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Heroes in Basic Medical Research – Robert J. Lefkowitz

Posted in Cardiovascular Pharmacogenomics, Cell Biology, Chemical Biology and its relations to Metabolic Disease, Clinical & Translational, Curation, Disease Biology, Frontiers in Cardiology and Cardiovascular Disorders, Gene Regulation, Genomic Endocrinology, Genomics Pharmacy, Historical relevance, Innovations in Neurophysiology & Neuropsychology, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Analytics, Pharmaceutical Drug Discovery, Technology Advance Assessment of, tagged , , on September 6, 2015| Leave a Comment »

Heroes in Basic Medical Research – Robert J. Lefkowitz

Author & Curator: Larry H Bernstein, MD, FCAP

Robert J. Lefkowitz, MD

Robert J. Lefkowitz MD, a Howard Hughes Medical Institute investigator who has spent his entire 39-year research career at the Duke University Medical Center, is sharing the 2012 Nobel Prize in Chemistry with Brian K. Kobilka of Stanford University School of Medicine, who was a post-doctoral fellow in Lefkowitz’s lab in the 1980s.

They are being recognized for their work on a class of cell surface receptors that have become the target of prescription drugs, including antihistamines, ulcer drugs and beta blockers to relieve hypertension, angina and coronary disease.

The receptors catch chemical signals from the outside and transmit their messages into the cell, providing the cell with information about changes occurring within the body. These particular receptors are called seven-transmembrane G protein-coupled receptors, or just “G-coupled receptors” for short. Serpentine in appearance, G-coupled receptors weave through the surface of the cell seven times.

The human genome contains code to make at least 1,000 different forms of these trans-membrane receptors, all of which are quite similar. The receptors also bear a strong resemblance to receptors that detect light in the eyes, smells in the nose and taste on the tongue. (See playlist of Lefkowitz science videos here.)

“Bob’s seminal discoveries related to G-protein coupled receptors ultimately became the basis for a great many medications that are in use today across many disease areas,” said Victor J. Dzau, MD, Chancellor for Health Affairs and CEO, Duke University Health System.  “He is an outstanding example of a physician-scientist whose impact can be seen in the lives of the countless patients who have benefited from his scientific discoveries. We are very proud of his magnificent achievements and grateful for his many contributions to Duke Medicine.”

After attending public elementary and junior high schools I entered The Bronx High School of Science (10th grade) in the autumn of 1956, graduating at age 16 in 1959. “Bronx Science” is one of several public high schools in New York City which admits students on the basis of a competitive examination. The student body, representing approximately the top 5% based on the exam, are gifted and interested in science and math. The accomplishments of graduates of this high school are quite remarkable. For example, I am the 8th Nobel Laureate to have graduated from this school, the 7 previous ones having received their prizes in Physics. For me, attending this school was a formative experience. Whereas in elementary and junior high school I was not greatly challenged, here I was among a group of remarkably bright, interesting and stimulating classmates. The curriculum featured many advanced classes at the college level. I was particularly drawn to chemistry and, as a result of taking these college level classes, I was able to receive full credit for two years of chemistry when I entered Columbia College in 1959. Thus I began as a college freshman with organic chemistry, a course generally taken by juniors.

The level of scholarship maintained by the student body was such that even with an average of about 94% my final class rank was about 100th out of 800. A classmate and friend at the time and at present, the famous geneticist David Botstein, had an almost identical average, a fact we tease each other about to this day.

Along with dozens of classmates, I moved on to Columbia University where I enrolled as a pre-medical student majoring in chemistry. The two year core curriculum in “Contemporary Civilization” was required of all students. With an emphasis on reading classic texts in history, philosophy, sociology and the political sciences and discussing these in small seminars, it was for me an opening to a whole new world. In addition, I took courses with and was exposed to, such intellectual giants as the literary critic Lionel Trilling, the cultural historian Jacques Barzun and the sociologist Daniel Bell, among others. I have very fond memories from this period of spending many hours in the public reading room at the 42nd Street New York Public Library, researching papers for those classes.

I also studied advanced Organic Chemistry with Cheves Walling and Physical Chemistry in a department which was strongly influenced by the then recently retired prominent physical organic chemist, Louis Hammett. However, the chemistry professor who had the most profound influence on me was actually a young Assistant Professor of Chemistry, Ronald Breslow. As a college senior I took an advanced seminar in biochemistry which he taught single handedly. This introduction to the chemistry of processes in living organisms really excited me in part, I suspect, because of his very lively teaching style. None of this, however, in any way diverted me from my goal of studying to become a practicing physician.

I greatly enjoyed my four years in medical school. I had dreamed about becoming a physician since grade school and now I was finally doing it. As a freshman immersed in the basic medical sciences I was able to deepen my interest in, and fascination with, biochemistry. Our biochemistry professors included a remarkable array of scholars (not that any of us appreciated that at the time). We heard lectures on metabolism from David Rittenberg, Chair of the Department; from David Shemin on porphyrins; from Irwin Chargaff on nucleic acids; and from David Nachmansohn on cholinergic neurotransmission.

One young professor left a lasting impression on me. Paul Marks was then a young academic hematologist who taught the Introduction to Clinical Medicine course in which we studied clinical problems for the first time, examined case histories, and looked at blood specimens. Not only was he a good clinician but he assigned readings from the basic science literature that were relevant in a very meaningful way to the cases we studied. This showed me how scientific information could be brought to bear on clinical problems. Among my classmates and friends in medical school was Harold Varmus, who was the co-recipient of the 1989 Nobel Prize for the discovery of oncogenes.

On July 1, 1968 I moved my family (now including the recently born Cheryl) to Rockville, Maryland to begin my research career at the NIH in nearby Bethesda, Maryland. I had been assigned, through a matching program, to work with Drs. Jesse Roth and Ira Pastan in the Clinical Endocrinology Branch of the National Institute of Arthritis and Metabolic Diseases (NIAMD), now known as NIDDK, the National Institute of Diabetes and Digestive and Kidney Diseases. I was a Clinical Associate, meaning that in addition to doing full time research ten months out of the year, for two months I also supervised a clinical endocrinology in-patient service. Because of this, I gained a remarkable exposure to unusual endocrine diseases which were under study at the time. An example of this was acromegaly.

It was the heyday of interest in second messenger signaling after the discovery of cAMP by Earl Sutherland. He would receive the Nobel Prize in Medicine and Physiology for this in 1971. One hormone after another was being shown to stimulate the enzyme adenylate cyclase thus increasing intracellular levels of cAMP. The idea that these different hormones might work through distinct receptors was talked about but was controversial. Moreover, at the time there were no direct methods for studying the receptors. I was assigned the challenging task of developing a radioligand binding method to study the putative receptors for adrenocorticotropic hormone (ACTH) in plasma membranes derived from an ACTH responsive adrenocortical carcinoma passaged in nude mice.

Recently, two Nobel Laureates, Mike Brown and Joe Goldstein, published a brief essay discussing the remarkable number of Nobel Laureates (9 so far) who have in common the fact that they came to the NIH as physicians during the brief space between 1964–1972 for postdoctoral research training. (1)

They dissect the unique convergence of circumstances which may have been responsible for this extraordinary result, including the quality of basic science mentors on the full time NIH staff, the competitiveness of “the best and the brightest” to obtain these positions during the Vietnam War years, and the now bygone emphasis on teaching of basic sciences in medical schools in the 1960s.

Lineages among Nobel Laureates are often commented upon. In my case, Jesse Roth had trained with Solomon Berson and Rosalyn Yalow whose development of radioimmunoassay led to the Nobel Prize in Medicine and Physiology to Yalow (1977) after Berson’s untimely death in 1972. Moreover, training in Ira Pastan’s laboratory contemporaneously with me was my medical school and house staff classmate and future Nobel Laureate, Harold Varmus. Ira had himself trained in the lab of another NIH career scientist, Earl Stadtman, who also trained a future Nobel Laureate, Mike Brown.

Dr. Edgar Haber, the Chief of Cardiology and a prominent immunochemist, allowed me to begin working in his lab. I was fascinated by receptors and what I saw as their potential to form the basis for a whole new field of research just waiting to be explored. I spent a great deal of time analyzing which receptor I should attempt to study. As an aspiring academic cardiologist I wanted to work on something related to the cardiovascular system. I also wanted a receptor known to be coupled to adenylate cyclase. I initially focused on two models, the cardiac glucagon and β-adrenergic receptors. However, my attention quickly became focused on the latter, for very practical reasons. Unlike the case for peptide hormones such as glucagon or ACTH, literally dozens, if not hundreds of analogs of adrenaline and noradrenaline, as well as their antagonists were available which could be chemically modified to develop the types of new tools which would need to be developed to study the receptors. These would include radioligands, photoaffinity probes, affinity chromatography matrices and the like. Moreover, the first β-adrenergic receptor blocker (“β-blocker”) had recently been approved for clinical use in the United States, adding further to the attractiveness of this target to me.

So in the early months of 1971 I began the quest to prove the existence of β-adrenergic receptors, to study their properties, to learn about their chemical nature, how they were regulated and how they functioned. This work has consumed me for the past forty years. Over the next several years in Boston, working mostly with membrane fractions derived from canine myocardium, I sought to develop radioligand binding approaches to tag the β-adrenergic receptors. I focused initially on the use of [3H]labeled catecholamines such as norepinephrine, which are agonists for the receptor. Specific saturable binding could be demonstrated, and I thought initially that we had developed a valid approach to label the receptors. However, it became increasingly clear over the next few years that the sites being labeled lacked many of the properties that would be expected for true physiological receptor binding sites. Coming to this realization was difficult.

During this time I also published some of the very first studies demonstrating GTP regulation of β-adrenergic receptor stimulated adenylate cyclase following after the work of Martin Rodbell on GTP regulation of glucagon sensitive adenylate cyclase. I was now a cardiology fellow. As at the NIH, nights on call were often spent in the lab doing experiments while hoping that my on call beeper would remain quiet. During these years, I had many stimulating and profitable discussions with Geoffrey Sharpe, a faculty member in the Nephrology Division with an interest in cell signaling and adenylate cyclase.

In work with postdoc Marc Caron in the spring of 1974, we succeeded in developing [3H]dihydroalprenolol. Contemporaneously, Gerald Aurbach at the NIH, and Alex Levitzki at the Hebrew University in Jerusalem also developed similar approaches using different radioligands. This was a watershed event because it finally opened the door to direct study of the receptors. Together with M.D./Ph.D. student Rusty Williams we developed comparable assays for the α-adrenergic receptors shortly thereafter.

Brian Kent Kobilka is an American physiologist and a corecipient of the 2012 Nobel Prize in Chemistry with Robert Lefkowitz for discoveries that reveal the inner workings of an important family G protein-coupled receptors.

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Sequencing yourself! and Learn more on Genome Sequencing on Tuesday, November 17, 2015 from 8am-5pm in the Joseph B. Martin Conference Center of the Harvard New Research Building at Harvard Medical School

Posted in Conference Coverage with Social Media, Gene Regulation, Gene Regulation and Evolution, Genetics & Innovations in Treatment, Genetics & Pharmaceutical, Genome Biology, Genomic Endocrinology, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Next Generation Sequencing (NGS), Personalized and Precision Medicine & Genomic Research, Scientific & Biotech Conferences: Press Coverage on July 7, 2015| Leave a Comment »

 Sequencing yourself! and Learn more on Genome Sequencing on Tuesday, November 17, 2015 from 8am-5pm in the Joseph B. Martin Conference Center of the Harvard New Research Building at Harvard Medical School, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

Sequencing yourself! and Learn more on Genome Sequencing on Tuesday, November 17, 2015 from 8am-5pm in the Joseph B. Martin Conference Center of the Harvard New Research Building at Harvard Medical School

Reporter: Aviva Lev-Ari, PhD, RN

Become one of the first humans to have your entire genome sequenced, while participating in an interactive set of presentations and debates about the promise and limitations of genome sequencing from some of the world’s leading genomic scientists.

The UYG Boston is an invitation-only, interactive symposium in which approximately 60 leaders from the Boston business and academic communities will have the opportunity to undergo whole genome sequencing, and to explore their own genome as part of an all-day educational conference with exciting presentations, debates and comments from some of the most thought-provoking leaders in the field of sequencing, informatics and genomic medicine.

Co-sponsors:

  • Brigham Genome Medicine, Brigham and Women’s Hospital
  • Partners Personalized Medicine and Laboratory for Molecular Medicine
  • Precision Medicine Program at Brigham and Women’s Hospital
  • Department of Pathology at Brigham and Women’s Hospital
  • Analytic and Translational Genetics Unit, Massachusetts General Hospital
  • The Broad Institute of Harvard and MIT
  • Department of Pathology at Massachusetts General Hospital
  • Division of Genetics, Department of Medicine, Brigham and Women’s Hospital

http://uygboston.uygsymposium.com/

 

Draft Agenda for UYG Agenda, November 17, 2015, NRB Rotunda Room

Registration is still open at this link: http://uygboston.uygsymposium.com

Breakfast and Registration

7:30-8:30

Module 1: Understanding the Basics of Genetics and Genomics

 

Moderator: __________________________________

8:30 am -9:55 am

(10) Robert Green: Welcome and Introductory Remarks

(20) Stacey Gabriel: Technical Overview of Sequencing, Alignment and Variant Calling

(20) Heidi Rehm: Variant Classification and Lab Reporting: the Good, the Bad and the VUS

(20) Daniel MacArthur: Using Large Datasets to Explore Penetrance

(15) Questions and Discussion

Coffee Break

9:55 am – 10:10 am

Module 2: Sequencing and Informatics in Clinical Care

 

Moderator: __________________________________

10:10 am-11:30 noon

(20) Dick Maas: Sequencing in Undiagnosed Cases

(20) Kricket Seidman: Sequencing in the Care of Specific Diseases (Cardiomyopathy)

(20) Zak Kohane: Sequencing and Informatics

(20) Discussion

Luncheon: Understand Your Genome®

11:30 noon – 1:00 pm

Pechet Room

Lunch for those who have been sequenced or wish to learn to use the MyGenome web portal with the demo genome (seating is limited to 40 WGS attendees + 10 additional attendees):

(30) Erica Ramos: Clinical Whole Genome Sequencing in a Healthy Population

(30) Erica Ramos: MyGenome Web Portal Revealed

(30) Erica Ramos and Genetic Counselors: Holding and Exploring Your Own Genome

Lunch served separately for those who do not wish to explore MyGenome Web App

Module 3: Sequencing in Research: from Discovery to Patient Care

 

Moderator: __________________________________

1:00 pm – 2:40 pm

(10) Jeff Flier: Afternoon welcome and remarks

(20) Sek Kathiresan: Developing Medicines that Mimic Natural Genomic Successes

(20) Calum MacRae: Global Phenotyping and the Clinic of the Future

(10) Heidi Rehm: ClinGen and Matchmaker Exchange

(20) Robert Green: Clinical Outcomes Research in Sequencing

(20) Discussion

Module 4: Academic Medical Centers and Personalized/Precision Medicine

 

Moderator: __________________________________

2:40- 3:35

(15) Betsy Nabel: Direct-to Consumer Sequencing and the Academic Medical Center

(20) Jeff Golden: Precision Medicine, Regulation and Reimbursement

(20) Discussion

Afternoon Break

3:35-3:50

Module 5: Debate on the Benefits, Harms and Costs of Sequencing Health Individuals by Individual Speakers with the Entire Panel of Speakers and the Attendees

3:50-4:55

Five Minute Pro or Con by Each Speaker and Select Audience Members, Followed by Debate

 

“DNA Team” Captains: “There is Benefit” Jeff Golden/Jeff Flier

“RNA Team” Captains: “There is No Benefit” Sek Kathiresan/Betsy Nabel

Closing Remarks

4:55 – 5:00

(5) Robert Green

Wine and Cheese Reception for Speakers and Attendees

5:00-6:00

Registration

– See more at: http://personalizedmedicine.partners.org/education/personalized-medicine-conference/program.aspx#sthash.cnydkNG1.dpuf

Fee:

Register by July 15th to attend for $3,100!
After July 15th registration will be $3,500.

Pricing includes:

$2,900 TruGenome™ Predisposition Screen plus a conference registration fee

When:

November 17, 2015
General Session: 8am – 5pm
Reception: 5pm – 7pm

Where:

The Joseph B. Martin Conference Center
Harvard Medical School
77 Avenue Louis Pasteur
Boston, MA 02115

Confirmed Speakers

  • George Church, PhD,
    Harvard Medical School
  • Stacey Gabriel, PhD
    The Broad Institute
  • Jeff Golden, MD
    Brigham and Women’s Hospital
  • Robert Green, MD, MPH
    Brigham and Women’s Hospital
  • Sek Kathiresan, MD
    Massachusetts General Hospital
  • Zak Kohane, MD, PhD
    Harvard Medical School
  • Richard Maas, MD, PhD
    Brigham and Women’s Hospital
  • Daniel MacArthur, PhD
    Massachusetts General Hospital
  • Calum MacRae, MD
    Brigham and Women’s Hospital
  • Betsy Nabel, MD
    Brigham and Women’s Hospital
  • Heidi Rehm, PhD
    Laboratory of Molecular Medicine
  • Christine Seidman, MD
    Brigham and Women’s Hospital

SOURCE

From: Robert Green <rcgreen@genetics.med.harvard.edu>

Date: Tuesday, July 7, 2015 at 1:46 PM

Subject: Learn about genome sequencing by sequencing yourself!

Robert C. Green, MD, MPH

Director, G2P Research Program

Associate Director for Research, Partners Center for Personalized Genetic Medicine

Division of Genetics, Department of Medicine

Brigham and Women’s Hospital and Harvard Medical School

EC Alumnae Building, Suite 301, 41 Avenue Louis Pasteur, Boston, MA 02115                                    

(office) 617-264-5834, (fax) 617-264-3018, (cell) 617-966-3216

(email) rcgreen@genetics.med.harvard.edu 

(web) www.genomes2people.org

Dear Colleagues:

We are inviting you, as one of a small group of forward looking thought leaders, to attend an exciting educational and experiential event: the Boston “Understand your Genome” conference. This conference will take place the day before this year’s Partners Personalized Medicine Conference at Harvard Medical School and will have two components.

First, a panel of world-renowned speakers will discuss the current progress and promise of genomic medicine, and debate the controversial issues surrounding the sequencing of healthy individuals for prediction and prevention.

Second, the conference will provide you with the option to become one of the first people on the planet to have your whole genome sequenced at a CLIA facility where a report will be generated by a board certified molecular geneticist on 1,691 genes with well-established associations to 1,232 Mendelian conditions, and 11 genes associated with responses to 16 different medications.

This conference is a non-profit educational event that is sponsored by the Division of Genetics, in the Department of Medicine at Brigham and Women’s Hospital with co-sponsorship by Partners Personalized Medicine and the Laboratory for Molecular Medicine, the Precision Medicine Program at Brigham and Women’s Hospital, the Department of Pathology at Brigham and Women’s Hospital, the Analytic and Translational Genetics Unit at Massachusetts General Hospital, the Department of Pathology at Massachusetts General Hospital and the Broad Institute. Together, we have assembled a remarkable panel of speakers for the first component of the program.

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Announcing Four e-Books from BioMed e-Series: Series B,C,D,E: Genomics, Cancer, Metabolomics, Physiology & Therapeutics

Posted in Academic Publishing, Cancer and Current Therapeutics, CANCER BIOLOGY & Innovations in Cancer Therapy, Computational Biology/Systems and Bioinformatics, Curation, Gene Regulation, Gene Regulation and Evolution, Genetics & Innovations in Treatment, Genetics & Pharmaceutical, Genome Biology, Genomic Expression, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Intellectual Property, Metabolomics, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Drug Discovery, Pharmacogenomics, Population Health Management, Population Health Management, Genetics & Pharmaceutical, Population Health Management, Nutrition and Phytochemistry, Proteomics on March 10, 2015| Leave a Comment »

Announcing Four e-Books from BioMed e-Series: Series B,C,D,E: Genomics, Cancer, Metabolomics, Physiology & Therapeutics

Editor-in-Chief: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/biomed-e-books/

 

onepage series BCDE covers

 

About Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/10/16/editorial-publication-of-articles-in-e-books-by-leaders-in-pharmaceutical-business-intelligence-contributions-of-larry-h-bernstein-md-fcap/

About Stephen J Williams, PhD

http://pharmaceuticalintelligence.com/contributors-biographies/senior-editors/stephen-j-williams-phd-pharmacology-bsc-toxicology-expert-author-writer/

About Aviva Lev-Ari, PhD, RN, BioMed e-Series, Editor-in-Chief

http://pharmaceuticalintelligence.com/founder/editorial-publication-of-articles-in-e-books-by-leaders-in-pharmaceutical-business-intelligence/

About Tilda Barliya, PhD

http://pharmaceuticalintelligence.com/contributors-biographies/senior-editors/tilda-barliya-phd-expert-author-writer-research-category-owner-nanotechnology-for-drug-delivery/

About Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/contributors-biographies/experts-authors-writers-eaws/ritu-saxena/

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Biomarker Guided Therapy

Posted in Cancer and Current Therapeutics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Screening, Cardiomyopathy, Cardiovascular Pharmacogenomics, Cardiovascular Research, Clinical Diagnostics, Computational Biology/Systems and Bioinformatics, Curation, Diabetes Mellitus, Diagnostics and Lab Tests, Electrophysiology, Frontiers in Cardiology and Cardiovascular Disorders, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Hematology, HTN, Myocardial Ischemia, Nephrology, Pharmacotherapy of Cardiovascular Disease, tagged , , , , , , , , , , on February 1, 2015| Leave a Comment »

Biomarker Guided Therapy

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

Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer

Liping Chung, K Moore, L Phillips, FM Boyle, DJ Marsh and RC Baxter
Breast Cancer Research 2014, 16:R63
http://breast-cancer-research.com/content/16/3/R63

Introduction: Serum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed  proteins in sera from BC and healthy volunteers (HV), with the
goal  of developing a new prognostic biomarker panel.
Methods: Training set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated.
Results: From 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P = 0.016). By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, immunoprecipitation and western blotting the proteins were identified as a fragment of apolipoprotein H (ApoH), ApoCI, complement C3a, transthyretin, and ApoAI. Kaplan-Meier analysis on 181 subjects after median follow-up of >5 years demonstrated that the panel significantly predicted disease-free survival (P = 0.005), its efficacy apparently greater in women with estrogen receptor (ER)-negative tumors (n = 50, P = 0.003) compared to ER-positive (n = 131, P = 0.161), although the influence of ER status needs to be confirmed after longer follow-up.
Conclusions: Protein mass profiling by MS has revealed five serum proteins which, in combination, can distinguish between serum from women with breast cancer and healthy control subjects with high sensitivity and specificity. The five-protein panel significantly predicts recurrence-free survival in women with ER-negative tumors and may have value in the management of these patients.

Variants of uncertain significance in BRCA: a harbinger of ethical and policy issues to come?

Jae Yeon Cheon, Jessica Mozersky and Robert Cook-Deegan
Genome Medicine 2014, 6:121
http://genomemedicine.com/content/6/12/121

After two decades of genetic testing and research, the BRCA1 and BRCA2 genes are two of the most well-characterized genes in the human genome. As a result, variants of uncertain significance (VUS; also called variants of unknown significance) are reported less frequently than for genes that have been less thoroughly studied. However, VUS continue to be uncovered, even for BRCA1/2. The increasing use of multi-gene panels and whole-genome and whole-exome sequencing will lead to higher rates of VUS detection because more genes are being tested, and most genomic loci have been far less intensively characterized than BRCA1/2. In this article, we draw attention to ethical and policy-related issues that will emerge. Experience garnered from BRCA1/2 testing is a useful introduction to the challenges of detecting VUS in other genetic testing contexts, while features unique to BRCA1/2 suggest key differences between the BRCA experience and the current challenges of multi-gene panels in clinical care. We propose lines of research and policy development, emphasizing the importance of pooling data into a centralized open-access database for the storage of gene variants to improve VUS interpretation. In addition, establishing ethical norms and regulated practices for sharing and curating data, analytical algorithms, interpretive frameworks and patient re-contact are important policy areas.

The Significance of Normal Pretreatment Levels of CA125 (<35 U/mL) in Epithelial Ovarian Carcinoma

Joseph Menczer,  Erez Ben-Shem,  Abraham Golan, and Tally Levy
Rambam Maimonides Med J 2015;6 (1):e0005. http://dx.doi.org:/10.5041/RMMJ.10180

Objective: To assess the association between normal CA125 levels at diagnosis of epithelial ovarian carcinoma (EOC) with prognostic factors and with outcome.
Methods: The study group consisted of histologically confirmed EOC patients with normal pretreatment CA125 levels, and the controls consisted of EOC patients with elevated (≥35 U/mL) pretreatment CA125 levels, diagnosed and treated between 1995 and 2112. Study and control group patients fulfilled the following criteria: 1) their pretreatment CA125 levels were assessed; 2) they had full standard primary treatment, i.e. cytoreductive surgery and cisplatin-based chemotherapy; and 3) they were followed every 2–4 months during the first two years and every 4–6 months thereafter.
Results: Of 114 EOC patients who fulfilled the inclusion criteria, 22 (19.3%) had normal pretreatment CA125 levels. The control group consisted of the remaining 92 patients with ≥35 U/mL serum CA125 levels pretreatment. The proportion of patients with early-stage and low-grade disease, with optimal cytoreduction, and with platin-sensitive tumors was significantly higher in the study group than in the control group. The progression-free survival (PFS) and overall survival (OS) were significantly higher in the study group than in the control group on univariate analysis but not on multivariate analysis.

Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia

Simone Ecker, Vera Pancaldi, Daniel Rico and Alfonso Valencia
Genome Medicine (2015) 7:8 http://dx.doi.org:/10.1186/s13073-014-0125-z

Background: Chronic lymphocytic leukemia (CLL) presents two subtypes which have drastically different clinical outcomes, IgVH mutated (M-CLL) and IgVH unmutated (U-CLL). So far, these two subtypes are not associated to clear differences in gene expression profiles. Interestingly, recent results have highlighted important roles for heterogeneity, both at the genetic and at the epigenetic level in CLL progression.
Methods: We analyzed gene expression data of two large cohorts of CLL patients and quantified expression variability across individuals to investigate differences between the two subtypes using different measures and statistical tests. Functional significance was explored by pathway enrichment and network analyses. Furthermore, we implemented a random forest approach based on expression variability to classify patients into disease subtypes.
Results: We found that U-CLL, the more aggressive type of the disease, shows significantly increased variability of gene expression across patients and that, overall, genes that show higher variability in the aggressive subtype are related to cell cycle, development and inter-cellular communication. These functions indicate a potential relation between gene expression variability and the faster progression of this CLL subtype. Finally, a classifier based on gene expression variability was able to correctly predict the disease subtype of CLL patients.
Conclusions: There are strong relations between gene expression variability and disease subtype linking significantly increased expression variability to phenotypes such as aggressiveness and resistance to therapy in CLL.

