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7:00 am Registration Open

7:30-8:30 Morning Coffee


Protein Biomarkers for Personalized
Medicine and Diagnostic Development

8:25-8:30 Chairperson’s Opening Remarks
Emanuel Petricoin, Ph.D., Co-Director, Center for Applied Proteomics and Molecular Medicine; Professor, Life Sciences, George Mason University


8:30-9:00 Implementation of Individualized Protein Drug Target Activation Mapping for Personalized Medicine Trials in Oncology Today

Emanuel Petricoin, Ph.D., Co-Director, Center for Applied Proteomics and Molecular Medicine; Professor, Life Sciences, George Mason University

We have originated a functional protein pathway activation mapping technique, called the reverse phase protein microarray that we have now graduated to full clinical trial implementation. Using this technique, we can map and measure the activation of all FDA approved targeted inhibitors within each patient’s tumor for the first time ever. This information is now being used in ongoing first-of-their-kind clinical trials for breast and colorectal cancers that are true personalized therapy trials and the first ever for metastatic disease.

9:00-9:30 FDA Regulation of Protein-Based Diagnostic Tests

Jeffrey N. Gibbs, J.D., Director, Hyman, Phelps and McNamara, P.C.

The use of protein-based assays is expected to play an increasingly important role in medicine. Regulation by the Food and Drug Administration will strongly influence the extent to which this promise is fulfilled. New protein-based assays will need to go through the FDA review process before they can be commercially distributed. While laboratory developed tests are generally not being currently regulated by FDA, these assays may face greater regulatory scrutiny in the future. Understanding the FDA regulatory process will be critical for those individuals and companies seeking to commercialize protein-based assays.

Sponsored by
9:30-10:00 Diagnostic and Treatment Monitoring Biomarkers for Intracellular Bacterial Infectious Disease

Eustache Paramithiotis, Ph.D., Senior Director, Cell & Molecular Biology, Caprion Proteomics, Inc.

Brucellosis is the world’s largest zoonosis. Diagnosis relies on serology or bacterial culture, both prone to false negatives. Treatment is by lengthy combination antibiotic therapy, with significant therapeutic failure, relapse, and adverse effects. Available biomarkers of relapse risk are not specific. Treatment monitoring biomarkers are not available. These limitations are common to most bacterial infections. To complement current diagnosis we propose to identify infection-specific proteins secreted by infected host cells, and follow these markers in sera. To identify treatment monitoring biomarkers we will identify serum protein expression changes associated with response to treatment, and develop assays for a multi-protein panel.

10:00-10:30 Streamlining the Regulatory Process of Multiplex Protein-Based Assays: An NCI and FDA Collaborative Effort

Emily Boja, Ph.D., Program Manager, Clinical Proteomic Technologies for Cancer, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health

The promise of protein biomarkers in cancer diagnostics is currently an area of considerable interest for application in personalized medicine. The rate of new protein analytes introduced, however, remains flat as reflected by an average of 0.3 cancer targets/year approved by the FDA. To close the gap between biomarker discovery and validation, the NCI-CPTC initiative has made significant progress since its inception to address analytical variability in current proteomic technologies/platforms, to introduce a bridging technology between these two distinct stages, and to collaborate with the FDA to understand regulatory science. This collaborative effort is highlighted in recently published workshop report and two mock 510(k) pre-submissions to illustrate the regulatory process of assay validation based on multiplex immunoaffinity MS and multiplex immunoaffinity array platforms.

10:30-11:30 Networking Coffee Break with Poster and Exhibit Viewing


Technology Showcase

11:30-11:45 Biomarkers for Drug Development
Austin Tanney, Ph.D., Scientific Liaison Manager, AlmacSponsored by

In the development of personalized medicine, the discovery and application of biomarkers in the drug development pipeline is critical. With applications including diagnosis/prognosis, drug pharmacodynamics and patient selection biomarkers can guide drug development and patient selection and treatment across the board. This presentation will outline Almac’s experience in biomarker discovery and development in a range of different tissues and disease indications.

