Biomarkers ARC

INITIATION DATE:

12.01.09

ARC DIRECTORS AND CO-DIRECTORS:

Mark McComb, PhD; Director; Assistant Professor; Medicine

Catherine Costello, PhD; Co-Director; Professor; Biochemistry

Richard A. Cohen, MD; Co-Director; Professor; Medicine/Vascular Biology

OVERVIEW OF GOALS AND MISSION:

Biomarkers constitute any multiplex of measurements that specifically detects normal or diseased physiology which may be used to achieve early detection of disease, to determine the effects of treatment on disease progression and aid in tracing disease mechanisms.

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Through a series of meetings beginning in May 2009, a diverse group of investigators from basic, translational, clinical and population science met together to launch the BUMC Biomarkers ARC.
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During these meetings the advanced proteomic capabilities of the Cardiovascular Proteomics Center (CPC) within the BUSM Center for Biomedical Mass Spectrometry (CBMS) were presented and discussed with an eye toward applying these technologies to biomarker discovery utilizing ongoing BU/BUSM/BMC projects with human patient populations. ARC attendees, including those experienced in population biomarkers, were enthusiastic that the capabilities demonstrated, if applied to human patient plasma, could result in novel biomarker discovery. The Biomarkers ARC has thus been created to maximize the likelihood that sufficient breadth and depth of data on plasma samples from patients may be obtained to represent “proof of principle” of experimental hypotheses that methodology developed in the CPC can be used in the discovery process of biomarker detection. This proof of principle approach should enable applications for funding of not only the direct participants, but also other investigators at BUMC doing human studies.

Specific Goals:

1. To provide a monthly forum for presentation and sharing of ideas and data aimed at discovery of novel biomarkers in order to take advantage of pre-existing expertise.

2. To establish new collaborations to improve on the technology, analysis, and the impact of new biomarkers. This includes input from CRC on nanotechnology (Goldberg) and systems biology (Collins).

3. To provide BUMC investigators with access to preliminary data and biological samples acquired in ongoing studies that might yield new biomarkers for different diseases.

4. To provide support for spanning the gaps between the initial detection of the biomarker, its validation, and its measurement in patients and community populations.

5. To provide support and preliminary data for funding applications for the development of biomarkers.

ARC Members:

Name/Title Dept/School Role in ARC Email Web Link
Mark McComb, PhD; Assist Prof Medicine Director mccomb@bu.edu http://www.bumc.bu.edu/bucbm/faculty/mark-e-mccomb/
Catherine Costello, PhD; Prof Biochemistry/ Biophysics/ Chemistry Co-Director cecmsms@bu.edu http://www.bumc.bu.edu/msr/staff-directory/catherine-e-costello-director/
Richard A. Cohen, MD; Prof Medicine/ Vascular Biology Co-Director racohen@bu.edu http://www.bumc.bu.edu/medicine/rcohen/
Vasan Ramachandran, MD; Prof Medicine/ Epidemiology API vasan@bu.edu http://www.bumc.bu.edu/medicine/ramachandran/
Wilson Colucci, MD; Prof Medicine/ Cardiology API wcolucci@bu.edu http://www.bumc.bu.edu/cardiovascularproteomics/project-12/
Robert Lafyatis, MD; Prof Medicine/ Rheumatology API lafyatis@bu.edu http://www.bumc.bu.edu/medicine/lafyatis/
Joseph Vita, MD; Prof Medicine/ Cardiology API
Emelia Benjamin, MD; Prof Medicine/ Cardiology ARC Member emelia@bu.edu http://www.bumc.bu.edu/medicine/benjamin/
Daniel Levy, MD; Prof Medicine/ Cardiology ARC Member
Francis Farraye, MD; Fellow Medicine ARC Member francis.farraye@bmc.org http://www.bumc.bu.edu/medicine/farraye/
James Collins, PhD; Prof Bioengineering ARC Member jcollins@bu.edu http://www.bu.edu/dbin/bme/people/primary/collins.php
Susan Fried, PhD; Prof Medicine/ Diabetes-metabolism ARC Member skfried@bu.edu http://www.bumc.bu.edu/medicine/fried/
Jane Freedman, MD; Prof Medicine/ Cardiology ARC Member freedmaj@bu.edu http://www.bumc.bu.edu/medicine/freedman/
Richard Myers, PhD; Prof Neurology/ Genome Science Center ARC Member rmyers@bu.edu http://www.bumc.bu.edu/genetics/genetics-people/faculty/myers/
M. Selim Unlu, PhD; Assist Prof Engineering/ Nanoscience ARC Member selim@bu.edu http://www.bu.edu/dbin/bme/people/joint/unlu.php
Bennett Goldberg, PhD; Prof Engineering/ Nanoscience ARC Member goldberg@bu.edu http://www.bu.edu/dbin/bme/people/joint/goldberg.php
Joseph Zaia, PhD; Prof Biochemistry ARC Member jzaia@bu.edu http://www.bumc.bu.edu/biochemistry/our-people/research-faculty/joseph-zaia/