The Emerging Roles of Thyroglobulin

Yuqian Luo, Yuko Ishido, Naoki Hiroi, Norihisa Ishii, and Koichi Suzuki
Advances in Endocrinology 2014, Article ID 189194, 7 pages http://dx.doi.org/10.1155/2014/189194

Thyroglobulin (Tg), the most important and abundant protein in thyroid follicles, is well known for its essential role in thyroid hormone synthesis. In addition to its conventional role as the precursor of thyroid hormones, we have uncovered a novel function of Tg as an endogenous regulator of follicular function over the past decade. The newly discovered negative feedback effect of Tg on follicular function observed in the rat and human thyroid provides an alternative explanation for the observation of follicle heterogeneity. Given the essential role of the regulatory effects of Tg, we consider that dysregulation of normal Tg function is associated with multiple human thyroid diseases including autoimmune thyroid disease and thyroid cancer. Additionally, extrathyroid Tg may serve a regulatory function in other organs. Further exploration of Tg action, especially at the molecular level, is needed to obtain a better understanding of both the physiological and pathological roles of Tg.

The GUIDE-IT trial will help doctors find a new standard of care for heart failure.

Heart failure affects more than 25 million people worldwide, including 5.8 million in the United States and 6.9 million in Europe. About one to two percent of adults in developed countries have been diagnosed with heart failure; this increases to more than 10 percent in people over age 70. Moreover, heart failure accounts for more than 17 percent of Medicare spending and about 5 percent of total US healthcare spending. The cost to society in the US is about 30 billion dollars a year—and rising.

For people hospitalized due to heart failure, the outlook isn’t encouraging. Following discharge, one in four patients is likely to be back in the hospital in less than a month. With every acute heart failure event that requires readmission, the chances of dying from the disease increase.

Heart failure occurs when the heart is unable to fill with or pump sufficient blood to meet the needs of the body. Some heart failure symptoms—shortness of breath, fatigue and fluid buildup—which are present in other health problems. Heart failure may develop from coronary artery disease, high blood pressure, cardiomyopathy, heart valve disease, arrhythmias, viral or bacterial infections, and congenital heart defects. As a consequence, these patients often have additional diseases (comorbidities) and managing heart failure can be extremely challenging.

There have been no new drugs for heart failure in more than a decade. The last breakthrough was cardiac resynchronization therapy, a device and not a drug. The goals of therapy are to treat heart failure’s underlying causes, reduce symptoms, improve the patient’s quality of life and keep the disease from getting worse.

More than a pump

The heart isn’t just a muscle pumping blood through the body. It is also an endocrine gland that secretes peptides and hormones. When the heart is failing, its stressed cells release larger amounts of substances known as natriuretic peptides, including N-terminal prohormone brain natriuretic peptide, or NT-proBNP.

Roche’s NT-proBNP test measures the levels of this peptide and helps doctors to determine whether patients are suffering from heart failure and to assess their prognosis. Most recently, NT-proBNP has also been shown to help physicians guide and adjust the patient’s drug therapy. The objective of the pivotal GUIDE-IT trial is to demonstrate the efficacy and safety of NT-proBNP guided heart failure therapy.

Sponsored by the National Institutes of Health (NIH), the GUIDE-IT trial will help doctors answer important questions about NT-proBNP’s impact on medical care. About 1100 patients are enrolled in this robustly powered, randomized controlled trial comparing NT-proBNP guided therapy on top of standard care versus standard care alone in high-risk heart failure patients. Its primary endpoint is time to cardiovascular death or first heart failure hospitalization.

With the NT-proBNP biomarker, doctors can create personalized treatment plans for patients to substantially reduce mortality and morbidity. It can be viewed as a companion diagnostic that works with all the drugs recommended by the major guidelines.

Finding new answers

GUIDE-IT will last five years and involve approximately 45 trial sites in the United States. The first group of patients will be enrolled by the end of 2012.

“We need to take a more strategic approach if we are going to meet the AHA/ASA’s 2020 goal of reducing heart failure hospitalizations by 20 percent,” Dr. O’Connor, Chief of the Division of Cardiovascular Medicine at Duke Heart Center in Durham, North Carolina, said at a media briefing held in October at Roche Diagnostics International in Rotkreuz, Switzerland.
The relative and combined ability of: high-sensitivity cardiac troponin T, and N-terminal pro-B-type natriuretic Peptide – to predict cardiovascular events and death in patients with type 2 diabetes.

Hillis GS; Welsh P; Chalmers J; Perkovic V; Chow CK; Li Q; Jun M; Neal B; et al.
http://reference.medscape.com/medline/abstract/24089534?src=wnl_ref_prac_diab

OBJECTIVE Current methods of risk stratification in patients with type 2 diabetes are suboptimal. The current study assesses the ability of N-terminal pro-B-type natriuretic peptide (NT-proBNP) and high-sensitivity cardiac troponin T (hs-cTnT) to improve the prediction of cardiovascular events and death in patients with type 2 diabetes.
RESEARCH DESIGN AND METHODS A nested case-cohort study was performed in 3,862 patients who participated in the Action in Diabetes and Vascular Disease: Preterax and Diamicron Modified Release Controlled Evaluation (ADVANCE) trial. RESULTS Seven hundred nine (18%) patients experienced a major cardiovascular event (composite of cardiovascular death, nonfatal myocardial infarction, or nonfatal stroke) and 706 (18%) died during a median of 5 years of follow-up. In Cox regression models, adjusting for all established risk predictors, the hazard ratio for cardiovascular events for NT-proBNP was 1.95 per 1 SD increase (95% CI 1.72, 2.20) and the hazard ratio for hs-cTnT was 1.50 per 1 SD increase (95% CI 1.36, 1.65). The hazard ratios for death were 1.97 (95% CI 1.73, 2.24) and 1.52 (95% CI 1.37, 1.67), respectively. The addition of either marker improved 5-year risk classification for cardiovascular events (net reclassification index in continuous model, 39% for NT-proBNP and 46% for hs-cTnT). Likewise, both markers greatly improved the accuracy with which the 5-year risk of death was predicted. The combination of both markers provided optimal risk discrimination.
CONCLUSIONS NT-proBNP and hs-cTnT appear to greatly improve the accuracy with which the risk of cardiovascular events or death can be estimated in patients with type 2 diabetes.

Genetics and Heart Failure: A Concise Guide for the Clinician

Cécile Skrzynia, Jonathan S. Berg, Monte S. Willis and Brian C. Jensen
Current Cardiology Reviews, 2013; 9.

Abstract: The pathogenesis of heart failure involves a complex interaction between genetic and environmental factors. Genetic factors may influence the susceptibility to the underlying etiology of heart failure, the rapidity of disease progression, or the response to pharmacologic therapy. The genetic contribution to heart failure is relatively minor in most multifactorial cases, but more direct and profound in the case of familial dilated cardiomyopathy. Early studies of genetic risk for heart failure focused on polymorphisms in genes integral to the adrenergic and renin-angiotensin-aldosterone system. Some of these variants were found to increase the risk of developing heart failure, and others appeared to affect the therapeutic response to neurohormonal antagonists. Regardless, each variant individually confers a relatively modest increase in risk and likely requires complex interaction with other variants and the environment for heart failure to develop. Dilated cardiomyopathy frequently leads to heart failure, and a genetic etiology increasingly has been recognized in cases previously considered to be “idiopathic”. Up to 50% of dilated cardiomyopathy cases without other cause likely are due to a heritable genetic mutation. Such mutations typically are found in genes encoding sarcomeric proteins and are inherited in an autosomal dominant fashion. In recent years, rapid advances in sequencing technology have improved our ability to diagnose familial dilated cardiomyopathy and those diagnostic tests are available widely. Optimal care for the expanding population of patients with heritable heart failure involves counselors and physicians with specialized training in genetics, but numerous online genetics resources are available to practicing clinicians.

Cardiac Troponin Testing Is Overused after the Rule-In or Rule-Out of Myocardial Infarction

Olaia Rodriguez Fraga, Y Sandoval, SA Love, ZJ McKinney, MAM Murakami, SW Smith, FS Apple
Clinical Chemistry 2015; 61:2 http://dx.doi.org:/10.1373/clinchem.2014.232694

No good studies have systematically evaluated appropriate clinical utilization of cardiac troponin testing in the clinical setting of the rule-in and rule-out of myocardial infarction (MI). Our collective 100-plus years of clinical and laboratory experience suggested that provider test ordering and use of cardiac troponin has been excessive after a diagnosis of MI or no MI has been determined. There is no evidence that supports continuation of cardiac troponin testing after a diagnosis is made.

Number of cTnI results demonstrating excessive orders by diagnosis

Number of cTnI results demonstrating excessive orders by diagnosis

Time and Frequency Domain Analysis of Heart Rate Variability and their orrelations in Diabetes Mellitus
T. Ahamed Seyd, V. I. Thajudin Ahamed, Jeevamma Jacob, Paul Joseph K
Intl J Biolog and Life Sciences 2008; 4(1)

Diabetes mellitus (DM) is frequently characterized by autonomic nervous dysfunction. Analysis of heart rate variability (HRV) has become a popular noninvasive tool for assessing the activities of autonomic nervous system (ANS). In this paper, changes in ANS
activity are quantified by means of frequency and time domain analysis of R-R interval variability. Electrocardiograms (ECG) of 16 patients suffering from DM and of 16 healthy volunteers were recorded. Frequency domain analysis of extracted normal to normal interval (NN interval) data indicates significant difference in very low frequency (VLF) power, low frequency (LF) power and high frequency (HF) power, between the DM patients and control group. Time domain measures, standard deviation of NN interval (SDNN), root mean square of successive NN interval differences (RMSSD), successive NN intervals differing more than 50 ms (NN50 Count), percentage value of NN50 count (pNN50), HRV triangular index and triangular interpolation of NN intervals (TINN) also show significant difference between the DM patients and control group.

Power Spectral Density of the RR interval of a 55 year old healthy volunteer

Power Spectral Density of the RR interval of a 55 year old healthy volunteer

Power Spectral Density of the RR interval of a 55 year old healthy volunteer

Power Spectral Density of the RR interval of a 62 year old woman suffering

Power Spectral Density of the RR interval of a 62 year old woman suffering

Power Spectral Density of the RR interval of a 62 year old woman suffering
from diabetes for the last 15 years

HRV analysis has gained much importance in recent years, as a technique employed to explore the activity of ANS, and as an important early marker for identifying different pathological conditions. DM is a disease in which the cardiac autonomic activity is progressively compromised. Our investigation indicates that different time domain and frequency domain measures of HRV would be able to provide valuable information regarding the autonomic dysfunction to DM.

Time domain and frequency domain analysis of the RR interval variability of diabetic and normal subjects shows that there is significant difference in these measures for DM patients with respect to normal subjects. Variation of the HRV parameters indicates changes in ANS activity of DM patients. This can provide valid information regarding autonomic neuropathy in people with diabetes. It may be noted that these methods can detect changes before clinical signs appear. So we can expect that these measures enable early detection and treatment/subsequent management of patients and thus can avoid acute and chronic complications.

Multiparametric diagnostics of cardiomyopathies by microRNA signatures

Christine S. Siegismund & Maria Rohde & Uwe Kühl & Dirk Lassner
Microchim Acta 2014   http://dx.doi.org:/10.1007/s00604-014-1249-y

The diagnosis of cardiomyopathies by endomyocardial biopsy analysis is the gold standard for confirmation of causative reasons but is failing if a sample does not contain the area of interest due to focal pathology. Biopsies are revealing an extract of the current situation of the heart muscle only, and the need for global organ-specific or systemic markers is obvious in order to minimize sampling errors. Global markers like specific gene expression signatures in myocardial tissue may therefore reflect the focal situation or condition of the whole myocardium. Besides gene expression profiles, microRNAs (miRNAs) represent a new group of stable biomarkers that are detectable both in tissue and body fluids. Such miRNAs may serve as cardiological biomarkers to characterize inflammatory processes, to confirm viral infections, and to differentiate various forms of infection.
The predictive power of single miRNAs for diagnosis of complex diseases may be further increased if several distinctly deregulated candidates are combined to form a specific miRNA signature. Diagnostic systems that generate disease related miRNA profiles are based on microarrays, bead-based oligo sorbent assays, or on assays based on real-time polymerase chain reactions and placed on microfluidic cards or nanowell plates. Multiparametric diagnostic systems that can measure differentially expressed miRNAs may become the diagnostic tool of the future due to their predictive value with respect to clinical course, therapeutic decisions, and therapy monitoring. We discuss here specific merits, limitations and the potential of currently available analytical platforms for diagnostics of heart muscle diseases based on miRNA profiling.

Predictive value of plasma galectin-3 levels in heart failure with reduced and preserved ejection fraction

Rudolf A. de Boer, DJA Lok, T Jaarsma, P van der Meer, AA Voors, et al.
Annals Med, 2011; 43: 60–68 http://dx.doi.org:/10.3109/07853890.2010.538080

We studied the prognostic value of base-line galectin-3 in a large HF cohort, with preserved and reduced left ventricular ejection fraction (LVEF), and compared this to other biomarkers.
Methods. We studied 592 HF patients who had been hospitalized for HF and were followed for 18 months. The primary end-point was a composite of all-cause mortality and HF hospitalization.
Results. A doubling of galectin-3 levels was associated with a hazard ratio (HR) of 1.97 (1.62–2.42) for the primary outcome (P= 0.001). After correction for age, gender, BNP, eGFR, and diabetes the HR was 1.38 (1.07–1.78; P= 0.015). Galectin-3 levels were correlated with higher IL -6 and CRP levels (P= 0.002). Changes of galectin-3 levels after 6 months did not add prognostic information to the base-line value (n= 291); however, combining plasma galectin-3 and BNP levels increased prognostic value over either biomarker alone (ROC analysis, P = 0.05). The predictive value of galectin-3 was stronger in patients with preserved LVEF (n= 114) compared to patients with reduced LVEF (P= 0.001).
Conclusions. Galectin-3 is an independent marker for outcome in HF and appears to be particularly useful in HF patients with preserved LVEF.

Criteria for the use of omics-based predictors in clinical trials

Lisa M. McShane, MM Cavenagh, TG Lively, DA Eberhard, et al.
Nature  17 Oct 2013; 502: 317-320. http://dx.doi.org:/10.1038/nature12564

The US National Cancer Institute (NCI), in collaboration with scientists representing multiple areas of expertise relevant to ‘omics’-based test development, has developed a checklist of criteria that can be used to determine the readiness of omics-based tests for guiding patient care in clinical trials. The checklist criteria cover issues relating to specimens, assays, mathematical modelling, clinical trial design, and ethical, legal and regulatory aspects. Funding bodies and journals are encouraged to consider the checklist, which they may find useful for assessing study quality and evidence strength. The checklist will be used to evaluate proposals for NCI-sponsored clinical
trials in which omics tests will be used to guide therapy.

M-Atrial Natriuretic Peptide and Nitroglycerin in a Canine Model of Experimental Acute Hypertensive Heart Failure: Differential Actions of 2 cGMP Activating Therapeutics.

Paul M McKie, Alessandro Cataliotti, Tomoko Ichiki, S Jeson Sangaralingham, Horng H Chen, John C Burnett
J Am Heart Assoc 01/2014; 3(1):e000206. http://dx.doi.org:/10.1161/JAHA.113.000206

Systemic hypertension is a common characteristic in acute heart failure (HF). This increasingly recognized phenotype is commonly associated with renal dysfunction and there is an unmet need for renal enhancing therapies. In a canine model of HF and acute vasoconstrictive hypertension we characterized and compared the cardiorenal actions of M-atrial natriuretic peptide (M-ANP), a novel particulate guanylyl cyclase (pGC) activator, and nitroglycerin, a soluble guanylyl cyclase (sGC) activator.
HF was induced by rapid RV pacing (180 beats per minute) for 10 days. On day 11, hypertension was induced by continuous angiotensin II infusion. We characterized the cardiorenal and humoral actions prior to, during, and following intravenous M-ANP (n=7), nitroglycerin (n=7), and vehicle (n=7) infusion. Mean arterial pressure (MAP) was reduced by M-ANP (139±4 to 118±3 mm Hg, P<0.05) and nitroglycerin (137±3 to 116±4 mm Hg, P<0.05); similar findings were recorded for pulmonary wedge pressure (PCWP) with M-ANP (12±2 to 6±2 mm Hg, P<0.05) and nitroglycerin (12±1 to 6±1 mm Hg, P<0.05). M-ANP enhanced renal function with significant increases (P<0.05) in glomerular filtration rate (38±4 to 53±5 mL/min), renal blood flow (132±18 to 236±23 mL/min), and natriuresis (11±4 to 689±37 mEq/min) and also inhibited aldosterone activation (32±3 to 23±2 ng/dL, P<0.05), whereas nitroglycerin had no significant (P>0.05) effects on these renal parameters or aldosterone activation.
Our results advance the differential cardiorenal actions of pGC (M-ANP) and sGC (nitroglycerin) mediated cGMP activation. These distinct renal and aldosterone modulating actions make M-ANP an attractive therapeutic for HF with concomitant hypertension, where renal protection is a key therapeutic goal.

Genome-Wide Association Study of a Heart Failure Related Metabolomic Profile Among African Americans in the Atherosclerosis Risk in Communities (ARIC) Study

Bing Yu, Y Zheng, D Alexander, TA Manolio, A Alonso, JA Nettleton, & E Boerwinkle
Genet Epidemiol 2013; 00:1–6, http://dx.doi.org:/10.1002/gepi.21752

Both the prevalence and incidence of heart failure (HF) are increasing, especially among African Americans, but no large-scale, genome-wide association study (GWAS) of HF-related metabolites has been reported. We sought to identify novel genetic variants that are associated with metabolites previously reported to relate to HF incidence. GWASs of three metabolites identified previously as risk factors for incident HF (pyroglutamine, dihydroxy docosatrienoic acid, and X-11787, being either hydroxy-leucine or hydroxy-isoleucine) were performed in 1,260 African Americans free of HF at the baseline examination of the Atherosclerosis Risk in Communities (ARIC) study. A significant association on chromosome 5q33 (rs10463316, MAF = 0.358, P-value = 1.92 × 10−10) was identified for pyroglutamine. One region on chromosome 2p13 contained a nonsynonymous substitution in N-acetyltransferase 8 (NAT8) was associated with X-11787 (rs13538, MAF = 0.481, P-value = 1.71 × 10−23). The smallest P-value for dihydroxy docosatrienoic acid was rs4006531 on chromosome 8q24 (MAF = 0.400, P-value = 6.98 × 10−7). None of the above SNPs were individually associated with incident HF, but a genetic risk score (GRS) created by summing the most significant risk alleles from each metabolite detected 11% greater risk of HF per allele. In summary, we identified three loci associated with previously reported HF-related metabolites. Further use of metabolomics technology will facilitate replication of these findings in independent samples.

Global Left Atrial Strain Correlates with CHADS2 Risk Score in Patients with Atrial Fibrillation

SK Saha, PL Anderson, G Caracciolo, A Kiotsekoglou, S Wilansky, S Govind, et al.
J Am Soc Echocardiogr 2011; 24(5): 506-512.
http://dx.doi.org:/10.1016/j.echo.2011.02.012

Background: The aim of this cross-sectional study was to explore the association between echocardiographic parameters and CHADS2 score in patients with nonvalvular atrial fibrillation (AF).
Methods: Seventy-seven subjects (36 patients with AF, 41 control subjects) underwent standard twodimensional, Doppler, and speckle-tracking echocardiography to compute regional and global left atrial (LA) strain.
Results: Global longitudinal LA strain was reduced in patients with AF compared with controls (P < .001) and was a predictor of high risk for thromboembolism (CHADS2 score $ 2; odds ratio, 0.86; P = .02). LA strain indexes showed good interobserver and intraobserver variability. In sequential Cox models, the prediction of hospitalization and/or death was improved by addition of global LA strain and indexed LA volume to CHADS2 score (P = .003).
Conclusions: LA strain is a reproducible marker of dynamic LA function and a predictor of stroke risk and cardiovascular outcomes in patients with AF.

Gene Expression and Genetic Variation in Human Atria

Honghuang Lin, EV Dolmatova, MP Morley, KL Lunetta, et al.
Heart Rhythm, HRTHM5533. PII: S1547-5271(13)01226-5
http://dx.doi.org/10.1016/j.hrthm.2013.10.051

Background— The human left and right atria have different susceptibilities to develop atrial fibrillation (AF). However, the molecular events related to structural and functional changes that enhance AF susceptibility are still poorly understood.
Objective— To characterize gene expression and genetic variation in human atria.
Methods— We studied the gene expression profiles and genetic variations in 53 left atrial and 52 right atrial tissue samples collected from the Myocardial Applied Genomics Network (MAGNet) repository. The tissues were collected from heart failure patients undergoing transplantation and from unused organ donor hearts with normal ventricular function. Gene expression was profiled using the Affymetrix GeneChip Human Genome U133A Array. Genetic variation was profiled using the Affymetrix Genome-Wide Human SNP Array 6.0.
Results— We found that 109 genes were differentially expressed between left and right atrial tissues. A total of 187 and 259 significant cis-associations between transcript levels and genetic variants were identified in left and right atrial tissues, respectively. We also found that a SNP at a known AF locus, rs3740293, was associated with the expression of MYOZ1 in both left and right atrial tissues. Conclusion— We found a distinct transcriptional profile between the right and left atrium, and extensive cis-associations between atrial transcripts and common genetic variants. Our results implicate MYOZ1 as the causative gene at the chromosome 10q22 locus for AF.

Atrial Natriuretic Peptide Single Nucleotide Polymorphisms in Patients with Nonfamilial Structural Atrial Fibrillation

Pietro Francia, A Ricotta, A Frattari, R Stanzione, A Modestino, et al.
Clinical Medicine Insights: Cardiology 2013:7 153–159
http://dx.doi.org:/10.4137/CMC.S12239

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.

N-terminal proBNP and mortality in hospitalized patients with heart failure and preserved vs. reduced systolic function: data from the prospective Copenhagen Hospital Heart Failure Study (CHHF)

Kirk, M. Bay, J. Parnerc, K. Krogsgaard, T.M. Herzog, S. Boesgaard, et al.
Eur Journal Heart Failure 6 (2004) 335–341
http://dx.doi.org:/10.1016/j.ejheart.2004.01.002

Preserved systolic function among heart failure patients is a common finding, a fact that has only recently been fully appreciated. The aim of the present study was to examine the value of NT-proBNP to predict mortality in relation to established risk factors among consecutively hospitalised heart failure patients and secondly to characterise patients in relation to preserved and reduced systolic function. Material: At the time of admission 2230 consecutively hospitalised patients had their cardiac status evaluated through determinations of NT-proBNP, echocardiography, clinical examination and medical history. Follow-up was performed 1 year later in all patients. Results: 161 patients fulfilled strict diagnostic criteria for heart failure (HF). In this subgroup of patients 1-year mortality was approximately 30% and significantly higher as compared to the remaining non-heart failure population (approx. 16%). Using univariate analysis left ventricular ejection fraction (LVEF), New York Heart Association classification (NYHA) and plasma levels of NT-proBNP all predicted mortality independently. However, regardless of systolic function, age and NYHA class, risk-stratification was provided by measurements of NT-proBNP. Having measured plasma levels of NT-proBNP, LVEF did not provide any additional prognostic information on mortality among heart failure patients (multivariate analysis).
Conclusion: The results show that independent of LVEF, measurements of NT-proBNP add additional prognostic information. It is concluded that NT-proBNP is a strong predictor of 1-year mortality in consecutively hospitalised patients with heart failure with preserved as well as reduced systolic function.

N-terminal pro-B-type natriuretic peptide and the prediction of primary cardiovascular events: results from 15-year follow-up of WOSCOPS

Paul Welsh, Orla Doolin, Peter Willeit, Chris Packard, Peter Macfarlane, et al.
Eur Heart Journal 2014. http://eurheartj.oxfordjournals.org/

Aims: To test whether N-terminal pro-B-type natriuretic peptide (NT-proBNP) was independently associated with, and improved the prediction of, cardiovascular disease (CVD) in a primary prevention cohort.
Methods and results:  In the West of Scotland Coronary Prevention Study (WOSCOPS), a cohort of middle-aged men with hypercholesterolemia at a moderate risk of CVD, we related the baseline NT-proBNP (geometric mean 28 pg/mL) in 4801 men to the risk of CVD over 15 years during which 1690 experienced CVD events. Taking into account the competing risk of non-CVD death, NT-proBNP was associated with an increased risk of all CVD [HR: 1.17 (95% CI: 1.11–1.23) per standard deviation increase in log NT-proBNP] after adjustment for classical and clinical cardiovascular risk factors plus C-reactive protein. N-terminal pro-B-type natriuretic peptide was more strongly related to the risk of fatal [HR: 1.34 (95% CI: 1.19–1.52)] than non-fatal CVD [HR: 1.17 (95% CI: 1.10–1.24)] (P ¼ 0.022). The addition of NT-proBNP to traditional risk factors improved the C-index (+0.013; P , 0.001). The continuous net reclassification index improved with the addition of NT-proBNP by 19.8% (95% CI: 13.6–25.9%) compared with 9.8% (95% CI: 4.2–15.6%) with the addition of C-reactive protein. N-terminal pro-B-type natriuretic peptide correctly reclassified 14.7% of events, whereas C-reactive protein correctly reclassified 3.4% of events. Results were similar in the 4128 men without evidence of angina, nitrate prescription, minor ECG abnormalities, or prior cerebrovascular disease.
Conclusion: N-terminal pro-B-type natriuretic peptide predicts CVD events in men without clinical evidence of CHD, angina, or history of stroke, and appears related more strongly to the risk for fatal events. N-terminal pro-B-type natriuretic peptide also provides moderate risk discrimination, in excess of that provided by the measurement of C-reactive protein.

