Valium,  subsequently bought out Boehringer Mannheim Diagnostics to gain entry into the IVD market, and established a huge presence in Molecular Diagnostics early.  If it did anything to gain a foothold in the treatment realm, it would more likely forge a relationship with Foundation Medicine.  Abbott Laboratories more than a decade ago was overextended, and it had become the leader in IVD as a result of the specialty tests, but it fell into difficulties with quality control of its products in the high volume testing market, and acceeded to Olympus, Roche, and in the mid volume market to Beckman and Siemens.  Of course, Dupont and Kodak, pioneering companies in IVD, both left the market.

The biggest challenge in the long run is identified by the ability to eliminate many treatments that would be failures for a large number of patients. That has already met the proof of concept.  However, when you look at the size of the subgroups, we are not anywhere near a large scale endeavor.  In addition, there is a lot that has to be worked out that is not related to genomic expression by the “classic” model, but has to take into account the emrging knowledge and greater understanding of regulation of cell metabolism, not only in cancer, but also in chronic inflammatory diseases.

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Biochemical Insights of Dr. Jose Eduardo de Salles Roselino

Larry H. Bernstein, MD, FCAP, Interviewer, Curator

Leaders in Pharmaceutical Intelligence

Biochemical Insights of Dr. Jose Eduardo de Salles Roselino

http://pharmaceuticalintelligence.com/12/24/2014/larryhbern/Biochemical_
Insights_of_Dr._Jose_Eduardo_de_Salles_Roselino/

Article ID #165: Biochemical Insights of Dr. Jose Eduardo de Salles Roselino. Published on 12/17/2014

WordCloud Image Produced by Adam Tubman

Biochemical Insights of Dr. Jose Eduardo de Salles Roselino

How is it that developments late in the 20th century diverted the attention of
biological processes from a dynamic construct involving interacting chemical
reactions under rapidly changing external conditions effecting tissues and cell
function to a rigid construct that is determined unilaterally by the genome
construct, diverting attention from mechanisms essential for seeing the complete
cellular construct?

Larry, I assume that in case you read the article titled Neo – Darwinism, The
Modern Synthesis and Selfish Genes that bares no relationship with Physiology
with Molecular Biology J. Physiol 2011; 589(5): 1007-11 by Denis Noble, you might
find that it was the key factor required in order to understand the dislodgment
of physiology as a foundation of medical reasoning. In the near unilateral emphasis
of genomic activity as a determinant of cellular activity all of the required general
support for the understanding of my reasoning. The DNA to protein link goes
from triplet sequence to amino acid sequence. That is the realm of genetics.
Further, protein conformation, activity and function requires that environmental
and micro-environmental factors should be considered (Biochemistry). If that
were not the case, we have no way to bridge the gap between the genetic
code and the evolution of cells, tissues, organs, and organisms.

  • Consider this example of hormonal function. I would like to stress in
    the cAMP dependent hormonal response, the transfer of information
    that 
    occurs through conformation changes after protein interactions.
    This mechanism therefore, requires that proteins must not have their
    conformation determined by sequence alone.
    Regulatory protein conformation is determined by its sequence plus
    the interaction it has in its micro-environment. For instance, if your
    scheme takes into account what happens inside the membrane and
    that occurs before cAMP, then production is increased by hormone
    action. A dynamic scheme  will show an effect initially, over hormone
    receptor (hormone binding causing change in its conformation) followed
    by GTPase change in conformation caused by receptor interaction and
    finally, Adenylate cyclase change in conformation and in activity after
    GTPase protein binding in a complex system that is dependent on self-
    assembly and also, on changes in their conformation in response to
    hormonal signals (see R. A Kahn and A. G Gilman 1984 J. Biol. Chem.
    v. 259,n 10 pp6235-6240. In this case, trimeric or dimeric G does not
    matter). Furthermore, after the step of cAMP increased production we
    also can see changes in protein conformation.  The effect of increased
    cAMP levels over (inhibitor protein and protein kinase protein complex)
    also is an effect upon protein conformation. Increased cAMP levels led
    to the separation of inhibitor protein (R ) from cAMP dependent protein
    kinase (C ) causing removal of the inhibitor R and the increase in C activity.
    R stands for regulatory subunit and C for catalytic subunit of the protein
    complex.
  • This cAMP effect over the quaternary structure of the enzyme complex
    (C protein kinase + R the inhibitor) may be better understood as an
    environmental information producing an effect in opposition to
    what may be considered as a tendency  towards a conformation
    “determined” by the genetic code. This “ideal” conformation
    “determined” by the genome  would be only seen in crystalline
    protein.
     In carbohydrate metabolism in the liver the hormonal signal
    causes a biochemical regulatory response that preserves homeostatic
    levels of glucose (one function) and in the muscle, it is a biochemical
    regulatory response that preserves intracellular levels of ATP (another
    function).
  • Therefore, sequence alone does not explain conformation, activity
    and function of regulatory proteins
    .  If this important regulatory
    mechanism was  not ignored, the work of  S. Prusiner (Prion diseases
    and the BSE crisis Stanley B. Prusiner 1997 Science; 278: 245 – 251,
    10  October) would be easily understood.  We would be accustomed
    to reason about changes in protein conformation caused by protein
    interaction with other proteins, lipids, small molecules and even ions.
  • In case this wrong biochemical reasoning is used in microorganisms.
    Still it is wrong but, it will cause a minor error most of the time, since
    we may reduce almost all activity of microorganism´s proteins to a
    single function – The production of another microorganism. However,
    even microorganisms respond differently to their micro-environment
    despite a single genome (See M. Rouxii dimorphic fungus works,
    later). The reason for the reasoning error is, proteins are proteins
    and DNA are DNA quite different in chemical terms. Proteins must
    change their conformation to allow for fast regulatory responses and
    DNA must preserve its sequence to allow for genetic inheritance.