MAIN ARC PROJECT(S) FOR 2009-2010:

Several considerations went into the choice of pilot projects for the Biomarkers ARC. Each of the chosen projects was required to have human subject samples that had already been collected and had significant other characteristics which would enhance the benefit of doing the studies, to both the investigators and wider community. The ARC projects were designed to build on current expertise and instrumentation within the CBMS, taking advantage of the fact that full-scale, in-depth proteomics methodologies have only recently reached a level of maturity that enables the proposed studies. Furthermore, the projects were designed to take advantage of preliminary studies performed in mice, in order to take advantage of the research being done at BUMC in transgenic mice and animal models of metabolic disease. Lastly, proteomic studies of the nature to be pursued are exceedingly costly requiring devoted personnel and expensive supplies and instrument support, thus a limited scale of each project was deemed necessary.

To meet these ends, a discovery based proteomics approach was designed to identify candidate biomarkers related to metabolic disease. Our hypothesis is that metabolic changes in diseased tissues may be detected by changes in plasma protein abundances that betray leakage of tissue-specific proteins, and by post-translational modifications (PTMs) that reflect abnormal tissue metabolism. To highlight and advance our capabilities in human biomarker discovery, we have specifically targeted three pilot projects that will demonstrate, to both the local community and funding agencies, the BUSM Center’s unique capabilities: 1) a highly controlled study of short-term insulin resistance in human subjects and mice, 2) extension of preliminary studies of mice with heart failure to patients, and 3) investigation of patients with scleroderma with/without pulmonary hypertension for whom gene array and plasma biomarker data is already available.

Project 1: Bed rest and diet-induced insulin resistance (Vita/Cohen).

As part of a SCCOR program grant on endothelial cell dysfunction associated with metabolic disease, Dr. Vita and colleagues are studying insulin-resistance induced by 5 days of bed rest in subjects (Hamburg NM et al. [PMID: 17932315]). In the published study, increases in glucose intolerance and serum lipids were correlated with deteriorated endothelial function. Samples are being collected from 40 subjects before and after bed rest: treated (20) or not (20), with an anti-inflammatory salicylate known to inhibit NFκB and insulin resistance (salsalate, 4g/d; PMID: 11533494). A recent abstract showed that the agent prevents endothelial dysfunction, blood monocyte gene changes, and serum inflammation markers caused by bed rest. This study is well controlled with only 5 days separating sample collection in the same subjects, and should show statistically significant changes in plasma markers of insulin resistance.

Preliminary studies exist on mice with diet-induced insulin resistance. In Drs. Cohen’s and Colucci’s lab normal mice were fed the “normal American diet” (30% fat, 30% carbohydrates as sucrose), this led to endothelial dysfunction, diastolic cardiac dysfunction, and vascular and cardiac protein oxidation. Amongst 40,000 peptides detected in the serum, about 500 increased with diet, but did not do so in mice treated with a polyphenol which prevented cardiovascular protein oxidation and inflammation. These included a ~30-fold increase in peptides of troponin I, a clinical cardiac biomarker, validating that tissue proteins could be examined, even with relatively mild diet-induced insulin resistance. The ARC funds will be used to start analysis of plasma samples from the human bed rest study. Subjects with insulin resistance will be examined for circulating vascular/endothelial cell proteins and peptides and/or protein modifications indicative of protein oxidation and lipid peroxidation. Data from insulin resistant mice will be cross-referenced with human data to search for biomarkers common to both sets.

Project 2: Heart failure in mice to men (Colucci):

This project will investigate samples from human CHF patients and also determine if a search for biomarkers can be accelerated by studies in a mouse model.