Effect of B-type natriuretic peptide-guided treatment of chronic heart failure on total mortality and hospitalization: an individual patient meta-analysis

Richard W. Troughton, Christopher M. Frampton, Hans-Peter Brunner-La Rocca,
Matthias Pfisterer, Luc W.M. Eurlings, Hans Erntell, Hans Persson, et al.
Eur Heart J 2014; 35: 1559–1567 http://dx.doi.org:/10.1093/eurheartj/ehu090

Aims Natriuretic peptide-guided (NP-guided) treatment of heart failure has been tested against standard clinically guided care in multiple studies, but findings have been limited by study size. We sought to perform an individual patient data metaanalysis to evaluate the effect of NP-guided treatment of heart failure on all-cause mortality.
Methods and results
Eligible randomized clinical trials were identified from searches of Medline andEMBASEdatabases and the Cochrane Clinical
Trials Register. The primary pre-specified outcome, all-cause mortality was tested using a Cox proportional hazards regression model that included study of origin, age (< 75 or ≥75 years), and left ventricular ejection fraction (LVEF, ≤45 or .45%) as covariates. Secondary endpoints included heart failure or cardiovascular hospitalization. Of 11 eligible studies, 9 provided individual patient data and 2 aggregate data. For the primary endpoint individual data from 2000 patients were included, 994 randomized to clinically guided care and 1006 to NP-guided care. All-cause mortality was significantly reduced by NP-guided treatment [hazard ratio = 0.62 (0.45–0.86);
P = 0.004] with no heterogeneity between studies or interaction with LVEF. The survival benefit from NP-guided therapy was seen in younger ( <75 years) patients [0.62 (0.45–0.85); P = 0.004] but not older (≥75 years) patients [0.98 (0.75–1.27); P = 0.96]. Hospitalization due to heart failure [0.80 (0.67–0.94); P = 0.009] or cardiovascular disease [0.82 (0.67–0.99); P = 0.048]was significantly lower in NP-guided patients with no heterogeneity between studies and no interaction with age or LVEF.
Conclusion: Natriuretic peptide-guided treatment of heart failure reduces all-cause mortality in patients aged < 75 years and overall reduces heart failure and cardiovascular hospitalization.

Diagnostic and prognostic evaluation of left ventricular systolic heart failure by plasma N-terminal pro-brain natriuretic peptide concentrations in a large sample of the general population

B A Groenning, I Raymond, P R Hildebrandt, J C Nilsson, M Baumann, F Pedersen
Heart 2004;90:297–303. http://dx.doi.org:/10.1136/hrt.2003.026021

Objective: To evaluate N-terminal pro-brain natriuretic peptide (NT-proBNP) as a diagnostic and prognostic marker for systolic heart failure in the general population.
Design: Study participants, randomly selected to be representative of the background population, filled in a heart failure questionnaire and underwent pulse and blood pressure measurements, electrocardiography, echocardiography, and blood sampling and were followed up for a median (range) period of 805 (6021171) days.
Setting: Participants were recruited from four randomly selected general practitioners and were examined in a Copenhagen university hospital.
Patients: 382 women and 290 men in four age groups (50259 (n = 174); 60269 (n = 204); 70279 (n = 174); > 80 years (n = 120)).
Main outcome measures: Value of NT-proBNP in evaluating patients with symptoms of heart failure and impaired left ventricular (LV) systolic function; prognostic value of NT-proBNP for mortality and hospital admissions.
Results: In 38 (5.6%) participants LV ejection fraction (LVEF) was (40%. NT-proBNP identified patients with symptoms of heart failure and LVEF (40% with a sensitivity of 0.92, a specificity of 0.86, positive and negative predictive values of 0.11 and 1.00, and area under the curve of 0.94. NT-proBNP was the strongest independent predictor of mortality (hazard ratio (HR) = 5.70, p = 0.0001), hospital admissions for heart failure (HR = 13.83, p = 0.0001), and other cardiac admissions (HR = 3.69, p = 0.0001). Mortality (26 v 6, p = 0.0003), heart failure admissions (18 v 2, p = 0.0002), and admissions for other cardiac causes (44 v 13, p = 0.0001) were significantly higher in patients with NTproBNP above the study median (32.5 pmol/l). Conclusions: Measurement of NT-proBNP may be useful as a screening tool for systolic heart failure in the general population.

Copeptin—Marker of Acute Myocardial Infarction

Martin Möckel & Julia Searle
Curr Atheroscler Rep 2014; 16:421 http://dx.doi.org:/10.1007/s11883-014-0421-5

The concentration of copeptin, the C-terminal part of pro-arginine vasopressin, has been shown to increase early after acute and severe events. Owing to complementary pathophysiology and kinetics, the unspecific marker copeptin, in combination with highly cardio-specific troponin, has been evaluated as an early-rule-out strategy for acute myocardial infarction in patients presenting with signs and symptoms of acute coronary syndrome. Overall, most studies have reported a negative predictive value between 97 and 100 % for the diagnosis of acute myocardial infarction in low- to intermediate-risk patients with suspected acute coronary syndrome. Additionally, a recent multicenter, randomized process study, where patients who tested negative for copeptin and troponin were discharged from the emergency department, showed that the safety of the new process was comparable to that of the current standard process. Further interventional trials and data from registries are needed to ensure the effectiveness and patient benefit of the new strategy.

The role of copeptin as a diagnostic and prognostic biomarker for risk stratification in the emergency department

Christian H Nickel1, Roland Bingisser and Nils G Morgenthaler
BMC Medicine 2012, 10:7 http://www.biomedcentral.com/1741-7015/10/7

The hypothalamic-pituitary-adrenal axis is activated in response to stress. One of the activated hypothalamic hormones is arginine vasopressin, a hormone involved in hemodynamics and osmoregulation. Copeptin, the C-terminal part of the arginine vasopressin precursor peptide, is a sensitive and stable surrogate marker for arginine vasopressin release. Measurement of copeptin levels has been shown to be useful in a variety of clinical scenarios, particularly as a prognostic marker in patients with acute diseases such as lower respiratory tract infection, heart disease and stroke. The measurement of copeptin levels may provide crucial information for risk stratification in a variety of clinical situations. As such, the emergency department appears to be the ideal setting for its potential use. This review summarizes the recent progress towards determining the prognostic and diagnostic value of copeptin in the emergency department.

Variability of the Transferrin Receptor 2 Gene in AMD

Daniel Wysokinski, Janusz Blasiak, Mariola Dorecka, Marta Kowalska, et al.
Disease Markers 2014, Article ID 507356, 8 pages http://dx.doi.org/10.1155/2014/507356

Oxidative stress is a major factor in the pathogenesis of age-related macular degeneration (AMD). Iron may catalyze the Fenton reaction resulting in overproduction of reactive oxygen species. Transferrin receptor 2 plays a critical role in iron homeostasis and variability in its gene may influence oxidative stress and AMD occurrence. To verify this hypothesis we assessed the association between  polymorphisms of the TFR2 gene and AMD. A total of 493AMDpatients and 171matched controls were genotyped for the two polymorphisms of the TFR2 gene: c.1892C>T (rs2075674) and c.−258+123T>C (rs4434553). We also assessed the modulation of some AMD risk factors by these polymorphisms.The CC and TT genotypes of the c.1892C>T were associated with AMD occurrence but the latter only in obese patients. The other polymorphism was not associated with AMD occurrence, but the CC genotype was correlated with an increasing AMD frequency in subjects with BMI < 26. The TT genotype and the T allele of this polymorphism decreased AMD occurrence in subjects above 72 years, whereas the TC genotype and the C allele increased occurrence of AMD in this group.The c.1892C>T and c.−258+123T>C polymorphisms of the TRF2 gene may be associated with AMD occurrence, either directly or by modulation of risk factors.

Urinary N-Acetyl-beta-D-glucosaminidase as an Early Marker for Acute Kidney Injury in Full-Term Newborns with Neonatal Hyperbilirubinemia

Bangning Cheng, Y Jin, G Liu, Z Chen, H Dai, and M Liu
Disease Markers 2014, Article ID 315843, 6 pages http://dx.doi.org/10.1155/2014/315843

Purpose. To investigate renal function estimated by markers in full-term newborns with hyperbilirubinemia.
Methods. A total of 332 full-term newborns with hyperbilirubinemia and 60 healthy full-term newborns were enrolled. Total serum bilirubin, serum creatinine (Cr), serum blood urea nitrogen (BUN), serum cystatin C (Cys-C), urinary beta-2-microglobulin (𝛽2MG) index, and urinary N-acetyl-beta-D-glucosaminidase (NAG) index were measured before and after treatment. All newborns were divided into three groups according to total serum bilirubin levels: group 1 (221-256), group 2 (256-342), and group 3 (>342). Results. The control group and group 1 did not differ significantly in regard to serum Cr, serum BUN, serum Cys-C, urinary 𝛽2MG index, and urinary NAG index. Urinary NAG index in group 2 was significantly higher than that in control group (𝑃 < 0.001). Between control group and group 3, serum Cys-C, urinary 𝛽2MG index, and urinary NAG index differed significantly. The significant positive correlation between total serum bilirubin and urinary NAG index was found in newborns when total serum bilirubin level was more than 272 𝜇mol/L.
Conclusions. High unconjugated bilirubin could result in acute kidney injury in full-term newborns. Urinary NAG might be the suitable marker for predicting acute kidney injury in full-term newborns with hyperbilirubinemia.

Urinary C-peptide creatinine ratio detects absolute insulin deficiency in Type 2 diabetes.

S V Hope, A G Jones, E Goodchild, M Shepherd, R E J Besser, B Shields, T McDonald, B A Knight, A Hattersley

Department of Geriatrics, Royal Devon and Exeter NHS Foundation Trust; NIHR Exeter Clinical Research Facility, University of Exeter.

Diabetic Medicine (impact factor: 2.9). 05/2013; http://dx.doi.org:/10.1111/dme.12222

Source: PubMed

ABSTRACT AIMS: To determine the prevalence and clinical characteristics of absolute insulin deficiency in long-standing Type 2 diabetes, using a strategy based on home urinary C-peptide creatinine ratio measurement.
METHODS: We assessed the urinary C-peptide creatinine ratios, from urine samples taken at home 2 h after the largest meal of the day, in 191 insulin-treated subjects with Type 2 diabetes (diagnosis age ≥45 years, no insulin in the first year). If the initial urinary C-peptide creatinine ratio was ≤0.2 nmol/mmol (representing absolute insulin deficiency), the assessment was repeated. A standardized mixed-meal tolerance test with 90-min stimulated serum C-peptide measurement was performed in nine subjects with a urinary C-peptide creatinine ratio ≤ 0.2 nmol/mmol (and in nine controls with a urinary C-peptide creatinine ratio >0.2 nmol/mmol) to confirm absolute insulin deficiency.
RESULTS: A total of 2.7% of participants had absolute insulin deficiency confirmed by a mixed-meal tolerance test. They were identified initially using urinary C-peptide creatinine ratio: 11/191 subjects (5.8%) had two consistent urinary C-peptide creatinine ratios ≤ 0.2 nmol/mmol; 9/11 subjects completed a mixed-meal tolerance test and had a median stimulated serum C-peptide of 0.18nmol/l. Five out of nine subjects had stimulated serum C-peptide <0.2 nmol/l and 9/9 subjects with urinary C-peptide creatinine ratio >0.2 had endogenous insulin secretion confirmed by the mixed-meal tolerance test. Compared with subjects with a urinary C-peptide creatinine ratio >0.2 nmol/mmol, those with confirmed absolute insulin deficiency had a shorter time to insulin treatment (median 2.5 vs. 6 years, P=0.005) and lower BMI (25.1 vs. 29.1kg/m(2) , P=0.04). Two out of five patients were glutamic acid decarboxylase autoantibody-positive.
CONCLUSIONS: Absolute insulin deficiency may occur in long-standing Type 2 diabetes, and cannot be reliably predicted by clinical features or autoantibodies. Its recognition should help guide treatment, education and management. The urinary C-peptide creatinine ratio is a practical non-invasive method to aid detection of absolute insulin deficiency, with a urinary C-peptide creatinine ratio > 0.2 nmol/mmol being a reliable indicator of retained endogenous insulin secretion.

Unlocking Biomarkers’ Full Potential

David Daniels, Ph.D.     genengnews  Feb 1, 2013 (Vol. 33, No. 3)

http://www.genengnews.com/gen-articles/unlocking-biomarkers-full-potential/4700/

Biomarker research and development has evolved over the past years from looking for a single marker (e.g., PSA) linked to a disease state to looking for a panel of markers that can capture the heterogeneity inherent in both the disease and the impacted patient population.

That is one of the key messages to be delivered at GTC’s “Biomarkers Summit” next month. Across the board, resources are being focused on the delivery of more precise, quantifiable biomarkers with predictive value in therapeutic decisions and for the prognosis of illness.

“Our focus on biomarker development is the recognition that the new products need to provide cost savings for the already strapped healthcare systems rather than just be cost effective,” shares Paul Billings, M.D., Ph.D., CMO at Life Technologies.

“We have built a new medical sciences group to address the needs of the multiple delivery systems in the world—from the sophisticated medical clinics in the developed world to the nurse-run shanty clinic in the third world. Providing tools for equitable access to quality diagnosis, on assay platforms that can provide care for all patients, is our goal.”

Life Tech’s medical sciences division has been built by acquisition of Pinpoint Genomics, Navigenics, and Compendia, and collaborations with partners such as Ingenuity Systems and CollabRx. The division is focused on taking the tools that have been used in the life science laboratories and providing molecular diagnostic data to the clinic. The intent is to deliver data in a valuable format that can be used by the molecular pathologist or the treating physician.

The division is developing the Pervenio™ Lung RS assay, a 14-gene expression profile that serves as a risk stratifier that uses a weighted algorithm for the expressed biomarkers within the tumor biopsy, a first-of-its-kind prognostic test for lung cancer, the firm reports.

Initially, tests will be offered as a service through Life Tech’s CLIA laboratory. Then, from the performance lessons learned, Life Tech’s will develop a simpler assay platform, with FDA approval, that can be dispersed globally without reduction of the essential content in the biomarker panel. The focus is on the workflow—screening for known mutations using established easy-to-use assay platforms, like RT-PCR. Should the screen not produce useful results, clinicians can search for new mutations via discovery platforms like next-gen sequencing (NGS).

http://www.genengnews.com/Media/images/Article/thumb_Sequenom_LungCartaPanel1722631391.jpg

Sequenom’s LungCarta panel of 214 somatic mutations in 26 tumor suppressors and oncogenes covers highly mutated pathways in lung adenocarcinomas.

At Sequenom, the company provides both the tools (DNA mass spectrometry and reagents) for confirmatory biomarker development as well as serving on the front lines as a diagnostic service provider (CLIA lab). The beauty of DNA mass spec is that it can process multiplexed PCR samples (10–60 loci) in a method that is quantitative when used for profiling tumor biopsies that are either archival or fresh tissue.

Given a tumor sample with multiple somatic mutations, the instrument enables the determination of the homogeneity of the cells, in which case the mutations will have the same allele frequency. Accuracy, as measured by coefficient of variance, is less than 2%. Despite this level of sensitivity, the mass spec can only be used as a confirmatory tool looking for known mutations. Discovery is best done using DNA sequencing. DNA mass spec can also be used to study methylation in tumor samples.

“In the not-too-distant future, we will be looking for mutations in plasma samples rather than biopsies,” predicts Charles Cantor, Ph.D., CSO at Sequenom.

“The key is to look noninvasively for mutations within plasma samples such that we can potentially catch the disease state earlier, rather than after tumor formation. Regardless of the tumor type, this approach will enable us to monitor therapeutic response and metastatic potential noninvasively. DNA mass spec is an ultrasensitive detection product that can detect somatic mutations at levels of 1 per 1,000. This level of sensitivity is critical for the future of plasma screening. NGS technology is not that sensitive.”

Sequenom’s CLIA lab is using automated DNA mass spec to provide three different test protocols: (1) carrier screening for cystic fibrosis looking at more than 100 different mutations, (2) adult macular degeneration progression using an SNP test with 13 loci, and (3) a noninvasive test for Rh compatibility between a mother and her unborn fetus.

http://www.genengnews.com/Media/images/Article/thumb_Illumina_HiSeq_Scientist2141841107.jpg

Scientists are using Illumina’s HiSeq system to discover molecular biomarkers that may provide opportunities for early detection of a range of diseases.

Sequenom has also set up an NGS facility within a CLIA lab in San Diego using Illumina’s HiSEQ platform. The NGS platform has been set up for noninvasive aneuploidy detection of maternal plasma (10 cc sample) looking at chromosomes 13, 18, and 21. The lab says it has analyzed more than 40,000 samples this year and is planning to increase that volume up to 100,000 samples per year. Most of these samples come from the U.S., but given the development of a new blood collection tube that allows for 72-hour ambient shipping, the lab is looking to increase the number of samples from outside the U.S.

Drug Development

During drug development, biomarkers function as pharmacodynamic markers to help assess the mechanism of action of a drug candidate, to define the downstream biological pathway, and to determine whether the drug is engaging the target with the anticipated biological effect. Later, biomarkers help determine whether a drug is effective using the tested regime (route of delivery, dosage level, and length of exposure time).

Following early development, the second stage is to use biomarkers to help segment patients for clinical trials. Part of the consideration here is how heterogeneous the disease is; are there homogeneous subsets of patients that will respond differentially to the drug based on different mechanisms of the disease?

“Biomarker research is focused on on- target effects,” says Nick Dracopoli, Ph.D., vp, head of oncology biomarkers at Janssen Research and Development, a J&J company.

“We look at indications and at patients with those indications that are most likely to respond to the drug candidates we’re developing. For oncology biomarkers, germ-line effects are weaker indicators than somatic changes in the tumor. As a consequence, SNP-based, genome-wide association studies are not very useful. It is better to focus on molecular changes within the tumor and define gene expression profiles and epigenetic modifications that correlate with the tumor phenotype. We are increasingly tracking patient immune response, particularly as more immuno-oncology products are moving into the drug development pipeline.”

The number of biomarkers being developed varies from project to project. But it is very clear that to be successful in the clinic, the biomarkers and the assays need to be of low complexity. Of the 10 to 12 companion diagnostics that have been approved by the FDA to date, all measure the status of the drug target (on-target markers). For example, EGFR measures the level of receptor expression; Braf and Kras markers measure the presence of the mutation and translocation in the ALK gene measures gene knockout.

It is important to realize that molecular profiles for first-in-class drugs are not optimal because they are based on only a few patients. Consequently they have weak predictive value overall.

“Aside from that rule of thumb, if you have a greater than 50% response rate for your drug, it is unlikely that you need a biomarker to predict response. Biomarker utility is best for drugs that would have a difficult road to approval, where it is critical to enrich for the subpopulation of responders. For example, Pfizer’s crizontinib was approved for non-small-cell lung patients but is only effective for 5% of all patients. If Pfizer was unable to demonstrate the relationship between activation of the ALK gene and disease, this inhibitor would not have been approved,” says Dr. Dracopoli.

“Drugs that are more broadly active can come to market without a companion diagnostic test. There is always a balance between the predictive values of the biomarker test and the response rates to treatment. That is, we should not treat if the chance of response is only 3–5%, rather than if it were 50% where the patient would want to take the chance if the drug were safe.”

An important take-home message is that mutations are not unique to an indication. So if you find a driver mutation in indications for which the drug has not been approved, you could discover new indications for the drug.

“At the end of the day, this is what cancer is—heterogeneous,” says Dr. Dracopoli. “We’d all love to treat one cancer with one drug and at one dose, but the story is more complex. The future of oncology is around understanding the molecular heterogeneity or underlying molecular pathology of the disease and the diversity of it, and then treat each patient accordingly.”

Clinical Considerations

“Given the complexity of biology,” says Achim Plum, Ph.D., principal consultant, Siemens, “whether is it cancer, metabolic disease, or any other disease state, we have been forced to move away from the idea that a single biomarker can capture the entire ‘story’ or mechanistic view of any disease. Hence newly developed biomarkers will be made up of a panel of markers that serve as a profile. In addition, with the sheer volume of DNA and protein analytics data, the clinic will need to employ software tools and algorithms to help the decision making.”

The task of getting broad profiling technologies that are analytical into a clinical setting and making them routine is difficult but not insurmontable. This will take a collaborative effort, something that Siemens among others are looking to develop. The key is to avoid technology hype and to establish good reliable software to process the data for decision making. “Data is not knowledge, and knowledge is not automatically decision making.”

As an academic, Daniel Chan, Ph.D., has a view of the whole value chain for biomarkers from discovery to development to use in the clinic. Dr. Chan holds the titles of professor in pathology, oncology, radiology, and urology, and is the director of the clinical chemistry division lab at Johns Hopkins Hospital.

Given his perspective from discovery to clinical use, Dr. Chan indicated that from the clinical point of view, “we need more markers.” He oversees the discovery of new biomarkers in his research lab, their validation in his translational research lab, and finally their utility in practice in his clinical chemistry lab. He is a strong advocate for collaboration of biomarker development from discovery to verification and validation to incorporation within the clinical practice.

Beyond the use of biomarkers for patient stratification and correlation between marker and therapeutic choice, as is the focus of the biopharma industry, for the clinic the use of biomarkers is for prevention and early detection. The earlier the detection, the better the outcome. That is, provide the “cure” before you need to initiate treatment.

To be successful in the future of biomarkers, we need to look beyond the biopharma focus and expand the horizon for early detection and monitor therapy later, says Dr. Chan. He describes a roadmap of developing bridges (to bridge the knowledge gaps), gates (decision gates for go/no go decisions as to whether a development path is viable), and partnerships (to collaborate with different points of view) for efficient new biomarker development.

According to Dr. Chan, we must define the intended use of the biomarker, which identifies the specific application and sets up the clinical study and study population to meet the clinical needs. We need to define specific assays to monitor biomarkers that will work within a clinical setting, not a research lab setting that uses disease models (tissue culture cells or small animals) and not real patient samples.

“The days when single markers are sufficient (PSA for prostate cancer or troponin for cardiovascular disease) are behind us. We need to develop a panel of markers or a profile pattern to address patient population heterogeneity and disease complexity that will guide our decision-making process,” remarks Dr. Chan. “Molecular biomarkers are giving way to protein biomarkers,” he adds.

Prevention and early detection will require the use of whole-body scans, so the sampling technology and analytical tools to be developed are critical to realize this goal. Assay ease of use, automation, and analytical performance that is suitable for the clinical lab are fundamental.

“An important future goal for biomarkers,” says Dr. Billings, “is to sample circulating tumor cells or circulating DNA in blood or plasma samples as a noninvasive measure of patient status. A decline in tumor biomarkers during chemotherapy, for example, could reflect the efficacy of the therapy. In contrast, an increase in tumor biomarkers, in a patient who had previously undergone surgery and therapy, might indicate disease recurrence, and is likely to do so before a tumor mass is detectable by imaging methods.”

STAT4 Gene Polymorphisms Are Associated with Susceptibility and ANA Status in Primary Biliary Cirrhosis

Satoru Joshita, T Umemura, M Nakamura, Y Katsuyama, S Shibata, et al.
Disease Markers  2014, Article ID 727393, 8 pages http://dx.doi.org/10.1155/2014/727393

Recent genome-wide association studies suggest that genetic factors contribute to primary biliary cirrhosis (PBC) susceptibility. Although several reports have demonstrated that the interleukin (IL) 12 signaling pathway is involved in PBC pathogenesis, its precise genetic factors have not been fully clarified. Here, we performed an association analysis between IL12A, IL12RB, and signal transducer and activator of transcription 4 (STAT4) genetic variations and susceptibility to PBC. Single nucleotide polymorphisms (SNPs) were genotyped in 395 PBC patients and 458 healthy subjects of Japanese ethnicity and evaluated for associations with PBC susceptibility, anti-nuclear antibody (ANA) status, and anti-mitochondrial antibody (AMA) status. We detected significant associations with PBC susceptibility for several STAT4 SNPs (rs10168266; p = 9.4 × 10−3, rs11889341; p = 1.2 × 10−3, rs7574865; p = 4.0 × 10−4, rs8179673; p = 2.0 × 10−4, and rs10181656; p = 4.2 × 10−5). Three risk alleles (rs7574865; p = 0.040, rs8179673; p = 0.032, and rs10181656; p = 0.031) were associated with ANA status, but not with AMA positivity. Our findings confirm that STAT4 is involved in PBC susceptibility and may play a role in ANA status in the Japanese population.

Serum Omentin-1 as a Disease Activity Marker for Crohn’s Disease

Yan Lu, Li Zhou, L Liu, Yan Feng, Li Lu, X Ren, X Dong, & W Sang
Disease Markers  2014, Article ID 162517, 5 pages   http://dx.doi.org/10.1155/2014/162517

Background and Aim. It remains challenging to determine the inflammatory activity in Crohn’s disease (CD) for lack of specific laboratory markers. Recent studies suggest that serum omentin-1 is associated with inflammatory response. We aimed to assess the potential of serum omentin-1 as a marker of disease activity in CD patients.
Methods. Serum omentin-1 concentrations were determined by enzyme-linked immunosorbent assay (ELISA) in patients with CD (n = 240), functional gastrointestinal disorders (FGDs, n = 120), and healthy controls (HC, n = 60) and evaluated for correlation with disease activity. Expression of omentin-1 in colonic tissues from patients with CD was also analyzed by real-time PCR and Western blotting. Serum omentin-1 levels as an activity index were evaluated using a receiver operating characteristic (ROC) curve.
Results. Serum omentin-1 concentrations were significantly decreased in active CD patients compared with patients in remission, FGDs, and HC (all p < 0.001). Expression of omentin-1 was decreased at mRNA and protein levels in inflamed colonic tissues in active CD than that in noninflamed colonic tissues. Serum omentin-1 levels were negatively correlated with disease activity in CD, better than C-reactive protein (CRP).
Conclusion. Our results indicate that serum and colonic omentin-1 expressions are decreased in active CD patients. The correlation of serum omentin-1 with disease activity in CD is superior to that of CRP. Serum omentin-1 is a potential marker for CD disease activity.
Serum Levels of Resistin, Adiponectin, and Apelin in Gastroesophageal Cancer Patients

Dorota Diakowska, K Markocka-Mdczka, P Szelachowski, and K Grabowski
Disease Markers 2014, Article ID 619649, 8 pages   http://dx.doi.org/10.1155/2014/619649

The aim of the study was the investigation of relationship between cachexia syndrome and serum resistin, adiponectin, and apelin in patients with gastroesophageal cancer (GEC).
Material and Methods. Adipocytokines concentrations were measured in sera of 85 GEC patients and 60 healthy controls. They were also evaluated in tumor tissue and appropriate normal mucosa of 38 operated cancer patients.
Results. Resistin and apelin concentrations were significantly higher in GEC patients than in the controls. The highest resistin levels were found in cachectic patients and in patients with distant metastasis. Serum adiponectin significantly decreased in GEC patients with regional and distant metastasis. Serum apelin was significantly higher in cachectic patients than in the controls. Apelin was positively correlated with hsCRP level. Resistin and apelin levels increased significantly in tumor tissues. Weak positive correlations between adipocytokines levels in serum and in tumor tissue were observed.
Conclusions. Resistin is associated with cachexia and metastasis processes of GEC. Reduction of serum adiponectin reflects adipose tissue wasting in relation to GEC progression. Correlation of apelin with hsCRP can reflect a presumable role of apelin in systemic inflammatory response in esophageal and gastric cancer.