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The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

Curator: Stephen J. Williams, Ph.D

Article ID #163: The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC. Published on 12/10/2014

WordCloud Image Produced by Adam Tubman

I am intending to do a series of posts highlighting interviews with Philadelphia area biotech startup CEO’s and show how a vibrant biotech startup scene is evolving in the city as well as the Delaware Valley area. Philadelphia has been home to some of the nation’s oldest biotechs including Cephalon, Centocor, hundreds of spinouts from a multitude of universities as well as home of the first cloned animal (a frog), the first transgenic mouse, and Nobel laureates in the field of molecular biology and genetics. Although some recent disheartening news about the fall in rankings of Philadelphia as a biotech hub and recent remarks by CEO’s of former area companies has dominated the news, biotech incubators like the University City Science Center and Bucks County Biotechnology Center as well as a reinvigorated investment community (like PCCI and MABA) are bringing Philadelphia back. And although much work is needed to bring the Philadelphia area back to its former glory days (including political will at the state level) there are many bright spots such as the innovative young companies as outlined in these posts.

First up I got to talk with Florian Schodel, M.D., Ph.D., CEO of Philimmune, which provides expertise in medicine, clinical and regulatory development and analytical sciences to support successful development and registration of vaccines and biologics. Before founding Philimmune, Dr. Schodel was VP in Vaccines Clinical Research of Merck Research Laboratories and has led EU vaccine clinical trials and the clinical development of rotavirus, measles, mumps, hepatitis B, and rubella vaccines. In addition Dr. Schodel and Philimmune consult on several vaccine development efforts at numerous biotech companies including:

 

\His specialties and services include: vaccines and biologics development strategy, clinical development, clinical operations, strategic planning and alliances, international collaborations, analytical and assay development, project and portfolio integration and leadership.

Successful development of vaccines and biologics poses some unique challenges: including sterile manufacturing and substantial early capital investment before initiated clinical trials, assay development for clinical trial support, and unique trail design. Therefore vaccines and biologics development is a highly collaborative process between several disciplines.

The Philadelphia area has a rich history in vaccine development including the discovery and development of the rubella, cytomegaolovirus, a rabies, and the oral polio vaccine at the Wistar Institute. Dr. Schodel answered a few questions on the state of vaccine development and current efforts in the Philadelphia area, including recent efforts by companies such as GSK’s efforts and Inovio’s efforts developing an Ebola vaccine.

In his opinion, Dr. Schodel believes our biggest hurdle in vaccine development in a societal issue, not a preclinic development issue. Great advances have been made to speed the discovery process and enhance quality assurance of manufacture capabilities like

however there has not been a great history or support for developing vaccines for the plethora of infectious diseases seen in the developing world. As Dr. Schodel pointed out, there are relatively few players in the field, and tough to get those few players excited for investing in new targets.

 

However, some companies are rapidly expanding their vaccine portfolios including

 

 

Why haven’t 3rd world countries developed their own vaccine programs?

 

  1. Hard to find partners willing to invest and support development
  2. Developing nations don’t have the money or infrastructure to support health programs
  3. Doctors in these countries need to be educated on how to conduct trials, conduct vaccine programs like Gates Foundation does. For more information see Nature paper on obstacles to vaccine introduction in third world countries.

 

Lastly, Dr. Schodel touched on a growing area, cancer vaccine development. Recent advances in bladder cancer vaccine, cervical, and promising results in an early phase metastatic breast cancer vaccine trial and phase I oral cancer vaccine trial have reinvigorated this field of cancer vaccinology.

 

Historic Timeline of Vaccine Development

vaccine development timeline

Graphic from http://en.pedaily.cn/Item.aspx?id=194125

 

Other posts on this site related to Biotech Startups in Philadelphia and some additional posts on infectious disease include:

 

RAbD Biotech Presents at 1st Pitch Life Sciences-Philadelphia

LytPhage Presents at 1st Pitch Life Sciences-Philadelphia

Hastke Inc. Presents at 1st Pitch Life Sciences-Philadelphia

1st Pitch Life Science- Philadelphia- What VCs Really Think of your Pitch

The History of Infectious Diseases and Epidemiology in the late 19th and 20th Century

 

 

 

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