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Posts Tagged ‘biomarkers’

Imaging-guided cancer treatment

Imaging-guided cancer treatment

Writer & reporter: Dror Nir, PhD

It is estimated that the medical imaging market will exceed $30 billion in 2014 (FierceMedicalImaging). To put this amount in perspective; the global pharmaceutical market size for the same year is expected to be ~$1 trillion (IMS) while the global health care spending as a percentage of Gross Domestic Product (GDP) will average 10.5% globally in 2014 (Deloitte); it will reach ~$3 trillion in the USA.

Recent technology-advances, mainly miniaturization and improvement in electronic-processing components is driving increased introduction of innovative medical-imaging devices into critical nodes of major-diseases’ management pathways. Consequently, in contrast to it’s very small contribution to global health costs, medical imaging bears outstanding potential to reduce the future growth in spending on major segments in this market mainly: Drugs development and regulation (e.g. companion diagnostics and imaging surrogate markers); Disease management (e.g. non-invasive diagnosis, guided treatment and non-invasive follow-ups); and Monitoring aging-population (e.g. Imaging-based domestic sensors).

In; The Role of Medical Imaging in Personalized Medicine I discussed in length the role medical imaging assumes in drugs development.  Integrating imaging into drug development processes, specifically at the early stages of drug discovery, as well as for monitoring drug delivery and the response of targeted processes to the therapy is a growing trend. A nice (and short) review highlighting the processes, opportunities, and challenges of medical imaging in new drug development is: Medical imaging in new drug clinical development.

The following is dedicated to the role of imaging in guiding treatment.

Precise treatment is a major pillar of modern medicine. An important aspect to enable accurate administration of treatment is complementing the accurate identification of the organ location that needs to be treated with a system and methods that ensure application of treatment only, or mainly to, that location. Imaging is off-course, a major component in such composite systems. Amongst the available solution, functional-imaging modalities are gaining traction. Specifically, molecular imaging (e.g. PET, MRS) allows the visual representation, characterization, and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In oncology, it can be used to depict the abnormal molecules as well as the aberrant interactions of altered molecules on which cancers depend. Being able to detect such fundamental finger-prints of cancer is key to improved matching between drugs-based treatment and disease. Moreover, imaging-based quantified monitoring of changes in tumor metabolism and its microenvironment could provide real-time non-invasive tool to predict the evolution and progression of primary tumors, as well as the development of tumor metastases.

A recent review-paper: Image-guided interventional therapy for cancer with radiotherapeutic nanoparticles nicely illustrates the role of imaging in treatment guidance through a comprehensive discussion of; Image-guided radiotherapeutic using intravenous nanoparticles for the delivery of localized radiation to solid cancer tumors.

 Graphical abstract

 Abstract

One of the major limitations of current cancer therapy is the inability to deliver tumoricidal agents throughout the entire tumor mass using traditional intravenous administration. Nanoparticles carrying beta-emitting therapeutic radionuclides [DN: radioactive isotops that emits electrons as part of the decay process a list of β-emitting radionuclides used in radiotherapeutic nanoparticle preparation is given in table1 of this paper.) that are delivered using advanced image-guidance have significant potential to improve solid tumor therapy. The use of image-guidance in combination with nanoparticle carriers can improve the delivery of localized radiation to tumors. Nanoparticles labeled with certain beta-emitting radionuclides are intrinsically theranostic agents that can provide information regarding distribution and regional dosimetry within the tumor and the body. Image-guided thermal therapy results in increased uptake of intravenous nanoparticles within tumors, improving therapy. In addition, nanoparticles are ideal carriers for direct intratumoral infusion of beta-emitting radionuclides by convection enhanced delivery, permitting the delivery of localized therapeutic radiation without the requirement of the radionuclide exiting from the nanoparticle. With this approach, very high doses of radiation can be delivered to solid tumors while sparing normal organs. Recent technological developments in image-guidance, convection enhanced delivery and newly developed nanoparticles carrying beta-emitting radionuclides will be reviewed. Examples will be shown describing how this new approach has promise for the treatment of brain, head and neck, and other types of solid tumors.

The challenges this review discusses

  • intravenously administered drugs are inhibited in their intratumoral penetration by high interstitial pressures which prevent diffusion of drugs from the blood circulation into the tumor tissue [1–5].
  • relatively rapid clearance of intravenously administered drugs from the blood circulation by kidneys and liver.
  • drugs that do reach the solid tumor by diffusion are inhomogeneously distributed at the micro-scale – This cannot be overcome by simply administering larger systemic doses as toxicity to normal organs is generally the dose limiting factor.
  • even nanoparticulate drugs have poor penetration from the vascular compartment into the tumor and the nanoparticles that do penetrate are most often heterogeneously distributed

How imaging could mitigate the above mentioned challenges

  • The inclusion of an imaging probe during drug development can aid in determining the clearance kinetics and tissue distribution of the drug non-invasively. Such probe can also be used to determine the likelihood of the drug reaching the tumor and to what extent.

Note: Drugs that have increased accumulation within the targeted site are likely to be more effective as compared with others. In that respect, Nanoparticle-based drugs have an additional advantage over free drugs with their potential to be multifunctional carriers capable of carrying both therapeutic and diagnostic imaging probes (theranostic) in the same nanocarrier. These multifunctional nanoparticles can serve as theranostic agents and facilitate personalized treatment planning.

  • Imaging can also be used for localization of the tumor to improve the placement of a catheter or external device within tumors to cause cell death through thermal ablation or oxidative stress secondary to reactive oxygen species.

See the example of Vintfolide in The Role of Medical Imaging in Personalized Medicine

vinta

Note: Image guided thermal ablation methods include radiofrequency (RF) ablation, microwave ablation or high intensity focused ultrasound (HIFU). Photodynamic therapy methods using external light devices to activate photosensitizing agents can also be used to treat superficial tumors or deeper tumors when used with endoscopic catheters.

  • Quality control during and post treatment

For example: The use of high intensity focused ultrasound (HIFU) combined with nanoparticle therapeutics: HIFU is applied to improve drug delivery and to trigger drug release from nanoparticles. Gas-bubbles are playing the role of the drug’s nano-carrier. These are used both to increase the drug transport into the cell and as ultrasound-imaging contrast material. The ultrasound is also used for processes of drug-release and ablation.

 HIFU

Additional example; Multifunctional nanoparticles for tracking CED (convection enhanced delivery)  distribution within tumors: Nanoparticle that could serve as a carrier not only for the therapeutic radionuclides but simultaneously also for a therapeutic drug and 4 different types of imaging contrast agents including an MRI contrast agent, PET and SPECT nuclear diagnostic imaging agents and optical contrast agents as shown below. The ability to perform multiple types of imaging on the same nanoparticles will allow studies investigating the distribution and retention of nanoparticles initially in vivo using non-invasive imaging and later at the histological level using optical imaging.

 multi

Conclusions

Image-guided radiotherapeutic nanoparticles have significant potential for solid tumor cancer therapy. The current success of this therapy in animals is most likely due to the improved accumulation, retention and dispersion of nanoparticles within solid tumor following image-guided therapies as well as the micro-field of the β-particle which reduces the requirement of perfectly homogeneous tumor coverage. It is also possible that the intratumoral distribution of nanoparticles may benefit from their uptake by intratumoral macrophages although more research is required to determine the importance of this aspect of intratumoral radionuclide nanoparticle therapy. This new approach to cancer therapy is a fertile ground for many new technological developments as well as for new understandings in the basic biology of cancer therapy. The clinical success of this approach will depend on progress in many areas of interdisciplinary research including imaging technology, nanoparticle technology, computer and robot assisted image-guided application of therapies, radiation physics and oncology. Close collaboration of a wide variety of scientists and physicians including chemists, nanotechnologists, drug delivery experts, radiation physicists, robotics and software experts, toxicologists, surgeons, imaging physicians, and oncologists will best facilitate the implementation of this novel approach to the treatment of cancer in the clinical environment. Image-guided nanoparticle therapies including those with β-emission radionuclide nanoparticles have excellent promise to significantly impact clinical cancer therapy and advance the field of drug delivery.

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Imaging-Biomarkers; from discovery to validation

Author: Dror Nir, PhD.

Preface

Recent technology advances such as miniaturization and improvement in electronic-processing components is driving increased introduction of innovative medical-imaging devices into critical nodes of major-diseases’ management pathways. Similarly, medical imaging bears outstanding potential to improve the process of drugs development and regulation (e.g. companion diagnostics and imaging surrogate markers. In; The Role of Medical Imaging in Personalized Medicine I discussed in length the role medical imaging assumes in drugs development.  Integrating imaging into drug development processes, specifically at the early stages of drug discovery, as well as for monitoring drug delivery and the response of targeted processes to the therapy is a growing trend. A nice (and short) review highlighting the processes, opportunities, and challenges of medical imaging in new drug development is: Medical imaging in new drug clinical development. An important aspect of drug development that is largely discussed is facilitating testing of the new drug through clinical studies. A major hurdle in development of many anti-cancer drugs is the long time that is required to determine the efficacy of the new drug through measurement of clinically meaningful endpoints; e.g. overall survival. Imaging is offering the opportunity to determine surrogate markers of clinical outcome (as a substitute for a clinically meaningful endpoints). The need for surrogate outcome markers is especially great with newer agents that may act by tumour stabilization as opposed to shrinkage.

To comply with current trends; e.g. personalized medicine and evidence-based medicine, medical imaging must support quantification of meaningful pathological phenomena; e.g. morphological deformations, enhanced/reduced chemical reactions, presence/absence of biological substances etc….

 

Two examples: 

Molecular imaging (e.g. PET, MRS) allows the visual representation, characterization, and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In oncology, it can be used to depict the abnormal molecules as well as the aberrant interactions of altered molecules on which cancers depend. An established biological process is neoplastic angiogenesis is associated with a number of detectable changes at molecular and microcirculatory levels. In Positron emission tomographic imaging of angiogenesis and vascular function the authors are offering that direct study of angiogenic molecular biology and tumour circulation before during and after treatment may offer useful surrogate markers for vascular-targeted therapies. The paper reviews two main areas: (a) the methodology behind PET imaging of tumour blood supply with 15O-oxygen labelled compounds; and (b) newer tracers in development as markers of angiogenetic biology.

A largely sought-for application for medical imaging is Monitoring quality of surgery: Cancer patients could benefit from a surgical procedure that helps the surgeon to determine adequate tumor resection margins. Variety of applications and work-flows; e.g. Systemic injection of tumor-specific fluorescence agents with subsequent intraoperative optical imaging to guide the surgeon in the process are offered. Recently, in order to overcome the problem of tumor heterogeneity it was proposed to shift the focus of tumor targeting towards the follicle-stimulating hormone receptor (FSHR).

Imaging bio-markers

Being able to discover and clinically validate fundamental finger-prints of cancer which can be detected and quantified through medical-imaging modalities is key to transforming the potential presented by medical imaging into clinical reality. Such specific finger-prints/characteristics are usually referred to as imaging bio-markers.

A critical step in the discovery and validation of imaging bio-markers is the matching of tissue location as depicted by imaging-products (most commonly images) to their histology, as underlined by a pathologist under the microscope.

Since histology requires extraction of organ tissue and some processing, it is impossible to achieve such matching in real time. Therefore, different techniques were developed to support the retrospective matching between histology and imaging. The most prevalent one rely on image registration: i.e. the products of medical imaging are registered to images of pathology slides. The main limitation of such methods has to do with:

  1. The fact that the two images poses largely different image resolution.
  2. The form-factor (shape and dimensions) of Histological tissue-slides are distorted in comparison to their in-vivo state.
  3. Histology-reading is subjective; i.e. the concordance between readings of different pathologist is far from being satisfactory. It gets worse when it comes to staging of the cancer.
  4. There is large variation in the quality of medical imaging products.

A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology presents a robust methodology validating imaging biomarkers in the case of prostate cancer. In this paper we describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. We hypothesized that integration of image registration principles into the histological workflow for radical prostatectomy specimens would increase the alignment accuracy. In this post I will include only few excerpts from this paper which I strongly recommend to read in full.

Materials and Methods

Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. The basic requirements of image registration were incorporated within the pathological protocol.

We demonstrate that the use of a simple, custom-made tissue-planer to slice the formalin-fixed prostate results in more uniform and parallel tissue blocks than conventional freehand techniques, and increases the accuracy of image alignment.  We also show that accounting for dimensional change due to formalin fixation is essential during image alignment.

Figure 1: Suggested workflow for registration of scanned histopathological data with radiological imaging

 fig1

 Figure 3

A sketch of the tissue cutting device is shown (A).  The formalin-fixed prostate was placed on the space marked “X” on the device with its flat posterior surface facing down.  With the probe in the urethra to align the AP axis with the device, the base of the gland was gently pressed onto “Y”.  The probe was then removed, and a mounted microtome blade was lowered along the 4mm raised edge of the device from top to bottom to cut away the block (B).  The sliced block was put aside with its apical face facing down, and the process was repeated by gently pressing the cut surface flush against the device before each cut (C).  The thickness of each block was measured in 5 locations marked (D).

fig3

Results

Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P < .0001), with higher sensitivity (85% vs. 69%) and specificity (94% vs. 73%) for margin prediction in a 5 × 5-mm grid analysis.

Figure 5. Assessment of alignment accuracy between radiological images and pathological sections

The method of assessing alignment accuracy between radiological images and pathological slides is shown using an example.  Each square within the grids overlaid onto histology and radiological images were scored either as a “1”, indicating the presence of a histological or radiological margin, respectively, or “0”.  Scored pathology grids were used as the reference, and scored radiology grids were used as the index.  Hence, we determined true positives i.e. grid points score “1” in both histology and radiology (yellow squares, n=25), false positives i.e. grid points on the radiology scores “1” but not on histology (green squares, n=4), false negatives i.e. grid points on the histology scores “0” but not on radiology (red squares, n=3), and true negatives (grey squares, n=38).

 fig5

Conclusions

A significantly better alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow.

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Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation: a Compilation of Articles in the Journal http://pharmaceuticalintelligence.com

Compilation of References by Leaders in Pharmaceutical Business Intelligence in the Journal http://pharmaceuticalintelligence.com about
Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation

Curator: Larry H Bernstein, MD, FCAP

Proteomics

  1. The Human Proteome Map Completed

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

http://pharmaceuticalintelligence.com/2014/08/28/the-human-proteome-map-completed/

  1. Proteomics – The Pathway to Understanding and Decision-making in Medicine

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/06/24/proteomics-the-pathway-to-
understanding-and-decision-making-in-medicine/

3. Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/10/22/advances-in-separations-technology-for-the-omics-and-clarification-         of-therapeutic-targets/

  1. Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-                metabolome/

5. Genomics, Proteomics and standards

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/06/genomics-proteomics-and-standards/

6. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

 

Metabolomics

  1. Extracellular evaluation of intracellular flux in yeast cells

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2014/08/25/extracellular-evaluation-of-intracellular-flux-in-yeast-cells/

  1. Metabolomic analysis of two leukemia cell lines. I.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2014/08/23/metabolomic-analysis-of-two-leukemia-cell-lines-_i/

  1. Metabolomic analysis of two leukemia cell lines. II.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2014/08/24/metabolomic-analysis-of-two-leukemia-cell-lines-ii/

  1. Metabolomics, Metabonomics and Functional Nutrition: the next step in nutritional metabolism and biotherapeutics

Reviewer and Curator, Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/22/metabolomics-metabonomics-and-functional-nutrition-the-next-step-          in-nutritional-metabolism-and-biotherapeutics/

  1. Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

http://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle-              metabolism-provides-homeomeostatic-regulation/

Metabolic Pathways

  1. Pentose Shunt, Electron Transfer, Galactose, more Lipids in brief

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

http://pharmaceuticalintelligence.com/2014/08/21/pentose-shunt-electron-transfer-galactose-more-lipids-in-brief/

  1. Mitochondria: More than just the “powerhouse of the cell”

Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2012/07/09/mitochondria-more-than-just-the-powerhouse-of-the-cell/

  1. Mitochondrial fission and fusion: potential therapeutic targets?

Ritu saxena

http://pharmaceuticalintelligence.com/2012/10/31/mitochondrial-fission-and-fusion-potential-therapeutic-target/

4.  Mitochondrial mutation analysis might be “1-step” away

Ritu Saxena

http://pharmaceuticalintelligence.com/2012/08/14/mitochondrial-mutation-analysis-might-be-1-step-away/

  1. Selected References to Signaling and Metabolic Pathways in PharmaceuticalIntelligence.com

Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/14/selected-references-to-signaling-and-metabolic-pathways-in-                     leaders-in-pharmaceutical-intelligence/

  1. Metabolic drivers in aggressive brain tumors

Prabodh Kandal, PhD

http://pharmaceuticalintelligence.com/2012/11/11/metabolic-drivers-in-aggressive-brain-tumors/

  1. Metabolite Identification Combining Genetic and Metabolic Information: Genetic association links unknown metabolites to functionally related genes

Writer and Curator, Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/10/22/metabolite-identification-combining-genetic-and-metabolic-                        information-genetic-association-links-unknown-metabolites-to-functionally-related-genes/

  1. Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation

Larry H Bernstein, MD, FCAP, author and curator

http://pharmaceuticalintelligence.com/2012/09/26/mitochondria-origin-from-oxygen-free-environment-role-in-aerobic-            glycolysis-metabolic-adaptation/

  1. Therapeutic Targets for Diabetes and Related Metabolic Disorders

Reporter, Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/08/20/therapeutic-targets-for-diabetes-and-related-metabolic-disorders/

10.  Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

http://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle-              metabolism-provides-homeomeostatic-regulation/

11. The multi-step transfer of phosphate bond and hydrogen exchange energy

Larry H. Bernstein, MD, FCAP, Curator:

http://pharmaceuticalintelligence.com/2014/08/19/the-multi-step-transfer-of-phosphate-bond-and-hydrogen-                          exchange-energy/

12. Studies of Respiration Lead to Acetyl CoA

http://pharmaceuticalintelligence.com/2014/08/18/studies-of-respiration-lead-to-acetyl-coa/

13. Lipid Metabolism

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

http://pharmaceuticalintelligence.com/2014/08/15/lipid-metabolism/

14. Carbohydrate Metabolism

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

http://pharmaceuticalintelligence.com/2014/08/13/carbohydrate-metabolism/

15. Update on mitochondrial function, respiration, and associated disorders

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

http://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated-                   disorders/

16. Prologue to Cancer – e-book Volume One – Where are we in this journey?

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

http://pharmaceuticalintelligence.com/2014/04/13/prologue-to-cancer-ebook-4-where-are-we-in-this-journey/

17. Introduction – The Evolution of Cancer Therapy and Cancer Research: How We Got Here?

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

http://pharmaceuticalintelligence.com/2014/04/04/introduction-the-evolution-of-cancer-therapy-and-cancer-research-          how-we-got-here/

18. Inhibition of the Cardiomyocyte-Specific Kinase TNNI3K

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

http://pharmaceuticalintelligence.com/2013/11/01/inhibition-of-the-cardiomyocyte-specific-kinase-tnni3k/