Serum Level of HER-2 Extracellular Domain in Iranian Patients with Breast Cancer: A Follow-up Study

Mehrnoosh Doroudchi, Abdolrasoul Talei, Helmout Modjtahedi, et al.
IJI 2005; 2(4): 191-200

Background: A soluble form of HER-2/neu extracellular domain (sHER-2) is reported to be released in the sera of metastatic breast cancer patients.
Objective: To measure the level of sHER-2 in sera of 115 breast cancer patients. Methods: Serial samples of 27 patients with metastasis, 18 non-metastatic patients, 15 patients in stage 0/I and 14 patients with accompanying benign breast disease were also included in this study.
Results: No significant difference was observed between sHER-2 level in the pre-operative sera of breast cancer patients and that of healthy individuals. Only 8 out of 27 patients whom later developed metastasis showed elevated levels of sHER-2 in their first serum sample. However, a trend of increase in the level of sHER-2 was observed in 14 (51.8%) of 27 metastatic sera before clinical diagnosis of the metastasis. A significant association between sHER-2 positive status and vascular invasion of the tumor was observed (P = 0.02). In addition, significant correlation of sHER-2 level with CEA (highest r = 0.74) and CA 15.3 (highest r = 0.74) tumor marker levels in the serial sera were observed. The mean time from sHER-2 positivity to tumor metastasis was calculated to be 98 days (range = 29-174).  Conclusion: Our results indicate that a relatively high percentage of Iranian patients with breast cancer show an elevated level of sHER-2 in their sera before clinical diagnosis of the tumor metastasis. Therefore, measuring the level of this oncoprotein, not only helps physicians in monitoring the patients during HERCEPTIN therapy, but also can be helpful in choosing more aggressive treatments at the early satges of tumor metastasis.
B-type natriuretic peptide is a biomarker for pulmonary hypertension in preterm infants with bronchopulmonary dysplasia

Alain Cuna, Jegen Kandasamy, Naomi Fineberg, Brian Sims
Research and Reports in Neonatology 2013:3 33–36
http://dx.doi.org/10.2147/RRN.S42236

Background: B-type natriuretic peptide (BNP) is a cardiac biomarker useful in screening for pulmonary hypertension (PH) in adults. It is possible that BNP may also be useful in detecting PH among preterm infants with bronchopulmonary dysplasia (BPD).
Objective: To determine the utility of BNP for identification of PH among preterm infants with BPD.
Methods: We retrospectively identified preterm infants with BPD who underwent screening echocardiography for suspected PH and had serum BNP levels measured within 10 days before or after echocardiography. Eligible infants were classified based on echocardiographic diagnosis of either PH or no PH. Median and interquartile ranges (IQR) of BNP values were compared, and area under the curve (AUC) of receiver operator characteristic (ROC) analysis was used to determine the optimum threshold value for detection of PH.
Results: Twenty-five preterm infants with BPD (mean gestational age 26.5 ± 1.7 weeks, mean birth weight 747 ± 248 g) were identified. The median difference in days between echocardiography and BNP measurement was 1 day (IQR 0–3, range 0–10 days). Based on echocardiography, 16 were diagnosed with PH and nine without PH. No significant difference in terms of gestational age, birth weight, sex, race, or respiratory support was found between the two groups. Median (IQR) BNP values of those with PH were higher than those without PH (413 [212–1178] pg/mL versus 55 [21–84] pg/mL, P , 0.001). AUC of ROC analysis showed that a BNP value of 117 pg/mL had 93.8% sensitivity and 100% specificity for detecting PH.
Conclusion: BNP estimation may be useful for screening of PH in infants with BPD.

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The Challenge of Antimicrobial Resistance

Posted in Anticancer Resistance, Bacterial Resistance, Genetics & Pharmaceutical, Genome Biology, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Human Immune System in Health and in Disease, Immunodiagnostics, Infectious Disease & New Antibiotic Targets, Infectious Disease Immunodiagnostics, Metabolomics, Microbiologial genetics, Microbiology, Nitric Oxide in Health and Disease, Nutrition and Phytochemistry, Pharmaceutical Analytics, Pharmaceutical Drug Discovery, Plant extract, Population Health Management, RNA Biology, tagged , , , , on January 28, 2015| Leave a Comment »

The Challenge of Antimicrobial Resistance

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

 

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

What is Drug Resistance?

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

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

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

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

Credit: NIAID

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

selected Staphylococcus aureus mechanisms for immune evasion.

selected Staphylococcus aureus mechanisms for immune evasion.

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

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

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

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

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

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

Table **

Interventions to Address the Antibiotic-Resistance Crisis.*

Intervention Status                                                   Preventing infection
and resistance

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

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

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

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

Refilling antibiotic pipeline by aligning
economic and regulatory approaches

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

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

Preserving available antibiotics,
slowing resistance

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

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

Elimination of use of antibiotics to                       Legislation proposed
promote livestock growth

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

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

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

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

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

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

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

Sequestration of host nutrients to
prevent microbial access to nutrients

Probiotics that compete with microbial
growth

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

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

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

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

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

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

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

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

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

Additional sources:

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

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

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

graphical abstract

graphical abstract

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

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

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

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

New protein detonates bacteria from within

By Tim Sandle     in Science

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

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

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

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

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

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

Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7

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

Author Affiliations

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

Significance

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

Abstract

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

New funding to fight antibiotic resistance SPECIAL

By Tim Sandle

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

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

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

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

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

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

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

The STAAR Act would:

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

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

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

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

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

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

Senator takes on antibiotic resistant organisms SPECIAL

By Tim Sandle     Apr 16, 2014 in Science

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See Instead:
S. 2236 (same title)

Referred to Committee — Apr 10, 2014

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

Read Full Post »

The Union of Biomarkers and Drug Development

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The Union of Biomarkers and Drug Development

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

There has been consolidation going on for over a decade in both thr pharmaceutical and in the diagnostics industry, and at the same time the page is being rewritten for health care delivery.  I shall try to work through a clear picture of these not coincidental events.

Key notables:

  1. A growing segment of the US population is reaching Medicare age
  2. There is also a large underserved population in both metropolitan and nonurban areas and a fragmentation of the middle class after a growth slowdown in the economy since the 2008 deep recession.
  3. The deep recession affecting worldwide economies was only buffered by availability of oil or natural gas.
  4. In addition, there was a self-destructive strategy to cut spending on national scales that withdrew the support that would bolster support for infrastrucrue renewl.
  5. There has been a dramatic success in the clinical diagnostics industry, with a long history of being viewed as a loss leader, and this has been recently followed by the pharmaceutical industry faced with inability to introduce new products, leading to more competition in off-patent medications.
  6. The introduction of the Accountable Care Act has opened the opportunities for improved care, despite political opposition, and has probably sustained opportunity in the healthcare market.

Let’s take a look at this three headed serpent. – Pharma, Diagnostics, New Entity
?  The patient  ?
?  Insurance    ?
?  Physician    ?

Part I.   The Concept

When Illumina Buys Roche: The Dawning Of The Era Of Diagnostics Dominance

Robert J. Easton, Alain J. Gilbert, Olivier Lesueur, Rachel Laing, and Mark Ratner
http://PharmaMedtechBI.com    | IN VIVO: The Business & Medicine Report Jul/Aug 2014; 32(7).

  • With current technology and resources, a well-funded IVD company can create and pursue a strategy of information gathering and informatics application to create medical knowledge, enabling it to assume the risk and manage certain segments of patients
  • We see the first step in the process as the emergence of new specialty therapy companies coming from an IVD legacy, most likely focused in cancer, infection, or critical care

When Illumina Inc. acquired the regulatory consulting firm Myraqa, a specialist in in vitro diagnostics (IVD), in July, the press release announcement characterized the deal as one that would bolster illumina’s in-house capabilities for clinical readiness and help prepare for its next growth phase in regulated markets. That’s not surprising given the US Food and Drug Administration’s (FDA) approval a year and a half ago of its MiSeq next-generation sequencer for clinical use. But the deal could also suggest illumina is beginning to move along the path toward taking on clinical risk – that is, eventually

  • advising physicians and patients, which would mean facing regulators directly

Such a move – by illumina, another life sciences tools firm, or an information specialist from the high-tech universe – is inevitable given

  • the emerging power of diagnostics and traditional health care players’ reluctance to themselves take on such risk.

Alternatively, we believe that a well-funded diagnostics company could establish this position. either way, such a champion would establish dominion over and earn higher valuation than less-aggressive players who

  • only supply compartmentalized drug and device solutions.

Diagnostics companies have long been dogged by a fundamental issue:

  1. they are viewed and valued more along the lines of a commodity business than as firms that deliver a unique product or service
  2. diagnostics companies are in position to do just that today because they are now advantaged by having access to more data points.
  3. if they were to cobble together the right capabilities, diagnostics companies would have the ability to turn information into true medical knowledge

Example: PathGEN PathChip

nucleic-acid-based platform detects 296 viruses, bacteria, fungi & parasites

http://ow.ly/d/2GvQhttp://ow.ly/DSORV

This puts the diagnostics player in an unfamiliar realm where it can ask the question of what value they offer compared with a therapeutic. The key is that diagnostics can now offer unique information and potentially unique tools to capture that information. In order to do so, it has to create information from the data it generates, and then to supply that knowledge to users who will value and act on that knowledge. Complex genomic tests, as much as physical examination, may be the first meaningful touch point for physicians’ classification of disease.

Even if lab tests are more expensive, it is a cheaper means for deciding what to do first for a patient than the trial and error of prescribing medication without adequate information. Information is gaining in value as the amount of treatment data available on genomically characterizable subpopulations increases. In such a circumstance
it is the ability to perform that advisory function that will add tremendous value above what any test provides, the leverage of being able to apply a proprietary diagnostics platform – and importantly, the data it generates. It is the ability to perform that advisory function that will add tremendous value above what any test provides.

Integrated Diagnostics Inc. and Biodesix Inc. with mass spectrometry has the tools for unraveling disease processes, and numerous players are quite visibly in or are getting into the business of providing medical knowledge and clinical decision support in pursuit of a huge payout for those who actually solve important disease mysteries. Of course one has to ask whether MS/MS is sufficient for the assigned task, and also whether the technology is ready for the kind of workload experienced in a clinical service compared to a research vehicle.  My impression (as a reviewer) is that it is not now the time to take this seriously.

Roche has not realized its intent with Ventana: failing to deliver on the promise of boosting Roche’s pipeline, which was a significant factor in the high price Roche paid. The combined company was to be “uniquely positioned to further expand Ventana’s business globally and together develop more cost-efficient, differentiated, and targeted medicines.  On the other hand,  Biodesix decided to use Veristrat to look back and analyze important trial data to try to ascertain which patients would benefit from ficlatuzumab (subset). The predictive effect for the otherwise unimpressive trial results was observed in both progression-free survival and overall survival endpoints, and encouraged the companies to conduct a proof-of-concept study of ficlatuzumab in combination with Tarceva in advanced Non Small Cell Lung Cancer Patients (NSCLC) selected using the Veristrat test.

A second phase of IVD evolution will be far more challenging to pharma, when the most accomplished companies begin to assemble and integrate much broader data
sets, thereby gaining knowledge sufficient to actually manage patients and dictate therapy, including drug selection. No individual physician has or will have access to all of this information on thousands of patients, combined with the informatics to tease out from trillions of data points the optimal personalized medical approach. When the IVD-origin knowledge integrator amasses enough data and understanding to guide therapy decisions in large categories, particularly drug choices, it will become more valuable than any of the drug suppliers.

This is an apparent reversal of fortune. The pharmaceutical industry has been considered the valued provider, while the IVD manufacturer has been the low valued cousin. Now, it is by an ability to make kore accurate the drug administration that the IVD company can control the drug bill, to the detriment of drug developers, by finding algorithms that generate equal-to-innovative-drug outcomes using generics for most of the patients, thereby limiting the margins of drug suppliers and the upsides for new drug discovery/development.

It is here that there appears to be a misunderstanding of the whole picture of the development of the healthcare industry.  The pharmaceutical industry had a high value added only insofar it could replace market leaders for treatment before or at the time of patent expiration, which largely depended either introducing a new class of drug, or by relieving the current drug in its class of undesired toxicities or “side effects”.  Otherwise, the drug armamentarium was time limited to the expiration date. In other words, the value was dependent on a window of no competition.  In addition, as the regulation of healthcare costs were tightening under managed care, the introduction of new products that were deemed to be only marginally better, could be substitued by “off-patent” drug products.

The other misunderstanding is related to the IVD sector.  Laboratory tests in the 1950’s were manual, and they could be done by “technicians” who might not have completed a specialized training in clinical laboratory sciences.  The first sign of progress was the introduction of continuous flow chemistry, with a sampling probe, tubing to bring the reacting reagents into a photocell, and the timing of the reaction controlled by a coiled glass tubing before introducing the colored product into a uv-visible photometer.  In perhaps a decade, the Technicon SMA 12 and 6 instruments were introduced that could do up to 18 tests from a single sample.

Part 2. Emergence of an IVD Clinical Automated Diagnostics Industry

Why tests are ordered

  1. Screening
  2. Diagnosis
  3. Monitoring

Historical Perspective

Case in Point 1:  Outstanding Contributions in Clinical Chemistry. 1991. Arthur Karmen.

Dr. Karmen was born in New York City in 1930. He graduated from the Bronx High School of Science in 1946 and earned an A.B. and M.D. in 1950 and 1954, respectively, from New York University. In 1952, while a medical student working on a summer project at Memorial-Sloan Kettering, he used paper chromatography of amino acids to demonstrate the presence of glutamic-oxaloacetic and glutaniic-pyruvic ransaminases (aspartate and alanine aminotransferases) in serum and blood. In 1954, he devised the spectrophotometric method for measuring aspartate aminotransferase in serum, which, with minor modifications, is still used for diagnostic testing today. When developing this assay, he studied the reaction of NADH with serum and demonstrated the presence of lactate and malate dehydrogenases, both of which were also later used in diagnosis. Using the spectrophotometric method, he found that aspartate aminotransferase increased in the period immediately after an acute myocardial infarction and did the pilot studies that showed its diagnostic utility in heart and liver diseases.  This became as important as the EKG. It was replaced in cardiology usage by the MB isoenzyme of creatine kinase, which was driven by Burton Sobel’s work on infarct size, and later by the troponins.

Case in point 2: Arterial Blood Gases.  Van Slyke. National Academy of Sciences.

The test is used to determine the pH of the blood, the partial pressure of carbon dioxide and oxygen, and the bicarbonate level. Many blood gas analyzers will also report concentrations of lactate, hemoglobin, several electrolytes, oxyhemoglobin, carboxyhemoglobin and methemoglobin. ABG testing is mainly used in pulmonology and critical care medicine to determine gas exchange which reflect gas exchange across the alveolar-capillary membrane.

DONALD DEXTER VAN SLYKE died on May 4, 1971, after a long and productive career that spanned three generations of biochemists and physicians. He left behind not only a bibliography of 317 journal publications and 5 books, but also more than 100 persons who had worked with him and distinguished themselves in biochemistry and academic medicine. His doctoral thesis, with Gomberg at University of Michigan was published in the Journal of the American Chemical Society in 1907.  Van Slyke received an invitation from Dr. Simon Flexner, Director of the Rockefeller Institute, to come to New York for an interview. In 1911 he spent a year in Berlin with Emil Fischer, who was then the leading chemist of the scientific world. He was particularly impressed by Fischer’s performing all laboratory operations quantitatively —a procedure Van followed throughout his life. Prior to going to Berlin, he published the  classic nitrous acid method for the quantitative determination of primary aliphatic amino groups,  the first of the many gasometric procedures devised by Van Slyke, and made possible the determination of amino acids. It was the primary method used to study amino acid

composition of proteins for years before chromatography. Thus, his first seven postdoctoral years were centered around the development of better methodology for protein composition and amino acid metabolism.

With his colleague G. M. Meyer, he first demonstrated that amino acids, liberated during digestion in the intestine, are absorbed into the bloodstream, that they are removed by the tissues, and that the liver alone possesses the ability to convert the amino acid nitrogen into urea.  From the study of the kinetics of urease action, Van Slyke and Cullen developed equations that depended upon two reactions: (1) the combination of enzyme and substrate in stoichiometric proportions and (2) the reaction of the combination into the end products. Published in 1914, this formulation, involving two velocity constants, was similar to that arrived at contemporaneously by Michaelis and Menten in Germany in 1913.

He transferred to the Rockefeller Institute’s Hospital in 2013, under Dr. Rufus Cole, where “Men who were studying disease clinically had the right to go as deeply into its fundamental nature as their training allowed, and in the Rockefeller Institute’s Hospital every man who was caring for patients should also be engaged in more fundamental study”.  The study of diabetes was already under way by Dr. F. M. Allen, but patients inevitably died of acidosis.  Van Slyke reasoned that if incomplete oxidation of fatty acids in the body led to the accumulation of acetoacetic and beta-hydroxybutyric acids in the blood, then a reaction would result between these acids and the bicarbonate ions that would lead to a lower than-normal bicarbonate concentration in blood plasma. The problem thus became one of devising an analytical method that would permit the quantitative determination of bicarbonate concentration in small amounts of blood plasma.  He ingeniously devised a volumetric glass apparatus that was easy to use and required less than ten minutes for the determination of the total carbon dioxide in one cubic centimeter of plasma.  It also was soon found to be an excellent apparatus by which to determine blood oxygen concentrations, thus leading to measurements of the percentage saturation of blood hemoglobin with oxygen. This found extensive application in the study of respiratory diseases, such as pneumonia and tuberculosis. It also led to the quantitative study of cyanosis and a monograph on the subject by C. Lundsgaard and Van Slyke.

In all, Van Slyke and his colleagues published twenty-one papers under the general title “Studies of Acidosis,” beginning in 1917 and ending in 1934. They included not only chemical manifestations of acidosis, but Van Slyke, in No. 17 of the series (1921), elaborated and expanded the subject to describe in chemical terms the normal and abnormal variations in the acid-base balance of the blood. This was a landmark in understanding acid-base balance pathology.  Within seven years after Van moved to the Hospital, he had published a total of fifty-three papers, thirty-three of them coauthored with clinical colleagues.

In 1920, Van Slyke and his colleagues undertook a comprehensive investigation of gas and electrolyte equilibria in blood. McLean and Henderson at Harvard had made preliminary studies of blood as a physico-chemical system, but realized that Van Slyke and his colleagues at the Rockefeller Hospital had superior techniques and the facilities necessary for such an undertaking. A collaboration thereupon began between the two laboratories, which resulted in rapid progress toward an exact physico-chemical description of the role of hemoglobin in the transport of oxygen and carbon dioxide, of the distribution of diffusible ions and water between erythrocytes and plasma,
and of factors such as degree of oxygenation of hemoglobin and hydrogen ion concentration that modified these distributions. In this Van Slyke revised his volumetric gas analysis apparatus into a manometric method.  The manometric apparatus proved to give results that were from five to ten times more accurate.

A series of papers on the CO2 titration curves of oxy- and deoxyhemoglobin, of oxygenated and reduced whole blood, and of blood subjected to different degrees of oxygenation and on the distribution of diffusible ions in blood resulted.  These developed equations that predicted the change in distribution of water and diffusible ions between blood plasma and blood cells when there was a change in pH of the oxygenated blood. A significant contribution of Van Slyke and his colleagues was the application of the Gibbs-Donnan Law to the blood—regarded as a two-phase system, in which one phase (the erythrocytes) contained a high concentration of nondiffusible negative ions, i.e., those associated with hemoglobin, and cations, which were not freely exchaThe importance of Vanngeable between cells and plasma. By changing the pH through varying the CO2 tension, the concentration of negative hemoglobin charges changed in a predictable amount. This, in turn, changed the distribution of diffusible anions such as Cl” and HCO3″ in order to restore the Gibbs-Donnan equilibrium. Redistribution of water occurred to restore osmotic equilibrium. The experimental results confirmed the predictions of the equations.

As a spin-off from the physico-chemical study of the blood, Van undertook, in 1922, to put the concept of buffer value of weak electrolytes on a mathematically exact basis.
This proved to be useful in determining buffer values of mixed, polyvalent, and amphoteric electrolytes, and put the understanding of buffering on a quantitative basis. A
monograph in Medicine entitled “Observation on the Courses of Different Types of Bright’s Disease, and on the Resultant Changes in Renal Anatomy,” was a landmark that
related the changes occurring at different stages of renal deterioration to the quantitative changes taking place in kidney function. During this period, Van Slyke and R. M. Archibald identified glutamine as the source of urinary ammonia. During World War II, Van and his colleagues documented the effect of shock on renal function and, with R. A. Phillips, developed a simple method, based on specific gravity, suitable for use in the field.

Over 100 of Van’s 300 publications were devoted to methodology. The importance of Van Slyke’s contribution to clinical chemical methodology cannot be overestimated.
These included the blood organic constituents (carbohydrates, fats, proteins, amino acids, urea, nonprotein nitrogen, and phospholipids) and the inorganic constituents (total cations, calcium, chlorides, phosphate, and the gases carbon dioxide, carbon monoxide, and nitrogen). It was said that a Van Slyke manometric apparatus was almost all the special equipment needed to perform most of the clinical chemical analyses customarily performed prior to the introduction of photocolorimeters and spectrophotometers for such determinations.

The progress made in the medical sciences in genetics, immunology, endocrinology, and antibiotics during the second half of the twentieth century obscures at times the progress that was made in basic and necessary biochemical knowledge during the first half. Methods capable of giving accurate quantitative chemical information on biological material had to be painstakingly devised; basic questions on chemical behavior and metabolism had to be answered; and, finally, those factors that adversely modified the normal chemical reactions in the body so that abnormal conditions arise that we characterize as disease states had to be identified.

Viewed in retrospect, he combined in one scientific lifetime (1) basic contributions to the chemistry of body constituents and their chemical behavior in the body, (2) a chemical understanding of physiological functions of certain organ systems (notably the respiratory and renal), and (3) how such information could be exploited in the
understanding and treatment of disease. That outstanding additions to knowledge in all three categories were possible was in large measure due to his sound and broadly based chemical preparation, his ingenuity in devising means of accurate measurements of chemical constituents, and the opportunity given him at the Hospital of the Rockefeller Institute to study disease in company with physicians.

In addition, he found time to work collaboratively with Dr. John P. Peters of Yale on the classic, two-volume Quantitative Clinical Chemistry. In 1922, John P. Peters, who had just gone to Yale from Van Slyke’s laboratory as an Associate Professor of Medicine, was asked by a publisher to write a modest handbook for clinicians describing useful chemical methods and discussing their application to clinical problems. It was originally to be called “Quantitative Chemistry in Clinical Medicine.” He soon found that it was going to be a bigger job than he could handle alone and asked Van Slyke to join him in writing it. Van agreed, and the two men proceeded to draw up an outline and divide up the writing of the first drafts of the chapters between them. They also agreed to exchange each chapter until it met the satisfaction of both.At the time it was published in 1931, it contained practically all that could be stated with confidence about those aspects of disease that could be and had been studied by chemical means. It was widely accepted throughout the medical world as the “Bible” of quantitative clinical chemistry, and to this day some of the chapters have not become outdated.

History of Laboratory Medicine at Yale University.

The roots of the Department of Laboratory Medicine at Yale can be traced back to John Peters, the head of what he called the “Chemical Division” of the Department of Internal Medicine, subsequently known as the Section of Metabolism, who co-authored with Donald Van Slyke the landmark 1931 textbook Quantitative Clinical Chemistry (2.3); and to Pauline Hald, research collaborator of Dr. Peters who subsequently served as Director of Clinical Chemistry at Yale-New Haven Hospital for many years. In 1947, Miss Hald reported the very first flame photometric measurements of sodium and potassium in serum (4). This study helped to lay the foundation for modern studies of metabolism and their application to clinical care.

The Laboratory Medicine program at Yale had its inception in 1958 as a section of Internal Medicine under the leadership of David Seligson. In 1965, Laboratory Medicine achieved autonomous section status and in 1971, became a full-fledged academic department. Dr. Seligson, who served as the first Chair, pioneered modern automation and computerized data processing in the clinical laboratory. In particular, he demonstrated the feasibility of discrete sample handling for automation that is now the basis of virtually all automated chemistry analyzers. In addition, Seligson and Zetner demonstrated the first clinical use of atomic absorption spectrophotometry. He was one of the founding members of the major Laboratory Medicine academic society, the Academy of Clinical Laboratory Physicians and Scientists.

Davenport fig 10.jpg

Case in Point 3.  Nathan Gochman.  Developer of Automated Chemistries.

Nathan Gochman, PhD, has over 40 years of experience in the clinical diagnostics industry. This includes academic teaching and research, and 30 years in the pharmaceutical and in vitro diagnostics industry. He has managed R & D, technical marketing and technical support departments. As a leader in the industry he was President of the American Association for Clinical Chemistry (AACC) and the National Committee for Clinical Laboratory Standards (NCCLS, now CLSI). He is currently a Consultant to investment firms and IVD companies.

Nathan Gochman

Nathan Gochman

The clinical laboratory has become so productive, particularly in chemistry and immunology, and the labor, instrument and reagent costs are well determined, that today a physician’s medical decisions are 80% determined by the clinical laboratory.  Medical information systems have lagged far behind.  Why is that?  Because the decision for a MIS has historical been based on billing capture.  Moreover, the historical use of chemical profiles were quite good at validating healthy dtatus in an outpatient population, but the profiles became restricted under Diagnostic Related Groups.    Thus, it came to be that the diagnostics was considered a “commodity”.  In order to be competitive, a laboratory had to provide “high complexity” tests that were drawn in by a large volume of “moderate complexity”tests.

