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Protein Biomarkers: Challenges in Clinical Implementation
June 17, 2009
1:00 - 3:00 p.m. EST

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1:00-1:10 Chairpersons Opening Remarks

1:10-1:40 Use of Activated Protein Pathway Biomarkers at the Bedside: Realizing the Promise of Personalized Therapy
Emanuel F. Petricoin III, Ph.D., Professor, Life Sciences & Company Director, Applied Proteomics & Molecular Medicine, George Mason University
Recently, whole genome mutational scanning analysis of a number of solid tumors has revealed that cancer is a protein pathway disease at the functional level. However, since genomic and transcript profiling likely cannot alone sufficiently predict protein pathway activation in each patient’s tumor, and it is these signaling pathways that represent the targets for new molecular guided therapeutics, it is critical that we begin to define human cancer at a functional pathway activation level. Post-translational modification such as phosphorylation drive and underpin nearly all cell signaling processes that are aberrantly activated in cancer and are epigenetic events, and not necessarily directly predictable using genomic approaches. Thus, the promise of proteomics resides in the study of molecules that are not just predictive or prognostic factors, but extend beyond correlation to causality. We have invented a new type of technology, called reverse phase protein microarrays, to generate a functional map of known cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen.  This patient-specific circuit diagram provides key information that identifies critical nodes or pathways that may serve as drug targets for individualized or combinatorial therapy through the quantification of phosphorylation states of proteins. The identification of activated networks on a patient-by-patient basis can be used as both a diagnostic and a therapeutic guide to patient selection and stratification.


1:40-1:50 A Novel Biomarker Workflow Strategy for Rapid Development of Biomarkers for Clinical Trials
Ruth A. VanBogelen, Ph.D., Director, Biomarkers & Proteomics, NextGen Sciences, Inc.
The ability to routinely test protein biomarker levels is a goal for researchers and clinicians. It is required for the validation of these biomarkers.  However, a typical timeline to discover biomarkers, develop assays for all the candidate protein biomarkers and confirm and validate the biomarkers is several years.  NextGen has developed a novel biomarker workflow strategy that decreases this timeline to months.  NextGen’s method of biomarker discovery and sample characterization generates the information crucial for assay development.  NextGen’s protein biomarker assay platform does not require antibodies and has high multiplexing capability.  Unique peptides are chosen for each protein in the assay to enable direct monitoring of the level of the peptide.  Once developed and validated, the assay takes less than 30 minutes to run (for all proteins in the assay).  In addition sample requirements are low (e.g., 15 microliters of plasma).  All the putative protein biomarkers can be tested in larger sample sets to select the best biomarkers.  The assay is further modified for biomarker validation in clinical samples.


1:50-2:20 Current Status of Protein Biomarkers: What We Have Learned and What Lies Ahead
Samir M. Hanash, M.D., Ph.D., Program Head, Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center
Although our understanding of the molecular pathogenesis of common types of cancers has improved considerably, the development of effective strategies for cancer diagnosis and treatment have lagged behind.  The vast dynamic range of protein abundance in plasma and the likely occurrence of tumor derived proteins in the lower range represent a major challenge in applying a proteomic based strategy for their identification.  A combination of innovative strategies promises to overcome these challenges.  Recent experience in comprehensive profiling of plasma proteins indicates that low abundance proteins may be identified and quantified with high confidence following extensive plasma fractionation and with the use of protein tagging procedures and high-resolution mass spectrometry.  From an experimental design point of view, most cancer biomarker studies, including those aimed at identifying markers for early detection, are initiated with analysis of specimens from newly diagnosed subjects.  The discovered candidate markers are subsequently investigated for their utility for early cancer diagnosis.  A preferred approach for discovery of such markers is to utilize plasma obtained at a pre-clinical stage, prior to the diagnosis of cancer.  Another implementation of this approach is through the use of mouse models of cancer that potentially represent an efficient means for uncovering diagnostic markers because of the ability to engineer mice that harbor genetic alterations known to be associated with tumors in humans, and because of the limited heterogeneity among mice bred under uniform conditions and the ability to sample blood in a standardized manner, at defined stages of tumor development.  The current status of these approaches will be presented.