19. The Binding of Oligonucleotides in DNA and 3-D Lattice Structures

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

http://pharmaceuticalintelligence.com/2013/05/15/the-binding-of-oligonucleotides-in-dna-and-3-d-lattice-structures/

20. Mitochondrial Metabolism and Cardiac Function

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

http://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-metabolism-and-cardiac-function/

21. How Methionine Imbalance with Sulfur-Insufficiency Leads to Hyperhomocysteinemia

Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/04/04/sulfur-deficiency-leads_to_hyperhomocysteinemia/

22. AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Author and Curator: Stephen J. Williams, PhD

http://pharmaceuticalintelligence.com/2013/03/12/ampk-is-a-negative-regulator-of-the-warburg-effect-and-suppresses-         tumor-growth-in-vivo/

23. A Second Look at the Transthyretin Nutrition Inflammatory Conundrum

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

http://pharmaceuticalintelligence.com/2012/12/03/a-second-look-at-the-transthyretin-nutrition-inflammatory-                         conundrum/

24. Mitochondrial Damage and Repair under Oxidative Stress

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

http://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

25. Nitric Oxide and Immune Responses: Part 2

Author and Curator: Aviral Vatsa, PhD, MBBS

http://pharmaceuticalintelligence.com/2012/10/28/nitric-oxide-and-immune-responses-part-2/

26. Overview of Posttranslational Modification (PTM)

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

http://pharmaceuticalintelligence.com/2014/07/29/overview-of-posttranslational-modification-ptm/

27. Malnutrition in India, high newborn death rate and stunting of children age under five years

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

http://pharmaceuticalintelligence.com/2014/07/15/malnutrition-in-india-high-newborn-death-rate-and-stunting-of-                   children-age-under-five-years/

28. Update on mitochondrial function, respiration, and associated disorders

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

http://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated-                  disorders/

29. Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/06/omega-3-fatty-acids-depleting-the-source-and-protein-insufficiency-         in-renal-disease/

30. Introduction to e-Series A: Cardiovascular Diseases, Volume Four Part 2: Regenerative Medicine

Larry H. Bernstein, MD, FCAP, writer, and Aviva Lev- Ari, PhD, RN

http://pharmaceuticalintelligence.com/2014/04/27/larryhbernintroduction_to_cardiovascular_diseases-                                  translational_medicine-part_2/

31. Epilogue: Envisioning New Insights in Cancer Translational Biology
Series C: e-Books on Cancer & Oncology

Author & Curator: Larry H. Bernstein, MD, FCAP, Series C Content Consultant

http://pharmaceuticalintelligence.com/2014/03/29/epilogue-envisioning-new-insights/

32. Ca2+-Stimulated Exocytosis:  The Role of Calmodulin and Protein Kinase C in Ca2+ Regulation of Hormone                         and Neurotransmitter

Writer and Curator: Larry H Bernstein, MD, FCAP and
Curator and Content Editor: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/12/23/calmodulin-and-protein-kinase-c-drive-the-ca2-regulation-of-                    hormone-and-neurotransmitter-release-that-triggers-ca2-stimulated-exocy

33. Cardiac Contractility & Myocardial Performance: Therapeutic Implications of Ryanopathy (Calcium Release-                           related Contractile Dysfunction) and Catecholamine Responses

Author, and Content Consultant to e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC
Author and Curator: Larry H Bernstein, MD, FCAP
and Article Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/08/28/cardiac-contractility-myocardium-performance-ventricular-arrhythmias-      and-non-ischemic-heart-failure-therapeutic-implications-for-cardiomyocyte-ryanopathy-calcium-release-related-                    contractile/

34. Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

Author and Curator: Larry H Bernstein, MD, FCAP Author: Stephen Williams, PhD, and Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/08/26/role-of-calcium-the-actin-skeleton-and-lipid-structures-in-signaling-and-cell-motility/

35. Identification of Biomarkers that are Related to the Actin Cytoskeleton

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2012/12/10/identification-of-biomarkers-that-are-related-to-the-actin-                           cytoskeleton/

36. Advanced Topics in Sepsis and the Cardiovascular System at its End Stage

Author: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/08/18/advanced-topics-in-Sepsis-and-the-Cardiovascular-System-at-its-              End-Stage/

37. The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

Demet Sag, PhD, Author and Curator

http://pharmaceuticalintelligence.com/2013/08/04/the-delicate-connection-ido-indolamine-2-3-dehydrogenase-and-               immunology/

38. IDO for Commitment of a Life Time: The Origins and Mechanisms of IDO, indolamine 2, 3-dioxygenase

Demet Sag, PhD, Author and Curator

http://pharmaceuticalintelligence.com/2013/08/04/ido-for-commitment-of-a-life-time-the-origins-and-mechanisms-of-             ido-indolamine-2-3-dioxygenase/

39. Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Homeostasis of Immune Responses for Good and Bad

Curator: Demet Sag, PhD, CRA, GCP

http://pharmaceuticalintelligence.com/2013/07/31/confined-indolamine-2-3-dehydrogenase-controls-the-hemostasis-           of-immune-responses-for-good-and-bad/

40. Signaling Pathway that Makes Young Neurons Connect was discovered @ Scripps Research Institute

Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/06/26/signaling-pathway-that-makes-young-neurons-connect-was-                     discovered-scripps-research-institute/

41. Naked Mole Rats Cancer-Free

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

http://pharmaceuticalintelligence.com/2013/06/20/naked-mole-rats-cancer-free/

42. Late Onset of Alzheimer’s Disease and One-carbon Metabolism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

http://pharmaceuticalintelligence.com/2013/05/06/alzheimers-disease-and-one-carbon-metabolism/

43. Problems of vegetarianism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

http://pharmaceuticalintelligence.com/2013/04/22/problems-of-vegetarianism/

44.  Amyloidosis with Cardiomyopathy

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

http://pharmaceuticalintelligence.com/2013/03/31/amyloidosis-with-cardiomyopathy/

45. Liver endoplasmic reticulum stress and hepatosteatosis

Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/03/10/liver-endoplasmic-reticulum-stress-and-hepatosteatosis/

46. The Molecular Biology of Renal Disorders: Nitric Oxide – Part III

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/the-molecular-biology-of-renal-disorders/

47. Nitric Oxide Function in Coagulation – Part II

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

http://pharmaceuticalintelligence.com/2012/11/26/nitric-oxide-function-in-coagulation/

48. Nitric Oxide, Platelets, Endothelium and Hemostasis

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/08/nitric-oxide-platelets-endothelium-and-hemostasis/

49. Interaction of Nitric Oxide and Prostacyclin in Vascular Endothelium

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/09/14/interaction-of-nitric-oxide-and-prostacyclin-in-vascular-endothelium/

50. Nitric Oxide and Immune Responses: Part 1

Curator and Author:  Aviral Vatsa PhD, MBBS

http://pharmaceuticalintelligence.com/2012/10/18/nitric-oxide-and-immune-responses-part-1/

51. Nitric Oxide and Immune Responses: Part 2

Curator and Author:  Aviral Vatsa PhD, MBBS

http://pharmaceuticalintelligence.com/2012/10/28/nitric-oxide-and-immune-responses-part-2/

52. Mitochondrial Damage and Repair under Oxidative Stress

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

53. Is the Warburg Effect the cause or the effect of cancer: A 21st Century View?

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/10/17/is-the-warburg-effect-the-cause-or-the-effect-of-cancer-a-21st-                 century-view/

54. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                  proteolysis-and-cell-apoptosis/

55. Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/02/14/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                   proteolysis-and-cell-apoptosis-reconsidered/

56. Nitric Oxide and iNOS have Key Roles in Kidney Diseases – Part II

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/nitric-oxide-and-inos-have-key-roles-in-kidney-diseases/

57. New Insights on Nitric Oxide donors – Part IV

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/new-insights-on-no-donors/

58. Crucial role of Nitric Oxide in Cancer

Curator and Author: Ritu Saxena, Ph.D.

http://pharmaceuticalintelligence.com/2012/10/16/crucial-role-of-nitric-oxide-in-cancer/

59. Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/09/16/nitric-oxide-has-a-ubiquitous-role-in-the-regulation-of-glycolysis-with-         a-concomitant-influence-on-mitochondrial-function/

60. Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

Curator and Author: Ziv Raviv, PhD, RN 04/06/2013

http://pharmaceuticalintelligence.com/2013/04/06/targeting-mitochondrial-bound-hexokinase-for-cancer-therapy/

61. Biochemistry of the Coagulation Cascade and Platelet Aggregation – Part I

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/biochemistry-of-the-coagulation-cascade-and-platelet-aggregation/

Genomics, Transcriptomics, and Epigenetics

  1. What is the meaning of so many RNAs?

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

http://pharmaceuticalintelligence.com/2014/08/06/what-is-the-meaning-of-so-many-rnas/

  1. RNA and the transcription the genetic code

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

http://pharmaceuticalintelligence.com/2014/08/02/rna-and-the-transcription-of-the-genetic-code/

  1. A Primer on DNA and DNA Replication

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

http://pharmaceuticalintelligence.com/2014/07/29/a_primer_on_dna_and_dna_replication/

4. Synthesizing Synthetic Biology: PLOS Collections

Reporter: Aviva Lev-Ari

http://pharmaceuticalintelligence.com/2012/08/17/synthesizing-synthetic-biology-plos-collections/

5. Pathology Emergence in the 21st Century

Author and Curator: Larry Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/03/pathology-emergence-in-the-21st-century/

6. RNA and the transcription the genetic code

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

http://pharmaceuticalintelligence.com/2014/08/02/rna-and-the-transcription-of-the-genetic-code/

7. A Great University engaged in Drug Discovery: University of Pittsburgh

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2014/07/15/a-great-university-engaged-in-drug-discovery/

8. microRNA called miRNA-142 involved in the process by which the immature cells in the bone  marrow give                              rise to all the types of blood cells, including immune cells and the oxygen-bearing red blood cells

Aviva Lev-Ari, PhD, RN, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/24/microrna-called-mir-142-involved-in-the-process-by-which-the-                   immature-cells-in-the-bone-marrow-give-rise-to-all-the-types-of-blood-cells-including-immune-cells-and-the-oxygen-             bearing-red-blood-cells/

9. Genes, proteomes, and their interaction

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

http://pharmaceuticalintelligence.com/2014/07/28/genes-proteomes-and-their-interaction/

10. Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator    Aviva Lev-Ari, PhD, RN, Curator

http://pharmaceuticalintelligence.com/2014/07/29/regulation-of-somatic-stem-cell-function/

11. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

http://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in-           adult-organisms/

12. Bzzz! Are fruitflies like us?

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/07/bzzz-are-fruitflies-like-us/

13. Long Non-coding RNAs Can Encode Proteins After All

Larry H Bernstein, MD, FCAP, Reporter

http://pharmaceuticalintelligence.com/2014/06/29/long-non-coding-rnas-can-encode-proteins-after-all/

14. Michael Snyder @Stanford University sequenced the lymphoblastoid transcriptomes and developed an
allele-specific full-length transcriptome

Aviva Lev-Ari, PhD, RN, Author and Curator

http://pharmaceuticalintelligence.com/014/06/23/michael-snyder-stanford-university-sequenced-the-lymphoblastoid-            transcriptomes-and-developed-an-allele-specific-full-length-transcriptome/

15. Commentary on Biomarkers for Genetics and Genomics of Cardiovascular Disease: Views by Larry H                                     Bernstein, MD, FCAP

Author: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/07/16/commentary-on-biomarkers-for-genetics-and-genomics-of-                        cardiovascular-disease-views-by-larry-h-bernstein-md-fcap/

16. Observations on Finding the Genetic Links in Common Disease: Whole Genomic Sequencing Studies

Author an curator: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/05/18/observations-on-finding-the-genetic-links/

17. Silencing Cancers with Synthetic siRNAs

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2013/12/09/silencing-cancers-with-synthetic-sirnas/

18. Cardiometabolic Syndrome and the Genetics of Hypertension: The Neuroendocrine Transcriptome Control Points

Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/12/12/cardiometabolic-syndrome-and-the-genetics-of-hypertension-the-neuroendocrine-transcriptome-control-points/

19. Developments in the Genomics and Proteomics of Type 2 Diabetes Mellitus and Treatment Targets

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2013/12/08/developments-in-the-genomics-and-proteomics-of-type-2-diabetes-           mellitus-and-treatment-targets/

20. Loss of normal growth regulation

Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/06/loss-of-normal-growth-regulation/

21. CT Angiography & TrueVision™ Metabolomics (Genomic Phenotyping) for new Therapeutic Targets to Atherosclerosis

Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/11/15/ct-angiography-truevision-metabolomics-genomic-phenotyping-for-           new-therapeutic-targets-to-atherosclerosis/

22.  CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics & Computational Genomics

Genomics Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/30/cracking-the-code-of-human-life-the-birth-of-bioinformatics-                      computational-genomics/

23. Big Data in Genomic Medicine

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/12/17/big-data-in-genomic-medicine/

24. From Genomics of Microorganisms to Translational Medicine

Author and Curator: Demet Sag, PhD

http://pharmaceuticalintelligence.com/2014/03/20/without-the-past-no-future-but-learn-and-move-genomics-of-                      microorganisms-to-translational-medicine/

25. Summary of Genomics and Medicine: Role in Cardiovascular Diseases

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/01/06/summary-of-genomics-and-medicine-role-in-cardiovascular-diseases/

 26. Genomic Promise for Neurodegenerative Diseases, Dementias, Autism Spectrum, Schizophrenia, and Serious                      Depression

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/02/19/genomic-promise-for-neurodegenerative-diseases-dementias-autism-        spectrum-schizophrenia-and-serious-depression/

 27.  BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

Sudipta Saha, PhD

http://pharmaceuticalintelligence.com/2012/12/04/brca1-a-tumour-suppressor-in-breast-and-ovarian-cancer-functions-         in-transcription-ubiquitination-and-dna-repair/

28. Personalized medicine gearing up to tackle cancer

Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2013/01/07/personalized-medicine-gearing-up-to-tackle-cancer/

29. Differentiation Therapy – Epigenetics Tackles Solid Tumors

Stephen J Williams, PhD

      http://pharmaceuticalintelligence.com/2013/01/03/differentiation-therapy-epigenetics-tackles-solid-tumors/

30. Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment

     Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/17/mechanism-involved-in-breast-cancer-cell-growth-function-in-early-          detection-treatment/

31. The Molecular pathology of Breast Cancer Progression

Tilde Barliya, PhD

http://pharmaceuticalintelligence.com/2013/01/10/the-molecular-pathology-of-breast-cancer-progression

32. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-                   signatures-2/

33. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine –                                                       Part 1 (pharmaceuticalintelligence.com)

Aviva  Lev-Ari, PhD, RN

http://pharmaceuticalntelligence.com/2013/01/13/paradigm-shift-in-human-genomics-predictive-biomarkers-and-personalized-medicine-part-1/

34. LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer                                         Personalized Treatment: Part 2

A Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-       drug-selection-in-cancer-personalized-treatment-part-2/

35. Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-        research-part-3/

36. Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of                           Cancer Scientific Leaders @http://pharmaceuticalintelligence.com

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/13/7000/Harnessing_Personalized_Medicine_for_ Cancer_Management-      Prospects_of_Prevention_and_Cure/

37.  GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico
effect of the inhibitor in its “virtual clinical trial”

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/11/14/gsk-for-personalized-medicine-using-cancer-drugs-needs-alacris-             systems-biology-model-to-determine-the-in-silico-effect-of-the-inhibitor-in-its-virtual-clinical-trial/

38. Personalized medicine-based cure for cancer might not be far away

Ritu Saxena, PhD

  http://pharmaceuticalintelligence.com/2012/11/20/personalized-medicine-based-cure-for-cancer-might-not-be-far-away/

39. Human Variome Project: encyclopedic catalog of sequence variants indexed to the human genome sequence

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/11/24/human-variome-project-encyclopedic-catalog-of-sequence-variants-         indexed-to-the-human-genome-sequence/

40. Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/10/inspiration-from-dr-maureen-cronins-achievements-in-applying-                genomic-sequencing-to-cancer-diagnostics/

41. The “Cancer establishments” examined by James Watson, co-discoverer of DNA w/Crick, 4/1953

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/09/the-cancer-establishments-examined-by-james-watson-co-discover-         of-dna-wcrick-41953/

42. What can we expect of tumor therapeutic response?

Author and curator: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/12/05/what-can-we-expect-of-tumor-therapeutic-response/

43. Directions for genomics in personalized medicine

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

http://pharmaceuticalintelligence.com/2013/01/27/directions-for-genomics-in-personalized-medicine/

44. How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis.

Stephen J Williams, PhD

http://pharmaceuticalintelligence.com/2012/10/31/how-mobile-elements-in-junk-dna-prote-cancer-part1-transposon-            mediated-tumorigenesis/

45. mRNA interference with cancer expression

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

 http://pharmaceuticalintelligence.com/2012/10/26/mrna-interference-with-cancer-expression/

46. Expanding the Genetic Alphabet and linking the genome to the metabolome

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-               metabolome/

47. Breast Cancer, drug resistance, and biopharmaceutical targets

Author and Curator: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/09/18/breast-cancer-drug-resistance-and-biopharmaceutical-targets/

48.  Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression                            Analysis

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/12/24/breast-cancer-genomic-profiling-to-predict-survival-combination-of-           histopathology-and-gene-expression-analysis

49. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva  Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-                   signatures-2/

50. Genomic Analysis: FLUIDIGM Technology in the Life Science and Agricultural Biotechnology

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/08/22/genomic-analysis-fluidigm-technology-in-the-life-science-and-                   agricultural-biotechnology/

51. 2013 Genomics: The Era Beyond the Sequencing Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2013_Genomics

52. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/Paradigm Shift in Human Genomics_/

Signaling Pathways

  1. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

  1. A Synthesis of the Beauty and Complexity of How We View Cancer:
    Cancer Volume One – Summary

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

http://pharmaceuticalintelligence.com/2014/03/26/a-synthesis-of-the-beauty-and-complexity-of-how-we-view-cancer/

  1. Recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes in
    serous endometrial tumors

Sudipta Saha, PhD

http://pharmaceuticalintelligence.com/2012/11/19/recurrent-somatic-mutations-in-chromatin-remodeling-ad-ubiquitin-           ligase-complex-genes-in-serous-endometrial-tumors/

4.  Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition

Stephen J Williams, PhD

http://pharmaceuticalintelligence.com/2012/11/30/histone-deacetylase-inhibitors-induce-epithelial-to-mesenchymal-              transition-in-prostate-cancer-cells/

5. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Author and Curator: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                   proteolysis-and-cell-apoptosis/

6. Signaling and Signaling Pathways

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2014/08/12/signaling-and-signaling-pathways/

7.  Leptin signaling in mediating the cardiac hypertrophy associated with obesity

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/11/03/leptin-signaling-in-mediating-the-cardiac-hypertrophy-associated-            with-obesity/

  1. Sensors and Signaling in Oxidative Stress

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/11/01/sensors-and-signaling-in-oxidative-stress/

  1. The Final Considerations of the Role of Platelets and Platelet Endothelial Reactions in Atherosclerosis and Novel
    Treatments

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/10/15/the-final-considerations-of-the-role-of-platelets-and-platelet-                      endothelial-reactions-in-atherosclerosis-and-novel-treatments

10.   Platelets in Translational Research – Part 1

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/10/07/platelets-in-translational-research-1/

11.  Disruption of Calcium Homeostasis: Cardiomyocytes and Vascular Smooth Muscle Cells: The Cardiac and
Cardiovascular Calcium Signaling Mechanism

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to e-SERIES A:
Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/09/12/disruption-of-calcium-homeostasis-cardiomyocytes-and-vascular-             smooth-muscle-cells-the-cardiac-and-cardiovascular-calcium-signaling-mechanism/

12. The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and
Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia,
Similarities and Differences, and Pharmaceutical Targets

     Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to
e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and
Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/09/08/the-centrality-of-ca2-signaling-and-cytoskeleton-involving-calmodulin-       kinases-and-ryanodine-receptors-in-cardiac-failure-arterial-smooth-muscle-post-ischemic-arrhythmia-similarities-and-           differen/

13.  Nitric Oxide Signalling Pathways

Aviral Vatsa, PhD, MBBS

http://pharmaceuticalintelligence.com/2012/08/22/nitric-oxide-signalling-pathways/

14. Immune activation, immunity, antibacterial activity

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/06/immune-activation-immunity-antibacterial-activity/

15.  Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator    Aviva Lev-Ari, PhD, RN, Curator

http://pharmaceuticalintelligence.com/2014/07/29/regulation-of-somatic-stem-cell-function/

16. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

http://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in-adult-organisms/

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Genomics, Proteomics and standards

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence/7/6/2014/Genomics, Proteomics and standards

This article is a look at where the biomedical research sciences are in developing standards for development in the near term.