Part 3. Biomarkers in Medical Practice

Case in Point 1.

A Solid Prognostic Biomarker

HDL-C: Target of Therapy or Fuggedaboutit?

Steven E. Nissen, MD, MACC, Peter Libby, MD

DisclosuresNovember 06, 2014

Steven E. Nissen, MD, MACC: I am Steve Nissen, chairman of the Department of Cardiovascular Medicine at the Cleveland Clinic. I am here with Dr Peter Libby, chief of cardiology at the Brigham and Women’s Hospital and professor of medicine at Harvard Medical School. We are going to discuss high-density lipoprotein cholesterol (HDL-C), a topic that has been very controversial recently. Peter, HDL-C has been a pretty good biomarker. The question is whether it is a good target.

Peter Libby, MD: Since the early days in Berkley, when they were doing ultracentrifugation, and when it was reinforced and put on the map by the Framingham Study,[1] we have known that HDL-C is an extremely good biomarker of prospective cardiovascular risk with an inverse relationship with all kinds of cardiovascular events. That is as solid a finding as you can get in observational epidemiology. It is a very reliable prospective marker. It’s natural that the pharmaceutical industry and those of us who are interested in risk reduction would focus on HDL-C as a target. That is where the controversies come in.

Dr Nissen: It has been difficult. My view is that the trials that have attempted to modulate HDL-C or the drugs they used have been flawed. Although the results have not been promising, the jury is yet out. Torcetrapib, the cholesteryl ester transfer protein (CETP) inhibitor developed by Pfizer, had anoff-target toxicity.[2] Niacin is not very effective, and there are a lot of downsides to the drug. That has been an issue, but people are still working on this. We have done some studies. We did our ApoA-1 Milano infusion study[3]about a decade ago, which showed very promising results with respect to shrinking plaques in coronary arteries. I remain open to the possibility that the right drug in the right trial will work.

Dr Libby: What do you do with the genetic data that have come out in the past couple of years? Sekar Kathiresan masterminded and organized an enormous collaboration[4] in which they looked, with contemporary genetics, at whether HDL had the genetic markers of being a causal risk factor. They came up empty-handed.

Dr Nissen: I am cautious about interpreting those data, like I am cautious about interpreting animal studies of atherosclerosis. We have both lived through this problem in which something works extremely well in animals but doesn’t work in humans, or it doesn’t work in animals but it works in humans. The genetic studies don’t seal the fate of HDL. I have an open mind about this. Drugs are complex. They work by complex mechanisms. It is my belief that what we have to do is test these hypotheses in well-designed clinical trials, which are rigorously performed with drugs that are clean—unlike torcetrapib—and don’t have off-target toxicities.

An Unmet Need: High Lp(a) Levels

Dr Nissen: I’m going to push back on that and make a couple of points. The HPS2-THRIVE study was flawed. They studied the wrong people. It was not a good study, and AIM-HIGH[8] was underpowered. I am not putting people on niacin. What do you do with a patient whose Lp(a) is 200 mg/dL?

Dr Libby: I’m waiting for the results of the PCSK9 and anacetrapib studies. You can tell me about evacetrapib.[9]Reducing Lp(a) is an unmet medical need. We both care for kindreds with high Lp(a) levels and premature coronary artery disease. We have no idea what to do with them other than to treat them with statins and lower their LDL-C levels.

Dr Nissen: I have taken a more cautious approach with respect to taking people off of niacin. If I have patients who are doing well and tolerating it (depending on why it was started), I am discontinuing niacin in some people. I am starting very few people on the drug, but I worry about the quality of the trial.

Dr Libby: So you are of the “don’t start don’t stop” school?

Dr Nissen: Yes. It’s difficult when the trial is fatally flawed. There were 11,000 patients from China in this study. I have known for years that if you give niacin to people of Asiatic ethnic descent, they have terrible flushing and they won’t continue the drug. One question is, what was the adherence? The adverse events would have been tolerable had there been efficacy. The concern here is that this study was destined to fail because they studied a low LDL/high HDL population, a group of people for whom niacin just isn’t used.

Triglycerides and HDL: Do We Have It Backwards?

Dr Libby: What about the recent genetic[10] and epidemiologic data that support triglycerides, and apolipoprotein C3 in particular as a causal risk factor? Have we been misled through all of the generations in whom we have been adjusting triglycerides for HDL-C and saying that triglycerides are not a causal risk factor because once we adjust for HDL, the risk goes away? Do you think we got it backwards?

Dr Nissen: The tricky factor here is that because of this intimate inverse relationship between triglycerides and HDL, we may be talking about the same phenomenon. That is one of the reasons that I am not certain we are not going to be able to find a therapy. What if you had a therapy that lowered triglycerides and raised HDL-C? Could that work? Could that combination be favorable? I want answers from rigorous, well-designed clinical trials that ask the right questions in the right populations. I am disappointed, just as I have been disappointed by the fibrate trials.[11,12] There is a class of drugs that raises HDL-C a little and lowers triglycerides a lot.

Dr Nissen: But the gemfibrozil studies (VA-HIT[13] and Helsinki Heart[14]) showed benefit.

The Dyslipidemia Bar Has Been Raised

Dr Libby: Those studies were from the pre-statin era. We both were involved in trials in which patients were on high-dose statins at baseline. Do you think that this is too high a bar?

Dr Nissen: The bar has been raised, and for the pharmaceutical industry, the studies that we need to find out whether lowering triglycerides or raising HDL is beneficial are going to be large. We are doing a study with evacetrapib. It has 12,000 patients. It’s fully enrolled. Evacetrapib is a very clean-looking drug. It doesn’t have such a long biological half-life as anacetrapib, so I am very encouraged that it won’t have that baggage of being around for 2-4 years. We’ve got a couple of shots on goal here. Don’t forget that we have multiple ongoing studies of HDL-C infusion therapies that are still under development. Those have some promise too. The jury is still out.

Dr Libby: We agree on the need to do rigorous, large-scale endpoint trials. Do the biomarker studies, but don’t wait to start the endpoint trial because that’s the proof in the pudding.

Dr Nissen: Exactly. We have had a little controversy about HDL-C. We often agree, but not always, and we may have a different perspective. Thanks for joining me in this interesting discussion of what will continue to be a controversial topic for the next several years until we get the results of the current ongoing trials.

Case in Point 2.

NSTEMI? Honesty in Coding and Communication?

Melissa Walton-Shirley

November 07, 2014

The complaint at ER triage: Weakness, fatigue, near syncope of several days’ duration, vomiting, and decreased sensorium.

The findings: O2sat: 88% on room air. BP: 88 systolic. Telemetry: Sinus tachycardia 120 bpm. Blood sugar: 500 mg/dL. Chest X ray: atelectasis. Urinalysis: pyuria. ECG: T-wave-inversion anterior leads. Echocardiography: normal left ventricular ejection fraction (LVEF) and wall motion. Troponin I: 0.3 ng/mL. CT angiography: negative for pulmonary embolism (PE). White blood cell count: 20K with left shift. Blood cultures: positive for Gram-negative rods.

The treatment: Intravenous fluids and IV levofloxacin—changed to ciprofloxacin.

The communication at discharge: “You had a severe urinary-tract infection and grew bacteria in your bloodstream. Also, you’ve had a slight heart attack. See your cardiologist immediately upon discharge-no more than 5 days from now.”

The diagnoses coded at discharge: Urosepsis and non-ST segment elevation MI (NSTEMI) 410.1.

One year earlier: This moderately obese patient was referred to our practice for a preoperative risk assessment. The surgery planned was a technically simple procedure, but due to the need for precise instrumentation, general endotracheal anesthesia (GETA) was being considered. The patient was diabetic, overweight, and short of air. A stress exam was equivocal for CAD due to poor exercise tolerance and suboptimal imaging. Upon further discussion, symptoms were progressive; therefore, cardiac cath was recommended, revealing angiographically normal coronaries and a predictably elevated left ventricular end diastolic pressure (LVEDP) in the mid-20s range. The patient was given a diagnosis of diastolic dysfunction, a prescription for better hypertension control, and in-depth discussion on exercise and the Mediterranean and DASH diets for weight loss. Symptoms improved with a low dose of diuretic. The surgery was completed without difficulty. Upon follow-up visit, the patient felt well, had lost a few pounds, and blood pressure was well controlled.

Five days after ER workup: While out of town, the patient developed profound weakness and went to the ER as described above. Fast forward to our office visit in the designated time frame of “no longer than 5 days’ postdischarge,” where the patient and family asked me about the “slight heart attack” that literally came on the heels of a normal coronary angiogram.

But the patient really didn’t have a “heart attack,” did they? The cardiologist aptly stated that it was likely nonspecific troponin I leak in his progress notes. Yet the hospitalist framed the diagnosis of NSTEMI as item number 2 in the final diagnoses.

The motivations on behalf of personnel who code charts are largely innocent and likely a direct result of the lack of understanding of the coding system on behalf of us as healthcare providers. I have a feeling, though, that hospitals aren’t anxious to correct this misperception, due to an opportunity for increased reimbursement. I contacted a director of a coding department for a large hospital who prefers to remain anonymous. She explained that NSTEMI ICD9 code 410.1 falls in DRG 282 with a weight of .7562. The diagnosis of “demand ischemia,” code 411.89, a slightly less inappropriate code for a nonspecific troponin I leak, falls in DRG 311 with a weight of .5662. To determine reimbursement, one must multiply the weight by the average hospital Medicare base rate of $5370. Keep in mind that each hospital’s base rate and corresponding payment will vary. The difference in reimbursement for a large hospital bill between these two choices for coding is substantial, at over $1000 difference ($4060 vs $3040).

Although hospitals that are already reeling from shrinking revenues will make more money on the front end by coding the troponin leak incorrectly as an NSTEMI, when multiple unnecessary tests are generated to follow up on a nondiagnostic troponin leak, the amount of available Centers for Medicare & Medicaid Services (CMS) reimbursement pie shrinks in the long run. Furthermore, this inappropriate categorization generates extreme concern on behalf of patients and family members that is often never laid to rest. The emotional toll of a “heart-attack” diagnosis has an impact on work fitness, quality of life, cost of medication, and the cost of future testing. If the patient lived for another 100 years, they will likely still list a “heart attack” in their medical history.

As a cardiologist, I resent the loose utilization of one of “my” heart-attack codes when it wasn’t that at all. At discharge, we need to develop a better way of communicating what exactly did happen. Equally important, we need to communicate what exactly didn’t happen as well.

Case in Point 3.

Blood Markers Predict CKD Heart Failure 

Published: Oct 3, 2014 | Updated: Oct 3, 2014

Elevated levels of high-sensitivity troponin T (hsTnT) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) strongly predicted heart failure in patients with chronic kidney disease followed for a median of close to 6 years, researchers reported.

Compared with patients with the lowest blood levels of hsTnT, those with the highest had a nearly five-fold higher risk for developing heart failure and the risk was 10-fold higher in patients with the highest NT-proBNP levels compared with those with the lowest levels of the protein, researcher Nisha Bansal, MD, of the University of Washington in Seattle, and colleagues wrote online in the Journal of the American Society of Nephrology.

A separate study, published online in theJournal of the American Medical Association earlier in the week, also examined the comorbid conditions of heart and kidney disease, finding no benefit to the practice of treating cardiac surgery patients who developed acute kidney injury with infusions of the antihypertensive drug fenoldopam.

The study, reported by researcher Giovanni Landoni, MD, of the IRCCS San Raffaele Scientific Institute, Milan, Italy, and colleagues, was stopped early “for futility,” according to the authors, and the incidence of hypotension during drug infusion was significantly higher in patients infused with fenoldopam than placebo (26% vs. 15%; P=0.001).

Blood Markers Predict CKD Heart Failure

The study in patients with mild to moderate chronic kidney disease (CKD) was conducted to determine if blood markers could help identify patients at high risk for developing heart failure.

Heart failure is the most common cardiovascular complication among people with renal disease, occurring in about a quarter of CKD patients.

The two markers, hsTnT and NT-proBNP, are associated with overworked cardiac myocytes and have been shown to predict heart failure in the general population.

However, Bansal and colleagues noted, the markers have not been widely used in diagnosing heart failure among patients with CKD due to concerns that reduced renal excretion may raise levels of these markers, and therefore do not reflect an actual increase in heart muscle strain.

To better understand the importance of elevated concentrations of hsTnT and NT-proBNP in CKD patients, the researchers examined their association with incident heart failure events in 3,483 participants in the ongoing observational Chronic Renal Insufficiency Cohort (CRIC) study.

All participants were recruited from June 2003 to August 2008, and all were free of heart failure at baseline. The researchers used Cox regression to examine the association of baseline levels of hsTnT and NT-proBNP with incident heart failure after adjustment for demographic influences, traditional cardiovascular risk factors, makers of kidney disease, pertinent medication use, and mineral metabolism markers.

At baseline, hsTnT levels ranged from ≤5.0 to 378.7 pg/mL and NT-proBNP levels ranged from ≤5 to 35,000 pg/mL. Compared with patients who had undetectable hsTnT, those in the highest quartile (>26.5 ng/mL) had a significantly higher rate of heart failure (hazard ratio 4.77; 95% CI 2.49-9.14).

Compared with those in the lowest NT-proBNP quintile (<47.6 ng/mL), patients in the highest quintile (>433.0 ng/mL) experienced an almost 10-fold increase in heart failure risk (HR 9.57; 95% CI 4.40-20.83).

The researchers noted that these associations remained robust after adjustment for potential confounders and for the other biomarker, suggesting that while hsTnT and NT-proBNP are complementary, they may be indicative of distinct biological pathways for heart failure.

Even Modest Increases in NP-proBNP Linked to Heart Failure

The findings are consistent with an earlier analysis that included 8,000 patients with albuminuria in the Prevention of REnal and Vascular ENd-stage Disease (PREVEND) study, which showed that hsTnT was associated with incident cardiovascular events, even after adjustment for eGFR and severity of albuminuria.

“Among participants in the CRIC study, those with the highest quartile of detectable hsTnT had a twofold higher odds of left ventricular hypertrophy compared with those in the lowest quartile,” Bansal and colleagues wrote, adding that the findings were similar after excluding participants with any cardiovascular disease at baseline.

Even modest elevations in NT-proBNP were associated with significantly increased rates of heart failure, including in subgroups stratified by eGFR, proteinuria, and diabetic status.

“NT-proBNP regulates blood pressure and body fluid volume by its natriuretic and diuretic actions, arterial dilation, and inhibition of the renin-aldosterone-angiotensin system and increased levels of this marker likely reflect myocardial stress induced by subclinical changes in volume or pressure, even in persons without clinical disease,” the researchers wrote.

The researchers concluded that further studies are needed to develop and validate risk prediction tools for clinical heart failure in patients with CKD, and to determine the potential role of these two biomarkers in a heart failure risk prediction and prevention strategy.

Fenoldopam ‘Widely Promoted’ in AKI Cardiac Surgery Setting

The JAMA study examined whether the selective dopamine receptor D agonist fenoldopam mesylate can reduce the need for dialysis in cardiac surgery patients who develop acute kidney injury (AKI).

Fenoldopam induces vasodilation of the renal, mesenteric, peripheral, and coronary arteries, and, unlike dopamine, it has no significant affinity for D2 receptors, meaning that it theoretically induces greater vasodilation in the renal medulla than in the cortex, the researchers wrote.

“Because of these hemodynamic effects, fenoldopam has been widely promoted for the prevention and therapy of AKI in the United States and many other countries with apparent favorable results in cardiac surgery and other settings,” Landoni and colleagues wrote.

The drug was approved in 1997 by the FDA for the indication of in-hospital, short-term management of severe hypertension. It has not been approved for renal indications, but is commonly used off-label in cardiac surgery patients who develop AKI.

Although a meta analysis of randomized trials, conducted by the researchers, indicated a reduction in the incidence and progression of AKI associated with the treatment, Landoni and colleagues wrote that the absence of a definitive trial “leaves clinicians uncertain as to whether fenoldopam should be prescribed after cardiac surgery to prevent deterioration in renal function.”

To address this uncertainty, the researchers conducted a prospective, randomized, parallel-group trial in 667 patients treated at 19 hospitals in Italy from March 2008 to April 2013.

All patients had been admitted to ICUs after cardiac surgery with early acute kidney injury (≥50% increase of serum creatinine level from baseline or low output of urine for ≥6 hours). A total of 338 received fenoldopam by continuous intravenous infusion for a total of 96 hours or until ICU discharge, while 329 patients received saline infusions.

The primary end point was the rate of renal replacement therapy, and secondary end points included mortality (intensive care unit and 30-day mortality) and the rate of hypotension during study drug infusion.

Study Showed No Benefit, Was Stopped Early

Yale Lampoon – AA Liebow.   1954

Not As a Doctor
[Fourth Year]

These lyrics, sung by John Cole, Jack Gariepy and Ed Ransenhofer to music borrowed from Gilbert and Sullivan’s The Mikado, lampooned Averill Liebow, M.D., a pathologist noted for his demands on students. (CPC stands for clinical pathology conference.)

If you want to know what this is,
it’s a medical CPC
Where we give the house staff
the biz, for there’s no one so
wise as we!
We pathologists show them how,
Although it is too late now.
Our art is a sacred cow!

American physician, born 1911, Stryj in Galicia, Austria (now in Ukraine); died 1978.

Averill Abraham Liebow, born in Austria, was the “founding father” of pulmonary pathology in the United States. He started his career as a pathologist at Yale, where he remained for many years. In 1968 he moved to the University of California School of Medicine, San Diego, where he taught for 7 years as Professor and Chairman, Department of Pathology.

His studies include many classic studies of lung diseases. Best known of these is his famous classification of interstitial lung disease. He also published papers on sclerosing pneumocytoma, pulmonary alveolar proteinosis, meningothelial-like nodules, pulmonary hypertension, pulmonary veno-occlusive disease, lymphomatoid granulomatosis, pulmonary Langerhans cell histiocytosis, pulmonary epithelioid hemangioendothelioma and pulmonary hyalinizing granuloma .

As a Lieutenant Colonel in the US Army Medical Corps, He was a member of the Atomic Bomb Casualty Commission who studied the effects of the atomic bomb in Hiroshima and Nagasaki.

We thank Sanjay Mukhopadhyay, M.D., for information submitted.

As a resident at UCSD, Dr. Liebow held “Organ Recitals” every morning, including Mother’s day.  The organs had to be presented in specified order… heart, lung, and so forth.  On one occasion, we needed a heart for purification of human lactate dehydrogenase for a medical student project, so I presented the lung out of order.  Dr. Liebow asked where the heart was, and I told the group it was noprmal and I froze it for enzyme purification (smiles).  In the future show it to me first. He was generous to those who showed interest.  As I was also doing research in Nathan Kaplan’s laboratory, he made special arrangements for me to mentor Deborah Peters, the daughter of a pulmonary physician, and granddaughter of the Peters who collaborated with Van Slyke.  I mentored many students with great reward since then.  He could look at a slide and tell you what the x-ray looked like.  I didn’t encounter that again until he sent me to the Armed Forces Institute of Pathology, Washington, DC during the Vietnam War and Watergate, and I worked in Orthopedic Pathology with Lent C. Johnson.  He would not review a case without the x-ray, and he taught the radiologists.

Part 3

My Cancer Genome from Vanderbilt University: Matching Tumor Mutations to Therapies & Clinical Trials

Reporter: Aviva Lev-Ari, PhD, RN

My Cancer Genome from Vanderbilt University: Matching Tumor Mutations to Therapies & Clinical Trials


GenomOncology and Vanderbilt-Ingram Cancer Center (VICC) today announced a partnership for the exclusive commercial development of a decision support tool based on My Cancer Genome™, an online precision cancer medicine knowledge resource for physicians, patients, caregivers and researchers.

Through this collaboration, GenomOncology and VICC will enhance My Cancer Genome through the development of a new genomics content management tool. The MyCancerGenome.org website will remain free and open to the public. In addition, GenomOncology will develop a decision support tool based on My Cancer Genome™ data that will enable automated interpretation of mutations in the genome of a patient’s tumor, providing actionable results in hours versus days.

Vanderbilt-Ingram Cancer Center (VICC) launched My Cancer Genome™ in January 2011 as an integral part of their Personalized Cancer Medicine Initiative that helps physicians and researchers track the latest developments in precision cancer medicine and connect with clinical research trials. This web-based information tool is designed to quickly educate clinicians on the rapidly expanding list of genetic mutations that impact cancers and enable the research of treatment options based on specific mutations. For more information on My Cancer Genome™visit www.mycancergenome.org/about/what-is-my-cancer-genome.

Therapies based on the specific genetic alterations that underlie a patient’s cancer not only result in better outcomes but often have less adverse reactions

Up front fee

Nominal fee covers installation support, configuring the Workbench to your specification, designing and developing custom report(s) and training your team.

Per sample fee

GenomOncology is paid on signed-out clinical reports. This philosophy aligns GenomOncology with your Laboratory as we are incentivized to offer world-class support and solutions to differentiate your clinical NGS program. There is no annual license fee.

Part 4

Clinical Trial Services: Foundation Medicine & EmergingMed to Partner

Reporter: Aviva Lev-Ari, PhD, RN

Clinical Trial Services: Foundation Medicine & EmergingMed to Partner


Foundation Medicine and EmergingMed said today that they will partner to offer clinical trial navigation services for health care providers and their patients who have received one of Foundation Medicine’s tumor genomic profiling tests.

The firms will provide concierge services to help physicians

  • identify appropriate clinical trials for patients
  • based on the results of FoundationOne or FoundationOne Heme.

“By providing clinical trial navigation services, we aim to facilitate

  • timely and accurate clinical trial information and enrollment support services for physicians and patients,
  • enabling greater access to treatment options based on the unique genomic profile of a patient’s cancer

Currently, there are over 800 candidate therapies that target genomic alterations in clinical trials,

  • but “patients and physicians must identify and act on relevant options
  • when the patient’s clinical profile is aligned with the often short enrollment window for each trial.

These investigational therapies are an opportunity to engage patients with cancer whose cancer has progressed or returned following standard treatment in a most favorable second option after relapse.  The new service is unique in notifying when new clinical trials emerge that match a patient’s genomic and clinical profile.

Google signs on to Foundation Medicine cancer Dx by offering tests to employees

By Emily Wasserman

Diagnostics luminary Foundation Medicine ($FMI) is generating some upward momentum, fueled by growing revenues and the success of its clinical tests. Tech giant Google ($GOOG) has taken note and is signing onto the company’s cancer diagnostics by offering them to employees.

Foundation Medicine CEO Michael Pellini said during the company’s Q3 earnings call that Google will start covering its DNA tests for employees and their family members suffering from cancer as part of its health benefits portfolio, Reuters reports.

Both sides stand to benefit from the deal, as Google looks to keep a leg up on Silicon Valley competitors and Foundation Medicine expands its cancer diagnostics platform. Last month, Apple ($AAPL) and Facebook ($FB) announced that they would begin covering the cost of egg freezing for female employees. A diagnostics partnership and attractive health benefits could work wonders for Google’s employee retention rates and bottom line.

In the meantime, Cambridge, MA-based Foundation Medicine is charging full speed ahead with its cancer diagnostics platform after filing for an IPO in September 2013. The company chalked up 6,428 clinical tests during Q3 2014, an eye-popping 149% increase year over year, and brought in total revenue for the quarter of $16.4 million–a 100% leap from last year. Foundation Medicine credits the promising numbers in part to new diagnostic partnerships and extended coverage for its tests.

In January, the company teamed up with Novartis ($NVS) to help the drugmaker evaluate potential candidates for its cancer therapies. In April, Foundation Medicine announced that it would develop a companion diagnostic test for a Clovis Oncology ($CLVS) drug under development to treat patients with ovarian cancer, building on an ongoing collaboration between the two companies.

Foundation Medicine also has its sights set on China’s growing diagnostics market, inking a deal in October with WuXi PharmaTech ($WX) that allows the company to perform lab testing for its FoundationOne assay at WuXi’s Shanghai-based Genome Center.

a nod to the deal with Google during a corporate earnings call on Wednesday, according to a person who listened in. Pellini said Google employees were made aware of this new benefit last week.

Foundation Medicine teams with MD Anderson for new trial of cancer Dx

Second study to see if targeted therapy can change patient outcomes

August 15, 2014 | By   FierceDiagnostics

Foundation Medicine ($FMI) is teaming up with the MD Anderson Cancer Center in Texas for a new trial of the the Cambridge, MA-based company’s molecular diagnostic cancer test that targets therapies matched to individual patients.

The study is called IMPACT2 (Initiative for Molecular Profiling and Advanced Cancer Therapy) and is designed to build on results from the the first IMPACT study that found

  • 40% of the 1,144 patients enrolled had an identifiable genomic alteration.

The company said that

  • by matching specific gene alterations to therapies,
  • 27% of patients in the first study responded versus
  • 5% with an unmatched treatment, and
  • “progression-free survival” was longer in the matched group.

The FoundationOne molecular diagnostic test

  • combines genetic sequencing and data gathering
  • to help oncologists choose the best treatment for individual patients.

Costing $5,800 per test, FoundationOne’s technology can uncover a large number of genetic alterations for 200 cancer-related genes,

  • blending genomic sequencing, information and clinical practice.

“Based on the IMPACT1 data, a validated, comprehensive profiling approach has already been adopted by many academic and community-based oncology practices,” Vincent Miller, chief medical officer of Foundation Medicine, said in a release. “This study has the potential to yield sufficient evidence necessary to support broader adoption across most newly diagnosed metastatic tumors.”

The company got a boost last month when the New York State Department of Health approved Foundation Medicine’s two initial cancer tests: the FoundationOne test and FoundationOne Heme, which creates a genetic profile for blood cancers. Typically,

  • diagnostics companies struggle to win insurance approval for their tests
  • even after they gain a regulatory approval, leaving revenue growth relatively flat.

However, Foundation Medicine reported earlier this week its Q2 revenue reached $14.5 million compared to $5.9 million for the same period a year ago. Still,

  1. net losses continue to soar as the company ramps up
  2. its commercial and business development operation,
  • hitting $13.7 million versus a $10.1 million deficit in the second quarter of 2013.

