DISTINGUISHED FACULTY
Prof. Christoph Borchers, Assistant Professor, Director, Biochemistry and Biophysics, University of North Carolina

Dr. David E. Clemmer, Robert and Marjorie Mann Chair; Chairman, Department of Chemistry, Indiana University

Dr. Richard R. Drake, Associate Professor, Center for Biomedical Proteomics, Eastern Virginia Medical School

Dr. Andrew Emili, Assistant Professor, Banting and Best Department Medical Research, University of Toronto

Dr. John Erve, Principal Scientist, Drug Safety and Metabolism, Wyeth Research

Dr. David Robinson Goodlett, Associate Professor, Department of Medicinal Chemistry, University of Washington

Dr. H. Barton Grossman, W. A. "Tex" and Deborah Moncrief, Jr. Distinguished Chair in Urology, Professor and Deputy Chairman, Department of Urology, The University of Texas M. D. Anderson Cancer Center

Dr. William S. Hancock, Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University

Dr. Ronald C. Hendrickson, Director Proteomics, Molecular Profiling, Merck Research Laboratories

Dr. Gerard Hoehn, Director, Clinical Proteomics Applications, Critical Care Medicine, NIH

Dr. Jennifer Colangelo, Principal Scientist, Safety Sciences, Pfizer Global Research and Development 

Dr. Neil L. Kelleher, Assistant Professor of Chemistry, Department of Chemistry, University of Illinois

Dr. James Lyons-Weiler, Assistant Professor, Pathology/Bionformatics, University of Pittsburgh Cancer Institute

Dr. Rod Mathews, Research Fellow, Proteomics & Biomarkers, Pfizer Global Research & Development 

Dr. Gary Means, Sr. Staff Scientist, Molecular Sciences, Amgen, Corp.

Dr. Greg Opiteck, Director, Protein Analysis, Caprion Pharmaceutical

Prof. Andrew Ottens, Associate Director, Neuroscience, Center for Neuroproteomics and Biomarkers Research, McKnight Brain Institute, University of Florida

Dr. Fred Regnier, Professor, Department of Chemistry, Purdue University

Dr. Salvatore Sechi, Director, Proteomics Program, NIDDK, NIH

Dr. Kerby Shedden, Assistant Professor, Department of Statistics, University of Michigan

Dr. David W. Speicher, Professor & Chair, Systems Biology Division; Director, Proteomics Laboratory, The Wistar Institute

Dr. Jim Stephenson, Senior Program Director, Mass Spectrometry Research, Research Triangle Institute

Dr. Jennifer Van Eyk, Director of The Johns Hopkins NHLBI Proteomics Center; Director of the Bayview Proteomics Group; and Associate Professor of Medicine, Division of Cardiology, Biological Chemistry and Biomedical Engineering, Johns Hopkins University

Dr. Timothy D. Veenstra, Director, Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc.

Dr. Miro Venturi, Head of Biomarker Lab, Preclinical Development, Nerviano Medical Sciences 

Dr. Richard Zangar, Senior Research Scientist, Biological Sciences, Pacific Northwest National Laboratory

7:00-8:30 Conference Registration

7:30-8:15 Technology Workshop (Spnorship Available)

8:30-8:35 Welcoming Remarks from Conference Director
Julia Boguslavsky, Conference Director, Cambridge Healthtech Institute

8:35-8:40 Chairperson's Opening Remarks

8:40-9:05 A Search for a Biomarker for Monitoring and Predicting Diabetes
Dr. Salvatore Sechi, Director, Proteomics Program, NIDDK, NIH
An estimated 6 million adults in the U.S. have undiagnosed type 2 diabetes. Additionally, 17 million adults have pre-diabetes. This is partially due to the lack of a simple and reliable way to detect diabetes and pre-diabetes. Several clinical studies (e.g. the Diabetes Prevention Program) have demonstrated effective interventions for preventing or delaying onset of diabetes in those with pre-diabetes. However, one of the limitations is the current method of diagnosing diabetes and pre-diabetes. The oral glucose tolerance test (OGTT), the gold standard for diagnosis of diabetes and pre-diabetes, requires fasting and is not very reproducible. In this presentation the main issues related to the development of a new biomarker for detecting pre-diabetes and diabetes will be discussed. Several projects mainly involving protein characterization by mass spectrometry and proteomic profiling of plasma samples will be described.