 

Let’s Not Wait for the FDA: Raising the Standards of Biomarker Development – A New Series

published by Theral Timpson on Tue, 07/01/2014 – 15:03

We talk a lot on this show about the potential of personalized medicine. Never before have we learned at such breakneck speed just how our bodies function. The pace of biological research staggers the mind and hints at a time when we will “crack the code” of the system that is homo sapiens, going from picking the low hanging fruit to a more rational approach. The high tech world has put at the fingertips of biologists just the tools to do it. There is plenty of compute, plenty of storage available to untangle, or decipher the human body. Yet still, we talk of potential.

Chat with anyone heavily involved in the life science industry–be it diagnostics or pharma– and you’ll quickly hear that we must have better biomarkers.

Next week we launch a series, Let’s Not Wait for the FDA: Raising the Standards of Biomarker Development, where we will pursue the “hotspots” that are haunting those in the field.

The National Biomarker Development Alliance (NBDA) is a non profit organization based at Arizona State University and led by the formidable Anna Barker, former deputy director of the NCI. The aim of the NBDA is to identify problem areas in biomarker development–from the biospecimen and sampling issues to experiment design to bioinformatics challenges–and raise the standards in each area. This series of interviews is based on their approach. We will purse each of these topics with a special guest.

The place to start is with samples. The majority of researchers who are working on biomarker assays don’t give much thought to the “story” of their samples. Yet the quality of their research will never exceed the quality of the samples with which they start–a very scary thought according toCarolyn Compton, a former pathologist, now professor of pathology at ASU and Johns Hopkins. Carolyn worked originally as a clinical pathologist and knows first hand the the issues around sample degradation. She left the clinic when she was recruited to the NCI with the mission of bringing more awareness to the issue of bio specimens. She joins us as our first guest in the series.

That Carolyn has straddled the world of the clinic and the world of research is key to her message. And it’s key to this series. As we see an increased push to “translate” research into clinical applications, we find that these two worlds do not work enough together.

Researchers spend a lot of time analyzing data and developing causal relationships from certain biological molecules to a disease. But how often do these researchers consider how the history of a sample might be altering their data?

“Garbage in, garbage out,” says Carolyn, who links low quality samples with the abysmal non-reproducable rate of most published research.

Two of our guests in the series have worked on the adaptive iSpy breast cancer trials. These are innovative clinical trials that have been designed to “adapt” to the specific biology of those in the trial. Using the latest advances in genetics, the iSPY trials aim to match experimental drugs with the molecular makeup of tumors most likely to respond to them. And the trials are testing multiple drugs at once.

Don Berry is known for bringing statistics to clinical trials. He designed the iSpy trials and joins us to explain how these new trials work and of the promise of the adaptive design.

Laura Esserman is the director of the breast cancer center at UCSC and has been heavily involved in the implementation of the iSpy trials. Esserman is concerned that “if we keep doing conventional clinical trials, people are going to give up on doing them.” An MBA as well as an MD, Esserman brings what she learned about innovation in the high-tech industry to treatment for breast cancer.

From there we turn to the topic of “systems biology” where we will chat with George Poste, a tour de force when it comes to considering all of the various aspects of biology. Anyone who has ever been present for one of George’s presentations has no doubt come away scratching your head wondering if we’ll ever really glimpse the whole system that is a human being. If there is one brain that has seen all the rooms and hallways of our complex system, it’s George Poste.

We’ll finish the series by interviewing David Haussler from UCSC of Genome Browser fame. Recently Haussler has worked extensively on an NCI project, The Cancer Genome Atlas, to bring together data sets and connect cancer researchers around the world. What is the promise and pitfalls David sees with the latest bioinformatics tools?

George Poste says that in the literature we have identified 150,000 biomarkers that have causal linkage to disease. Yet only 100 of these have been commercialized and are used in the clinic. Why is the number so low? We hope to come up with some answers in this series.

 

 

Why Hasn’t Clinical Genetics Taken Off? (part 2)

published by Sultan Meghji on Fri, 06/20/2014 – 14:49

 

In my previous post, I made the broad comment that education of the patient and front line doctors was the single largest barrier to entry for clinical genetics. Here I look at the steps in the scientific process and where the biggest opportunities lie:

The Sequencing (still)

PCR is a perfectly reasonable technology for sequencing in the research lab today, but the current configuration of technologies need to change. We need to move away from an expert level skill set and a complicated chemistry process in the lab to a disposable, consumer friendly set of technologies. I’m not convinced PCR is the right technology for that and would love to see nanopore be a serious contender, but lack of funding for a broad spectrum of both physics-only as well as physical-electrical startups have slowed the progress of these technologies. And waiting in the wings, other technologies are spinning up in research labs around the world. Price is no longer a serious problem in the space – reliable, repeatable, easy to use sequencing technologies are. The complexity of the current technology (both in terms of sample preparation and machine operation) is a big hurdle.

The Analysis (compute)

Over the last few years, quite a bit of commentary and effort has been put into making the case that the compute is a significant challenge (including more than a few comments by yours truly in that vein!). Today, it can be said with total confidence that compute is NOT a problem. Compute has been commoditized. Through excellent new software to advanced platforms and new hardware, it is a trivial exercise to do the analysis and costs tiny amounts of money ($<25 per sample on a cloud provider appears to be the going rate for a clinical exome in terms of platform & infrastructure cost). Integration with the sequencer and downstream medical middleware is the biggest opportunity.

The Analysis (value)

The bigger challenge on the analysis is the specific things being analyzed as mapped to the needs of the patient. We are still in a world where the vast majority of the sequencing work is being done in support of a specific patient with a specific disease. There isn’t even broad consensus yet in the scientific community about the basics of the pipeline (see my blog posthere for an attempt at capturing what I’m seeing in the market). A movement away from the recent trend in studying specific indications (esp. cancer) is called for. Broadening the sample population will allow us to pick simpler, clearer and easier pipelines which will then make them more adoptable. It would be a massive benefit to the world if the scientific, medical and regulatory communities would get together and start creating, in a crowdsourced manner, a small number of databases that are specifically useful to healthy people. Targeting things like nutrition, athletics, metabolism, and other normal aspects of daily life. A dataset that could, when any one person’s DNA is references, would find something useful. Including the regulators is key so that we can begin to move away from the old fashioned model of clearances that still permeate the industry.

The Regulators

Beyond the broader issues around education I referenced in my previous post, there is a massive upgrade in the regulation infrastructure that is needed. We still live in a world of fax machines, overnight shipping of paper documents and personal relationships all being more important than the quality of the science you as an innovator are bringing to bear.

Consider the recent massive growth in wearables, fitness trackers and other instrumentation local to the human body. Why must we treat clinical genetics simply as a diagnostic and not, as it should be, as a fundamental set of quantitative data about your body that you can leverage in a myriad of ways. Direct to consumer (DTC) genetics companies, most notably 23andme, have approached this problem poorly – instead of making it valuable to the average consumer, what they’ve done is attempted to straddle the line between medical and not. The Fitbit model has shown very clearly that lifestyle activities can be directly harnessed to build commercial value in scaling health related activities without becoming a regulatory issue. It’s time for genetics to do the same thing.

 

 

Development and Role of the Human Reference Sequence in Personal Genomics

Posted by @finchtalk on July 3, 2014

discovery in a digital world

 

 

 

A few weeks back, we published a review about the development and role of the human reference genome. A key point of the reference genome is that it is not a single sequence. Instead it is an assembly of consensus sequences that are designed to deal with variation in the human population and uncertainty in the data. The reference is a map and like a geographical maps evolves though increased understanding over time.

From the Wiley On Line site:

Abstract

Genome maps, like geographical maps, need to be interpreted carefully. Although maps are essential to exploration and navigation they cannot be completely accurate. Humans have been mapping the world for several millennia, but genomes have been mapped and explored for just a single century with the greatest advancements in making a sequence reference map of the human genome possible in the past 30 years. After the deoxyribonucleic acid (DNA) sequence of the human genome was completed in 2003, the reference sequence underwent several improvements and today provides the underlying comparative resource for a multitude genetic assays and biochemical measurements. However, the ability to simplify genetic analysis through a single comprehensive map remains an elusive goal.

Key Concepts:

  • Maps are incomplete and contain errors.
  • DNA sequence data are interpreted through biochemical experiments or comparisons to other DNA sequences.
  • A reference genome sequence is a map that provides the essential coordinate system for annotating the functional regions of the genome and comparing differences between individuals’ genomes.
  • The reference genome sequence is always product of understanding at a set point in time and continues to evolve.
  • DNA sequences evolve through duplication and mutation and, as a result, contain many repeated sequences of different sizes, which complicates data analysis.
  • DNA sequence variation happens on large and small scales with respect to the lengths of the DNA differences to include single base changes, insertions, deletions, duplications and rearrangements.
  • DNA sequences within the human population undergo continual change and vary highly between individuals.
  • The current reference genome sequence is a collection of sequences, an assembly, that include sequences assembled into chromosomes, sequences that are part of structurally complex regions that cannot be assembled, patches (fixes) that cannot be included in the primary sequence, and high variability sequences that are organised into alternate loci.
  • Genetic analysis is error prone and the data require validation because the methods for collecting DNA sequences create artifacts and the reference sequence used for comparative analyses is incomplete.

Keywords:DNA sequencing

 

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Genomics and Medicine: The Physician’s View

Genomics and Medicine: The Physician’s View

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

 

Genomics has had a rapid growth of research into variability of human genetics in both healthy populations in the study of population migration, and in the study of genetic sequence alterations that may increase the risk of expressed human disease.  This is the case for cardiology, cancer, inflammtory conditions, and gastrointestinal diseases. For the most part, genomics research in the last decade has shed light on potential therapeutic targets, but the identification of drug toxicities in late phase trials has been associated with a 70 percent failure rate in bringing new drugs to the market.   Despite good technologies for investigative studies, initial work is carried out on animals and then the transferrability of the work from a “model” to man has to be assured.  That is the first issue of concern.

Secondly, there is a well considered reluctance on the part of experienced and well prepared physicians to be “early” adopters to newly introduced drugs, with the apprehension that unidentified clinical problems can be expected to be unmasked.  It is, however, easier to consider when a new drug belongs to an established class of medications, and it has removed known adverse effects.  In this case, the adverse effects are known side effects, but not necessarily serious drug reactions that would preclude use.

A third consideration is the cost of drug development, and the cost of development is passed on to the healthcare organization in the purchasing cost. We can rest assured that the Pharmacy and Therapeutics Review Committee will not cease meeting on a regular schedule anytime soon.  Further, how do the drug failures become embedded in the cost of the pharmaceutical budget passed on to the recipient.  Historically, insurance is an actuarial discipline.  But in the lifetime of an individual, they are bound to see a physician for acute or chronic medical attention.  Only the timing cannot be predicted.  As a result, dealing with the valid introduction of new medications is a big concern for both the public and the private insurer.

How does this compute for the physician provider.  The practice of medicine is not quickly adaptive, as the physician’s primary concern is to do no harm.   Genomics testing is not widely available, and it is for the most part not definitive for diagnostic purposes as things stand today.  It may provide assessment of risk, or of survival expectation.  The physician uses a step by step assessment, using the patient and family history, a focused physical exam, laboratory and radiology, proceeding to other more specialized exams.  Much of the laboratory testing is based on the appearance in the circulation of changes in blood chemistry of the nature of electrolytes, circulating cells in the blood and of the blood forming organ, proteins, urea and uric acid.  They are not exquisitely sensitive, but they might be sufficient for their abnormal concentrations appearing at the time the patient presents with a complaint. What tests are ordered is determioned by a need for relevant information to make a medical decision.

The relevant questions are:

1. acuity of symptoms and signs.
2. actions to be taken.
3. tests that are needed to clarify the examination findings.

once a provisional diagnosis is obtained, referrals, additional testing, and medication orders are provided based on the assessment.

Where does genetic testing fit into this? At this point, it will only be used

  1. to confirm a restricted list of diagnoses that have a high association with the condition, and
  2. only with the participation of a medical geneticist, when
  3. profiling the patient and other members of the family is required.

10d0de1 Vitruvian Man by Leonardo da Vinci

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Cancer Biomarkers for Companion Diagnostics

Author and Curator: Larry H Bernstein, MD, FCAP

 

Scientists from around the world gathered to share some of their newest biomarker research at the “Oncology Biomarkers Conference”.

Honing in on Cancer Biomarkers

Caitlin Smith
G
EN  15 Nov 2013; 33(20)

Introduction and Goals

Some of the newest cancer treatments aim to individualize the therapy to the specific type of cancer and patient. The large and growing number of different genetic alterations that researchers observe in cancer cells have made it unfeasible to test for only a handful of targets. Instead, clinical testing is moving toward testing for many targets simultaneously.

“This approach of multiplexed tumor genotyping allows for the simultaneous evaluation of a broad range of common and rare tumor alterations,” said Darrell Borger, Ph.D., director of biomarker and co-director of translational research laboratories at the Massachusetts General Hospital Cancer Center. “This is important for expanding the application of targeted therapy across a greater number of patients who undergo testing, and directing those patients into the most relevant clinical trials.”

Dr. Borger and colleagues are uncovering “molecular signatures of tumors,” or collections of targets present in specific tumor types. “A molecular signature of a tumor is in essence a map of the abnormalities within a particular tumor that are thought to be critical in driving the disease process,” said Dr. Borger. “We know that each tumor will have a unique combination of genetic alterations.”

These signatures are useful because the ability to genotype a certain kind of cancer can help find the most effective treatment possible. “The more comprehensive the tumor profiling, the more detailed the roadmap we can draw for directing that patient’s care,” Dr. Borger said.

Uncovering the molecular signatures of tumors has another important role—to better understand the differences among cells within the same tumor. “Tumor heterogeneity is an important mechanism of emerging drug resistance,” said Dr. Borger. “Broad-based tumor profiling and the use of sensitive testing platforms are essential in identifying these potential mechanisms of disease resistance, so that targeted approaches can be aimed at circumventing those mechanisms.”

Target Signaling

Also working to help physicians figure out which treatments among many might work best for individual patients is Selventa. Focusing on gene expression biomarkers, Selventa researchers correlate gene expression patterns from patient data with changes in target signaling mechanisms.

“We operate on the hypothesis that patients with high or low levels of target (or downstream target) pathway signaling correspond to potential responders or nonresponders to target therapy, respectively,” said Renée Deehan Kenney, Ph.D., vp of research. “If we know who responded and who did not respond to treatment, then we can use that information to hone the biomarker using machine-learning approaches.”

Selventa is using its Systems Diagnostics (SysDx) platform to identify biomarkers used in diagnosing immune disorders such as rheumatoid arthritis (RA). Their product Clarify-RA is based on the SysDx approach using a blood biomarker. It is designed to aid clinicians in matching RA patients with those RA drugs that will be most beneficial to them. Such matching is valuable because RA is a heterogeneous disease, but different patients respond differently to the over 15 RA drugs that are available. Moreover, RA is a debilitating disease that cannot wait for a trial-and-error treatment approach.

“To compound this clinical challenge, drugs approved for RA offer about 50% improvement for only 40% of the patients,” said Dr. Deehan Kenney. For example, one biomarker Selventa found can identify RA patients who are likely to respond to anti-TNF therapy. Similarly, Selventa’s SysDx approach also found a biomarker from tumor biopsy tissue that identifies ER+ breast cancer patients whose cancer tends to progress with tamoxifen treatment.

IHC-Based Testing

President and CEO of Precision Biologics, Philip Arlen, M.D., discussed his company’s research on a new monoclonal antibody (NPC-1C), which targets tumors in both pancreatic and colorectal cancer. The antibody’s target is specific to tumors, and the antibody has negligible reactions with normal tissue, he said.

Precision Biologics took an unconventional tack to making NPC-1C, using a cancer vaccine that had been developed from colorectal cancer tissue removed from patients with varying stages of disease. They screened for antibodies that were specific for tumors, but nonreactive with normal tissue.

In both cell cultures and in animal models, they found that NPC-1C destroyed pancreatic cancer cells. “Furthermore, we had very encouraging Phase I/IIa data demonstrating prolongation in overall survival in patients that had exhausted all standards of therapy,” said Dr. Arlen.

Precision Biologics has developed an immunohistochemistry-based diagnostic test for expression of NPC-1C’s target. “Patients’ tumors are tested, and if the target is present, the patients can receive treatment with NPC-1C,” said Dr. Arlen. “We are also developing a diagnostic assay with NPC-1C for early detection and prognosis of colorectal and pancreatic cancer.”

NMR Technology

LipoScience researchers using NMR technology to look for cancer biomarkers expect that panels of metabolites covering a range biochemical processes will need to be analyzed. They produced these 1H NMR spectra of unprocessed serum focusing on (A) macromolecular signals and (B) the small molecule metabolome.

LipoScience is also developing new ways to search for biomarkers. Specifically, to find biomarkers of clinical value, they are using NMR technology. “We take advantage of two of the key features of the NMR platform,” explained Thomas O’Connell, Ph.D., senior director of research and development. “These are the lack of required sample preparation for routine biofluids and the inherently quantitative signals.” This means that they can profile large sample sets very quickly.

LipoScience researchers are now using NMR to look for cancer biomarkers. “Given the heterogeneity of most cancers, it is not likely that a single biomarker will provide the necessary clinical performance,” said Dr. O’Connell, “so we are examining panels of metabolites that cover a range of biochemical processes, including lipid and lipoprotein metabolism, energy perturbations, inflammatory processes, and others.”