2:20-2:30 Sponsored Presentation
Opportunity available. Contact Ilana Quigley, Business Development, 781-972-5457 or iquigley@healthtech.com


2:30-3:00 Discussion with the Speakers

 

 

About the Speakers:

Emanuel F. Petricoin III, Ph.D., Professor, Life Sciences & Company Director, Applied Proteomics & Molecular Medicine, George Mason University
Dr. Emanuel F. Petricoin is the Co-Director of the Center for Applied Proteomics and Molecular Medicine (CAPMM) at George Mason University. Prior to this position, he served as Co-Director of the FDA-NCI Clinical Proteomics Program from 2001-2005, and a Senior Investigator within the Center for Biologics Evaluation and Research at the U.S. Food and Drug Administration from 1993-2005. Dr. Petricoin received his Ph.D. in Microbiology from the University of Maryland in 1990. As a post-doctoral fellow at the U.S. Food and Drug Administration, he concentrated on signal transduction analysis using proteomic technologies. The focus of the CAPMM is the invention and use of proteomics technologies for signal transduction analysis, phosphoproteomics and nanoparticle-based peptidomic biomarker discovery for direct clinical applications at the bedside. His expertise centers on translational research for applications of novel proteomics and nano- technologies for patient tailored medicine and clinical diagnostics. He and his colleague, Dr. Lance Liotta, have recently spun-out two companies based on technologies and discoveries made in their GMU laboratories. The first company, Theranostics Health, was founded in 2006, and focuses on personalized therapy. Dr. Petricoin serves as Acting Vice President, Chief Science Officer of the company. The second company, Ceres Nanosciences, was founded in 2008, and focuses on the use of a novel nanoparticle technology for early disease detection and measurement of ultra low abundance proteins such as human growth hormone for anti-doping applications. He is a co-inventor on 40 filed and published patents, and has authored over 210 peer-reviewed publications and invited reviews. He has authored over 40 book chapters, is the Co-Editor-in-Chief of Human Genomics and Proteomics, is on the editorial board of Proteomics, Biomedical Microdevices, Proteomics- Clinical Applications, Proteomics- Protocols, Molecular Carcinogenesis, Journal of Personalized Medicine and is a Senior Editor for Cancer Epidemiology Biomarkers and Prevention. He was the founding Co-Editor-in-Chief of Clinical Proteomics. Dr. Petricoin is a founding member of the Human Proteomic Organization (HUPO) as well as the U.S. HUPO, and served on the Executive Committee and Treasurer for HUPO from 2002-2004. He has received numerous awards including the NIH Director’s Award, FDA Distinguished Scientist Award, American Society of Cytopathology Basic Research Award, the Roche Diagnostics/CLAS Distinguished Scientist Award and the Harvard University Leading Edge Award.

Ruth A. VanBogelen, Ph.D., Director, Biomarkers & Proteomics, NextGen Sciences, Inc.
Dr. VanBogelen has over 30 years of proteomics experience. She joined the company in April 2008 after a 16 year tenure of increasing responsibility at Pfizer/Warner Lambert. At Pfizer, Dr. VanBogelen was Director of the Proteomics Center, working globally with scientists from all therapeutic areas and Pfizer sites to address the needs for proteomics (80% biomarker projects) using both internal resources and outsourcing. Dr. VanBogelen began exploring the use of peptide MRM technology to overcome the bottleneck in biomarker assay development (which included outsourcing and collaborations with 3 different companies). Dr. VanBogelen also worked to identify external collaborations for establishing knowledgebases (both machine-readable and human-readable) for computational deductive reasoning and to address issues with institutional memory (collaborations with 2 companies). Previous to Pfizer, she spent 14 years at the University of Michigan studying E. coli physiology using proteomics (over 40 publications).

Samir M. Hanash, M.D., Ph.D., Program Head, Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center
Dr. Hanash is program head for Molecular Diagnostics at the Fred Hutchinson Cancer Research Center in Seattle, Washington. Dr. Hanash’s interests and expertise focus on the development and application of integrated approaches to the molecular profiling of cancer, with particular emphasis on proteomics. He has been a program principal investigator for several multi-investigator projects aimed at biomarker discovery and validation using proteomics.  Dr. Hanash has organized and participated in several workshops and initiatives related to diagnostics and proteomics.  He is the inaugural president of the Human Proteome Organization.

 


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