9:05-9:30 Biochemical Insight and Biomarkers Discovered via Proteomic Analysis of Bronchoalveolar Lavage Fluid from Acute Respiratory Distress Syndrome (ARDS) Patients and Normals
Dr. David Robinson Goodlett, Associate Professor, Department of Medicinal Chemistry, University of Washington
To gain insight into the airspace environment during acute lung injury, we analyzed the proteome of bronchoalveolar lavage fluid (BALF) from normal subjects and from ARDS patients. Shotgun proteomics on an LTQFT was used to generate hypotheses regarding proteins of interest to ARDS in the BALF samples. A total of 200 unique proteins were identified, including proteins associated with apoptosis, C-reactive protein, signal transduction regulators, and proteins made by macrophages. Of these proteins we identified several growth factors and cytokines not previously described in BALF, including insulin growth factor binding protein-3 (IGFBP-3). Because IGFBP-3 has role in regulating cell survival, we asked whether there was a correlation of IGFBP-3 levels with acute lung injury. We measured IGFBP-3 levels in BALF by ELISA and found that average IGFBP-3 level in normal was 3 ng/ml, peaked at 80 ng/ml in ARDS day 1, and decreased to 16 ng/ml in ARDS day 14. Because IGFBP-3 increased with early ARDS, we asked whether IGFBP-3 induced apoptosis of lung epithelial cells, independent of IGF. We found no affect of IGFBP-3 on epithelial cell apoptosis. However, we showed that the IGF pathway, acting through the type 1 IGF-receptor (IGF-1R), represses apoptosis of lung fibroblasts but not lung epithelial cells. The data suggest IGFBP-3/IGF pathway is involved in pathogenesis of lung injury.

9:30-9:55 Proteomic Biomarkers of Heart Failure: Discovery and Validation
Dr. Andrew Emili, Assistant Professor, Banting and Best Dept. Medical Research, University of Toronto
Cardiovascular disease is the leading cause of suffering, morbidity and death in the developed world and the new challenge is the emerging epidemic of heart failure. The molecular basis of heart failure is complex and precise diagnostic and prognostic tools are missing. To this end, our research team has created an analytical platform allowing for comprehensive comparative proteomic analysis of the global patterns of protein abundance in early-stage disease-affected cardiac tissue using mouse models (genetic and acquired) of heart failure. Our platform is based on exhaustive gel-free shotgun tandem mass spectrometry, using multi-dimensional protein identification technology (MudPIT), as well as coupled to extensive pattern-recognition, data mining, and machine learning computational methods. This project is generating an extensive database of protein expression "signatures" linked to clinically-relevant pathological perturbations associated with disease progression.

9:55-10:45 Coffee Break with Exhibit and Poster Viewing

10:45-11:10 Discovery and Development of Translational Biomarkers for Osteoarthritis
Dr. Rod Mathews, Research Fellow, Proteomics & Biomarkers, Pfizer Global Research & Development 
Osteoarthritis (OA) is characterized by degeneration of articular cartilage in synovial joints. A directed MS approach was used to identify cartilage degradation products as potential biomarkers for OA. A sensitive immunocapture LC/MS/MS method was developed to quantify a specific degradation product. This biomarker can be measured in several biological fluids in both clinical and pre-clinical models.

11:10-11:35 Comprehensive Proteomic Analysis of Patients with Carotid Atherosclerosis
Dr. Gerard Hoehn, Director, Clinical Proteomics Applications, Critical Care Medicine, NIH
Successful biomarker discovery projects involve the coordination of many different disciplines, including proteomics, clinical chemistry and bioinformatics, and the integration of data from multiple analytical platforms. In an effort to find biomarkers predictive for increased risk of ischemic stroke and to further elucidate the pathophysiologic mechanisms of carotid atherosclerosis, we have begun examining protein expression differences in patients undergoing carotid endarterectomy for high grade carotid atherosclerotic stenosis. Comparisons of both serum and tissue samples from carotid endarterectomy patients using 2D gel electrophoresis, SELDI-TOF-MS, and cytokine arrays demonstrate multiple protein differences between symptomatic (incidence of stroke) and asymptomatic (no history of stroke) patients. The analytical and informational challenges of integrating data output from these disparate analytical tools to develop multivariate models that distinguish at-risk patients with high sensitivity and specificity will be discussed.

11:35-12:00 Integrating Tissue and Serum Resources for Clinical Proteomic Approaches to Cancer Biomarker Discovery
Dr. Richard R. Drake, Associate Professor, Center for Biomedical Proteomics, Eastern Virginia Medical School
Just as there are increasingly more options available for different proteomic analysis platforms, there are likewise many choices of clinical samples that could be utilized for biomarker discovery. Serum or plasma are more readily attainable, and would be ideal for future high-throughput diagnostic applications, however, overcoming current dynamic range issues has hindered biomarker discovery efforts. Tissue is less commonly available, but offers a potentially more biomarker rich target. Our goal has been to integrate robotic, multiplexed affinity-based processing of serum and tissue to attain biomarkers out of clinically relevant sample collections. This approach attempts to maximize the utility of evaluating matched serum/tissue resources by linking identified serum markers to the affected cancer tissues, and vice versa, by identifying potential tissue biomarkers that could be detected in serum/plasma. Unique combinations of robotic sample fractionation methods that retain throughput capabilities coupled with quantitative MALDI-TOF/TOF strategies, fluorescent 2D-DIGE gels, and laser capture microscopy will be presented.