They plan to use NMR and metabolomic profiling to develop clinical assays that help to choose patient-specific therapies. “We are hopeful that one day in the near future, panels of biomarkers could provide clinicians with much more objective, quantifiable, and personalized information regarding the diagnosis and management of their patients,” added Dr. O’Connell.

Single Molecule Arrays

The Simoa (for single molecule array) instrument from Quanterix uses a digital ELISA technique, trapping fluorescent reaction product in indiv-idual wells, to speed blood testing for HIV.

Researchers at Quanterix have developed a method of testing for a different type of biomarker—one that indicates the early and acute (and most contagious) stage of HIV infection. Their method is faster, cheaper, and more sensitive than previous tests.

Previously, the gold standard HIV test with the highest sensitivity was nucleic acid testing, which detects viral genetic material. The new test from Quanterix, called Simoa for “single molecule arrays,” is a digital ELISA technique. Simoa works by preventing the sensitivity loss that can occur in conventional ELISAs because of the dilution of reaction product into the reaction volume. Simoa essentially miniaturizes the ELISA principle, trapping fluorescent reaction product in individual wells to prevent dilution.

“The technology basically supercharges a standard ELISA to give 1,000-times greater sensitivity,” said David Wilson, Ph.D., vp of product development. “Due to this extreme sensitivity of Simoa to enzyme label, label molecules can be reduced, which lowers nonspecific interactions and improves signal background. This drives the sensitivity of Simoa digital immunoassays down to the level of nucleic acid testing.”

Simoa assays are easily amenable to high-throughput fluidics instrumentation and automation. So Dr. Wilson hopes Simoa will be applied to HIV screening in blood banks, as well as other blood-borne viruses to which Quanterix is developing new Simoa assays. “A key need in many blood banking centers is high throughput,” Dr. Wilson said. “Blood units are screened for a number of pathogens, so effective throughput is measured in number of units processed in a given period of time.”

Simoa immunoassays can be multiplexed to test for up to 10 different target proteins simultaneously, which may benefit blood banks. However, blood banking is highly regulated, so introducing Simoa assays may take time. “As with any new test used to ensure a blood unit is pathogen-free,” explained Dr. Wilson, “a substantial amount of data is needed to prove to regulatory bodies that the test exhibits the claimed performance, and that the manufacturing processes are fully validated and controlled.”

Perhaps one day, it will be possible to detect biomarkers of viral infection, cancer, and other diseases for many people very quickly. Then, armed with the relevant information, healthcare providers will be able to fight disease more effectively.

 

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Cancer Biomarkers

Larry H Bernstein, MD, FCAP, Reporter    Reblog

Article ID #85: Cancer Biomarkers. Published on 11/18/2013

WordCloud Image Produced by Adam Tubman

http://pharmaceuticalintelligence.org/2013-11-17/larryhbern/cancer-biomarkers

Clinical Laboratory News Nov 2013;  39( 11)

  The Vicious Cycle of  Under-Valued Cancer Biomarkers

 Could Sweeping Changes Bring More Tests Into Clinical Practice?

By Genna Rollins

It’s a classic conundrum: biomarkers are essential to

  • diagnosing,
  • staging,
  • treating, and
  • monitoring cancer,

yet despite an explosion of research, only a trickle have made it into clinical practice. The factors behind this less-than-desirable circumstance are complex at best, but according to some observers, boil down to the healthcare system’s placing

  • more value on cancer therapeutics relative to biomarkers.

Without a better means of demonstrating the difference biomarkers make in clinical outcomes or management, they remain stuck in a loop of low value:

  1. inadequate funding for research that, in turn,
  2. limits the evidence for clinical utility,
  3. keeping their value low.

A panel of leading scholars, clinicians, and executives recently collaborated about this dilemma in the hopes of starting a national dialogue toward breaking what they call a vicious cycle. Their proposed solutions—as ambitious as the problem is convoluted—can be implemented if the industry has the will to do so, they contend.

“People don’t value tumor biomarkers. They value therapeutics. We all talk about personalized medicine but we don’t really mean it if we’re not willing to value biomarkers the way we value therapeutics,” said Daniel Hayes, MD, Stuart B. Padnos professor of breast cancer research and clinical director of the breast oncology program at the University of Michigan Comprehensive Cancer Center in Ann Arbor. “However,

  • if we insist on doing biomarker research the same way we do therapeutic research, it gets very expensive.

But without putting the kind of money and research into it that’s necessary to determine clinical utility, payers don’t want to pay as much for a diagnostic as a therapeutic, and we’re stuck in this vicious cycle.”

Hayes has been on the forefront of thinking about how to bring more clinically meaningful biomarkers into cancer care, and he was the lead author of the group’s commentary, which was published

  • in the July 31, 2013 issue of Science Translational Medicine (Sci Transl Med 2013;196:1–7).

 A Bad Track Record

Whether or not they concur with all elements of Hayes’ and his colleagues’ vicious cycle concept, many in the cancer field agree that biomarkers have an anemic batting average. The scientific literature is replete with reports of promising cancer biomarkers, but

  • fewer than two dozen protein tumor markers have been cleared by the Food and Drug Administration (FDA)—
  • only about half in the past decade—and not all have been embraced by clinicians.
  • The same is true of lab-developed tests (LDTs).

While some paradigm-shifting cancer biomarkers with obvious clinical utility have been implemented rapidly in practice, others—be they FDA-cleared or LDTs—never really have found a niche. An example of the latter is

  • UGT1A1 testing prior to starting irinotecan hydrochloride chemotherapy in colorectal cancer patients.

Individuals who are homozygous for the UGT1A1*28 allele are at increased risk for neutropenia when taking irinotecan, but this testing just hasn’t caught on, according to Hayes’ co-author, Richard L. Schilsky, MD, chief medical officer of the American Society of Clinical Oncology (ASCO). “Practically no oncologist orders the test because

  • it’s not clear what you’re supposed to do if you get a result back that shows your patient is high-risk.

There’s not a specific recommendation about whether you’re supposed to

  1. omit the drug,
  2. lower the dose,
  3. lower the dose by how much, and
  4. whether lowering the dose actually mitigates the side-effects and
  5. whether or not it actually reduces the effectiveness of the treatment,” he explained.

On the other end of the spectrum is KRAS genetic testing in metastatic colon cancer. After seminal research published in 2008 showed that

  • patients without this mutation were more likely to respond to anti-epidermal growth factor receptor (anti-EGFR) monoclonal antibody therapy,

the test, even as an LDT, quickly became the de facto standard-of-care.

“A wealth of data came out all at the same time, and almost overnight

  • oncologists started ordering KRAS testing and
  • stopped prescribing the relevant drugs for patients whose tumors had KRAS mutations,” recalled Schilsky.

“That was a clear example of where if the tumor has a mutation,

  1. the drug doesn’t work, and
  2. you shouldn’t give it.

That’s the kind of discrete information that oncologists are always looking for.”

The KRAS test also hit the medical economics jackpot:

  • one anti-EGFR agent, cetuximab, costs anywhere from $110,000–160,000 per year,
  • making an easy argument for reserving this treatment for patients most likely to benefit from it.

At the same time, the cost of KRAS testing, about $400, speaks to Hayes’ and his colleagues’ arguments about the vicious cycle. If the test has that much clinical impact, shouldn’t it be valued higher in the medical system?

  Is Drug Development a Model?

“The pharmaceutical industry

  • potentially could be a model for how to do biomarker validation and evidence generation.

But then we’d have to charge a whole lot more for the tests, which everybody sees as commodities right now,” said Hayes’ co-author Debra Leonard, MD, PhD, professor and chair of pathology at the University of Vermont College of Medicine in Burlington.

  1. “Payers pay the cost of doing the test, but they
  2. aren’t calculating in the cost of all that evidence generation.

That’s why drug companies can charge so much, because all the cost of generating evidence is built into the price of a drug when it comes onto the market. There’s also good evidence to say that it does or doesn’t work, and

  • that’s not the case for tests.”

To Leonard’s point about evidence, the authors cited one cause of the vicious cycle as how FDA regulates approvals for diagnostic tests (See Figure, below). The agency by statute does not have authority to require that

  • proposed tests show clinical utility by improving clinical outcomes,

but that is exactly what the authors would like to see. “In the current regulatory environment, many tumor-biomarker tests

  • enter the market with analytical and clinical validity but insufficient information to establish their impact on healthcare outcomes.
  • Thus, few of these tests are included in evidence-based guidelines,

leaving healthcare professionals or third-party payers unsure of whether and how to use the tests or how much to pay for them,” they wrote.

 Vicious to Virtuous

A. Vicious Cycle

B. Virtuous Cycle

(A) The vicious cycle of tumor-biomarker research and clinical utility.

(B) A proposed virtuous cycle of tumor-biomarker research and clinical utility based on proposals herein.

Used with permission of Science Translational Medicine

  Shaking Up the FDA

The authors proposed several solutions to this challenge, some more audacious than others. On the bold side, they suggested that

  • FDA reorganize how it reviews oncology products, consolidating now separate drug and diagnostic reviews into a single oncologic product line managed jointly by the respective drug and biomarker divisions;
    • in the case of the former, the Office of Hematology and Oncology Products in the Center for Drug Evaluation and Research, and
    • in the latter, the Office of In Vitro Diagnostics in the Center for Devices and Radiological Health
  • In the same vein,
    • the authors proposed that FDA approve or clear tests only with rigorous evidence of both clinical utility and analytical validity, using ASCO level 1 evidence criteria.

If those recommendations might be long-term goals, possibly even requiring Congressional approval, others seem more approachable, but perhaps no less controversial. One is that

  • FDA begins regulating LDTs.

This contentious topic, under review for more than 3 years at FDA, would, the authors suggest, subject all proposed tests to a risk-based review process, regardless of the manufacturer or commercialization strategy behind them. However, not even all the authors back the idea.

“I don’t believe we can do away with LDTs,” said Leonard. “If the FDA had a better mechanism for looking at LDTs in their risk-based system, that might be helpful. But I worry about everything having to go through FDA because of the slowness of the FDA process and the expense of using the FDA process. There also doesn’t seem to be any idea of how we’re going to get from where we are today to an FDA approval process that actually works.”

Leonard also expressed skepticism that the FDA approval process inherently produces better or more clinically useful tests than do LDTs. “The FDA process does not look at

  1. clinical utility, and there is no evidence that
  2. FDA-cleared or -approved tests do any better when
    • they get into clinical practice than ones that haven’t gone through the FDA process and are LDTs,” she said,

citing the Health and Human Services Secretary’s Advisory Committee on Genetics, Health, and Society, which, in its 2008 report on the U.S. system of overseeing genetic testing found

  • a “paucity” of information about the clinical utility of genetic testing.

Other researchers who have thought about how to speed up the biomarker pipeline also find this recommendation troubling. “Basically eliminating LDTs, especially if this were not accompanied by a prior increase in reimbursement and research dollars, would be extremely negative,” said Leigh Anderson, PhD, CEO of Washington, D.C.-based SISCAPA Assay Technologies. “I’m involved in collaborative work with a number of groups trying to develop new tests mainly in the cancer area and I don’t think any of them would be in the position

  • to think seriously about going forward with those if the LDT route didn’t exist.

They would have to raise hundreds of millions of additional dollars to take that approach. It’s not trivial to develop an LDT, but to say

  • a proposed assay has to be treated as an FDA-cleared in vitro diagnostic [IVD] represents a significant additional barrier.”

  The Benefits of Biospecimen Banks

Although Anderson wasn’t on board with the authors’ proposal about LDTs, he lauded their recommendation that

  • all drug registration trials maintain a biospecimen bank,
  • funded by the sponsoring drug company,
  • so that subsequent researchers could access the samples for prospective-retrospective studies.

In fact, writing in a Clinical Chemistry opinion piece along with the journal’s editor-in-chief Nader Rifai, PhD, he recommended that

  • the National Institutes of Health develop a list of key clinical diagnostic questions
  • prioritized by disease impact and linked to studies or medical centers with corresponding biospecimens.

This “would allow

  • a much more informed and productive application of the existing biomarker resources and
  • would provide a much-needed basis for arguing for the enormous potential health-economic value of successful new tests,” they wrote (Clin Chem 2013;59:194–7).

Along with the need to provide higher levels of evidence for candidate cancer biomarkers, the authors called for a significant

  • ramp-up in biomarker research investment and higher reimbursement for tests that demonstrate clinical utility.

In addition, they recommended that

  • scientific journals adhere to higher standards in publishing tumor biomarker studies and
  • be as willing to publish biomarker studies that have negative results as those with positive findings.

Finally, they proposed that guideline bodies follow evidence-based recommendations for tumor biomarker test use.

  Emulating the PET Registry

To up the ante on these sweeping reforms, the authors believe addressing them in concert is the only way to break the vicious cycle. But how can the healthcare industry essentially reinvent a new paradigm for better valuing cancer biomarkers when the elements of doing so are like a gyrating Medusa’s head of knotty, seemingly intractable challenges? The authors agree the problem is too daunting if considered only in its entirety. But they and other experts suggest that several tangible actions could move the field along substantially without too much chaos or pain.

For example, in the area of building evidence that would open the door for better reimbursement for cancer biomarker tests,

  • Schilsky envisions a tissue or blood test equivalent to the National Oncologic PET Registry (NOPR).

This ground-breaking initiative managed by the American College of Radiology (ACR) and the ACR Imaging Network developed evidence for Medicare to reimburse PET scanning with F-18 fluorodeoxyglucose when it wasn’t covered at all. NOPR enabled reimbursement for this testing in cancer patients on the proviso that physicians agreed to enter data in a registry that would enable a fair assessment of the impact PET had on cancer patient management. Started in 2006, NOPR led in 2009 to coverage of PET scans as part of the initial treatment strategy for most solid tumors, coverage that recently

  • was expanded to include payment for up to three PET scans in patients with advanced cancer after their initial treatment, according to Schilsky.

By doing the same thing with selected tumor biomarkers, Schilsky suggested, “we immediately begin to capture information that we’re not currently getting on

  • the prevalence of use of certain tests,
  • the kinds of clinical decisions based on those tests, and
  • the outcomes of the patients who undergo the testing,”

he explained. “Then, for payers, it becomes much less of a Wild West environment. They will have information they can analyze and use to inform their coverage decisions.” Such a system also would differentiate the most clinically useful tests from less relevant ones, enabling payers to shift resources to the winning tests. This, in turn, would incentivize test developers “to put tests out that are likely to perform well,” Schilsky added.

The authors also point to efforts like the National Human Genome Research Institute’s recent decision to fund more than $25 million over 4 years to develop the Clinical Genome Resource for

  • authoritative information on genetic variants relevant to human disease and patient care.

The National Cancer Institute (NCI) also is planning a

  • web-based inventory of all biospecimens collected under its clinical trials cooperative group program, according to Schilsky.

  The Impact of Technology

Anderson believes the authors overlooked the impact technological advances could have on the vicious cycle, by speeding up the process of vetting candidate biomarkers. “An alternative way of doing mass spectrometry [MS]-based protein assays is

  • to analyze for specific targeted proteins in smaller numbers, so you might measure 10 or 100, but accurately and quickly,” he explained.

“Those kinds of directed assay methods which are not looking for everything, but instead for specific things that you hypothesize are important biomarkers, can be run

  • fast enough and cheaply enough that you can run hundreds and hundreds of samples in a practical way.

That then removes the primary technological limitation to getting the validation of biomarkers done.”

Anderson added that this type of MS-based directed protein analysis also could speed up the bench-to-bedside time for biomarkers. “The advantage is that the same method used in biomarker verification studies at the research stage can be

  • implemented at least in the large reference labs as LDTs, where
  • it provides a significant technology improvement over immunoassays,” said Anderson.

“That it can be taken all the way from research to LDT in a capable reference lab takes a lot of delay out of the introduction into clinical practice. That’s because you don’t need to redevelop immunoassays for different platforms. Eventually you might not even need to redevelop it for an IVD platform, once mass spectrometry IVD platforms exist.” He predicted that this approach could shave 5–10 years from the biomarker development process. Anderson’s company, SISCAPA Assay Technologies, provides mass-spec-based specific assays for biomarker proteins.

Researchers also have a responsibility to think about the clinical need they want to address before diving deep into discovery, suggested Ivan Blasutig, PhD, a clinical biochemist and assistant professor at Toronto General Hospital and the University of Toronto. “Many of the biomarkers discovered may have statistically significant results but when it comes to actual clinical use they don’t cut it. That’s one of the biggest issues,” he said.

 Analytics: The Achilles Heel

Blasutig collaborates closely with Eleftherios Diamandis, MD, PhD, who has written extensively about the challenges of bringing proposed cancer biomarkers into clinical practice. He, Diamandis, and others have emphasized how important robust analytics are in the early stages of biomarker discovery. In fact Blasutig and Diamandis recently wrote about how using what turned out to be an unreliable commercial kit for CUZD1 detection set back their research team by 2 years and about $500,000 in their quest to find a new pancreatic cancer biomarker (Clin Chem 2013 doi:10.1373/clinchem.2013.215236).

Blasutig and others encouraged clinical laboratorians to participate actively in biomarker discovery, as they bring a wealth of knowledge about analytical issues in validation that research chemists don’t necessarily share. Laboratorians also are more likely to be aware of resources like the NCI’s Early Detection Research Network, which gives guidance on topics such as completing sample collections and avoiding analytical bias, Blasutig suggested.

If the vicious cycle seems completely unwieldy and unrepairable, each person CLN contacted expressed confidence that even in the face of long odds, it can be changed. Leonard spoke for many: “I’m optimistic that we have to do this for our patients, and for our healthcare delivery system. There are a lot of good people around who are interested in having this conversation. So if we can just get all the parties at the table and see if there are some concrete steps that we can take, that would be a major step in the right direction.”

 Comment by reviewer:

The clinical laboratory has been concentrating on technical accuracy considerably beyond the clinical utility of many observations in clinical medicine.  This is not necessarily appreciated, so when a test is inconsistent with the clinical hypothesis, it may be rejected as error.  Errors may occur, but are rare, except if there is specimen misidentification.  However, we are still focused on a “silver bullet” approach to use of diagnostic tests.  There is some variability of the expression of cancer cells, so that there are subclusters to be expected within a major class.  The level of applied mathematics that is needed to analyze this data has been refined enormously in the last decade, and has to be used on the selected groups of tests referred to with all due respect by Leigh Anderson, who has the imagination to pursue the highest accuracy in large scale MS analysis that his laboratory has pursued for many years.  This reviewer is interested in the “information content” of a combination of tests, when the accuracy of testing is no longer an issue.  By combining the high throuput and lower cost of processing, with vastly better mathematical technology than is customary – on the fly – would be a breakthrough.  That would not be the end of this journey because there would have to be centers for analysis distributed within a few hours of the treatment centers (or at those sites), so that testing and processing would enable better facilitation of treatment.