Preliminary studies exist (CPC renewal). Plasma samples were analyzed from a transgenic mouse in which the growth factor driven G-protein, Gq, is over-expressed in the heart leading to cardiac hypertrophy and heart failure. Results of the full-sequence of serum albumin showed many amino acids that had oxidized lipid PTMs, such as 4-hydroxynonenal and malondialdehyde. These PTMs were abundantly increased on proteins in the hearts of the mice with heart failure. Cardiac MB isoform of creatine kinase was detected in modified form in both the heart and the serum. In addition, Dr. Colucci and co-investigators in the BMC Heart Failure Center have samples of patients with stable or decompensated heart failure. A recent publication  (Biolo,S.A. et al, 2009 Circulation) used longitudinal samples in the same patients during an episode of worsening CHF which showed changes in several circulating proteins related to myocardial remodeling, including troponin. Frozen samples, 40+ patients with heart failure, and age-matched controls are available. Our initial study will analyze paired samples from 5 subjects, obtained at decompensation and after re-compensation. Serum proteins including albumin and those originating in the heart (creatine kinase MB isoform, myosin heavy chain) will be examined for OPTMs that were also observed in mouse heart and serum. Data obtained in this study also will go towards verifying the hypothesis that findings in mouse serum and tissue are relevant to biomarker discovery in patients.

Project 3: Scleroderma-induced pulmonary hypertension (PAH) (Lafyatis)

Dr. Lafyatis and colleagues have archived samples of patients with scleroderma, with and without PAH, and controls. They completed (Pendergrass et al.) a cross-sectional comparison of these 3 groups with microarray analyses of mRNA from blood monocytes. At the same time, serum was analyzed for multiple cytokines, inflammatory and metabolic markers. Several serum biomarkers were increased in patients with PAH, including inflammatory cytokines such as IL-6 and TNF-alpha, and markers of vascular injury such as ICAM, VCAM and vWF. This study was selected because of the special interest in scleroderma at this institution, and the genomic and known biomarker measurements already performed. In addition, ongoing proteomic studies in sickle cell patients with and without PAH (Steinberg) will enable comparisons that may differentiate fibrotic PAH (scleroderma) and occlusive PAH (sickle cell). This study will be undertaken in year 2.

ARC AS A RESOURCE:

The Biomarker ARC was envisioned as a highly collaborative group, and attendees have included specialists in cardiovascular, hematology, oncology, neurology, population studies, as well as biochemistry and nanotechnology. The ARC members realize that obtaining proteomics data represents only the first step in identification of potential biomarkers, and that once potential biomarkers are identified, that they need to be validated in small patient cohorts, and larger patient populations. We also believe that the BUMC community is ideally equipped to perform not only the discovery phase of biomarker development, but that we can rely on the expertise of investigators who have been and are associated with many large scale clinical research programs here, and are thus experienced in biomarker evaluation. From the very beginning, we have involved Drs. Vasan Ramachandran and Emelia Benjamin because of their extensive experience in evaluating biomarkers in the Framingham Heart Study, and Dr. Dan Levy, Director of the FHS, has attended and supports the goals of the ARC.

Monthly meetings are designed to encourage discussion and foster collaboration and will consist of presentations by basic and clinical investigators or invited guests interested in biomarker detection and development. The interdisciplinary discussions have already demonstrated that valuable insights can result from this format, particularly with respect to study design. Data presentations consisting of on-going research, both within and outside the ARC project, will provide the focus of the studies with an aim towards facilitating evaluation and development of biomarkers for human disease.

Pictures, Images, Figures:

mccomb-3The Cardiovascular Proteomics Center (CPC) is a state-of-the-art proteomics facility housed within the BUSM Center for Biomedical Mass Spectrometry (CBMS) directed by Drs. Chen, Zaia, McComb and Costello. The CPC Core Laboratory directed by Dr. McComb houses a comprehensive mass spectrometry-based proteomics platform consisting of protein purification, multi-dimensional protein and peptide fractionation and on-line and off-line protein and peptide characterization via MS and MS/MS. In addition to simple protein identification by database search methods and relative quantification via spectral counting, a comprehensive bioinformatics platform is available to researchers within the CPC/CBMS for data interrogation of large scale ‘omics projects.

Investigators who are interested in pursuing proteomics based projects are encourage to contact Dr Costello or Dr McComb to discuss logistics, experimental design and  access to resources within the CBMS.

CBMS: http://www.bumc.bu.edu/bucbm/

CPC: http://www.bumc.bu.edu/cardiovascularproteomics/

CPC Core Laboratory: http://www.bumc.bu.edu/cardiovascularproteomics/proteomics-core-laboratory/

Contact|Directory|BUMC
May 17, 2010
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of BU School of Medicine