1:00-1:15	Integrated Proteomics/Genomics Platform for Biomarker Discovery	Sponsored by
	Dr. Christian Rohlff, CEO, Oxford Genome Sciences Oxford Genome Sciences (OGeS) supports the global pharmaceutical industry by identifying new drug targets and biomarkers important at all stages of drug development and disease management. Our proteomics platforms are geared towards the systematic high-throughput characterisation of proteins expressed in clinical samples for integrated drug target and biomarker discovery. OGeS integrates clinical, genomic and proteomic information from different platforms such as 1D & 2D GE, ICAT, MudPIT and glycol-capture LC MS to accelerate the discovery and validation of candidate targets and biomarkers in man. OGAP™ database is the world’s largest proprietary collection of proteins represented by the Oxford Genome Anatomy Project (OGAP) database containing over one million peptide sequences from 50 tissues and 60 disease states, mapped to approximately 15,000 genes and over five million SNPs. These services and tools can be customized for each of our partners individually to support and enhance their preclinical and clinical drug development activities. We see an increasing number of biomarkers in our data, where SNPs may be responsible for certain protein isoform changes and post-translational modifications in a subset of people, that will be discussed.
1:15-1:30	Low to High Throughput Protein Sample Preparation for Biomarker Studies
	Dr. Lisa Bradbury, Director R&D, Pall Corporation

1:30-1:45 Technology Short Talks 
(Sponsorship Available, contact Arnold Wolfson at 781-972-5431 or awolfson@healthtech.com)

Protein Biomarker Validation and Translation: Case Studies

2:00-2:05 Chairperson's Opening Remarks

2:05-2:30 Recognition and Validation of Oxidative Stress Biomarkers
Dr. Fred Regnier, Professor, Department of Chemistry, Purdue University

2:30-2:55 Biomarker Discovery and Validation Using Accurate Mass and Time Tag (AMT) Proteomics and ELISA Microarrays
Dr. Richard Zangar, Senior Research Scientist, Biological Sciences, Pacific Northwest National Laboratory
Discovery of new cancer biomarkers is problematic due to the limited sensitivity and throughput of proteomic methods combined with the heterogeneity of the human population. To overcome these challenges, we are evaluating nipple aspirate fluid (NAF), a concentrated source of breast proteins, using a very sensitive proteomics method called the accurate mass and time tag (AMT) approach. Biomarker candidates identified in the proteomic studies will be validated in plasma and NAF using an ELISA microarray system that can simultaneously analyze up to 50 candidate biomarkers. This system can process sufficient numbers (i.e., thousands) of plasma samples to evaluate the effects of potentially confounding factors such as age, race, weight, etc. on the clinical utility of a biomarker or profile of biomarkers.

2:55-3:20 A Point of Care Proteomic Test for the Detection and Surveillance of Bladder Cancer
Dr. H. Barton Grossman, W. A. "Tex" and Deborah Moncrief, Jr. Distinguished Chair in Urology, Professor and Deputy Chairman, Department of Urology, The University of Texas M. D. Anderson Cancer Center
Bladder cancer arises in the urothelium and is the fourth most common cancer in men. The prevalence of bladder cancer in the United States is greater than 500,000. Cystoscopy (endoscopic visualization of the bladder) is used both for initial detection and surveillance but can fail to detect some cancers. The NMP22 BladderChek is a point of care test that detects a nuclear matrix protein in urine. In combination with cystoscopy, this test improves the identification of both initial and recurrent urothelial cancer.

3:20-4:10 Refreshment Break with Exhibit and Poster Viewing (last chance to view)

4:10-4:15 Chairperson's Opening Remarks

4:15-4:40 Advances and Challenges in Cancer Detection via Mass Spectrometry
Dr. James Lyons-Weiler, Assistant Professor, Pathology/Bionformatics, University of Pittsburgh Cancer Institute
In this overview, I will outline advances made in the comparative evaluation of methods for the analysis of data from mass-spectrometry based proteomic profiling in cancer, highlighting the importance of careful evaluative comparisons of methods for preprocessing, feature selection, classification, and for the evaluation of methods for comparative evaluation. I will outline open questions and challenges, and address a number of developing perspectives on serum proteomic based profiling in cancer, including the process of data characterization, the evaluation and validation process, the need to identify peptides prior to clinical implementation, and the need for careful study design. The need for progress in validating prediction models for early cancer detection is as urgent as ever, and, therefore, rapid, intense but careful and systematic research in this area is needed.