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Landscape of Cardiac Biomarkers for Improved Clinical Utilization

Curator and Author: Larry H Bernstein, MD, FCAP

Curation

This reviewer has been engaged in the development, the application, and the validation of cardiac biomarkers for over 30 years. There has been a nonlinear introduction of new biomarkers in that period, with an explosion of methods discovery and large studies to validate them in concert with clinical trials. The improvement of interventional methods, imaging methods, and the unraveling of patient characteristics associated with emerging cardiovascular disease is both cause for alarm (technology costs) and for raised expectations for both prevention, risk reduction, and treatment. What is strikingly missing is the kind of data analyses on the population database that could alleviate the burden of physician overload. It is an urgent requirement for the EHR, and it needs to be put in place to facilitate patient care.

Introduction

This is a journey through the current status of biochemical markers in cardiac evaluation. 

In the traditional use of cardiac biomarkers, the is a timed blood sampling from the decubital fossa. This was the case with alanine aminotransferase (AST, then SGOT), creatine kinase (CK) or its isoenzyme MB, and lactic dehydrogenase (or the isoenzyme-1). The time of sampling was based on time to appearance from time of damage, and the release of the biomarker is a stochastic process. The earliest studies of CK-MB appearance, peak height, and disappearance was by Burton Sobel and associates related to measuring the extent of damage, and determined that reperfusion had an effect. A significant reason for using a combination of CK-MB and LD-1 was that a patient who is a late arrival might have a CK-MB on the decline (peak at 18 h) while the LD-1 is rising (peak at 48 h).

The introduction of the troponins was accompanied by a serial 4 h measurement, usually for 4 draws (0, 4, 8, 12 h). The computational power of laboratory information systems was limited until recently, so it is somewhat surprising, given what we have seen – in addition to published work in the 1980’s – that this capability is not in use today, when regression and nonparametric classification algorithms are now so advanced that would enable much improved and effective communication to the physician needing the information.

J Adan, LH Bernstein, J Babb. Can peak CK-MB segregate patients with acute myocardial infarction into different outcome classes? Clin Chem 1985; 31(2):996-997. ICID: 844986.

RA Rudolph, LH Bernstein, J Babb. Information induction for predicting acute myocardial infarction. Clin Chem 1988; 34(10):2031-2038. ICID: 825568.

LH Bernstein, IJ Good, GI Holtzman, ML Deaton, J Babb. Diagnosis of acute myocardial infarction from two measurements of creatine kinase isoenzyme MB with use of nonparametric probability estimation. Clin Chem 1989; 35(3):444-447. ICID: 825570.

L H Bernstein, A Qamar, C McPherson, S Zarich, R Rudolph. Diagnosis of myocardial infarction: integration of serum markers and clinical descriptors using information theory. Clin Chem 1999; 72(1):5-13. ICID: 825618

Vermunt, J.K. & Magidson, J. (2000a). “Latent Class Cluster Analysis”, chapter 3 in J.A. Hagenaars and A.L. McCutcheon (eds.), Advances in Latent Class AnalysisCambridge University Press.

Vermunt, J.K. & Magidson, J. (2000b). Latent GOLD 2.0 User’s Guide. Belmont, MA: Statistical Innovations Inc.

LH Bernstein, A Qamar, C McPherson, S Zarich. Evaluating a new graphical ordinal logit method (GOLDminer) in the diagnosis of myocardial infarction utilizing clinical features and laboratory data. Yale J Biol Med. 1999; 72(4):259-268. ICID: 825617.

L Bernstein, K Bradley, S Zarich. GOLDmineR: improving models for classifying patients with chest pain.
Yale J Biol Med. 2002; 75(4):183-198. ICID: 825624

SA Haq, M Tavakol, LH Bernstein, J Kneifati-Hayek, M Schlefer, et al. The ACC/ESC Recommendation for 99th Percentile of the Reference NormalTroponin I Overestimates the Risk of an Acute Myocardial Infarction: a novel enhancement in the diagnostic performance of troponins. “6th Scientific Forum on Quality of Care and Outcomes Research in Cardiovascular Disease and Stroke.” Circulation 2005; 111(20):e313-313. ICID: 939931.

LH Bernstein, MY Zions, SA Haq, S Zarich, J Rucinski, B Seamonds, …., John F Heitner. Effect of renal function loss on NT-proBNP level variations. Clin Biochem 2009; 42(10-11):1091-1098. ICID: 937529

SA Haq, M Tavakol, S Silber, L Bernstein, J Kneifati-Hayek, et al. Enhancing the diagnostic performance of troponins in the acute care setting. J Emerg Med 2008; ICID: 937619

Gil David, LarryH Bernstein, Ronald Coifman. Generating Evidence Based Interpretation of Hematology Screens via Anomaly Characterization. OCCJ 2011; 4(1):10-16. ICID: 939928

The use and limitations of high-sensitivity cardiac troponin and natriuretic peptide concentrations in at risk populations

Background: High-sensitivity cardiac troponin (hs-cTn) assays are now available that can detect measurable troponin in significantly more individuals in the general population than conventional assays. The clinical use of these hs-cTn assays depends on the development of proper reference values. However, even with a univariate biomarker for risk and/or severity of ischemic heart disease, a single reference value for the cardiac biomarker does not discriminate the probabilities between 2 or 3 different cardiac disorders, or identify any combination of these, such as, heart failure or renal disease > stage 2 and acute coronary syndrome. True, the physician has a knowledge of the history and presentation as a guide. Do we know how adequate the information is in a patient who has an atypical presentation? Again, the same problem arises with the use of the natriuretic peptides, but the value of these tests is improved over the previous generation tests. Let us parse through the components of this diagnostic problem, which is critical for reaching the best decisions under the circumstances.

Issue 1. The use of the clinical information, such as, patient age, gender, past medical history, known medical illness, CHEST PAIN, ECG, medications, are the basis of longstanding clinical practice. These may be sufficient in a patient who presents with acute coronary syndrome and a Q-wave not previously seen, or with ST-elevation, ST-depression, T-wave inversion, or rhythm abnormality. Many patients don’t present that way.

Issue 2. The use of a single ‘decision-value’ for critical situations decribed, leaves us with a yes-no answer. If you use a receiver-operator characteristic curve, all of the patients used to construct the sensitivity/specificity analysis have to be decisively known for identification. Otherwise, one might just take the median of a very large population, and the median represents the best value for a data set that is not normal distribution. However, the ROC method may inform about an acute event, if that is the purpose, but with a single value for a single variable, it can’t identify a likelihood of an event in the next six months.

Issue 3. There are several quantitative biomarkers that are considerably better than were available 15 years prior to this discussion. These can be used alone, but preferably in combination for diagnostic evaluation, for predictiong prognosis, and for therapeutic decision-making. What is now available was unimagined 20 years ago, both in test selection and in treatment selection.

Cardiac troponin assays were recently reviewed in Clin Chem by Fred Apple and Amy Seenger. (The State of Cardiac Troponin Assays: Looking Bright and Moving in the Right Direction).

Cardiac troponin assays have evolved substantially over 20 years, owing to the efforts of manufacturers to make them more precise and sensitive. These enhancements have led to high-sensitivity cardiac troponin assays, which ideally would give measureable values above the limit of detection (LoD) for 100% of healthy individuals and demonstrate an imprecision (CV) of ≤10% at the 99th percentile.

As laboratorians, we wish to comment on the recently published “ACCF 2012 Expert Consensus Document on Practical Clinical Considerations in the Implementation of Troponin Elevations”. Our purpose is to address 8 analytical issues that we believe have the potential to cause confusion and that therefore deserve clarification.

Since the initial publications by the National Academy of Clinical Biochemistry (NACB) in 1999 and by the European Society of Cardiology/American College of Cardiology in 2000, when both organizations endorsed cardiac troponin I (cTnI) or cTnT as the preferred biomarker for the detection of myocardial infaction, numerous other organizations have followed suit and promoted the sole use of cardiac troponin in this clinical application. The American College of Cardiology Foundation (ACCF) 2012 Expert Consensus Document summarizes the recently published 2012 Third Universal Definition of Myocardial Infarction by the Global Task Force, thus providing some practical recommendations on the use and interpretation of cardiac troponin in clinical practice.

This commentator has already expressed the view that there is no ‘silver bullet’, and the potential for confusion is not yet going to be resolved. The potential for greater accuracy in diagnosis is bolstered by currently available imaging.

Current strength of cardiac biomarker opportunities:

A recent study measured hs-tnI in 1716 (93%) of the community-based study cohort and 499 (88%) of the healthy reference cohort. Parameters that significantly contributed to higher hs-cTnI concentrations in the healthy reference cohort included age, male sex, systolic blood pressure, and left ventricular mass. Glomerular filtration rate and body mass index were not independently associated with hs-cTnI in the healthy reference cohort. Individuals with diastolic and systolic dysfunction, hypertension, and coronary artery disease (but not impaired renal function) had significantly higher hs-cTnI values than the healthy reference cohort.

The authors concluded that hs-cTnI assay with the aid of echocardiographic imaging in a large, well-characterized community-based cohort demonstrated hs-cTnI to be remarkably sensitive in the general population, and there are important sex and age differences among healthy reference individuals. Even though the results have important implications for defining hs-cTnI reference values and identifying disease, the reference value is not presented, and the question remains about how many subjects in the 88% (499) healthy reference consort had elevated systolic blood pressure or left ventricular hypertrophy (LVH) measured by imaging. Furthermore, while impaired renal function dropped out as an independent predictor of associated hs-cTnI, one would expect it to have a strong association with LVH.

Defining High-Sensitivity Cardiac Troponin Concentrations in the Community.
PM McKie, DM Heublein, CG. Scott, ML Gantzer, …and AS Jaffe.
Depart Med & Lab Med and Pathology, Mayo Clinic and Foundation, Rochester, MN; Siemens Diagnostics, Newark, DE. Clin Chem 2013.

hsTnI with NSTEMI

Another study looks at the prognostic performance of hs-TnI assay with non-STEMI. High-sensitivity assays for cardiac troponin enable more precise measurement of very low concentrations and improved diagnostic accuracy. However, the prognostic value of these measurements, particularly at low concentrations, is less well defined. (This is the sensitivity vs specificity dilemma raised with regard to the impoved hs-cTn assays.) But the value of low measured values is a matter for prognostic evaluation, based on the hypothesis that any cTnI that is measured in serum is leaked from cardiomyocytes. This assay evaluation used the Abbott ARCHITECT. The data were 4695 patients with non–ST-segment elevation acute coronary syndromes (NSTE-ACS) from the EARLY-ACS (Early Glycoprotein IIb/IIIa Inhibition in NSTE-ACS) and SEPIA-ACS1-TIMI 42 (Otamixaban for the Treatment of Patients with NSTE-ACS–Thrombolysis in Myocardial Infarction 42) trials. The primary endpoint was cardiovascular death or new myocardial infarction (MI) at 30 days. Baseline cardiac troponin was categorized at the 99th percentile reference limit (26 ng/L for hs-cTnI; 10 ng/L for cTnT) and at sex-specific 99th percentiles for hs-cTnI.

All patients at baseline had detectable hs-cTnI compared with 94.5% with detectable cTnT. With adjustment for all other elements of the TIMI risk score, patients with hs-cTnI ≥99th percentile had a 3.7-fold higher adjusted risk of cardiovascular death or MI at 30 days relative to patients with hs-cTnI <99th percentile (9.7% vs 3.0%; odds ratio, 3.7; 95% CI, 2.3–5.7; P < 0.001). Similarly, when stratified by categories of hs-cTnI, very low concentrations demonstrated a graded association with cardiovascular death or MI (P-trend < 0.001). Thus, Application of this hs-cTnI assay identified a clinically relevant higher risk of recurrent events among patients with NSTE-ACS, even at very low troponin concentrations.

Prognostic Performance of a High-Sensitivity Cardiac Troponin I Assay in Patients with Non–ST-Elevation Acute Coronary Syndrome. EA Bohula May, MP Bonaca, P Jarolim, EM Antman, …and DA Morrow. Clin Chem 2013.

Combination test with cTnI and a troponin

The next study looks at the value of a combination of cTnT and N-Terminal pro-B-type-natriuretic-peptide (NT proBNP) to predict heart failure risk. Recall that NT proBNP has been a stabd-alone biomarker for CHF. The study was done with the consideration that heart failure (HF) is projected to have the largest increases in incidence over the coming decades. Therefore, would cardiac troponin T (cTnT) measured with a high-sensitivity assay and N-terminal pro-B–type natriuretic peptide (NT-proBNP), biomarkers strongly associated with incident HF, improve HF risk prediction in the Atherosclerosis Risk in Communities (ARIC) study?

Using sex-specific models, we added cTnT and NT-proBNP to age and race (“laboratory report” model) and to the ARIC HF model (includes age, race, systolic blood pressure, antihypertensive medication use, current/former smoking, diabetes, body mass index, prevalent coronary heart disease, and heart rate) in 9868 participants without prevalent HF; area under the receiver operating characteristic curve (AUC), integrated discrimination improvement, net reclassification improvement (NRI), and model fit were described.

Over a mean follow-up of 10.4 years, 970 participants developed incident HF. Adding cTnT and NT-proBNP to the ARIC HF model significantly improved all statistical parameters (AUCs increased by 0.040 and 0.057; the continuous NRIs were 50.7% and 54.7% in women and men, respectively). Interestingly, the simpler laboratory report model was statistically no different than the ARIC HF model.

Troponin T and N-Terminal Pro-B–Type Natriuretic Peptide: A Biomarker Approach to Predict Heart Failure Risk: The Atherosclerosis Risk in Communities Study. V Nambi, X Liu, LE Chambless, JA de Lemos, SS Virani, et al.
Clin Chem 2013.

BCM Researchers Discover Simpler, Improved Biomarkers to Predict Heart Failure As Accurate As Complex Models     Posted by: Anna Ishibashi Sep 17, 2013

Biomarkers for heart failure Researchers at the Baylor College of Medicine and the Michael E. DeBakey Veterans Affairs hospital discovered two improved biomarkers in the bloodstream that predict who is at higher risk of having heart failure in 10 years. The study was published in the journal Clinical Chemistry.

In the Atherosclerosis Risk in Communities (ARIC) clinical study, researchers measured the blood concentration of troponin T and N-terminal-pro-B-type natriuretic peptide (NT-proBNP) in the models, while also collecting age and race data. The important point taken from the study was that researchers did not find any difference in the accuracy of heart failure risk prediction statistically between this simpler test and the traditional, more complex one, which includes information of age, race, systolic blood pressure, antihypertensive medication use, smoking status, diabetes, body-mass index, prevalent coronary heart disease and heart rate.

Troponin T is an indicator of damaged heart muscle and can be detected in low levels even in individuals with no symptoms through this simpler, improved testing method. Similarly, NT-proBNP is a by-product of brain natriuretic peptide (BNP), which is a small neuropeptide hormone that has been shown to be effective in diagnosing congestive heart failure.

The critical issues that we must now address is what lifestyle and drug therapies can prevent the development of heart failures for individuals who are at high risk – according to Dr. Christie Ballantyne, professor of medicine and section chief of cardiology and cardiovascular research at BCM and the Houston Methodist Center for Cardiovascular Disease Prevention.

Although chest pain is widely considered a key symptom in the diagnosis of myocardial infarction (MI), not all patients with MI present with chest pain. This study was done the frequency with which patients with MI present without chest pain and to examine their subsequent management and outcome. A total of 434,877 patients with confirmed MI enrolled June 1994 to March 1998 in the National Registry of Myocardial Infarction, which includes 1674 hospitals in the United States. Outcome measures were prevalence of presentation without chest pain; clinical characteristics, treatment, and mortality among MI patients without chest pain vs those with chest pain.

Of all patients diagnosed as having MI, 142,445 (33%) did not have chest pain on presentation to the hospital. This group of MI patients was, on average, 7 years older than those with chest pain (74.2 vs 66.9 years), with a higher proportion of women (49.0% vs 38.0%) and patients with diabetes mellitus (32.6% vs 25.4%) or prior heart failure (26.4% vs 12.3%). Also, MI patients without chest pain had a longer delay before hospital presentation (mean, 7.9 vs 5.3 hours), were less likely to be diagnosed as having confirmed MI at the time of admission (22.2% vs 50.3%), and were less likely to receive thrombolysis or primary angioplasty (25.3% vs 74.0%), aspirin (60.4% vs 84.5%), β-blockers (28.0% vs 48.0%), or heparin (53.4% vs 83.2%). Myocardial infarction patients without chest pain had a 23.3% in-hospital mortality rate compared with 9.3% among patients with chest pain (adjusted odds ratio for mortality, 2.21 [95% confidence interval, 2.17-2.26]).

We tested the hypotheses that MI patients without chest pain compared with those with chest pain would present later for medical attention, would be less likely to be diagnosed as having acute MI on initial evaluation, and would receive fewer appropriate medical treatments within the first 24 hours. We also evaluated the association between the presence of atypical presenting symptoms and hospital mortality related to MI.

Our results suggest that patients without chest pain on presentation represent a large segment of the MI population and are at increased risk for delays in seeking medical attention, less aggressive treatments, and in-hospital mortality.

Prevalence, Clinical Characteristics, and Mortality Among Patients With Myocardial Infarction Presenting Without Chest Pain. JG Canto, MG Shlipak, WJ Rogers, JA Malmgren, PD Frederick, et al. JAMA 2013; 283(24):3223-3229. http://dx.doi.org/10.1001/jama.283.24.3223

cTnT degraded forms in circulation

This recent study questions whether degraded cTnT forms circulate in the patient’s blood. Separation of cTnT forms by gel filtration chromatography (GFC) was performed in sera from 13 AMI patients to examine cTnT degradation. The GFC eluates were subjected to Western blot analysis with the original antibodies from the Roche immunoassay used to mimic the clinical cTnT assay. GFC analysis of AMI patients’ sera revealed 2 cTnT peaks with retention volumes of 5 and 21 mL. Western blot analysis identified these peaks as cTnT fragments of 29 and 14–18 kDa, respectively. Furthermore, the performance of direct Western blots on standardized serum samples demonstrated a time-dependent degradation pattern of cTnT, with fragments ranging between 14 and 40 kDa. Intact cTnT (40 kDa) was present in only 3 patients within the first 8 h after hospital admission.

Time-Dependent Degradation Pattern of Cardiac Troponin T Following Myocardial Infarction. EPM Cardinaels, AMA Mingels T van Rooij, PO Collinson, FW Prinzen and MP van Dieijen-Visser. Clin Chem 2013.

Older patients with higher cTNI

One of the problems of interpretation of cTnI is the age relationship to the 99th percentile of the elderly. cTnI was measured using a high-sensitivity assay (Abbott Diagnostics) in 814 community-dwelling individuals at both 70 and 75 years of age. The cTnI 99th percentiles were determined separately using nonparametric methods in the total sample, in men and women, and in individuals with and without CVD.