Oncology

There has been a remarkable transformation in our understanding of

  • the molecular genetic basis of cancer and its treatment during the past decade or so.

In depth genetic and genomic analysis of cancers has revealed that

  • each cancer type can be sub-classified into many groups based on the genetic profiles and
  • this information can be used to develop new targeted therapies and treatment options for cancer patients.

This panel will explore the technologies that are facilitating our understanding of cancer, and

  • how this information is being used in novel approaches for clinical development and treatment.
Oncology _ Reprted by Dr. Aviva Lev-Ari, Founder, Leaders in Pharmaceutical Intelligence

Opening Speaker & Moderator:

Lynda Chin, M.D.
Department Chair, Department of Genomic Medicine
MD Anderson Cancer Center

  • Who pays for PM?
  • potential of Big data, analytics, Expert systems, so not each MD needs to see all cases, Profile disease to get same treatment
  • business model: IP, Discovery, sharing, ownership — yet accelerate therapy
  • security of healthcare data
  • segmentation of patient population
  • management of data and tracking innovations
  • platforms to be shared for innovations
  • study to be longitudinal,
  • How do we reconcile course of disease with PM
  • phinotyping the disease vs a Patient in wait for cure/treatment

Panelists:

Roy Herbst, M.D., Ph.D.
Ensign Professor of Medicine and Professor of Pharmacology;
Chief of Medical Oncology, Yale Cancer Center and Smilow Cancer Hospital

Development new drugs to match patient, disease and drug – finding the right patient for the right Clinical Trial

  • match patient to drugs
  • partnerships: out of 100 screened patients, 10 had the gene, 5 were able to attend the trial — without the biomarker — all 100 patients would participate for the WRONG drug for them (except the 5)
  • patients wants to participate in trials next to home NOT to have to travel — now it is in the protocol
  • Annotated Databases – clinical Trial informed consent – adaptive design of Clinical Trial vs protocol
  • even Academic MD can’t read the reports on Genomics
  • patients are treated in the community — more training to MDs
  • Five companies collaborating – comparison og 6 drugs in the same class
  • if drug exist and you have the patient — you must apply PM

Summary and Perspective:

The current changes in Biotechnology have been reviewed with an open question about the relationship of In Vitro Diagnostics to Biopharmaceuticals switching, with the potential, particularly in cancer and infectious diseases, to added value in targeted therapy by matching patients to the best potential treatment for a favorable outcome.

This reviewer does not see the movement of the major diagnostics leaders entering into the domain of direct patient care, even though there are signals in that direction.  The Roche example is perhaps the most interesting because Roche already became the elephant in the room after the introduction of Valium,  subsequently bought out Boehringer Mannheim Diagnostics to gain entry into the IVD market, and established a huge presence in Molecular Diagnostics early.  If it did anything to gain a foothold in the treatment realm, it would more likely forge a relationship with Foundation Medicine.  Abbott Laboratories more than a decade ago was overextended, and it had become the leader in IVD as a result of the specialty tests, but it fell into difficulties with quality control of its products in the high volume testing market, and acceeded to Olympus, Roche, and in the mid volume market to Beckman and Siemens.  Of course, Dupont and Kodak, pioneering companies in IVD, both left the market.

The biggest challenge in the long run is identified by the ability to eliminate many treatments that would be failures for a large number of patients. That has already met the proof of concept.  However, when you look at the size of the subgroups, we are not anywhere near a large scale endeavor.  In addition, there is a lot that has to be worked out that is not related to genomic expression by the “classic” model, but has to take into account the emrging knowledge and greater understanding of regulation of cell metabolism, not only in cancer, but also in chronic inflammatory diseases.

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@MIT, Biological Engineering : new computer model that allows to design the most complex three-dimensional DNA shapes ever produced

Posted in Genetics & Pharmaceutical, Genome Biology, Genomics Pharmacy on December 9, 2014| Leave a Comment »

@MIT, Biological Engineering : new computer model that allows to design the most complex three-dimensional DNA shapes ever produced

Reporter: Aviva Lev-Ari, PhD, RN

NATURE COMMUNICATIONS | ARTICLE OPEN

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

Nature Communications 5, 5578 doi:10.1038/ncomms6578

Abstract

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science.

http://www.nature.com/ncomms/2014/141203/ncomms6578/full/ncomms6578.html

 

Computer model enables design of complex DNA shapes

Engineers computer-design the most complicated 3-D structures ever made from DNA.

Watch Video

Anne Trafton | MIT News Office
December 3, 2014

Press Inquiries
SOURCE
https://newsoffice.mit.edu/2014/computer-model-for-complex-dna-shapes-1203
 

MIT biological engineers have created a new computer model that allows them to design the most complex three-dimensional DNA shapes ever produced, including rings, bowls, and geometric structures such as icosahedrons that resemble viral particles.

This design program could allow researchers to build DNA scaffolds to anchor arrays of proteins and light-sensitive molecules called chromophores that mimic the photosynthetic proteins found in plant cells, or to create new delivery vehicles for drugs or RNA therapies, says Mark Bathe, an associate professor of biological engineering.

“The general idea is to spatially organize proteins, chromophores, RNAs, and nanoparticles with nanometer-scale precision using DNA. The precise nanometer-scale control that we have over 3-D architecture is what is centrally unique in this approach,” says Bathe, the senior author of a paper describing the new design approach in the Dec. 3 issue of Nature Communications.

The paper’s lead authors are postdoc Keyao Pan and former MIT postdoc Do-Nyun Kim, who is now on the faculty at Seoul National University. Other authors of the paper are MIT graduate student Matthew Adendorff and Professor Hao Yan and graduate student Fei Zhang, both of Arizona State University.

DNA by design

Because DNA is so stable and can easily be programmed by changing its sequence, many scientists see it as a desirable building material for nanoscale structures. Around 2005, scientists began creating tiny two-dimensional structures from DNA using a strategy called DNA origami — the construction of shapes from a DNA “scaffold” strand and smaller “staple” strands that bind to the scaffold. This approach was later translated to three dimensions.

Designing these shapes is tedious and time-consuming, and synthesizing and validating them experimentally is expensive and slow, so researchers including Bathe have developed computer models to aid in the design process. In 2011, Bathe and colleagues came up with a program called CanDo that could generate 3-D DNA structures, but it was restricted to a limited class of shapes that had to be built on a rectangular or hexagonal close-packed lattice of DNA bundles.

In the new paper, Bathe and colleagues report a computer algorithm that can take sequences of DNA scaffold and staple strands and predict the 3-D structure of arbitrary programmed DNA assemblies. With this model, they can create much more complex structures than were previously possible.

The new approach relies on virtually cutting apart sequences of DNA into subcomponents called multi-way junctions, which are the fundamental building blocks of programmed DNA nanostructures. These junctions, which are similar to those that form naturally during DNA replication, consist of two parallel DNA helices in which the strands unwind and “cross over,” binding to a strand of the adjacent DNA helix.

After virtually cutting DNA into these smaller sections, Bathe’s program then reassembles them computationally into larger programmed assemblies, such as rings, discs, and spherical containers, all with nanometer-scale dimensions. By programming the sequences of these DNA components, designers can also easily create arbitrarily complex architectures, including symmetric cages such as tetrahedrons, octahedrons, and dodecahedrons.

“The principal innovation was in recognizing that we can virtually cut these junctions apart only to reassemble them in silico to predict their 3-D structure,” Bathe says. “Predicting their 3-D structure in silico is central to diverse functional applications we’re pursuing, since ultimately it is 3-D structure that gives rise to function, not DNA sequence alone.”

MIT engineers demonstrate the complex 3-D DNA structures made by their novel computer program.

Video: Melanie Gonick/MIT

The new program should enable researchers to design many more structures than those allowed by the CanDo program, says Paul Rothemund, a senior research associate at Caltech who was not part of the research team.

“Since a large fraction of the DNA nanotech community is currently using molecules whose structures could not be treated by the original CanDo, the current work is a highly welcome advance,” Rothemund says.

The researchers plan to make their algorithm publicly available within the next few months so that other DNA designers can also benefit from it. In the current version of the model, the designer has to come up with the DNA sequence, but Bathe hopes to soon create a version in which the designer can simply give the computer model a specific shape and obtain the sequence that will produce that shape. This would enable true nanometer-scale 3-D printing, where the “ink” is synthetic DNA.

Scaffolds and molds

Once researchers have access to printing 3-D nanoscale DNA objects of arbitrary geometries, they can use them for many different applications by combining them with other kinds of molecules. “These DNA objects are passive structural scaffolds,” Bathe says. “Their function comes from other molecules attached to them.”

One type of molecule that Bathe has begun working with is light-harvesting molecules called chromophores, which are a key component of photosynthesis. In living cells, these molecules are arranged on a protein scaffold, but proteins are more difficult to engineer into nanoscale assemblies, so Bathe’s team is trying to mimic the protein scaffold structure with DNA.

Another possible application is designing scaffolds that would allow researchers to mimic bacterial toxin assemblies made from multiple protein subunits. For example, the Shiga toxin consists of five protein subunits arranged in a specific pentameric structure that enables stealthy entry into cells. If researchers could reproduce this structure, they could create a version whose toxic parts are disabled, so that the remainder can be used for delivering drugs and micro- or messenger RNAs.

“This targeting subunit is very effective at getting into cells, and in a way that does not set off a lot of alarms, or result in its degradation by cellular machinery,” Bathe says. “With DNA we can build a scaffold for that entry vehicle part and then attach it to other things — cargo like microRNAs, mRNAs, cancer drugs, and other therapeutics.”

The researchers have also used DNA nanostructures as molds to form tiny particles of gold or other metals. In a recent Science paper, Bathe and colleagues at Harvard University’s Wyss Institute for Biologically Inspired Engineering demonstrated that DNA molds can shape gold and silver into cubes, spheres, and more complex structures, such as Y-shaped particles, with programmed optical properties that can be predicted by computer model. This approach offers a “made-to-order” nanoparticle design and synthesis procedure with diverse applications in nanoscale science and technology.

The current research was funded by the Office of Naval Research and the National Science Foundation.

Topics:DNANanoscience and nanotechnologyBiological engineeringSchool of EngineeringResearchAlgorithms

 

 

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CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121

Posted in Academic Publishing, Conference Coverage with Social Media, Gene Regulation, Gene Regulation and Evolution, Genetics & Pharmaceutical, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Immunodiagnostics, Infectious Disease & New Antibiotic Targets, Infectious Disease Immunodiagnostics, Innovation in Immunology Diagnostics, Intellectual Property, Intellectual Property, Innovations, Commercialization, Investment in technological breakthrough, Interviews with Scientific Leaders, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmacogenomics, Population Health Management, Genetics & Pharmaceutical, Proteomics, RNA Biology, RNA Biology, Cancer and Therapeutics, Scientific & Biotech Conferences: Press Coverage on October 26, 2014| Leave a Comment »

LIVE – Now –>> CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121

Reporter: Aviva Lev-Ari, PhD, RN

Article ID #157: Article ID #159: CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121. Published on 10/26/2014

WordCloud Image Produced by Adam Tubman

REAL TIME Conference Coverage by Dr. Aviva Lev-Ari, PhD, RN

For more Biotech Conferences Covered in Real Time by Dr. Aviva Lev-Ari, PhD, RN for Leaders in Pharmaceutical Business Intelligence using Social Media and Open Access Online Scientific Journal http://pharmaceuticalintelligence.com

click on

http://pharmaceuticalintelligence.com/press-coverage/

For articles on CRISPR-Cas9 in Open Access Online Scientific Journal http://pharmaceuticalintelligence.com

click on

http://pharmaceuticalintelligence.com/?s=CRISPR-Cas9

 

LIVE CONTENT from 

Gabbay Award Lecture in Biotechnology and Medicine @Brandeis

is been added 0n 10/27 @3;30PM

InVivo Target Search Mechanism – Fast Cas9 Diffusion in Live Cells

First Speaker

Emmanuelle Charpentier (Dept. of Molecular Biology. Umea University; Dept. of Regulation in Infection Biology, Helmholtz Centre for Infection Research)

CRISPR-Cas9: How a Bacterial Immune System Revolutionizes Life Sciences and Medicine

application in dairy industry basilicum, bacteria

Second Speaker

Jennifer Doudna (Dept. of Biochemistry, Biophysics and Structural Biology, UC Berkeley)CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering

Bacterial/archaeal chromosome

a single gene CAs9m- enzyme single-guide RNAs (sgRNAs)

crRNA

A Programmable Dual-RNA- Genome editing begins with dsDNA cleavange

ZFHs, TALENs, HEs, Cas9:sgRNA

protein DNA recognition

Genome targeting technologies: ZFN & TALEN

/Cas9/targeting RNA bound by a nuclease

2012-RNA-guided DNA endonuclease

1/2013 Church, Zhang

Re-Writing the Genome:

DNA structu

restriction enzymes

PCR

Specific genome editing in cell and in organizmism

robust transcriptional control with ccatalyrtic

In the Lab @Berkeley

Hoe Cas9 find DNA targets with high specificity

Mechanism of DNA interrogation

  • high affinity product binding, no substrate turnover
  • binding first occur at PAM motifs
  • PAM binding triggers Cas9 catalytic activity

CRISPR: Clusters of Regulary

three steps to acquire immunity in bacteria

1. adaptation

2. crRNA biogenesis

3. Interference

CRISPR in Structural Biology

  • RNA-induced conversion of Cas9 into an active confrontation – crystal structure morphology

Models for DNA interrogation by Cas9:RNA

Programmed RNA cleavage using Cas9:gRNA in O’Connell at al. (2014) Nature

 

  • Therapeutic Applications

1. Delivery of antibiotic small molecule

2. Animal models live cell (catalitic inactive version vs active version)

 

Third Speaker

Feng Zhang (McGovern Inst. for Brain Research, MIT)
Development and Applications of CRISPR-Cas9 for Genome Editing

Brain Research – Applications for CRISPER

  • Genetics & epigenetics
  • signals – optogenetics Neuromodulation
  • optogenetics — fibers — cells

The CRISPR/Cas bacterial

Crispr RNA maturation

E.coli – immunity for using Crispr

Streptococcus thermophilus – CRISPr editing applied

Development of a Technology Platform

  • expand modes of Genomic Pertubation

develop efficient co-transduction of primary neurons

multiplex knockout un the denate

  • demonstrate uses in biological therapeutic context

CRISPR — Reagents development, protocol developed, discussion forums

targeting of MeCP2 gyrus leads to robust protein depletion and behavior change

toxicity potential researched

Cre-dedendent CAs9 MOUSE FOR CANCER MODELING – mouth lung

  • develop an open source for the community

Genome-scale CRISPR knockout (GeCKO) Screen – generate library pool of cell – mutation identification – melanoma treated by BRAF inhibitor – targets for menanoma resistence

Comparison of shRNA vs GeCKO – CRISPR more robust and statisticaly significant, However, GeCKO provides higher sensitivity than shRNA

  •  foundational technology development

Crystal structure of Cas9 in complex wiht guided RNA and target DNA

Cre-dependent Cas9 Mouse

 

For Twitter.com

#Cas9
#CRISPR
#molecularbiology
#biotechnology
#GeneEditing
#genetic#engineering (sometimes these two # are put together like this)
#Boston

@BrandeisU
@MIT
@UCBerkeley
@CRISPRpapers
@UmeaUniversity
@mcgovernmit (this is for Feng Zhang)
@pharma_BI

 

CRISPR Service / Cas9

Commercialization by

 http://www.appliedstemcell.com/services/cell-line-models/cell-line-modification/

The CRISPR/Cas9 system uses the Cas9 nuclease to facilitate RNA-guided site-specific DNA cleavage. The system consists of two components:

(1) Mammalian codon-optimized version of the Cas9 protein carrying a nuclear localization signal to ensure nuclear compartmentalization in mammalian cells

(2) Guide RNAs (gRNAs) to direct Cas9 protein to sequence-specifically cleave the targeted DNA

The advantage of CRISPR/Cas9 over ZFNs or TALENs is its scalability and multiplexibility in that multiple sites within the mammalian genome can be simultaneously modified, providing a robust, high-throughput approach for gene editing in mammalian cells.

CRISPR Service (Point mutation, Deletion, Small DNA insertion)

crispr

We are experts in CRISPR Service! Applied StemCell is in Nature Biotechnology as one of the select companies for CRISPR-Cas9 tools! Monya Baker, “Gene Editing at CRISPR Speed,” Nature Biotechnology, 32: 309-312, April 2014.

Since Applied Stem Cell started out as a company focused on induced pluripotent stem cells (iPSCs), we have excellent capabilities of correcting mutations in disease-model iPSCs using CRISPR/ Cas9.

 

 

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Mechanisms of Drug Resistance

Posted in Biochemical pathways, Ca2+ triggered activation, Calcium Signaling, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Clinical Diagnostics, Cytoskeleton, Disease Biology, Drug Toxicity, Enzyme Induction, Gene Regulation, Gene Regulation and Evolution, Genetics & Pharmaceutical, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Infectious Disease & New Antibiotic Targets, Innovations, Intellectual Property, Ionic Transporters Na+, Lipid metabolism, Lipids, Metabolism, Metabolomics, Methods, Molecular Genetics & Pharmaceutical, Mutant Gene Expression, Nitric Oxide in Health and Disease, Nutrigenomics, Nutrition and Phytochemistry, Patents, Pharmaceutical Analytics, Pharmaceutical Discovery, Pharmaceutical Drug Discovery, Phosphorylation, Plant extract, Proteins, Proteomics, Signaling, Systemic Inflammatory Response Related Disorders, Transcriptomics, Translational Research, Translational Science, tagged , , , , , , , , , , , , , , , , , , , , , , on October 9, 2014| Leave a Comment »

Mechanisms of Drug Resistance

Curator: Larry H. Bernstein, MD, FCAP

Leaders in Pharmaceutical Intelligence, CSO

 

Mechanisms of Drug Resistance

This discussion is a continuing discussion of matters of metabolomics and the
essential role of genomic or epigenetic mechanisms to guide the development of
proteomic driven effectors of resistance to drug therapy.
We start with the elucidation of efflux pumps in bacteria, and we conclude with
consideration of cancer cells.

Part 1. Antimicrobial Resistance

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

difference between non-resistant bacteria and drug resistant bacteria

difference between non-resistant bacteria and drug resistant bacteria

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

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

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

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

According to the Centers for Disease Control and Prevention (April 2011), antibiotic
resistance in the United States costs an estimated $20 billion a year in excess health
care costs. In addition, a cost of $35 million in other societal costs and more than 8
million additional days that people spend in the hospital. This is because people
infected with antimicrobial-resistant organisms are more likely to have longer hospital stays and may require more complicated treatment.

Diagnostic tests designed to determine which microbe is causing infection and to
which antimicrobials the microbe might be resistant take a few days or weeks to give
results because of a requirement for the microbe to grow for it to be identified.

Part 2. Antibiotic Tolerance   
Reported By Jef Akst | June 25, 2014

Optimization of lag time underlies antibiotic tolerance in evolved bacterial
populations
O. Fridma et al.    Nature, 2014 
http://dx.doi.org://10.1038/nature13469

Populations of Escherichia coli grown in the lab develop tolerance when exposed to
repeated treatments with the antibiotic ampicillin. The bacteria evolved to stay in a
dormant “lag” phase for just longer than three-, five-, or eight-hour-long treatment
courses. Antibiotic tolerance, which allows bacteria to survive even high levels of
antibiotics by remaining dormant. Tolerance may lead to an inaccurate assumption
that an unsuccessful antibiotic treatment failed as a result of resistance, in which
the microbe has evolved to grow in the presence of the drug. Resistance is very well
known; but the issue of tolerance is much less known,” according to Tom Coenye of
the Laboratory of Pharmaceutical Microbiology (LPM) at Gent University in Belgium,
who was not involved in the research.  This is a new phenomenon, extended lag,
where mutants have a longer lag time, and that extended lag allows them to survive
an attack by antibiotics.

To gain a better understanding of how bacterial populations might evolve to tolerate
antibiotic exposure, Nathalie Q. Balaban, a microbiologist and physicist at The Hebrew
University of Jerusalem in Israel and her colleagues exposed cultures of E. coli to high
concentrations of ampicillin for three, five, or eight hours, then washed the drug away
and suspended the bacteria in fresh media to be grown overnight. The next day, the
team repeated these treatments. In 10 cycles we could see that tolerance had evolved,
” Balaban said. Indeed, while the ampicillin treatments killed more than 99.9 percent of
the E. coli, by day 10, bacterial survival had increased 100-fold.

Moreover, the bacteria were also tolerant to norfloxacin, an antibiotic with a different mechanism of action than ampicillin but also ineffective during the dormant stage,
further supporting the idea that the E. coli populations had evolved to tolerate certain
durations of antibiotic exposure. “This is characteristic of tolerance,” said Balaban.
“The bacteria that have evolved tolerance under ampicillin are also more tolerant to
this completely different class of antibiotics.” Resistance, on the other hand, is usually
class-specific, she noted.

The researchers identified three genes that seemed to play a functional role in antibiotic
tolerance. While the exact mechanism of how mutations in these genes may have
lengthened the bacteria’s lag time is not yet known, two of the genes are part of pathways
that were previously implicated in bacterial persistence, including an antitoxin in a
common toxin-antitoxin module that may help regulate that bacteria’s growth.

Part 3. Multidrug Resistance Perspective

Mechanisms of antibiotic resistance in salmonella: efflux pumps, genetics,
quorum sensing and biofilm formation.

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

Multidrug resistance (MDR) to antibiotics presents a serious therapeutic problem
in the treatment of bacterial infections. The importance of this mechanism of resistance
in clinical settings is reflected in the increasing number of reports of multidrug resistant
isolates. In Salmonella enterica, the most common etiological agent of food borne
salmonellosis worldwide, MDR is becoming a major concern.

In Salmonella the main mechanisms of antibiotic resistance are mutations in target
genes (such as DNA gyrase and topoisomerase IV) and the over-expression of efflux pumps. However, other mechanisms such as

  1. changes in the cell envelope;
  2. down regulation of membrane porins;
  3. increased lipopolysaccharide (LPS) component of the outer cell membrane;
  4. quorum sensing and
  5. biofilm formation

can also contribute to the resistance seen in this microorganism. To overcome
this problem new therapeutic approaches are urgently needed.

In the case of efflux-mediated multidrug resistant isolates, one of the treatment
options could be

  • the use of efflux pump inhibitors (EPIs)
  • in combination with the antibiotics to which the bacteria is resistant.

By blocking the efflux pumps

  • resistance is partly or wholly reversed,
  • allowing antibiotics showing no activity against the MDR strains
  • to be used to treat these infections.

Compounds that show potential as an EPI are therefore of interest, as well as new
strategies to target the efflux systems. Quorum sensing (QS) and biofilm formation
are systems also known to be involved in antibiotic resistance. Consequently,
compounds that

  • can disrupt or inhibit these bacterial “communication systems” will be of use in
    the treatment of these infections.

Part 5. Effux pumps and S. Aureus

Multidrug Efflux Pumps in Staphylococcus aureus: an Update

SS Costa, M Viveiros, L Amaral and I Couto
1Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e
Medicina Tropical, Universidade Nova de Lisboa (IHMT, UNL), 2Centro de Recursos
Microbiológicos (CREM), UNL, Portugal,3COST ACTION BM0701 (ATENS), Brussels,
Belgium
The Open Microbiology Journal 2013;(Suppl 1-M5): 59-71

The emergence of infections caused by multi- or pan-resistant bacteria in the hospital
or in the community settings is an increasing health concern. Albeit there is no single
resistance mechanism behind multi-resistance, multidrug efflux pumps,

  • proteins that cells use to detoxify from noxious compounds,

seem to play a key role in the emergence of these multidrug resistant (MDR) bacteria.
During the last decades, experimental data has established their contribution to low
level resistance to antimicrobials in bacteria and their

  • potential role in the appearance of MDR phenotypes, by the extrusion of multiple,
    unrelated compounds.

Recent studies suggest that

  • efflux pumps may be used by the cell as a first-line defense mechanism,

avoiding the drug to reach lethal concentrations, until a stable, more efficient alteration
occurs, that allows survival in the presence of that agent.

In this paper we review the current knowledge on

  • MDR efflux pumps and their
  • intricate regulatory network in Staphylococcus aureus,

a major pathogen, responsible from mild to life-threatening infections. Particular emphasis will be given to the potential role that

  • aureus MDR efflux pumps,
  • either chromosomal or plasmid-encoded, have
  • on resistance towards different antimicrobial agents and
  • on the selection of drug – resistant strains.

We will also discuss the many questions that still remain on the role of each specific
efflux pump and the need to establish appropriate methodological approaches to
address all these questions.