4:40-5:05 Cancer Profiling and Outcome Prediction Using Gene Expression Microarrays
Dr. Kerby Shedden, Assistant Professor, Department of Statistics, University of Michigan
I will discuss recent advances in cancer profiling and outcome prediction based on statistical analysis of gene expression measurements. After discussing some recent work on the comparison of quantitation methods for Affymetrix expression array data, I will turn to several issues relating to building predictive models for disease outcome and treatment response. I will discuss methods for accommodating the effects of heterogeneity in disease patient populations, and the use of surrogate and intermediate outcomes for purposes of predicting survival and treatment response. Finally I will discuss methods for identifying complex interactions among the expression levels of several genes that may be predictive of outcome in a way that is quite distinct from the information encoded in more traditional predictive measures.

8:30-8:35 Chairperson's Opening Remarks

8:35-9:00 Reactive Metabolites and Drug Toxicity: What is the Role of Protein Adducts?
Dr. John Erve, Principal Scientist, Drug Safety and Metabolism, Wyeth Research
Reactive metabolites have been implicated in causing drug toxicity, in part, through reactions leading to covalent adducts with proteins. Advances in analytical approaches to study proteins, such as mass spectrometry and SDS-PAGE, have allowed both identification of susceptible amino acids and specific protein targets of reactive metabolites. Knowledge about which proteins are targeted by reactive metabolites should help increase our mechanistic understanding of drug toxicity and may also point to potential biomarkers of toxicity. This talk will highlight the field of protein adducts with special focus on drug toxicity.

9:00-9:25 A Novel Plasma Proteomic Approach to Identify Specific Biomarkers of Toxicity
Dr. Miro Venturi, Head of Biomarker Lab, Preclinical Development, Nerviano Medical Sciences 
We will describe a novel approach for the identification and validation of toxicity biomarkers in plasma samples. This includes specific depletion of irrelevant proteins, fractionation of less abundant ones and quantitative assay set-up and validation. The approach spans a range of technologies such as RT-PCR, antibody arraying and multiplexing and guarantees bridging assay development from preclinical to clinical studies.

9:25-9:50 Proteome Profiling in the Discovery of Pre-clinical Biomarkers
Dr. Jennifer Colangelo, Principal Scientist, Safety Sciences, Pfizer Global Research and Development 
Proteomic approaches are increasingly used to identify toxicity biomarkers in pre-clinical studies. Serum profiling often leads to the identification of acute phase markers, instead of targeted toxicity biomarkers. Experimental design and comprehensive bioinformatics analyses are critical for producing valuable markers that are not a result of treatment effects. A case study for the identification of biomarkers for drug-induced, testicular toxicity will be presented.

9:50-10:15 Networking Coffee Break

10:15-10:40 Pharmacodynamic Biomarkers: Preparing for Secretase Inhibitors
Dr. Greg Opiteck, Director, Protein Analysis, Caprion Pharmaceuticals
Clinical scientists are anticipating that the coming wave of secretase inhibitors will severely tax their ability to design, power, and conduct trials in the field of Alzheimer's Disease. Simple questions with regard to dosing recommendations and drug manufacturing/supply will be extremely difficult to answer without pharmacodynamic markers that can be measured in real time during Phase I and IIa trials. Recognizing that imaging is an incredibly expensive option, which will limit the development options to a small number of sites and negatively impact enrolment, Caprion Pharmaceuticals is identifying circulating pharmacodynamic markers that can be measured in AD trials as readily as LDL is measured in cardiovascular trials. The present study found circulating protein markers of disease through quantitative plasma profiling followed by peptide sequencing via tandem mass spectrometry. These proteins are in the process of being developed as PD markers for measurement in subsequent trials by traditional immunoassay instrumentation.

10:40-11:05 Flow Cytometric Analysis of Receptor Signaling in Whole Blood
Dr. Gary Means, Sr. Staff Scientist, Molecular Sciences, Amgen, Corp.
Receptor activation is being evaluated by multi-color flow cytometry in specific subsets of cells found in whole blood. We demonstrate dose- and time-dependent activation of signaling based upon phosphoprotein readouts and dose-dependent inhibition using antagonistic antibodies. In addition to the valuable multi-dimensional pharmacodynamic data, these receptor proximal assays are providing data which is being evaluated for its potential to stratify patients with respect to therapeutic responses.

11:30 Close of Conference

For more information please contact: 
Julia Boguslavsky, Conference Director, Cambridge Healthtech Institute
Phone: 781-972-5482 or E-mail: juliab@healthtech.com

For sponsorship information please contact:
Arnie Wolfson at 781-972-5431 or awolfson@healthtech.com.