The cTnI 99th percentile at baseline was 55.2 ng/L for the total cohort. Higher 99th percentiles were noted in men (69.3 ng/L) and individuals with CVD (74.5 ng/L). The cTnI 99th percentile in individuals free from CVD at baseline (n = 498) increased by 51% from 38.4 to 58.0 ng/L during the 5-year observation period. Relative increases ranging from 44% to 83% were noted across all subgroups. Male sex [odds ratio, 5.3 (95% CI, 1.5–18.3)], log-transformed N-terminal pro-B-type natriuretic peptide [odds ratio, 1.9 (95% CI, 1.2–3.0)], and left-ventricular mass index [odds ratio, 1.3 (95% CI, 1.1–1.5)] predicted increases in cTnI concentrations from below the 99th percentile (i.e., 38.4 ng/L) at baseline to concentrations above the 99th percentile at the age of 75 years.

cTnI concentration and its 99th percentile threshold depend strongly on the characteristics of the population being assessed. Among elderly community dwellers, higher concentrations were seen in men and individuals with prevalent CVD. Aging contributes to increasing concentrations, given the pronounced changes seen with increasing age across all subgroups. These findings should be taken into consideration when applying cTnI decision thresholds in clinical settings.

KM Eggers, Lars Lind, Per Venge and Bertil Lindahl. Factors Influencing the 99th Percentile of Cardiac Troponin I Evaluated in Community-Dwelling Individuals at 70 and 75 Years of Age/. Clin Chem 2013.

Background: Atrial natriuretic peptide (ANP) has antihypertrophic and antifibrotic properties that are relevant to AF substrates. The −G664C and rs5065 ANP single nucleotide polymorphisms (SNP) have been described in association with clinical phenotypes, including hypertension and left ventricular hypertrophy. A recent study assessed the association of early AF and rs5065 SNPs in low-risk subjects. In a Caucasian population with moderate-to-high cardiovascular risk profile and structural AF, we conducted a case-control study to assess whether the ANP −G664C and rs5065 SNP associate with nonfamilial structural AF.
Methods: 168 patients with nonfamilial structural AF and 168 age- and sex-matched controls were recruited. The rs5065 and −G664C ANP SNPs were genotyped.
Results: The study population had a moderate-to-high cardiovascular risk profile with 86% having hypertension, 23% diabetes, 26% previous myocardial infarction, and 23% left ventricular systolic dysfunction. Patients with AF had greater left atrial diameter (44 ± 7 vs. 39 ± 5 mm; P , 0.001) and higher plasma NTproANP levels (6240 ± 5317 vs. 3649 ± 2946 pmol/mL; P , 0.01). Odds ratios (ORs) for rs5065 and −G664C gene variants were 1.1 (95% confidence interval [CI], 0.7–1.8; P = 0.71) and 1.2 (95% CI, 0.3–3.2; P = 0.79), respectively, indicating no association with AF. There were no differences in baseline clinical characteristics among carriers and noncarriers of the −664C and rs5065 minor allele variants.
Conclusions: We report lack of association between the rs5065 and −G664C ANP gene SNPs and AF in a Caucasian population of patients with structural AF. Further studies will clarify whether these or other ANP gene variants affect the risk of different subphenotypes of AF driven by distinct pathophysiological mechanisms.

P Francia, A Ricotta, A Frattari, R Stanzione, A Modestino, et al.
Atrial Natriuretic Peptide Single Nucleotide Polymorphisms in Patients with Nonfamilial Structural Atrial Fibrillation.
Clinical Medicine Insights: Cardiology 2013:7 153–159   http://dx.doi.org/10.4137/CMC.S12239  http://www.la-press.com/atrial-natriuretic-peptide-single-nucleotide-polymorphisms-in-patients-article-a3882

Cystatin C and eGFR predict AMI or CVD mortality

BACKGROUND: The estimated glomerular filtration rate (eGFR) independently predicts cardiovascular death or myocardial infarction (MI) and can be estimated by creatinine and cystatin C concentrations. We evaluated 2 different cystatin C assays, alone or combined with creatinine, in patients with acute coronary syndrome.
METHODS: We analyzed plasma cystatin C, measured with assays from Gentian and Roche, and serum creatinine in 16 279 patients from the PLATelet Inhibition and Patient Outcomes (PLATO) trial. We evaluated Pearson correlation and agreement (Bland–Altman) between methods, as well as prognostic value in relation to cardiovascular death or MI during 1 year of follow up by multivariable logistic regression analysis including clinical variables, biomarkers, c-statistics, and relative integrated discrimination improvement (IDI).
RESULTS: Median cystatin C concentrations (interquartile intervals) were 0.83 (0.68–1.01) mg/L (Gentian) and 0.94 (0.80–1.14) mg/L (Roche). Overall correlation was 0.86 (95% CI 0.85–0.86). The level of agreement was within 0.39 mg/L (2 SD) (n = 16 279).
The areas under the curve (AUCs) in the multivariable risk prediction model with cystatin C (Gentian, Roche) or Chronic Kidney Disease Epidemiology Collaboration eGFR (CKD-EPI) added were 0.6914, 0.6913, and 0.6932. Corresponding relative IDI values were 2.96%, 3.86%, and 4.68% (n = 13 050). Addition of eGFR by the combined creatinine–cystatin C equation yielded AUCs of 0.6923 (Gentian) and 0.6924 (Roche) with relative IDI values of 3.54% and 3.24%.
CONCLUSIONS: Despite differences in cystatin C concentrations, overall correlation between the Gentian and Roche assays was good, while agreement was moderate. The combined creatinine–cystatin C equation did not outperform risk prediction by CKD-EPI.
A Åkerblom, L Wallentin, A Larsson, A Siegbahn, et al.
Cystatin C– and Creatinine-Based Estimates of Renal Function and Their Value for Risk Prediction in Patients with Acute Coronary Syndrome: Results from the PLATelet Inhibition and Patient Outcomes (PLATO) Study.
 

T2Dm has many subphenotypes in the prediabetic phase

For decades, glucose, hemoglobin A1c, insulin, and C peptide have been the laboratory tests of choice to detect and monitor diabetes. However, these tests do not identify individuals at risk for developing type 2 diabetes (T2Dm) (so-called prediabetic individuals and the subphenotypes therein), which would be a prerequisite for individualized prevention. Nor are these parameters suitable to identify T2Dm subphenotypes, a prerequisite for individualized therapeutic interventions. The oral glucose tolerance test (oGTT) is still the only means for the early and reliable identification of people in the prediabetic phase with impaired glucose tolerance (IGT). This procedure, however, is very time-consuming and expensive and is unsuitable as a screening method in a doctor′s office. Hence, there is an urgent need for innovative laboratory tests to simplify the early detection of alterations in glucose metabolism.
The search for diabetic risk genes was the first and most intensively pursued approach for individualized diabetes prevention and treatment. Over the last 20 years cohorts of tens of thousands of people have been analyzed, and more than 70 susceptibility loci associated with T2Dm and related metabolic traits have been identified. But despite extensive replication, no susceptibility loci or combinations of loci have proven suitable for diagnostic purposes.
Why did the genomic studies fail? One reason might be that T2Dm is a polygenetic disease, but there is another more important reason. The large diabetes cohorts investigated in these studies were very heterogeneous, consisting of poorly characterized individuals who were usually selected because they had an increase in blood glucose. Subsequently it has become clear that many different subphenotypes already exist in the prediabetic phase.
Metabolomics represents a new potential approach to move the diagnosis of diabetes beyond the application of the classical diabetic laboratory tests.
Rainer Lehmann. Diabetes Subphenotypes and Metabolomics: The Key to Discovering Laboratory Markers for Personalized Medicine?
 

Ca2+/calmodulin-dependent protein kinase II (CaMKII) has recently emerged as a ROS activated proarrhythmic signal

Background—Atrial fibrillation is a growing public health problem without adequate therapies. Angiotensin II (Ang II) and reactive oxygen species (ROS) are validated risk factors for atrial fibrillation (AF) in patients, but the molecular pathway(s) connecting ROS and AF is unknown. The Ca2+/calmodulin-dependent protein kinase II (CaMKII) has recently emerged as a ROS activated proarrhythmic signal, so we hypothesized that oxidized CaMKII􀄯(ox-CaMKII) could contribute to AF.
Methods and Results—We found ox-CaMKII was increased in atria from AF patients compared to patients in sinus rhythm and from mice infused with Ang II compared with saline. Ang II treated mice had increased susceptibility to AF compared to saline treated WT mice, establishing Ang II as a risk factor for AF in mice. Knock in mice lacking critical oxidation sites in CaMKII􀄯 (MM-VV) and mice with myocardial-restricted transgenic over-expression of methionine sulfoxide reductase A (MsrA TG), an enzyme that reduces ox-CaMKII, were resistant to AF induction after Ang II infusion.
 
RyR and Ca+ release from SR
 
ANS-   autonomic innervation of heart
 
 
mongillo_fig1  regulation of cardiac Ca++ cycling by ANS
 
jce561317.fig3    cardiac contraction
 
 
 
 
serum levels of MAA differentiated stable CAD from MI. For IgM antibodies to MAA, results were consistent with IgGantibodies to MAA
 
 
 
Conclusions—Our studies suggest that CaMKII is a molecular signal that couples increased ROS with AF and that therapeutic strategies to decrease ox-CaMKII may prevent or reduce AF.
Key words: atrial fibrillation, calcium/calmodulin-dependent protein kinase II, angiotensin II, reactive oxygen species, arrhythmia (mechanisms)
A Purohit, AG Rokita, X Guan, B Chen, et al.  Oxidized CaMKII Triggers Atrial Fibrillation.  Circulation. Sep 12, 2013;
 

Microparticles (MP)s give clues about vascular endothelial injury

BACKGROUND: Endothelial dysfunction is an early event in the development and progression of a wide range of cardiovascular diseases. Various human studies have identified that measures of endothelial dysfunction may offer prognostic information with respect to vascular events. Microparticles (MPs) are a heterogeneous population of small membrane fragments shed from various cell types. The endothelium is one of the primary targets of circulating MPs, and MPs isolated from blood have been considered biomarkers of vascular injury and inflammation.
CONTENT: This review summarizes current knowledge of the potential functional role of circulating MPs in promoting endothelial dysfunction. Cells exposed to different stimuli such as shear stress, physiological agonists, proapoptotic stimulation, or damage release MPs, which contribute to endothelial dysfunction and the development of cardiovascular diseases. Numerous studies indicate that MPs may trigger endothelial dysfunction by disrupting production of nitric oxide release from vascular endothelial cells and subsequently modifying vascular tone. Circulating MPs affect both proinflammatory and proatherosclerotic processes in endothelial cells. In addition, MPs can promote coagulation and inflammation or alter angiogenesis and apoptosis in endothelial cells.
SUMMARY: MPs play an important role in promoting endothelial dysfunction and may prove to be true biomarkers of disease state and progression.
Fina Lovren and Subodh Verma.  Evolving Role of Microparticles in the Pathophysiology of Endothelial Dysfunction.
 
Outcomes of STEMI and NSTEMI different predicted by NPs after MI
Patients with increased blood concentrations of natriuretic peptides (NPs) have poor cardiovascular outcomes after myocardial infarction (MI). Data from 41 683 patients with non–ST-segment elevation MI (NSTEMI) and 27 860 patients with ST-segment elevation MI (STEMI) at 309 US hospitals were collected as part of the ACTION Registry®–GWTG™ (Acute Coronary Treatment and Intervention Outcomes Network Registry–Get with the Guidelines) (AR-G) between July 2008 and September 2009.

B-type natriuretic peptide (BNP) or N-terminal pro-BNP (NT-proBNP) was measured in 19 528 (47%) of NSTEMI and 9220 (33%) of STEMI patients. Patients in whom NPs were measured were older and had more comorbidities, including prior heart failure or MI. There was a stepwise increase in the risk of in-hospital mortality with increasing BNP quartiles for both NSTEMI (1.3% vs 3.2% vs 5.8% vs 11.1%) and STEMI (1.9% vs 3.9% vs 8.2% vs 17.9%). The addition of BNP to the AR-G clinical model improved the C statistic from 0.796 to 0.807 (P < 0.001) for NSTEMI and from 0.848 to 0.855 (P = 0.003) for STEMI. The relationship between NPs and mortality was similar in patients without a history of heart failure or cardiogenic shock on presentation and in patients with preserved left ventricular function.

NPs are measured in almost 50% of patients in the US admitted with MI and appear to be used in patients with more comorbidities. Higher NP concentrations were strongly and independently associated with in-hospital mortality in the almost 30 000 patients in whom NPs were assessed, including patients without heart failure.

BM Scirica, MB Kadakia, JA de Lemos, MT Roe, DA Morrow, et al. Association between Natriuretic Peptides and Mortality among Patients Admitted with Myocardial Infarction: A Report from the ACTION Registry®–GWTG™.

Predictive value of processed forms of BNP in circulation

B-type natriuretic peptide (BNP) is secreted in response to pathologic stress from the heart. Its use as a biomarker of heart failure is well known; however, its diagnostic potential in ischemic heart disease is less explored. Recently, it has been reported that processed forms of BNP exist in the circulation. We characterized processed forms of BNP by a newly developed mass spectrometry–based detection method combined with immunocapture using commercial anti-BNP antibodies.

Measurements of processed forms of BNP by this assay were found to be strongly associated with presence of restenosis. Reduced concentrations of the amino-terminal processed peptide BNP(5–32) relative to BNP(3–32) [as the index parameter BNP(5–32)/BNP(3–32) ratio] were seen in patients with restenosis [median (interquartile range) 1.19 (1.11–1.34), n = 22] vs without restenosis [1.43 (1.22–1.61), n = 83; P < 0.001] in a cross-sectional study of 105 patients undergoing follow-up coronary angiography. A sensitivity of 100% to rule out the presence of restenosis was attained at a ratio of 1.52. Processed forms of BNP may serve as viable potential biomarkers to rule out restenosis.

H Fujimoto, T Suzuki, K Aizawa, D Sawaki, J Ishida, et al. Processed B-Type Natriuretic Peptide Is a Biomarker of Postinterventional Restenosis in Ischemic Heart Disease. Clin Chem 2013.

Circulating proteins from patients requiring revascularization

More than a million diagnostic cardiac catheterizations are performed annually in the US for evaluation of coronary artery anatomy and the presence of atherosclerosis. Nearly half of these patients have no significant coronary lesions or do not require mechanical or surgical revascularization. Consequently, the ability to rule out clinically significant coronary artery disease (CAD) using low cost, low risk tests of serum biomarkers in even a small percentage of patients with normal coronary arteries could be highly beneficial. METHODS: Serum from 359 symptomatic subjects referred for catheterization was interrogated for proteins involved in atherogenesis, atherosclerosis, and plaque vulnerability. Coronary angiography classified 150 patients without flow-limiting CAD who did not require percutaneous intervention (PCI) while 209 required coronary revascularization (stents, angioplasty, or coronary artery bypass graft surgery). Continuous variables were compared across the two patient groups for each analyte including calculation of false discovery rate (FDR [less than or equal to]1%) and Q value (P value for statistical significance adjusted to [less than or equal to]0.01).

Significant differences were detected in circulating proteins from patients requiring revascularization including increased apolipoprotein B100 (APO-B100), C-reactive protein (CRP), fibrinogen, vascular cell adhesion molecule 1 (VCAM-1), myeloperoxidase (MPO), resistin, osteopontin, interleukin (IL)-1beta, IL-6, IL-10 and N-terminal fragment protein precursor brain natriuretic peptide (NT-pBNP) and decreased apolipoprotein A1 (APO-A1). Biomarker classification signatures comprising up to 5 analytes were identified using a tunable scoring function trained against 239 samples and validated with 120 additional samples. A total of 14 overlapping signatures classified patients without significant coronary disease (38% to 59% specificity) while maintaining 95% sensitivity for patients requiring revascularization. Osteopontin (14 times) and resistin (10 times) were most frequently represented among these diagnostic signatures. The most efficacious protein signature in validation studies comprised osteopontin (OPN), resistin, matrix metalloproteinase 7 (MMP7) and interferon gamma (IFNgamma) as a four-marker panel while the addition of either CRP or adiponectin (ACRP-30) yielded comparable results in five protein signatures.

Proteins in the serum of CAD patients predominantly reflected

  1. a positive acute phase, inflammatory response and

  2. alterations in lipid metabolism, transport, peroxidation and accumulation.

    There were surprisingly few indicators of growth factor activation or extracellular matrix remodeling in the serum of CAD patients except for elevated OPN. These data suggest that many symptomatic patients without significant CAD could be identified by a targeted multiplex serum protein test without cardiac catheterization thereby eliminating exposure to ionizing radiation and decreasing the economic burden of angiographic testing for these patients.

WA Laframboise, R Dhir, LA Kelly, P Petrosko, JM Krill-Burger, et al. Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography.
BMC Medicine (impact factor: 6.03). 12/2012; 10(1):157. http://dx.doi.org/10.1186/1741-7015-10-157

miRNAs in CAD

MicroRNAs are small RNAs that control gene expression. Besides their cell intrinsic function, recent studies reported that microRNAs are released by cultured cells and can be detected in the blood. To address the regulation of circulating microRNAs in patients with stable coronary artery disease. To determine the regulation of microRNAs, we performed a microRNA profile using RNA isolated from n=8 healthy volunteers and n=8 patients with stable coronary artery disease that received state-of-the-art pharmacological treatment. Interestingly, most of the highly expressed microRNAs that were lower in the blood of patients with coronary artery disease are known to be expressed in endothelial cells (eg, miR-126 and members of the miR-17 approximately 92 cluster). To prospectively confirm these data, we detected selected microRNAs in plasma of 36 patients with coronary artery disease and 17 healthy volunteers by quantitative PCR. Consistent with the data obtained by the profile, circulating levels of miR-126, miR-17, miR-92a, and the inflammation-associated miR-155 were significantly reduced in patients with coronary artery disease compared with healthy controls. Likewise, the smooth muscle-enriched miR-145 was significantly reduced. In contrast, cardiac muscle-enriched microRNAs (miR-133a, miR-208a) tend to be higher in patients with coronary artery disease. These results were validated in a second cohort of 31 patients with documented coronary artery disease and 14 controls. Circulating levels of vascular and inflammation-associated microRNAs are significantly downregulated in patients with coronary artery disease.

S Fichtlscherer, S De Rosa, H Fox, T Schwietz, A Fischer, et al. Circulating microRNAs in patients with coronary artery disease. Circulation Research 09/2010; 107(5):677-84.

Imaging modalities compared

This review compares the noninvasive anatomical imaging modalities of coronary artery calcium scoring and coronary CT angiography to the functional assessment modality of MPI in the diagnosis and prognostication of significant CAD in symptomatic patients. A large number of studies investigating this subject are analyzed with a critical look on the evidence, underlying the strengths and limitations. Although the overall findings of the presented studies are favoring the use of CT-based anatomical imaging modalities over MPI in the diagnosis and prognosticating of CAD, the lack of a high number of large- scale, multicenter randomized controlled studies limits the generalizability of this early evidence. Further studies comparing the short- and long-term clinical outcomes and cost-effectiveness of these tests are required to determine their optimal role in the management of symptomatic patients with suspected CAD.

Y Hacioglu, M Gupta, Matthew J Budoff. Noninvasive anatomical coronary artery imaging versus myocardial perfusion imaging: which confers superior diagnostic and prognostic information?
Journal of computer assisted tomography 34(5):637-44.