        Table 1. Multidrug Efflux Pumps Described for Staphylococcus aureus

Efflux Pump  Familya  Regulator(s)b  Substrate Specificity  References 
Chromosomally-encoded Efflux Systems 
NorA MFS MgrA,
NorG(?)		 Hydrophilic fluoroquinolones (ciprofloxacin,
norfloxacin) QACs (tetraphenylphosphonium,
benzalkonium chloride) Dyes (e.g. ethidium
bromide, rhodamine)		 [16,18,19]
NorB MFS MgrA,
NorG		 Fluoroquinolones (e.g. hydrophilic: ciprofloxacin,
norfloxacin and hydrophobic: moxifloxacin,
sparfloxacin) Tetracycline QACs (e.g.
tetraphenylphosphonium, cetrimide) Dyes (e.g. ethidium bromide)		 [31]
NorC MFS MgrA(?),
NorG		 Fluoroquinolones (e.g. hydrophilic: ciprofloxacin
and hydrophobic: moxifloxacin) Dyes
(e.g. rhodamine)		 [35,36]
MepA MATE MepR Fluoroquinolones (e.g. hydrophilic: ciprofloxacin,
norfloxacin and hydrophobic: moxifloxacin,
sparfloxacin) Glycylcyclines (e.g. tigecycline) QACs (e.g. tetraphenylphosphonium, cetrimide, benzalkonium chloride) Dyes
(e.g. ethidium bromide)		 [37,38]
MdeA MFS n.i. Hydrophilic fluoroquinolones (e.g. ciprofloxacin,
norfloxacin) Virginiamycin, novobiocin, mupirocin,
fusidic acid QACs (e.g. tetraphenylphosphonium,
benzalkonium chloride, dequalinium) Dyes (e.g. ethidium bromide)		 [39,40]
SepA n.d. n.i. QACs (e.g. benzalkonium chloride) Biguanidines
(e.g. chlorhexidine) Dyes (e.g. acriflavine)		 [41]
SdrM MFS n.i. Hydrophilic fluoroquinolones (e.g. norfloxacin) Dyes (e.g. ethidium bromide, acriflavine) [42]
LmrS MFS n.i. Oxazolidinone (linezolid) Phenicols
(e.g. choramphenicol, florfenicol) Trimethoprim, erythromycin, kanamycin,
fusidic acid QACs (e.g. tetrapheny-
lphosphonium) Detergents (e.g. sodium
docecyl sulphate) Dyes (e.g. ethidium
bromide)		 [43]
Plasmid-encoded Efflux Systems

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

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

Identification of the plasmid-encoded qacA efflux pump gene
in meticillin-resistant Staphylococcus aureus (MRSA)
strain HPV107, a representative of the MRSA Iberian clone

S.S. Costaa,b, E. Ntokouc, A. Martinsa,d, M. Viveirosa,e, S. Pournarasc,
I. Coutoa,b, L. Amarala,d,e,∗
a Unidade de Micobactérias, Instituto de Higiene e Medicina Tropical,
Universidade Nova de Lisboa (IHMT, UNL), b Centro de Recursos Microbiológicos,
Universidade Nova de Lisboa (CREM, UNL), d Unidade de Parasitologia e
Microbiologia Médica (UPMM), Instituto de Higiene e Medicina Tropical, Universidade
Nova de Lisboa (IHMT, UNL), Lisbon, Portugal; e COST ACTION BM0701 (ATENS)
c Department of Microbiology, Medical School, University of Thessaly, Larissa, Greece;
Int J Antimicrobial Agents  2010; 36: 557–561
http://www.elsevier.com/locate/ijantimicag

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial
bacterium for which prevention and control measures consist mainly of

  • the application of biocides with antiseptic and disinfectant activity.

In this study, we demonstrated the presence of

  • the plasmid-located efflux pump gene qacA in MRSA strain HPV107,

a clinical isolate representative of the MRSA Iberian clone. The existence
of efflux activity in strain HPV107 due to the QacA pump was found and

  • this QacA efflux activity was linked with a phenotype of
  • reduced susceptibility towards several biocide compounds.

No association could be made with antibiotic resistance. This work
emphasises the potential of QacA pump activity in

  • the maintenance and dissemination of important MRSA strains in
    the hospital setting and, increasingly, in the community.

Efflux-mediated response of Staphylococcus aureus exposed to
ethidium bromide

I Couto1,2, S S Costa1, M Viveiros1, M Martins1,3 and L Amaral1,3*
1Unidade de Micobacterias, Instituto de Higiene e Medicina Tropical,
Universidade Nova de Lisboa (UNL), 2Centro de Recursos Microbiolo´gicos (CREM), Faculdade de Cieˆncias e Tecnologia, UNL,3UPMM,
Instituto de Higiene e Medicina Tropical, UNL, Portugal
J Antimicrob Chemother  (2008) 62, 504–513
http://dx.doi.org:/10.1093/jac/dkn217

By adapting an antibiotic-susceptible Staphylococcus aureus strain to
increasing concentrations of ethidium bromide, a known substrate
of efflux pumps (EPs), and

  • by phenotypically and genotypically analysing the resulting progeny,
  • we characterized the molecular mechanisms of S. aureus
    adaptation to ethidium bromide.

ATCC 25923 was grown in increasing concentrations of ethidium bromide.
The MICs of representatives of eight classes of antibiotics, eight biocides
and two dyes against ATCC 25923 and its ethidium bromide-resistant progeny
ATCC 25923EtBr were determined

  • with or without six efflux pump inhibitors (EPIs).

Efflux activity in the presence/absence of EPIs was evaluated by realtime
fluorometry. The presence and expression of eight EP genes were assayed
by PCR and quantitative RT–PCR (qRT–PCR), respectively. Mutations in
grlA, gyrA and norA promoter regions were screened by DNA sequencing.

Compared with its parental strain, ATCC 25923EtBr was

  • 32-fold more resistant to ethidium bromide and
  • also more resistant to biocides and hydrophilic fluoroquinolones.
  • Resistance to these could be reduced by the EPIs chlorpromazine,
    thioridazine and reserpine.

Increased efflux of ethidium bromide by ATCC 25923EtBr could be
inhibited by the same EPIs. qRT–PCR showed that

  • norA was 35-fold over-expressed in ATCC 25923EtBr,

whereas the remaining EP genes showed no significant increase in their

expression. Sequencing of the norA promoter region revealed

  • a 70 bp deletion in ATCC 25923EtBr.

Exposure of S. aureus to quaternary compounds such as ethidium bromide
results in decreased susceptibility of the organism to a wide variety of
compounds, including quinolones and biocides

  • through an efflux-mediated response, which
  • for strain ATCC 25923 is mainly NorA-mediated.

This altered expression may result from alterations in the norA
promoter region.

Ethnic consumption of plant leaf extracts and appraisal of
their nutraceutical efficacy against multidrug resistant
staphylococcus aureus

Kaushik S1, 2*, Tomar Rs1, Shrivastav V1, Shrivastav A2 And Jain Sk3
Amity Institute of Biotechnology, Amity University Madhya Pradesh,
Gwalior (M.P.);  2: College of Life Sciences, Cancer Hospital and
Research Institute, Gwalior (M.P.); 3: Department of Microbiology,
Vikram University, Ujjain (M.P.), INDIA
IJBPAS, Feb, 2014, 3(2): 204-209

Nutraceuticals are natural bioactive chemical compounds that have
health promoting, disease preventing or medicinal properties.
Emergence of Multi Drug Resistant Staphylococci is increasing at
alarming rates and diseases caused by these strains leave patients
against multiple resistant Staphylococcus aureus.

The test bacteria were isolated and characterized by standard and
NCCLS recommended microbiological techniques. A total of eighteen
plant extracts were analysed for their antimicrobial activity. The
selection of medicinal plants was based on their traditional uses in
India. However most of these plants were not previously screened.
Antibacterial activity of these components was performed by standard
Kirby Bauer Disk Diffusion method approved by NCCLS and the
inhibitory effect was analysed by calculating Zone of inhibition.

Among the eighteen plant extracts analysed we found highest
activity in the effect of chemotherapy and as promising bio control agents

  • Guava,
  • Mango,
  • Jamun and
  • Pomengrate plant extracts,

while most of the other plants were either showing very moderate/
least activity against test bacteria. Our recent experiment indicated
that phytochemicals extracted with methanol can be utilized as
nutraceutical to lower the side.

Part 6. Efflux pumps and gram-negative organisms

Efflux Pumps that Bestow Multi-Drug Resistance of Pathogenic Gram-
negative Bacteria 

Amaral L1,2*, Spengler G2, Martins A2,3 and Molnar J2
1Travel Medicine of the Centre for Malaria and Other Tropical Diseases (CMDT),
Institute of Hygiene and Tropical Medicine, Lisbon, Portugal 2Department of
Medical Microbiology and Immunobiology, Faculty of Medicine, University of
Szeged, Szeged, Hungary 3Unit of Parasitology and Medical Microbiology
(UPMM), Institute of Hygiene and Tropical Medicine, Lisbon, Portugal
Amaral et al., Biochem Pharmacol 2013; 2:3
http://dx.doi.org/10.4172/2167-0501.1000119

The efflux pump

The efflux pump

Efflux pumps are integral plasma membrane protein systems that recognize and bind
noxious compounds present in the cytoplasm (toxic products produced by metabolism;
compounds that have penetrated the cell), or periplasm of the bacterial cell and extrude
it into the environment in which the bacterium resides [1].

The efflux pump machinery gives the cell additional protection to the one provided by

  • the constituents of its cell wall (example: lipopolysaccharides), and
  • provides an initial protection to noxious agents present in its
    natural environment that have penetrated into the cell (example: bile
    salts in the colon) [1].

The efflux pump machinery is divided into five superfamily classes;

  • the major facilitator (MF),
  • the ATP-binding cassette (ABC),
  • the resistance-nodulation-division (RND),
  • the small multi-drug resistance (SMR) and
  • the multi-drug and toxic compound extrusion (MATE).

With respect to Gram-negative bacteria, although they all play
important roles in the protection of the bacterium from noxious
agents present in the environment, the

  • main efflux pump of the Gram negative bacterium is a
    member of the RND superfamily, and
  • because multi-drug resistance of clinical isolates have
    been associated with the over-expression of this pump,

it has received a great deal of attention [2].

The first in vitro response of bacteria to a given noxious agent,
such as an antibiotic, is to over-express its main efflux pump [2].
If the bacterium is serially exposed in vitro to increasing
concentrations of that compound, it responds by increasing
the effective number of its main efflux pump, as well as others
that provide redundant protection [2].

However, if that “adapted” bacterium is now maintained at a
constant level of a noxious agent, the level of efflux pump
activity increases up to a maximum, followed by a gradual
return of efflux pump activity to its basal level. Concomitant
to this process, an accumulation of mutations of essential
proteins located in the plasma membrane (example penicillin
binding proteins), mutations 30 S component of the ribosome
and gyrase take place [3]. These events suggest that when
the organism is faced with an environment that contains a
constant toxic level of a compound, and the cost for
maintaining an energy consuming system, such as that
needed for the energy dependent efflux pump, is too
great a price to pay.

Therefore, in order to survive in this unchanging environment,
other mechanisms are activated. For example, activation of a
mutator master gene is thought to be an important step at this
level, which results in the mutation of genes that code for
essential proteins, reversing the over-expression of efflux-
pumps, but still conferring the bacterial resistant to the
environmental pressure via other mechanism(s), yet
to be understood [4,5].

During therapy, the level of resistance increases many fold
higher than that of the initial infecting strain. Hence, clinical
isolates from treated patients often show much higher levels
of antibiotic resistance than that of their wild type counterpart
(sometimes it can even present a 1000 fold increase) [6].
At this stage, resistance is usually related to the presence
of mutations, which reduces the survival of the resistant
bacteria,

  • once it is transferred to a noxious agent-free environment

that contains the competing wild type counterpart [3,4].

Depending upon when during therapy a clinical strain is isolated,
its resistance to two or more antibiotic classes (multi-drug
resistance (MDR)), may be due entirely to over-expressed
efflux pumps; to a mixture of over-expressed efflux pumps
and increasing accumulation of mutations; and only to mutations [3,4].

The degree of resistance can readily be determined with
methods that employ compounds known for their modulation
of efflux pump activity, such as

  • phenothiazines [7] or phenyl-arginine-betanaphthylamide
    (PAβN),
  • the latter which competes with the antibiotic as
    substrate of the efflux pump [8].

If in presence of such compounds,

  • the MDR bacterium is rendered fully susceptible
    to the antibiotic(s) to which it was initially resistant,
  • resistance is most likely due to its overexpressed
    efflux pump systems.
  • Contributions made by accumulated mutations
    render the organism less and less affected by the EPI.

This type of information is of great value to clinicians faced
with long-term therapy of a bacterial infection that
progresses to an MDR phenotype. It should be understood
that although the Gram-negative bacterium has essentially
one main efflux pump, such as

  • the AcrAB (Escherichia coli) or
  • the MexAB (Pseudomonas aeruginosa),

the deletion of the main efflux pump results in the over-
expression of one or more other RND efflux pumps,
such as is the case for deletion of the AcrAB, followed by

  • the over-expression of the AcrEF pump [2].

Redundancy of as many as nine RND efflux pumps [2],
provides additional protection to the organism.

The pumps belonging to the RND family form

  • a tripartite complex together with
  • the periplasmic proteins belonging to the
    membrane fusion-protein (MFP) family and
  • the outer membrane channels.

RND transporters consist of

  • a transporter protein that recognises and
    binds the noxious agent
    in the cytoplasm or periplasm and
  • transports it to the contiguous channel (TolC),
  • ending at the surface of the outer membrane.

The transporter is attached to the plasma membrane
by two or three fusion proteins, which are believed to assist the

  • extrusion of the substrate by peristaltic actions [9].

Although the actual structure of RND efflux pumps
in the cell envelop is not completely understood,

  • the structure of the transporter, TolC and fusion
    proteins are well established for major Gram-negative
    bacteria [10].

The PMF energy dependent efflux pump most likely needs the
passage of hydronium ions through its internal cavity,

  • for the release of the substrate that is
  • in turn ejected into the TolC channel via the
  • peristaltic action of the fusion proteins [11].

A low pH,

  • the concentration of hydronium ions at the surface of the cell
  • results in a pH difference of 2 or 3 pH units compared
    to that of the milieu,

the surface concentration of hydronium ions

  • provides the force for the mobility of hydronium ions
  • through porins leading to the acidification of the periplasm,
  • providing the low pH needed by the transporter
  • for the release of the substrate.

At high pH, these hydronium ions come from

  • hydrolysis of ATP by ATP synthase, and
  • are passed into the transporter, thereby
  • reducing its internal pH, so that
  • the release of the substrates can take place [11,12].

EPIs, such as the phenothiazines chlorpromazine or thioridazine,

  • exert their inhibition at pH above 6, and
  • are thought to affect hydrolysis of ATP
  • denying the efflux pump transporter hydronium ions needed

for release of the bound substrate [11,12].

The search for EPIs that are clinically useful continues, although

with respect to thioridazine, this old neuroleptic has been shown

  • to inhibit efflux pumps of pathogenic mycobacteria [13], and
  • has been successfully used to treat extensively drug resistant
    tuberculosis infections [14].

The regulation of the main efflux pump of Escherichia coli may
take place via   distinct pathways. The induced synthesis of the
transporter component of the AcrAB efflux pump, when the
organism is exposed in vitro to a noxious agent,

  1. involves the activation of the stress gene soxS,
  2. followed by the activation of the local regulator marA,
  3. then by the activation of the transporter gene acrB [8].

In the case of Salmonella spp. two component resistance
mechanisms, such as the PmrA/PmrB system, directly
activate the master efflux pump regulator ram A gene [15].
The activation of the PmrA/PmrB system takes place
readily when Salmonella spp. is phagocytosed due to
the acidic nature of the phagolysosome [15], as follows:

  1. PmrB is a sensor that self-phosphorylates, and
  2. then transfers the phosphate to PmrA.
  3. PmrA activates a nine gene operon, which
  4. codes for Lipid A introduced into the nascent
    lipopolysaccharide layer of the outer membrane.
  5. The increased presence of Lipid A renders the
    phagocytosed bacterium practically immune to
    everything, including the hydrolases of the
    phagolysososome [15].

Although some EPIs are in clinical trials, none have yet to
reach the marketplace,    mainly due to their common
toxicity against healthy mammalian cells, affecting
intrinsic mammalian efflux pumps, as for example
those of the blood brain barrier. Lastly, it should be
noted that compounds that inhibit the efflux pump
of bacteria also have the capacity to promote the
removal of plasmids that carry antibiotic resistant
genes [16,17].

  1. Nikaido H, Pages JM (2012) Broad-specificity efflux
    pumps and their role in multidrug resistance of Gram-
    negative bacteria. FEMSMicrobiol Rev 36: 340-363.
  2. Viveiros M, Jesus A, Brito M, Leandro C, Martins M,
    et al. (2005) Inducement and reversal of tetracycline
    resistance in Escherichia coli K-12 and expression of
    proton gradient-dependent multidrug efflux pump
    genes. Antimicrob Agents Chemother 49: 3578-3582.
  3. Martins A, Couto I, Aagaard L, Martins M, Viveiros M
    (2007) Prolonged exposure of methicillin-resistant
    Staphylococcus aureus (MRSA) COL strain to
    increasing concentrations of oxacillin results in a
    multidrug-resistant phenotype. Int J Antimicrob
    Agent 29: 302-305.
  4. Martins A, Spengler G, Molnar J, Amaral L (2012)
    Sequential responses of bacteria to noxious agents
    (antibiotics) leading to accumulation of mutations
    and permanent resistance. Biochem Pharmacol J
    Open Access 1: 7.

Inhibitors of efflux pumps of Gram-negative
bacteria inhibit Quorum Sensing

Leonard Amaral, Joseph Molnar
1 Grupo de Micobacterias, Unidade de Microbacterilogia,
Centro de Malaria e Doenças Tropicais (CMDT), Instituto de
Higiene e Medicina Tropical, Universidade Nova de Lisboa,
Lisbon, Portugal; 2 Cost Action BM0701 (ATENS) of the
European Commission/European Science Foundation;
3 Department of Medical Microbiology and Immunobiology,
University of Szeged, Szeged, Hungary
Open Journal of Pharmacology, 2012, 2-2

Quorum Sensing (QS) systems of bacteria consist of

  • a producer of the QS signal and the responder.

The generation of a QS signal provides the means by which
a population can behave in a concerted manner such as

  • swarming, swimming and secretion of biofilm, etc.

Because concerted bahaviour bestows protection to the bacterial
species, and hence factors involved in the severity of an infection
such as virulence are products of QS systems, compounds that
inhibit the QS system have significant clinical relevance. Recent
evidence suggests that

  • the secretion of QS signals takes place via
  • the efflux pump system of the producer of the signal.

Interestingly, compounds such as phenothiazines and
trifluoromethyl ketones (TFs)

  • that inhibit proton motive force (PMF) activities such
    as swarming and swimming also
  • inhibit the PMF dependent efflux pump systems of
    bacteria and their QS   systems.

This review discusses the relationship between the efflux
pump, the QS system and the compounds that affect both.
Lastly, suggestions are made regarding classes of compounds
that have been shown

  • to inhibit PMF dependent efflux pumps and the need
  • to evaluate them for QS inhibitory properties.

Keywords: Quorum Sensing, QS signal, acylated hydroxyl
lactone (AHL), efflux pumps, Proton Motive Force (PMF),
inhibitors of efflux pumps, inhibitors of QS systems,
phenothiazines, Trifluormethyl Ketones (TFs), plants
sources for QS inhibitors

Efflux pumps of bacteria provide protection from noxious
agents that are present in the environment in which they
exist. Noxious agents may be naturally occurring compounds
present in environments outside and within the human.

Because over-expressed efflux pumps render antibiotic
therapy problematic, an intense search for agents that
inhibit specific efflux pumps of specific bacteria has
been conducted during the past decade [9].

Communication between bacteria of the same strain
or species and between species contributes to their
survival [11-13]. Communication involves the secretion
of signals that invoke a specific response from the responder
[11-13]. This  communication process is termed Quorum
sensing (QS). When it takes place between strains of the
same species,

  • communication is directed towards the reduction
    of population growth and
  • reducing the possibility of exceeding the nutritional
    support of the environment

Other signals may involve a population response that involves

  • the secretion of bioactive molecules that inhibit the
    replication of a competing population species [14-16]
    or even kill [biocidins) [17-21] or
  • promote a swarming effect that recruits members
    of the same species to migrate  to a specific location [22-24]
    similar to swarming by insects subsequent to signals
    indicating site of food [example bees).
  • biofilm, encase the bacteria at distances from each other
    [25-29] and within the matrix of this biofilm are
    channels used for further communication [30].

Biofilms are produced in the wild, at sites such as surfaces
of rocks which maintain the bacterial population in situ [31]
and are also produced at sites of the human colonized by
infecting bacteria [32, 33].

Agents that inhibit the QS response of the infecting bacterium
are obviously important and hence, the search for such agents
that inhibit the QS system and biofilm formation has been in
effect for the past two decades [11-13].

There is a relationship between efflux pumps (EP), QS and
biofilm (BF) secretion which has come to the forefront only
recently [13]. Control of this relationship is critical for
successful therapy of MDR bacterial infections which have
become rather commonplace. It is the intent of this review
to identify agents which may serve to interfere with the
complex system of EP-QS-BF interaction.

Proton motive force (PMF) dependent transporters obtain
their energy for function from the proton motive force. The
proton motive force is the result of cellular metabolism which
yields protons that are not used for coupling with molecular
oxygen and which are exported to the surface of the cell [43-45]
where they are distributed and bound to components of
the protective lipopolysaccharide layer that covers the cell
and constitutes a part of the outer cell wall of Gram-negative
[46] and the cell wall of Gram positive bacteria [47].

The larger the concentration of protons (hydronium ions)
on the surface of the cell with respect to their lower
concentration on the medial side of the cytoplasmic
membrane creates an electrochemical gradient that
is termed the proton motive force (PMF) [48].

Because hydronium ions cannot penetrate the cell wall
or the membrane, they may re-enter the cell only
through channels such as porins in general [49, 50].
The movement of these hydromium ions from the
surface of the cell to the periplasm or cytoplasm is
predicated upon systems that use the PMF as source
of energy-namely the resistance nodulation division
(RND) family of transporters.

E. coli has a multiplicity of efflux pumps that may
exceed 30 in number [51]. However, the main
efflux pump of this organism is the AcrAB-TolC
efflux pump [52, 53] which when deleted, its
function is replaced by the AcrEF-TolC efflux
pump [51]. Both efflux pumps are members
of the resistance nodulation division family of
transporters [51] and consist of three proteins:

  1. The transporter AcrB coded by the gene acrB and
    is intimately attached to the  plasma membrane;
  2. Two fusion proteins AcrA coded by the gene acrA
    that flank the AcrB transporter and are thought
    to assist the movement of a substrate through
    the AcrB transporter [35]; and,
  3. TolC which is also part of other tri-unit efflux pumps
    of the organism [35], is contiguous with the AcrB
    transporter and provides a conduit for the extrusion
    of the substrate [38].

Although the means for the recognition of the substrate to
be extruded appears to involve a pocket within the transporter,
it appears to be

  • defined by a phenyalanine residue [54].

Nevertheless, studies employing fluorochromes recognised by
the AcrB transporter indicate that the binding and release of
the substrate are pH dependent [55].

  • At low pH the dissociation of the substrate is high and
  • at high pH it is very slow.

In a physiological environment of ca. pH 7, if the dissociation
of the substrate is slow or not at all, then the effectiveness of
the pump to extrude a noxious agent would be nullified.
However, since the pump functions at this pH, conditions that
result in the dissociation of the substrate needed for continuous
pump action must involve a

  • decrease of the pH of the internal cavity of the pump
    to which the substrate is bound.

It has been postulated that the lowering of the pH takes place
by the generation of hydronium ions from metabolism [6] which

  • pass from the cytoplasmic side of the plasma membrane
    through the transporter.

At lower pH, there is no need for the generation of metabolically
derived  hydronium ions since these ions can be

  • diverted by the PMF from the surface of the cell
    to the periplasm via porins.

Whether hydronium ions are to be generated from the
hydrolysis of ATP at high pH or used for the synthesis
of ATP at low pH is a special

  • function of ATP synthase [56-58].

Model of the AcrAB-TolC efflux pump of a Gram-
negative bacterium

AcrAB-TolC efflux pump of a Gram-negative bacterium

AcrAB-TolC efflux pump of a Gram-negative bacterium

Hypothesis. At near neutral pH, Hydronium ions from hydrolysis of ATP
by ATP synthase pass through the AcrB

transporter, reduce the pH to a point that causes the release of the
substrate. When the hydronium ions reach the surface of the cell they
are distributed over that surface and bind to lipopolysaccharides
and basic amino acids. When there is a need for hydronium ions for
activity of the efflux pump and the pH is lower than neutral, and
the hydrolysis of ATP is not favoured, hydronium ions from the
surface of cell via the PMF mobilize through the Aqua porins
and reach the transporter where they are pushed through
the transporter by the peristaltic action caused by the fusion
proteins. Substrates bound to the transporter dissociate
when the pH is reduced by the flow of hydronium ions and
are carried out by the flow of water.

Inhibitors of bacterial efflux pumps
Inhibitors of the QS of bacteria

Because phenothiazines inhibit many energy dependent systems
of bacteria such as motility [89, 90, 95], and these phenothiazines
also inhibit efflux pumps of bacteria [6, 7, 9, 41, 51, 73, 74, 76-83],
there seems to be a correlation between an active efflux pump
system and a functional QS system. That this assumption is correct,
recent evidence has been provided showing that the efflux pumps of
the AHL responding environmental Chromobacterium violaceum
(CV026) bacterium and that of E. coli are inhibited by the phenothiazine
thioridazine (TZ) [12]. Because TZ is known to inhibit genes that
regulate and code for efflux pumps of bacteria [41, 119, 120], it is
possible that the inhibition of the responding CV0126 bacterium to
AHLs [12] involves the inhibition of genes that code and regulate
the efflux pump of the responder which is assumed to recognise the
AHL signal as an noxious agent and hence would extrude it to the
environment [12]. The inhibition of an efflux pump should manifest
itself as an inhibitor of the QS component responsible for biofilm
formation.

Since the discovery of berberine a powerful inhibitor of bacterial
efflux pumps [159], plants have become sources of inhibitors of
efflux pumps [160-164]. Given that efflux pumps and the  QS of
bacteria have an intimate relationship as described in this review,
attention has been focused on plants for potential sources of inhibitors
of efflux pumps and QS systems. Essential oils from Columbian
plants have yielded a large number of compounds that inhibit the
QS system of responding bacteria such as

  1. limonene-carvone , the
  2. citral (geranial-neral) (isolated from Lippia alba),
  3. α-pinene (from Ocotea sp.),
  4. β-pinene (from Swinglea glutinosa),
  5. cineol (from Elettaria cardamomun),
  6. α-zingiberene (from Zingiber officinale) and
  7.  pulegone (from Minthostachys mollis) [165].

Several other essential oils, in particular were shown to present
promising inhibitory properties for the short chain AHL quorum
sensing (QS) system in Escherichia coli containing the biosensor

  •  plasmid pJBA132, in  particular Lippia alba.

Citral was the only  essential oil that presented some activity for
the long chain AHL QS system in Pseudomonas putida containing

  •  the plasmid pRK-C12 [165].

The essence of this review is to correlate the relationship of the
efflux pump system to the QS system of bacteria via the use of
compounds that inhibit both systems. Simply put, inhibitors of
the efflux pump system also, when studied, inhibit the QS system
as well. Because the PMF dependent efflux pump system of Gram-
negatives that is overexpressed is responsible for the multi-drug
phenotype of the bacterium, compounds that affect the PMF of
the bacterium are candidates that will inhibit the activity of the
pump. Consequently, this inhibition will inhibit the secretion of
biofilm, and because biofilm is a deterrent to the action of antibiotics,
compounds that affect the efflux pump system are promising
candidates for clinical evaluation.

Limiting and controlling carbapenem-resistant
Klebsiella pneumonia

L Saidel-Odes, A Borer.
1Infection Control and Hospital Epidemiology Unit, 2Infectious
Diseases Institute, Soroka University Medical Center and the
Faculty of Health Sciences, Ben-Gurion University of the Negev,
Beer-Sheva, Israel
Infection and Drug Resistance 2014:7 9–14

Carbapenem-resistant Klebsiella pneumoniae (CRKP)

  • is resistant to almost all antimicrobial agents,
  • is associated with substantial morbidity and mortality, and
  • poses a serious threat to public health.

The ongoing worldwide spread of this pathogen emphasizes the
need for immediate intervention. This article reviews the global
spread and risk factors for CRKP colonization/infection, and
provides an overview of the strategy to combat CRKP dissemination

Outbreaks of CRKP that have occurred around the world have
been associated with the plasmid-encoded carbapenemase
K. pneumoniae carbapenemase (KPC),

  • a carbapenem-hydrolyzing β-lactamase.19

CRKP isolates are resistant to almost all available antimicrobials
and are susceptible

  • only to polymyxins and tigecycline;
  • a minority to the few remaining aminoglycosides,
    though resistance to these agents is increasingly reported.20,21

Several investigators have evaluated predictors for CRKP colonization.
The following summarizes various studies.

  1. In a multivariate analysis, prior use of macrolides and
    any antibiotic exposure $14 days remained the only
    independent factors associated with CRKP bacteremia
  2. Nosocomial isolation of CRKP was strongly favored by the
    selection pressure of carbapenem. In this study, prior
    treatment with fluoroquinolones was associated with
    decreased risk for the emergence of CRKP.
  3. Previous use of carbapenem and cephalosporin
  4. Nursing home residency before hospital admission, bedridden
    status, and previous antibiotic therapy
  5. exposure to fluoroquinolones
  6. the recipient of antibiotics
  7. intensive care unit (ICU) stay, and
  8. Poor functional status,
  9. Independent predictors of subsequent carbapenem-
    resistant Enterobacteriaceae (CRE) infection were
  • admission to the ICU,
  • having a central venous  catheter,
  • receipt of antibiotics, and
  • diabetes mellitus

Schwaber et al and the Israeli CRE Working Group enforced the
Israel Ministry of Health guidelines mandating physical separation
of hospitalized carriers of CRE and dedicated staffing and appointed
a professional task force charged with containment.19 The monthly
incidence of nosocomial CRE was reduced from 55.5 to 11.7 cases
per 100,000 patient days within 15 months.

Part 7.  Tuberculosis

The Mechanism by which the Phenothiazine Thioridazine
Contributes to Cure Problematic Drug-Resistant Forms
of Pulmonary Tuberculosis: Recent Patents for “New Use”

L Amaral1*, A Martins2,3, G Spengler2, A Hunyadi4 and J Molnar2
Recent Patents on Anti-Infective Drug Discovery 2013; 8(3):000-000

At this moment, over half million patients suffer from multi-drug
resistant tuberculosis (MDR-TB) according to the data from the WHO.
A large majority is terminally ill with essentially incurable pulmonary
tuberculosis. This herein mini-review provides the experimental and
observational evidence that a specific phenothiazine,

  • thioridazine,

will contribute to cure any form of drug-resistant tuberculosis. This
antipsychotic agent is no longer under patent  protection for its
initial use. The reader is informed on the recent developments

  • in patenting this compound for “new use” with a special
  • emphasis on the aspects of drug-resistance.

Given that economic motivation can stimulate the use of this drug
as an antitubercular agent, future prospects are also discussed.

Thioridazine is not the only phenothiazine that has been recommended
for therapy of pulmonary tuberculosis. In general, many phenothiazines
have been implicated for antitubercular activity [62, 80-86]. Among
these are

  • trifluoperazine [87-94],
  • methdilazine [95, 96],
  • promazine [97, 98],
  • promethazine [97, 98],
  • fluphenazin [99],
  • propiomazine [100], and
  • the methylene blue related toluidine blue [101].

There are phenothiazine compounds derived from the parental
methylene blue for therapy of pathologies unrelated to tuberculosis
that also possess

  •  antitubercular [44, 48] and/or antimalarial properties [44].

Moreover, derivatives made from any of the phenothiazines that
have in vitro activity against Mycobacterium tuberculosis are also
active [61, 67, 102, 103], suggesting ample opportunities for
patenting of new analogs developed from known, active phenothiazines
with even less side effects than those of TZ, as recently suggested by
Musuka and co-authors [104]. It is important to mention, that the
commercially available phenothiazines such as for example

  •  trifluoperazine, methdilazine, promazine, promethazine,
    fluphenazin and propiomazine

are beyond patent protection as initially intended. Nevertheless,
these compounds have been patented as adjuvants for the treatment
of MDR cancer (patent expired in 2011 [105]; and, right afterwards,
a new patent has been filed with a priority date of 28th March, 2012,
claiming combination therapy of cancer with a chemotherapeutic
agent and a dopamine receptor antagonist against Cancer stem cells (CSC).

Taking into account that intrinsic MDR is considered as one of the key
properties of CSCs [107], the subject to be covered is indeed related.
According to the MDR, XDR and TDR Mycobacterium tuberculosis,
subjects of this herein paper, the initial step for actually reaching those
in need has been made: a patent has been published in December, 2007,
for the use of TZ and its derivatives for reversing anti-microbial drug
resistance [108]. We must note, however, that, despite the six years
passed since, we were unable to find any related clinical trials, which
would certainly be of outmost importance and urgency in order to
proceed towards an effective therapy of highly resistant mycobacterial
infections.

Mechanism Of Action Of Tz: Why It Cures Multi-Drug,
Extensively Drug Resistant And Probably Totally Drug
Resistant Tuberculosis

Over-expressed efflux pumps of Mycobacterium tuberculosis render
the organism multi-drug resistant [13]. Special attention has been
given to those coded by the

  • mmpL7, p55, efpA, mmr, Rv1258c and Rv2459 genes [109].

The activity of these efflux pumps can be suppressed by

  • concentrations of TZ that have no effect on the viability of
    Mycobacterium tuberculosis
  • rendering the organism susceptible to the antibiotic to
    which it was initially resistant
  • as a consequence of the over-expression of its
    efflux pumps [109].

TZ has also been shown to inhibit the activity of the main

  • efflux pumps of bacteria belonging to other species.

TZ has strong inhibitory activity against the genes that code for
essential proteins of M. tuberculosis [122-124].  Consequently, we
may conclude that the in vitro activity of TZ involves

  • the inhibition of the efflux pumps of M. tuberculosis and that
  • the in vitro exposure of this organism to TZ renders the organism
  • susceptible to antibiotics to which it was initially resistant
  • as a consequence of over-expressed efflux pumps [21].

Phenothiazines such as CPZ, TZ, trifluoperazine, etc., also inhibit

  • the binding of calcium to calcium binding proteins such as

calmodulin in eukaryotes [125], and

  • interfere with other proteins involved in
  • the regulation of cellular activity [126].

They inhibit the transport of calcium and potassium systems

  • in eukaryotic cells [127-129] as well as in
  • mycobacteria [89, 130] and
  • E. coli [113].

In fact, in the latter case, calcium was shown essential to

  • the continuous activity of the thioridiazine sensitive
    efflux system [113].

The killing activity of the human macrophage as well as that
of the neutrophil

  • is dependent upon the retention of calcium and potassium
  • within the phagolysosome of the cell [131].

Considering this, several alternative choices are available for
patenting under “new use”, which would allow a “fresh start”
for the compound to be developed. However, the needed
experimental proof that these phenothiazine agents have
activity at the pulmonary macrophage of the alveolar unit
(the site where the causative organism of pulmonary tuberculosis
resides) is still absent.

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

Marta Martins
UCD Centre for Food Safety, School of Agriculture, Food Science and
Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
& Unit of Mycobacteriology and UPMM; Instituto de Higiene e Medicina
Tropical, Universidade Nova de Lisboa (IHMT/UNL),  Lisbon, Portugal
Recent Patents on Anti-Infective Drug Discovery, 2011, 6, 000-000

The emergence of resistance in Tuberculosis has become a serious
problem for the control of this disease. For that reason, new therapeutic
strategies that can be implemented in the clinical setting are urgently
needed. The design of new compounds active against mycobacteria
must take into account that Tuberculosis is mainly an intracellular
infection of the alveolar macrophage and therefore must maintain
activity within the host cells.

An alternative therapeutic approach will be described in this review,
focusing on the activation of the phagocytic cell and the subsequent
killing of the internalized bacteria. This approach explores the combined
use of antibiotics and phenothiazines, or Ca2+ and K+ flux inhibitors,
in the infected macrophage.

Targeting the infected macrophage and not the internalized bacteria
could overcome the problem of bacterial multi-drug resistance. This
will potentially eliminate the appearance of new multi-drug resistant
tuberculosis (MDR-TB) cases and subsequently prevent the emergence
of extensively-drug resistant tuberculosis (XDR-TB).

Patents resulting from this novel and innovative approach could be
extremely valuable if they can be implemented in the clinical setting.
Other patents will also be discussed such as the treatment of TB
using immunomodulator compounds (for example: betaglycans).

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

SG. Dastidar 1, JE. Kristiansen 2, J Molnar 3 and L Amaral
Antibiotics 2013; 2: 58-71;
http://dx.doi.org:/10.3390/antibiotics2010058

Phenothiazines have their primary effects on the plasma membranes
of prokaryotes and eukaryotes. Among the components of the
prokaryotic plasma membrane affected are

  • efflux pumps,
  • their energy sources
  • and energy providing enzymes, such as ATPase,
  • and genes that regulate and code for the permeability
    aspect of a bacterium.

The response of multidrug and extensively drug resistant
tuberculosis to phenothiazines shows an alternative therapy for the
treatment of these dreaded diseases, which are claiming more and
more lives every year throughout the world.

Many phenothiazines have shown

  • synergistic activity with several antibiotics thereby
  • lowering the doses of antibiotics administered to patients
    suffering from specific bacterial infections.

Trimeprazine is synergistic with trimethoprim. Flupenthixol (Fp)
has been found to be synergistic with penicillin and chlorpromazine
(CPZ); in addition, some antibiotics are also synergistic. Along with
the antibacterial action described in this review,

  • many phenothiazines possess plasmid curing activities, which
  • render the bacterial carrier of the plasmid sensitive to antibiotics.

Thus, simultaneous applications of a phenothiazine like TZ would not
only act as an additional antibacterial agent but also would help

  • to eliminate drug resistant plasmid from
    the infectious bacterial cells.

Part 8.  Cancer Cytotherapy

Synthesis and Structure-Activity Relationships of Novel
Dioxolanes as MDR Modulators in Cancer

A Martins 1,2,†,*, J Csábi 3,†, A Balázs 4, DKitka 1, L Amaral 5,
J Molnár 1, A Simon 6, G Tóth 6 and A Hunyadi 3,
Molecules 2013, 18, 15255-15275;
http://dx.doi.org:/10.3390/molecules181215255

Ecdysteroids, molting hormones of insects, can exert several mild,
non-hormonal bioactivities in mammals, including humans. In a
previous study, we have found a significant effect of certain derivatives

  • on the ABCB1 transporter mediated multi-drug resistance of a
  • transfected murine leukemia cell line.

In this paper, we present a structure-activity relationship study
focused on

  • the apolar dioxolane derivatives of 20-hydroxyecdysone.

Semi-synthesis and bioactivity of a total of 32 ecdysteroids, including
20 new compounds, is presented, supplemented with their

  • complete 1H- and 13C-NMR signal assignment

As published before [9], the 20,22-diol moiety of 20E is more reactive
than the 2,3-diol, probably due to the free rotation of the 20,22-bond
of 20E that allows the 20,22-dioxolane ring to form with less strain.

This allowed us to selectively obtain the 20,22-mono-dioxolane
derivatives 2–14, or, depending on the amount of reagent and the
reaction time, the 2,3;20,22-bis-homo-dioxolanes 17 and 21–25.

By utilizing the 20,22-monodioxolane ecdysteroids, another aldehyde
or ketone could be coupled to position 2,3, resulting in several bis-hetero-
dioxolane derivatives 26–33. For this, however, gradually decreasing
reactivity with the increase of the size of the reagent was a limiting factor:

  • larger aldehydes or ketones (mainly those containing a
    substituted aromatic ring) could not be coupled at the 2,3-position.
  • The 2,3-monodioxolane derivatives also appeared to be present as
    minor side-products of the reactions, and as a consequence of their
    low amount, only one such compound (compound 15) was isolated and studied.

To selectively obtain this kind of a compound (16) in a more reasonable
yield, another, three-step approach was successfully applied:

  • after protecting the 20,22-diol with phenylboronic acid, the
    2,3-acetonide could be prepared, and
  • removal of the 20,22 protecting group afforded the desired
    2,3-monoacetonide in a one-pot procedure.

In the case of the reactions with aldehydes or asymmetric ketones,
the new C-28 and C-29 central atoms of the dioxolane rings are
stereogenic centers and thus two possible diastereomers can be
formed at both diols. Their configuration was elucidated by two-
dimensional ROESY or selective one-dimensional ROESY experiments,
e.g., in the doubly substituted

  • dioxolane derivative 22 (R1 = R4 = n-Bu, R2 = R3 = H)
  • the unambiguous differentiation of the 1H and 13C signals of
    the two n-butyl groups was achieved in the following way
    (see Figure 2).

Assignment of the H-C(28) atoms (δ = 4.93/105.9 ppm) was supported by

  • the H-2/C-28 and H-3/C-28 HMBC correlations, and
  • that of H-C(29) (δ = 4.91/105.6 ppm) by the H-22/C-29
    cross peak, respectively.

The selective ROESY experiment irradiating at 4.93 ppm showed

  • contacts with the Hα-2 and Hα-3 atoms proving the
    α position of the R2 = H atom.

The ROESY response obtained irradiating H = R3 signal (δ = 4.91)
on H-22 (δ = 3.64 ppm) revealed their

  • cis arrangement and the R configuration around C-29.

The unambiguous assignments of the signals

  • of the two n-butyl groups R1 and R4 were achieved by
  • selective TOCSY experiments (irradiation at
  • δ = 4.93 and 4.91, respectively).

Figure 2

Stereostructure of 22. Red-ROESY proximitries. Blue- 1H. Black-1 001

Stereostructure of 22. Red-ROESY proximitries. Blue- 1H. Black-1 001

Stereostructure of 22. Red arrows indicate the detected ROESY
steric proximities, the blue numbers give the characteristic 1H,
and the black numbers the 13C chemical shifts.

 

Related Material

Identification of Efflux Pump-mediated Multidrug-resistant
Bacteria by the Ethidium Bromide-agar Cartwheel Method
M Martins, M Viveiros, I Couto, SS. Costa, T Pacheco, S Fanning,
Jean-Marie Pagès, and L Amaral
in vivo 2011; 25: 171-178  

Index for efflux activity of the MDR strains. The capacity to efflux EtBr
of each bacterial strain was ranked relative to the reference strain
according to the following formula:

 

Index for efflux activity of the MDR strains

Index for efflux activity of the MDR strains

A Simple Method for Assessment of MDR Bacteria for
Over-Expressed Efflux Pumps
M Martinsa,b*, MP. McCuskera,b, M Viveirosa,c, I Coutoc,d,
S Fanninga,b, Jean-Marie Pagès b,e, L Amaral,b,
The Open Microbiol J 2013; 7: 1-5  1874-2858/13 Bentham

Flowchart followed to test bacterial strains using the EtBr-agar
Cartwheel method.

Flowchart followed to test bacterial strains using the EtBr-agar Cartwheel method.

Flowchart followed to test bacterial strains using the EtBr-agar Cartwheel method.

EtBr-agar cartwheel method applied to different bacterial species

EtBr-agar cartwheel method applied to different bacterial species

EtBr-agar cartwheel method applied to different bacterial species

The effect of selected EPIs on the resistance of the induced and
MDR Gram-positive bacteria.

TET
Enterococcus EFC
ATCC29212
HSEFM-D		 1.5
>2.5		 w/o
EPI		 +
TZ		 +
CPZ		 +
RES
4
16		 4
4		 4
4		 4
8
(4×) (4×) (2×)
                                MCEtBr NOR  (mg/l) MIC NOR (mg/l)
HSEFM-E >2.5 0.125 0.125 0.125 0.125

EPI: Efflux pump inhibitor; w/o: without; TZ: thioridazine; CPZ:
chlorpromazine; PAN: phenyl arginine β-naphthylamide. Values
in bold-type correspond to a decrease of 4-fold or higher on
the MIC values in comparison to those in the absence of inhibitor.
Values in parenthesis indicate the MIC decrease relative to that
of the original culture. The concentration of each EPI used is
defined in the Materials and Methods section.

Macrocyclic diterpenes resensitizing multidrug
resistant phenotypes 
MA. Reis a, A Paterna a, RJ. Ferreira a, H Lage b,
Maria-José U. Ferreira a,⇑
a Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade
de Farmácia, Universidade de Lisboa, Lisboa, Portugal
b Charité Campus Mitte, Institute of Pathology, Berlin, Germany
Bioorganic & Medicinal Chemistry xxx (2014) xxx–xxx

Herein, collateral sensitivity effect was exploited as a strategy to
select effective compounds to overcome multidrug resistance in
cancer. Thus, eleven macrocyclic diterpenes, namely jolkinol D (1),
isolated from Euphorbia piscatoria, and its derivatives (2–11) were
evaluated for their activity on three different Human cancer entities:

  • gastric (EPG85-257), pancreatic (EPP85-181) and colon (HT-29)

each with a variant selected for resistance to mitoxantrone

  1. EPG85-257RN;
  2. EPP85-181RN;
  3. HT-29RN and
  • one to daunorubicin (EPG85-257RD; EPP85-181RD; HT-29RD).

Jolkinol D (1) and most of its derivatives (2–11) exhibited significant
collateral sensitivity effect towards the cell lines

  • EPG85-257RN (associated with P-glycoprotein overexpression) and
  • HT-29RD (altered topoisomerase II expression).

The benzoyl derivative, jolkinoate L (8) demonstrated ability to

  • target different cellular contexts with
  • concomitant high antiproliferative activity.

These compounds were previously assessed as
P-glycoprotein modulators,

  • at non-cytotoxic doses, on MDR1-mouse lymphoma cells.

A regression analysis between

  1. the antiproliferative activity presented herein and
  2. the previously assessed P-glycoprotein modulatory effect

showed a strong relation between the compounds that presented

  • both high P-glycoprotein modulation and cytotoxicity.

Molecular Docking Characterizes Substrate-Binding Sites
and Efflux Modulation Mechanisms within P‑Glycoprotein.

Ferreira,† Maria-José U. Ferreira,† and DJVA dos Santos*,†,‡
†Research Institute for Medicines and Pharmaceutical Sciences
(iMed.UL), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
‡REQUIMTE, Department of Chemistry & Biochemistry, Faculty of
Sciences, University of Porto, Porto, Portugal
J. Chem. Inf. Model. XXXX, XXX, XXX−XXX
http://dx.doi.org:/10.1021/ci400195v

P-Glycoprotein (Pgp) is one of the best characterized ABC
transporters, often involved

  • in the multidrug-resistance phenotype
  • overexpressed by several cancer cell lines.

Experimental studies contributed to important knowledge concerning
substrate polyspecificity, efflux mechanism, and drug binding sites.
This information is, however, scattered through different perspectives,
not existing a unifying model for the knowledge available for this transporter.
Using a previously refined structure of murine Pgp,

  • three putative drug-binding sites were hereby characterized
  • by means of molecular docking.

The modulator site (M-site) is characterized by

  • cross interactions between both Pgp halves

herein defined for the first time, having an important role in

  • impairing conformational changes leading to substrate efflux.

Two other binding sites, located next to the inner leaflet of the lipid bilayer,

  • were identified as the substrate binding H and R sites
  • by matching docking and experimental results.

A new classification model

  • with the ability to discriminate substrates from modulators

is also proposed, integrating a vast number of theoretical and experimental data.

conformational changes leading to substrate efflux

conformational changes leading to substrate efflux

conformational changes leading to substrate efflux

http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jcisd8/
2013/jcisd8.2013.53.issue-7/ci400195v/production/pdfimages_v02/normal.img-000.jpg

 

 

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10th Annual Personalized Medicine Conference at the Harvard Medical School, November 12-13, 2014, The Joseph B. Martin Conference Center at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA

Posted in Academic Publishing, Conference Coverage with Social Media, Genome Biology, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, Personalized and Precision Medicine & Genomic Research on October 9, 2014| Leave a Comment »

10th Annual Personalized Medicine Conference at the Harvard Medical School, November 12-13, 2014, The Joseph B. Martin Conference Center at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA

2014 Personalized Medicine Program 

  • Partners HealthCare Personalized Medicine
  • Harvard Business School
  • Harvard Medical School
  • American Association for Cancer Research
  • Personalized Medicine Coalition

10th Annual Personalized Medicine Conference at the

Harvard Medical School

November 12-13, 2014

The Joseph B. Martin Conference Center

Harvard Medical School

77 Avenue Louis Pasteur, Boston, MA

Announcement

LEADERS IN PHARMACEUTICAL BUSINESS INTELLIGENCE

will cover the event for the Scientific Media

Dr. Lev-Ari will be in attendance at the Pre-event Reception on 11/11/2014 @Hotel Commonwealth, Boston and on 11/12 and 11/13/2014 – Covering the Event in REALTIME using Social Media

 

AGENDA

http://personalizedmedicine.partners.org/Education/Personalized-Medicine-Conference/Program.aspx

10th Annual Personalized Medicine Conference at the Harvard Medical School, November 12-13, 2014, The Joseph B. Martin Conference Center at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA

 Reporter: Aviva Lev-Ari, PhD, RN

2014 Personalized Medicine Program 

Partners HealthCare, HMS, HBS 

November 12-13, 2014, 

The Joseph B. Martin Conference Center at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA

Event Home Page

http://personalizedmedicine.partners.org/education/personalized-medicine-conference/default.aspx

About the The 10th Annual Personalized Medicine Conference
The Personalized Medicine Conference is an annual two-day event co-hosted and presented by Partners HealthCare Personalized Medicine, Harvard Business School, and Harvard Medical School in association with the American Association for Cancer Research and Personalized Medicine Coalition. Widely considered the most prestigious event in the field, this conference attracts hundreds of national and international thought leaders across multiple disciplines as speakers, panelists, and attendees.

See more at: http://personalizedmedicine.partners.org/education/personalized-medicine-conference/default.aspx#sthash.TbFlbDn6.dpuf

AGENDA

http://personalizedmedicine.partners.org/Education/Personalized-Medicine-Conference/Program.aspx

 

Personalized Medicine Conference Speakers

Speakers for the 2014 Personalized Medicine Conference are being added as they are confirmed. Please refer to the Program for the topics being discussed.

SOURCE

http://personalizedmedicine.partners.org/Education/Personalized-Medicine-Conference/Speakers.aspx

  

SPEAKERS

 

Personalized Medicine Conference

Speakers for the 2014 Personalized Medicine Conference are being added as they are confirmed. Please refer to the Program for the topics being discussed.

– See more at: http://personalizedmedicine.partners.org/Education/Personalized-Medicine-Conference/Speakers.aspx#sthash.MnMgQjdA.dpuf

 

LEADERS IN PHARMACEUTICAL BUSINESS INTELLIGENCE

 

Editorials of event coverage via our Open Access Scientific Journal

http://pharmaceuticalintelligence.com

Scientific Journal Site Statistics

Date |Views to Date |# of articles |NIH Clicks |Nature Clicks

07/29/2013   217,356 1,138 1,389 705
12/01/2013   287,645 1,428 1,676 828
02/09/2014   325,039 1,665 1,793 892
03/05/2014   338,958 1,717 1,830 965
03/21/2014   347,667 1,750 1,838 974

03/31/2014  352,683 1,768 1,869 991

05/12/2014  373.696  1,878  1,944  1,035

06/18/2014  393,111  1,992  1,982  1,087

7/27/2014  418,570  2,098  2.050  1,124

9/2/2014  444,222  2,226  2,104  1,170

10/9/2014 471,117  2,337  2,147  1,216

11/4/2014  492,736  2,471  2,194 1,234

 

 

Pre e-Pub e-Books Flyers


Series A: e-Books on Cardiovascular Diseases 

Series A Content Consultant: Justin D Pearlman, MD, PhD, FACC

VOLUME THREE

Etiologies of Cardiovascular Diseases:

Epigenetics, Genetics and Genomics

 

by  

Larry H Bernstein, MD, FCAP, Senior Editor, Author and Curator

and

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

SACHS FLYER 2014 CVD Title

SACHS FLYER 2014 CVD Seriescindividual-page2

SACHS FLYER 2014 CVD Seriescindividual2-page3

SACHS FLYER 2014 CVD Seriescindividual-page4

Please see Further Titles on Cardiovascular Diseases at

http://pharmaceuticalintelligence.com/biomed-e-books/series-a-e-books-on-cardiovascular-diseases/

Please see Further Titles in our BioMed e-Series at

http://pharmaceuticalintelligence.com/biomed-e-books/

 

on TWITTER follow us @

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Series C: e-Books on Cancer & Oncology

Volume One: Cancer Biology and Genomics for Disease Diagnosis

http://pharmaceuticalintelligence.com/biomed-e-books/series-c-e-books-on-cancer-oncology/cancer-biology-and-genomics-for-disease-diagnosis/

Volume Two: Therapies in Cancer – Surgery, Radiation, Chemo and Immunotherapies

http://pharmaceuticalintelligence.com/biomed-e-books/series-c-e-books-on-cancer-oncology/volume-2-immunotherapy-in-oncology/

Series B: Frontiers in Genomics Research

Volume One: Genomics Orientations for Individualized Medicine

http://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/volume-one-genomics-orientations-for-personalized-medicine/

GENOMICS related articles in the JOURNAL

  • Cardiovascular Pharmacogenomics – 134 articles
  • Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics – 55 articles
  • Nutrigenomics – 43 articles
  • Pharmacogenomics – 88 articles
  • Genomic Testing: Methodology for Diagnosis – 241 articles
  • Personalized Medicine & Genomic Research – 390 articles
  • Genome Biology – 421 articles

Genomics Orientations for Individualized Medicine

Volume One

genomicsebook31

 

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