Three Dimensional In-Room Imaging (3DCA) in PCI

Introduction: Coronary angiography is a two-dimensional (2D) imaging modality and thus is limited in its ability to represent complex three-dimensional (3D) vascular anatomy. Lesion length, bifurcation angles/lesions, and tortuosity are often inadequately assessed using 2D angiography due to vessel overlap and foreshortening. 3D Rotational Angiography (3DRA) with subsequent reconstruction generates models of the coronary vasculature from which lesion length measurements and Optimal View Maps (OVM) defining the amount of vessel foreshortening for each gantry angle can be derived. This study sought to determine if 3DRA-assisted percutaneous coronary interventions resulted in improved procedural results by minimizing foreshortening and optimizing stent selection.
 Rotational angiographic acquisitions were performed and a 3D model was generated from two images greater than 30° apart. An optimal view map identifying the least amount of vessel foreshortening and overlap was derived from the 3D model.
The clinical validation of in-room image-processing tools such as 3DCA and optimal view maps is important since FDA approval of these tools does not require the presentation of any data on clinical experience and impact on clinical outcomes. While the technology of 3DRA and optimal view calculations has been well validated by the work of Chen and colleagues, this study is important in demonstrating how clinical care may be impacted [4,5,7]. This study was biased toward minimizing the impact of these tools on clinical decision-making since the study site, cardiologists, and staff have extensive experience in rotational angiography, 3-D modeling and reconstruction, and the impact of foreshortening on the assessment of lesion length and choice of stent size.
3DRA assistance significantly reduced target vessel foreshortening when compared to operator’s choice of working view for PCI (2.99% ± 2.96 vs. 9.48% ± 7.56, p=0.0001). The operators concluded that 3DRA recommended better optimal view selection for PCI in 14 of 26 (54%) total cases. In 9 (35%) of 26 cases 3DRA assistance facilitated stent positioning. 3DRA based imaging prompted stent length changes in 4/26 patients (15%).
MH. Eng, PA Hudson, AJ Klein, SYJ Chen, … , JA Garcia. Impact of Three Dimensional In-Room Imaging (3DCA) in the Facilitation of Percutaneous Coronary Interventions. J Cardio Vasc Med 2013; 1: 1-5.

 

Related References from PharmaceuticalIntelligence.com:

Genomics & Genetics of Cardiovascular Disease Diagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013
Curators: Aviva Lev-Ari, PhD, RN and Larry H. Bernstein, MD, FCAP
http://pharmaceuticalintelligence.com/2013/03/07/genomics-genet…cs-32010-32013/
http://wp.me/p2kEDv-2Jp

Prognostic Marker Importance of Troponin I in Acute Decompensated Heart Failure (ADHF)
Larry H Bernstein and  Aviva Lev-Ari
http://pharmaceuticalintelligence.com/2013/06/30/troponin-i-in-…-heart-failure
http://wp.me/p2kEDv-41S

A Changing expectation from cardiac biomarkers.
Larry H Bernstein
http://pharmaceuticalintelligence.com/2012/12/25/assessing-card…ith-biomarkers/
http://wp.me/p2kEDv-1DN

Dealing with the Use of the High Sensitivity Troponin (hs cTn) Assays
Larry H Bernstein and Aviva Lev-Ari
http://pharmaceuticalintelligence.com/2013/05/18/dealing-with-t…-hs-ctn-assays/
http://pharmaceuticalintelligence.com/wp-admin/post.php?post=13255
http://wp.me/p2kEDv-3rN

For Disruption of Calcium Homeostasis in Cardiomyocyte Cells, see

Part VI: Calcium Cycling (ATPase Pump) in Cardiac Gene Therapy: Inhalable Gene Therapy for Pulmonary Arterial Hypertension and Percutaneous Intra-coronary Artery Infusion for Heart Failure: Contributions by Roger J. Hajjar, MD

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/08/01/calcium-molecule-in-cardiac-gene-therapy-inhalable-gene-therapy-for-pulmonary-arterial-hypertension-and-percutaneous-intra-coronary-artery-infusion-for-heart-failure-contributions-by-roger-j-hajjar/

Part VII: Cardiac Contractility & Myocardium Performance: Ventricular Arrhythmias and Non-ischemic Heart Failure – Therapeutic Implications for Cardiomyocyte Ryanopathy (Calcium Release-related Contractile Dysfunction) and Catecholamine Responses

Justin Pearlman, MD, PhD, FACC, Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/08/28/cardiac-contractility-myocardium-performance-ventricular-arrhythmias-and-non-ischemic-heart-failure-therapeutic-implications-for-cardiomyocyte-ryanopathy-calcium-release-related-contractile/

Part VIII: Disruption of Calcium Homeostasis: Cardiomyocytes and Vascular Smooth Muscle Cells: The Cardiac and Cardiovascular Calcium Signaling Mechanism

Justin Pearlman, MD, PhD, FACC, Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/09/12/disruption-of-calcium-homeostasis-cardiomyocytes-and-vascular-smooth-muscle-cells-the-cardiac-and-cardiovascular-calcium-signaling-mechanism/

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The Delicate Connection:  IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

Author and Curator: Demet Sag, PhD, CRA, GCP      

Table of Contents:

  1. Abstract
  2. Dual role for IDO
  3. Immune System and IDO
  4. Autoimmune disorders and IDO
  5. Cancer and Ido
  6. Clinical Interventions
  7. Clinical Trials
  8. Future Actions for Molecular Dx and Targeted Therapies:
  9. Conclusion
  10. References

TABLE 1- IDO Clinical Trials

TABLE 2- Kyn induced Genes

TABLE 3 Possible biomarkers and molecular diagnostics targets

TABLE 4: Current Interventions ______________________________________________________________________________________________________________

ABSTRACT:

Overall purpose is to find a method to manipulate IDO for clinical applications, mainly the focus of this review is is cancer prevention and treatment.  The first study proving the connection between IDO and immune response came from, a very natural event, a protection of pregnancy in human. This led to discover that high IDO expression is a common factor in cancer tumors. Thus, attention promoted investigations on IDO’s role in various disease states, immune disorders, transplantation, inflammation, women health, mood disorders.
Many approaches, vaccines and adjuvants are underway to find new immunotherapies by combining the power of DCs in immune response regulation and specific direction of siRNA.  As a result, with this unique qualities of IDO, DCs and siRNA, we orchestrated a novel intervention for immunomodulation of IDO by inhibiting with small interference RNA, called siRNA-IDO-DCvax.  Proven that our DCvax created a delay and regression of tumor growth without changing the natural structure and characterization of DCs in melanoma and breast cancers in vivo. (** The shRNA IDO- DCvax is developed by Regen BioPhrama, San Diego, CA ,  Thomas Ichim, Ph.D, CSO. and David Koos, CEO)

______________________________________________________________________________________________________________

Double-Edged Sword of IDO: The Good and The Bad for Clinical intervention and Developments

IDO almost has a dual role. There is a positive side of high expression of IDO during pregnancy (29; 28; 114), transplants (115; 116; 117; 118; 119), infectious diseases (96) and but this tolerance is negative during autoimmune-disorders (120; 121; 122), tumors of cancer (123; 124; 117; 121; 125; 126; 127) (127), and mood disorders (46). The increased IDO expression has a double-edged sword in human physiology provides a positive role during protection of fetus and grafts after transplantations but becomes a negative factor during autoimmune disorders, cancer, sepsis and mood disorders.

Prevention of allogeneic fetal rejection is possible by tryptophan metabolism (26) rejecting with lack of IDO but allocating if IDO present (29; 28; 114). These studies lead to find “the natural regulation mechanism” for protecting the transplants from graft versus host disease GVHD (128) and getting rid of tumors.

The plasticity of  mammary and uterus during reproduction may hold some more answers to prevent GVHD and tumors of cancer with good understanding of IDO and tryptophan mechanism (129; 130). After allogeneic bone marrow transplants the risk of solid tumor development increased about 80% among 19,229 patients even with a greater risk among patients under 18 years old (117).  The adaptation of tolerance against host mechanism is connected to the IDO expression (131). During implantation and early pregnancy IDO has a role by making CD4+CD25+Foxp3+ regulatory T cells (Tregs) and expressing in DCs and  MQs  (114; 132; 133).

Clonal deletion mechanism prevents mother to react with paternal products since female mice accepted the paternal MHC antigen-expressing tumor graft during pregnancy and rejected three weeks after delivery (134). CTLA-4Ig gene therapy alleviates abortion through regulation of apoptosis and inhibition of spleen lymphocytes (135).  

 Immune System and IDO DCs are the orchestrator of the immune response (56; 57; 58) with list of functions in uptake, processing, and presentation of antigens; activation of effector cells, such as T-cells and NK-cells; and secretion of cytokines and other immune-modulating molecules to direct the immune response. The differential regulation of IDO in distinct DC subsets is widely studied to delineate and correct immune homeostasis during autoimmunity, infection and cancer and the associated immunological outcomes. Genesis of antigen presenting cells (APCs), eventually the immune system, require migration of monocytes (MOs), which is originated in bone marrow. Then, these MOs move from bloodstream to other tissues to become macrophages and DCs (59; 60).

Initiation of immune response requires APCs to link resting helper T-cell with the matching antigen to protect body. DCs are superior to MQs and MOs in their immune action model. When DCs are first described (61) and classified, their role is determined as a highly potent antigen-presenting cell (APC) subset with 100 to 1000-times more effective than macrophages and B-cells in priming T-cells. Both MQs and monocytes phagocytize the pathogen, and their cell structure contains very large nucleus and many internal vesicles. However, there is a nuance between MQ and DCs, since DCs has a wider capacity of stimulation, because MQs activates only memory T cells, yet DCs can activate both naïve and memory T cells.

DCs are potent activators of T cells and they also have well controlled regulatory roles. DC properties determine the regulation regardless of their origin or the subset of the DCs. DCs reacts after identification of the signals or influencers for their inhibitory, stimulatory or regulatory roles, before they express a complex repertoire of positive and negative cytokines, transmembrane proteins and other molecules. Thus, “two signal theory” gains support with a defined rule.  The combination of two signals, their interaction with types of cells and time are critical.

In short, specificity and time are matter for a proper response. When IDO mRNA expression is activated with CTL40 ligand and IFNgamma, IDO results inhibition of T cell production (4).  However, if DCs are inhibited by 1MT, an inhibitor of IDO, the response stop but IgG has no affect (10).  In addition, if the stimulation is started by a tryptophan metabolite, which is downstream of IDO, such as 3-hydroxyantranilic or quinolinic acids, it only inhibits Th1 but not Th2 subset of T cells (62).

Furthermore, inclusion of signal molecules, such as Fas Ligand, cytochrome c, and pathways also differ in the T cell differentiation mechanisms due to combination, time and specificity of two-signals.  The co-culture experiments are great tool to identify specific stimuli in disease specific microenvironment (63; 12; 64) for discovering the mechanism and interactions between molecules in gene regulation, biochemical mechanism and physiological function during cell differentiation.

As a result, the simplest differential cell development from the early development of DCs impact the outcome of the data. For example, collection of MOs from peripheral blood mononuclear cells (PBMCs) with IL4 and GM-CSF leads to immature DCs (iDCs). On next step, treatment of iDCs with tumor necrosis factor (TNF) or other plausible cytokines (TGFb1, IFNgamma, IFNalpha,  IFNbeta, IL6 etc.) based on the desired outcome differentiate iDCs  into mature DCs (mDCs). DCs live only up to a week but MOs and generated MQs can live up to a month in the given tissue. B cells inhibit T cell dependent immune responses in tumors (65).

AutoImmune Disorders:

The Circadian Clock Circuitry and the AHR

The balance of IDO expression becomes necessary to prevent overactive immune response self-destruction, so modulation in tryptophan and NDA metabolisms maybe essential.  When splenic IDO-expressing CD11b (+) DCs from tolerized animals applied, they suppressed the development of arthritis, increased the Treg/Th17 cell ratio, and decreased the production of inflammatory cytokines in the spleen (136).

The role of Nicotinamide prevention on type 1 diabetes and ameliorates multiple sclerosis in animal model presented with activities of  NDAs stimulating GPCR109a to produce prostaglandins to induce IDO expression, then these PGEs and PGDs converted to the anti-inflammatory prostaglandin, 15d-PGJ(2) (137; 138; 139).  Thus, these events promotes endogenous signaling mechanisms involving the GPCRs EP2, EP4, and DP1 along with PPARgamma. (137).

Modulating the immune response at non-canonical at canonocal pathway while keeping the non-canonical Nf-KB intact may help to mend immune disorders. As a result, the targeted blocking in canonical at associated kinase IKKβ and leaving non-canonocal Nf-kB pathway intact, DCs tips the balance towards immune supression. Hence, noncanonical NF-κB pathway for regulatory functions in DCs required effective IDO induction, directly or indirectly by endogenous ligand Kyn and negative regulation of proinflammatory cytokine production. As a result, this may help to treat autoimmune diseases such as rheumatoid arthritis, type 1 diabetes, inflammatory bowel disease, and multiple sclerosis, or allergy or transplant rejection.

While the opposite action needs to be taken during prevention of tumors, that is inhibition of non-canonical pathway.  Inflammation induces not only relaxation of veins and lowering blood pressure but also stimulate coagulopathies that worsen the microenvironment and decrease survival rate of patients after radio or chemotherapies.Cancer Generating tumor vaccines and using adjuvants underway (140).

Clinical correlation and genetic responses also compared in several studies to diagnose and target the system for cancer therapies (127; 141; 131).  The recent surveys on IDO expression and human cancers showed that IDO targeting is a candidate for cancer therapy since IDO expression recruiting Tregs, downregulates MHC class I and creating negative immune microenvironment for protection of development of tumors (125; 27; 142).  Inhibition of IDO expression can make advances in immunotherapy and chemotherapy fields (143; 125; 131; 144).

IDO has a great importance on prevention of cancer development (126). There are many approaches to create the homeostasis of immune response by Immunotherapy.  However, given the complexity of immune regulations, immunomodulation is a better approach to correct and relieve the system from the disease.  Some of the current IDO targeted immunotherapy or immmunomodulations with RNA technology for cancer prevention (145; 146; 147; 148; 149; 150) or applied on human or animals  (75; 151; 12; 115; 152; 9; 125) or chemical, (153; 154) or  radiological (155).  The targeted cell type in immune system generally DCs, monocytes (94)T cells (110; 156)and neutrophils (146; 157). On this paper, we will concentrate on DCvax on cancer treatments.

 T-reg, regulatory T cells; Th, T helper; CTLA-4, cytotoxic T lymphocyte-associated antigen 4; TCR, T cell receptor; IDO, indoleamine 2,3-dioxygenase. (refernece: http://www.pnas.org/content/101/28/10398/suppl/DC)

T-reg, regulatory T cells; Th, T helper; CTLA-4, cytotoxic T lymphocyte-associated antigen 4; TCR, T cell receptor; IDO, indoleamine 2,3-dioxygenase. (refernece: http://www.pnas.org/content/101/28/10398/suppl/DC)

IDO and the downstream enzymes in tryptophan pathway produce a series of immunosuppressive tryptophan metabolites that may lead into Tregs proliferation or increase in T cell apoptosis (62; 16; 27; 158), and some can affect NK cell function (159).

The interesting part of the mechanism is even without presence of IDO itself, downstream enzymes of IDO in the kynurenine tryptophan degradation still show immunosuppressive outcome (160; 73) due to not only Kyn but also TGFbeta stimulated long term responses. DC vaccination with IDO plausible (161) due to its power in immune response changes and longevity in the bloodstream for reversing the system for Th17 production (162).

Clinical Interventions are taking advantage of the DC’s central role and combining with enhancing molecules for induction of immunity may overcome tolerogenic DCs in tumors of cancers (163; 164).

The first successful application of DC vaccine used against advanced melanoma after loading DCs with tumor peptides or autologous cell lysate in presence of adjuvants keyhole limpet hematocyanin (KLH) (165).  Previous animal and clinical studies show use of DCs against tumors created success (165; 166; 167) as well as some problems due to heterogeneity of DC populations in one study supporting tumor growth rather than diminishing (168).

DC vaccination applied onto over four thousand clinical trial but none of them used siRNA-IDO DC vaccination method. Clinical trials evaluating DCs loaded ex vivo with purified TAAs as an anticancer immunotherapeutic interventions also did not include IDO (Table from (169). This table presented the data from 30 clinical trials, 3 of which discontinued, evaluating DCs loaded ex vivo with TAAs as an anticancer immunotherapy for 12 types of cancer [(AML(1), Breast cancer (4), glioblastoma (1), glioma (2), hepatocellular carcinoma (1), hematological malignancies (1), melanoma (6), neuroblastoma sarcoma (2), NSCLC (1), ovarian cancer (3), pancreatic cancer (3), prostate cancer (10)] at phase I, II or I/II.

Tipping the balance between Treg and Th17 ratio has a therapeutic advantage for restoring the health that is also shown in ovarian cancer by DC vaccination with adjuvants (161).  This rebalancing of the immune system towards immunogenicity may restore Treg/Th17 ratio (162; 170) but it is complicated. The stimulation of IL10 and IL12 induce Treg produce less Th17 and inhibiting CTL activation and its function (76; 171; 172) while animals treated with anti-TGFb before vaccination increase the plasma levels of IL-15 for tumor specific T cell survival in vivo (173; 174) ovarian cancer studies after human papilloma virus infection present an increase of IL12 (175).

Opposing signal mechanism downregulates the TGFb to activate CTL and Th1 population with IL12 and IL15 expression (162; 173).  The effects of IL17 on antitumor properties observed by unique subset of CD4+ T cells (176) called also CD8+ T cells secrete even more IL17 (177).

Using cytokines as adjuvants during vaccination may improve the efficacy of vaccination since cancer vaccines unlike infections vaccines applied after the infection or disease started against the established adoptive immune response.  Adjuvants are used to improve the responses of the given therapies commonly in immunotherapy applications as a combination therapy (178).

Enhancing cancer vaccine efficacy via modulation of the microenvironment is a plausible solution if only know who are the players.  Several molecules can be used to initiate and lengthen the activity of intervention to stimulate IDO expression without compromising the mechanism (179).  The system is complicated so generally induction is completed ex-vivo stimulation of DCs in cell lysates, whole tumor lysates, to create the microenvironment and natural stimulatory agents. Introduction of molecules as an adjuvants on genetic regulation on modulation of DCs are critical, because order and time of the signals, specific location/ tissue, and heterogeneity of personal needs (174; 138; 180). These studies demonstrated that IL15 with low TGFb stimulates CTL and Th1, whereas elevated TGFb with IL10 increases Th17 and Tregs in cancer microenvironments.

IDO and signaling gene regulation

For example Ret-peptide antitumor vaccine contains an extracellular fragment of Ret protein and Th1 polarized immunoregulator CpG oligonucleotide (1826), with 1MT, a potent inhibitor of IDO, brought a powerful as well as specific cellular and humoral immune responses in mice (152).

The main idea of choosing Ret to produce vaccine in ret related carcinomas fall in two criterion, first choosing patients self-antigens for cancer therapy with a non-mutated gene, second, there is no evidence of genetic mutations in Ret amino acids 64-269. Demonstration of proliferating hemangiomas, benign endothelial tumors and often referred as hemangiomas of infancy appearing at head or neck, express IDO and slowly regressed as a result of immune mediated process.

After large scale of genomic analysis show insulin like growth factor 2 as the key regulator of hematoma growth (Ritter et al. 2003). We set out to develop new technology with our previous expertise in immunotherapy and immunomodulation (181; 182; 183; 184), correcting Th17/Th1 ratio (185), and siRNA technology (186; 187).  We developed siRNA-IDO-DCvax. Patented two technologies “Immunomodulation using Altered DCs (Patent No: US2006/0165665 A1) and Method of Cancer Treatments using siRNA Silencing (Patent No: US2009/0220582 A1).

In melanoma cancer DCs were preconditioned with whole tumor lysate but in breast cancer model pretreatment completed with tumor cell lysate before siRNA-IDO-DCvax applied. Both of these studies was a success without modifying the autanticity of DCs but decreasing the IDO expression to restore immunegenity by delaying tumor growth in breast cancer (147) and in melanoma (188).  Thus, our DCvax specifically interfere with Ido without disturbing natural structure and content of the DCs in vivo showed that it is possible to carry on this technology to clinical applications.

Furthermore, our method of intervention is more sophisticated since it has a direct interaction mechanism with ex-vivo DC modulation without creating long term metabolism imbalance in Trp/Kyn metabolite mechanisms since the action is corrective and non-invasive.

There were several reasons.

First, prevention of tumor development studies targeting non-enzymatic pathway initiated by pDCs conditioned with TGFbeta is specific to IDO1 (189).

Second, IDO upregulation in antigen presenting cells allowing metastasis show that most human tumors express IDO at high levels (123; 124).

Third, tolerogenic DCs secretes several molecules some of them are transforming growth factor beta (TGFb), interleukin IL10), human leukocyte antigen G (HLA-G), and leukemia inhibitory factor (LIF), and non-secreted program cell death ligand 1 (PD-1 L) and IDO, indolamine 2.3-dioxygenase, which promote tumor tolerance. Thus, we took advantage of DCs properties and Ido specificity to prevent the tolerogenicity with siRNA-IDO DC vaccine in both melanoma and breast cancer.

Fourth, IDO expression in DCs make them even more potent against tumor antigens and create more T cells against tumors. IDOs are expressed at different levels by both in broad range of tumor cells and many subtypes of DCs including monocyte-derived DCs (10), plasmacytoid DCs (142), CD8a+ DCs (190), IDO compotent DCs (17), IFNgamma-activated DCs used in DC vaccination.  These DCs suppress immune responses through several mechanisms for induction of apoptosis towards activated T cells (156) to mediate antigen-specific T cell anergy in vivo (142) and for enhancement of Treg cells production at sites of vaccination with IDO-positive DCs+ in human patients (142; 191; 192; 168; 193; 194). If DCs are preconditioned with tumor lysate with 1MT vaccination they increase DCvax effectiveness unlike DCs originated from “normal”, healthy lysate with 1MT in pancreatic cancer (195).  As a result, we concluded that the immunesupressive effect of IDO can be reversed by siRNA because Treg cells enhances DC vaccine-mediated anti-tumor-immunity in cancer patients.

Gene silencing is a promising technology regardless of advantages simplicity for finding gene interaction mechanisms in vitro and disadvantages of the technology is utilizing the system with specificity in vivo (186; 196).  siRNA technology is one of the newest solution for the treatment of diseases as human genomics is only producing about 25,000 genes by representing 1% of its genome. Thus, utilizing the RNA open the doors for more comprehensive and less invasive effects on interventions. Thus this technology is still improving and using adjuvants. Silencing of K-Ras inhibit the growth of tumors in human pancreatic cancers (197), silencing of beta-catenin in colon cancers causes tumor regression in mouse models (198), silencing of vascular endothelial growth factor (VGEF) decreased angiogenesis and inhibit tumor growth (199).

Combining siRNA IDO and DCvax from adult stem cell is a novel technology for regression of tumors in melanoma and breast cancers in vivo. Our data showed that IDO-siRNA reduced tumor derived T cell apoptosis and tumor derived inhibition of T cell proliferation.  In addition, silencing IDO made DCs more potent against tumors since treated or pretreated animals showed a delay or decreased the tumor growth (188; 147)

 

Clinical Trials:

First FDA approved DC-based cancer therapies for treatment of hormone-refractory prostate cancer as autologous cellular immunotherapy (163; 164).  However, there are many probabilities to iron out for a predictive outcome in patients.

Table 2 demonstrates the current summary of clinical trials report.  This table shows 38 total studies specifically Ido related function on cancer (16), eye (3), surgery (2), women health (4), obesity (1), Cardiovascular (2), brain (1), kidney (1), bladder (1), sepsis shock (1), transplant (1),  nervous system and behavioral studies (4), HIV (1) (Table 4).  Among these only 22 of which active, recruiting or not yet started to recruit, and 17 completed and one terminated.

Most of these studies concentrated on cancer by the industry, Teva GTC ( Phase I traumatic brain injury) Astra Zeneca (Phase IV on efficacy of CRESTOR 5mg for cardiovascular health concern), Incyte corporation (Phase II ovarian cancer) NewLink Genetics Corporation Phase I breast/lung/melanoma/pancreatic solid tumors that is terminated; Phase II malignant melanoma recruiting, Phase II active, not recruiting metastatic breast cancer, Phase I/II metastatic melanoma, Phase I advanced malignancies) , HIV (Phase IV enrolling by invitation supported by Salix Corp-UC, San Francisco and HIV/AIDS Research Programs).

Many studies based on chemotherapy but there are few that use biological methods completed study with  IDO vaccine peptide vaccination for Stage III-IV non-small-cell lung cancer patients (NCT01219348), observational study on effect of biological therapy on biomarkers in patients with untreated hepatitis C, metastasis melanoma, or Crohn disease by IFNalpha and chemical (ribavirin, ticilimumab (NCT00897312), polymorphisms of patients after 1MT drug application in treating patients with metastatic or unmovable refractory solid tumors by surgery (NCT00758537), IDO expression analysis on MSCs (NCT01668576), and not yet recruiting intervention with adenovirus-p53 transduced dendric cell vaccine , 1MT , radiation, Carbon C 11 aplha-methyltryptophan- (NCT01302821).

Among the registered clinical trials some of them are not interventional but  observational and evaluation studies on Trp/Kyn ratio (NCT01042847), Kyn/Trp ratio (NCT01219348), Kyn levels (NCT00897312, NCT00573300),  RT-PCR analysis for Kyn metabolism (NCT00573300, NCT00684736, NCT00758537), and intrinsic IDO expression of mesenchymal stem cells in lung transplant with percent inhibition of CD4+ and CD8+ T cell proliferation toward donor cells (NCT01668576), determining polymorphisms (NCT00426894). These clinical trials/studies are immensely valuable to understand the mechanism and route of intervention development with the data collected from human populations   

Future Actions for Molecular Dx and Targeted Therapies:

Viable tumor environment. Tumor survival is dependent upon an exquisite interplay between the critical functions of stromal development and angiogenesis, local immune suppression and tumor tolerance, and paradoxical inflammation. TEMs: TIE-2 expressing monocytes; “M2” TAMs: tolerogenic tumor-associated macrophages; MDSCs: myeloid-derived suppressor cells; pDCs: plasmacytoid dendritic cells; co-stim.: co-stimulation; IDO: indoleamine 2,3-dioxygenase; VEGF: vascular endothelial growth factor; EGF: epidermal growth factor; MMP: matrix metaloprotease; IL: interleukin; TGF-β: transforming growth factor-beta; TLRs: toll-like receptors.  (reference: http://www.hindawi.com/journals/cdi/2012/937253/fig1/)

Viable tumor environment. Tumor survival is dependent upon an exquisite interplay between the critical functions of stromal development and angiogenesis, local immune suppression and tumor tolerance, and paradoxical inflammation. TEMs: TIE-2 expressing monocytes; “M2” TAMs: tolerogenic tumor-associated macrophages; MDSCs: myeloid-derived suppressor cells; pDCs: plasmacytoid dendritic cells; co-stim.: co-stimulation; IDO: indoleamine 2,3-dioxygenase; VEGF: vascular endothelial growth factor; EGF: epidermal growth factor; MMP: matrix metaloprotease; IL: interleukin; TGF-β: transforming growth factor-beta; TLRs: toll-like receptors. (reference: http://www.hindawi.com/journals/cdi/2012/937253/fig1/)

Current survival or response rate is around 40 to 50 % range.  By using specific cell type, selected inhibition/activation sequence based on patient’s genomic profile may improve the efficacy of clinical interventions on cancer treatments. Targeted therapies for specific gene regulation through signal transduction is necessary but there are few studies with genomics based approach.

On the other hand, there are surveys, observational or evaluations (listed in clinical trials section) registered with www.clinicaltrials.gov that will provide a valuable short-list of molecules.  Preventing stimulation of Ido1 as well as Tgfb-1gene expression by modulating receptor mediated phosphorylation between TGFb/SMAD either at Mad-Homology 1 (MH1) or Mad-Homology 1 (MH2) domains maybe possible (79; 82; 80). Within Smads are the conserved Mad-Homology 1 (MH1) domain, which is a DNA binding module contains tightly bound Zinc atom.

Smad MH2 domain is well conserved and one the most diverse protein-signal interacting molecule during signal transduction due to two important Serine residues located extreme distal C-termini at Ser-Val-Ser in Smad 2 or at pSer-X-PSer in RSmads (80). Kyn activated orphan G protein–coupled receptor, GPR35 with unknown function with a distinct expression pattern that collides with IDO sites since its expression at high levels of the immune system and the gut (63) (200; 63).  

The first study to connect IDO with cancer shows that group (75).  The directly targeting to regulate IDO expression is another method through modulating ISREs in its promoter with RNA-peptide combination technology. Indirectly, IDO can be regulated through Bin1 gene expression control over IDO since Bin1 is a negative regulator of IDO and prevents IDO expression.  IDO is under negative genetic control of Bin1, BAR adapter–encoding gene Bin1 (also known as Amphiphysin2). Bin1 functions in cancer suppression since attenuation of Bin1 observed in many human malignancies (141; 201; 202; 203; 204; 205; 206) .  Null Bin-/- mice showed that when there is lack of Bin1, upregulation of IDO through STAT1- and NF-kB-dependent expression of IDO makes tumor cells to escape from T cell–dependent antitumor immunity.

This pathway lies in non-enzymatic signal transducer function of IDO after stimulation of DCs by TGFb1.  The detail study on Bin1 gene by alternative spicing also provided that Bin1 is a tumor suppressor.  Its activities also depends on these spliced outcome, such as  Exon 10, in muscle, in turn Exon 13 in mice has importance in role for regulating growth when Bin1 is deleted or mutated C2C12 myoblasts interrupted due to its missing Myc, cyclinD1, or growth factor inhibiting genes like p21WAF1 (207; 208).

On the other hand alternative spliced Exon12A contributing brain cell differentiation (209; 210). Myc as a target at the junction between IDO gene interaction and Trp metabolism.  Bin1 interacts with Myc either early-dependent on Myc or late-independent on Myc, when Myc is not present. This gene regulation also interfered by the long term signaling mechanism related to Kynurenine (Kyn) acting as an endogenous ligand to AHR in Trp metabolite and TGFb1 and/or IFNalpha and IFNbeta up regulation of DCs to induce IDO in noncanonical pathway for NF-kB and myc gene activations (73; 74).  Hence, Trp/Kyn, Kyn/Trp, Th1/Th17 ratios are important to be observed in patients peripheral blood. These direct and indirect gene interactions place Bin1 to function in cell differentiation (211; 212; 205).

Regulatory T-cel generation via reverse and non-canonical signaliing to pDCs

Table 3 contains the microarray analysis for Kyn affect showed that there are 25 genes affected by Kyn, two of which are upregulated and 23 of them downregulated (100). This list of genes and additional knowledge based on studies creating the diagnostics panel with these genes as a biomarker may help to analyze the outcomes of given interventions and therapies. Some of these molecules are great candidate to seek as an adjuvant or co-stimulation agents.  These are myc, NfKB at IKKA, C2CD2, CREB3L2, GPR115, IL2, IL8, IL6, and IL1B, mir-376 RNA, NFKB3, TGFb, RelA, and SH3RF1. In addition, Lip, Fox3P, CTLA-4, Bin1, and IMPACT should be monitored.

In addition, Table 4 presents the other possible mechanisms. The highlights of possible target/biomarkers are specific TLRs, conserved sequences of IDO across its homologous structures, CCR6, CCR5, RORgammat, ISREs of IDO, Jak, STAT, IRFs, MH1 and MH2 domains of Smads. Endothelial cell coagulation activation mechanism and pDC maturation or immigration from lymph nodes to bloodstream should marry to control not only IDO expression but also genesis of preferred DC subsets. Stromal mesenchymal cells are also activated by these modulation at vascular system and interferes with metastasis of cancer. First, thrombin (human factor II) is a well regulated protein in coagulation hemostasis has a role in cell differentiation and angiogenesis.

Protein kinase activated receptors (PARs), type of GPCRs, moderate the actions. Second, during hematopoietic response endothelial cells produce hematopoietic growth factors (213; 214). Third, components of bone marrow stroma cells include monocytes, adipocytes, and mesenchymal stem cells (215). As a result, addressing this issue will prevent occurrence of coagulapathologies, namely DIC, bleeding, thrombosis, so that patients may also improve response rate towards therapies. Personal genomic profiles are powerful tool to improve efficacy in immunotherapies since there is an influence of age (young vs. adult), state of immune system (innate vs. adopted or acquired immunity). Table 5 includes some of the current studies directly with IDO and indirectly effecting its mechanisms via gene therapy, DNA vaccine, gene silencing and adjuvant applications as an intervention method to prevent various cancer types.

CONCLUSION

IDO has a confined function in immune system through complex interactions to maintain hemostasis of immune responses. The genesis of IDO stem from duplication of bacterial IDO-like genes.  Inhibition of microbial infection and invasion by depleting tryptophan limits and kills the invader but during starvation of trp the host may pass the twilight zone since trp required by host’s T cells.  Thus, the host cells in these small pockets adopt to new microenvironment with depleted trp and oxygen poor conditions. Hence, the cell metabolism differentiate to generate new cellular structure like nodules and tumors under the protection of constitutively expressed IDO in tumors, DCs and inhibited T cell proliferation.

On the other hand, having a dichotomy in IDO function can be a potential limiting factor that means is that IDOs impact on biological system could be variable based on several issues such as target cells, IDO’s capacity, pathologic state of the disease and conditions of the microenvironment. Thus, close monitoring is necessary to analyze the outcome to prevent conspiracies since previous studies generated paradoxical results.

Current therapies through chemotherapies, radiotherapies are costly and effectiveness shown that the clinical interventions require immunotherapies as well as coagulation and vascular biology manipulations for a higher efficacy and survival rate in cancer patients. Our siRNA and DC technologies based on stem cell modulation will provide at least prevention of cancer development and hopefully prevention in cancer.

11.       References

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2. Molecular insights into substrate recognition and catalysis by indolamine 2,3-dioxygenase. Forouhar, F., Anderson, R., Mowat, C.F, et al. 2006, PNAS, pp. vol. 104, no:2, 473-478.

3. Importance of the Two Interferon-stimulated Response Element. Konan KV, Taylor, MW. 1996, J. Biol. Chem.-, pp. 19140-5.

4. Induction of indolamine 2,3 dioxygenase: A mechanism of the anti-tumor activity of interferon gamma. Ozaki, Y., Edelstein, M.P., Duch, D.S. 1998, PNAS USA., pp. vol:85, 1242-1246.

5. Localization of the human indoleamine 2,3-dioxygenase (IDO) gene to the pericentromeric region of human chromosome . Burkin, D. J., Kimbro, K. S., Barr, B. L., Jones, C., Taylor, M. W., Gupta, S. L. 1993, Genomics , pp. 17: 262-263.

6. Localization of indoleamine 2,3-dioxygenase gene (INDO) to chromosome 8p12-p11 by fluorescent in situ hybridization. Najfeld, V., Menninger, J., Muhleman, D., Comings, D. E., Gupta, S. L. 1993, Cytogenet. Cell Genet. , pp. 64: 231-232.

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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

Hepatocellular carcinoma is one of the most common malignancies worldwide, and it has a poor prognosis due to its rapid development and early metastasis. An understanding of tumor metabolism would be helpful for the clinical diagnosis and therapy of hepatocellular carcinoma. Chronic hepatitis B virus infection is the primary risk factor for hepatocellular carcinoma, and the majority of hepatocellular carcinoma cases develop from hepatitis infections and subsequent cirrhosis. Rapid development and early metastasis are the typical characteristics of hepatocellular carcinoma, which always results in a poor prognosis. Therefore, investigating the hepatocarcinogenesis mechanism is very important for decreasing the incidence and mortality of hepatocellular carcinoma. The abnormal metabolism of cancer has been considered an important characteristic of tumors, which could clarify the pathogenesis and provide potential therapeutic targets for clinical treatments. According to the Warburg effect, the deregulated energy metabolism of cancer cells may also modify many related metabolic pathways that influence various biological processes, such as cell proliferation and apoptosis. As a common characteristic of cancer cells, modified metabolism has been the focus of cancer research.

Because of its asymptomatic nature, hepatocellular carcinoma is usually diagnosed at late and advanced stages, for which there are no effective therapies. Thus, biomarkers for early detection and molecular targets for treating hepatocellular carcinoma are urgently needed. Emerging high-throughput metabolomics technologies have been widely applied, aiming at the discovery of candidate biomarkers for cancer staging, prediction of recurrence and prognosis, and treatment selection. Tissue metabolomics is a useful tool for studying the abnormal metabolisms of diseases, and it can provide information about the metabolic modifications and the upstream regulative mechanism in diseases. More importantly, the systemic metabolic characteristics of tissues could provide opportunities for exploring novel diagnostic markers or therapeutic targets for clinical applications. Tissue metabolomics is conducted using a pairwise comparison of different parts of tissue from each patient, which can remove individual differences, such as age, sex, region, etc. The differences between the tumor cells and their surrounding host cells may reflect the interactions of the tumor and the host, which are important clues for studying the invasion and metastasis of tumors. Metabolic profiles, which are affected by many physiological and pathological processes, may provide further insight into the metabolic consequences of this severe liver disease. Small-molecule metabolites have an important role in biological systems and represent attractive candidates to understand hepatocellular carcinoma phenotypes. The power of metabolomics allows an unparalleled opportunity to query the molecular mechanisms of hepatocellular carcinoma.

Source References:

http://www.ncbi.nlm.nih.gov/pubmed/23824744

http://www.ncbi.nlm.nih.gov/pubmed/23150189

http://onlinelibrary.wiley.com/doi/10.1002/hep.26350/abstract

http://www.ncbi.nlm.nih.gov/pubmed/21114800

http://www.ncbi.nlm.nih.gov/pubmed/19305372

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