Sponsored by
11:45-12:15 pm A Multiplexed Electrochemiluminescent Technology for the Simultaneous Analysis of Multiple Biomarkers from Complex Samples
David Sloan, Ph.D., Meso Scale Discovery
Meso Scale Discovery’s plate based electrochemiluminescent platform allows for the rapid development of high sensitivity immunoassays that cover a large dynamic range allowing for the quant-ification of biomolecules that can vary hundred to thousand fold in
concentration without the requirement for multiple sample dilutions. Assays generally have a high matrix tolerance enabling samples to be run in high concentrations of sample matrix. The platform is compatible with a wide variety of both simple and complex biological matrices such as serum and plasma, cell and tissue extracts, and other biological fluids. Other advantages of the platform for ligand binding assays include the ability to multiplex assays, minimal sample requirements, reduced wash steps and flexibility in assay design or format. While many of the traditional optimization and validation parameters of ligand binding assays apply, the increased complexity of multiplexed immunoassays requires that additional considerations be taken into account during the development and validation of these assays. Strategies and examples of the development and characterization of multiplexed immunoassays on MSD’s plate based electrochemiluminescent platform will be discussed.

Sponsored by
12:15-12:30 Analysis of Human Kidney Toxicity/Damage Using Multiplex Immunoassays

Wei Zheng, Ph.D., R&D Immunoassay Group Leader, EMD Chemicals

The FDA and EMEA have issued guidelines for 7 new urinary biomarkers of drug-induced kidney damage in rats. A natural continuation of this is to build on such efforts in studies performed in human patient material to advance the “rolling qualification.” To this end, a screen for potential protein biomarkers in relation to kidney toxicity/damage was performed in a set of urine and plasma samples from patients with documented renal damage. Multiplexed immunoassays were used to quantify protein analytes and standard blood and urine chemistry were determined. Statistical analyses using both univariate and multivariate tools indicated discrepancies in protein levels when comparing case and control samples. Future analysis aiming to qualify these biomarkers will indicate the potential of these candidates as markers for renal toxicity in humans.

12:30-12:45 Layered-Immunohistochemistry: A Novel Technology for "So many markers and so little tissue"Sponsored by
20 20 GeneSystems logo

Michael S. Lebowitz, Ph.D., Director of R&D, 20/20 GeneSystems, Inc.
Analysis of tissue biomarkers is key to understanding the activation status of particular pathways in specific cell types and can be indicative of disease diagnosis, prognosis, prediction of therapeutic efficacy and monitoring of treatment outcomes.  This information is of further importance in identifying and validating novel drug targets.  While in certain instances detection of single biomarkers is sufficient, it is rapidly becoming clear that both panels of multiple markers and variations in biomarker levels relative to each other is more informative and more diagnostic of cell and disease status.  The ideal biomarker tests conserve precious tissue by multiplexing marker measurements, retain information regarding tissue morphology and cell type localization, and normalize marker levels to objective standards.  20/20 GeneSystems, Inc. has introduced Layered-Immunohistochmistry (L-IHC) a tissue biomarker platform that meets all of these requirements.  In L-IHC the proteins of the tissue are channeled upward through the membrane stack with each layer capturing a certain percentage of total protein.  Thus each membrane represents a “carbon” copy of the tissue and can be probed for different biomarkers using standard immunostaining techniques.  Specific marker staining is detected using fluorescently labeled secondary antibodies and is always normalized to total protein to account for differences in protein transfer.  L-IHC has already been applied to a case of disease prognosis and 20/20 is actively involved in the development of L-IHC-based tests to predict therapeutic outcomes.  20/20 is now offering L-IHC-based testing to the research market on a contract basis.

12:45-2:00 Lunch on Your Own


Protein Biomarker Discovery
and Profiling Approaches

Chairperson's Opening Remarks
Gilbert S. Omenn, M.D., Ph.D., Director, Center for Computational Medicine and Bioinformatics, University of Michigan School of Medicine

2:00-2:40 Discovery and Characterization of Alternative Splice Variant Peptides: A New Class of Protein Cancer Biomarker Candidates

Gilbert S. Omenn, M.D., Ph.D., Director, Center for Computational Medicine and Bioinformatics, University of Michigan School of Medicine

Alternative splicing generates protein diversity without increasing genome size. Our analytical pipeline identifies and quantifies known and novel splice isoforms from peptide sequences determined by mass spectrometry. Alternative splice variant peptides are a new class of protein cancer bio-markers. We have conducted extensive proteomic analyses on plasma and tissue specimens from genetically-designed mouse models of human pancreatic and breast cancers. Mass spectra are interrogated against a non-redundant database of exhaustive 3-frame translation of Ensemble transcripts and gene models from Ecgene using X!Tandem software. The search results are processed for peptide-to-protein integration by Trans Proteomic Pipeline (TPP) and/or Michigan Peptide to Protein Integration (MPPI). Over-expressed novel variants are validated by qRT-PCR. The exact splicing findings and the biological annotations for over-expressed variants in these cancers are quite interesting.

2:40-3:20 Self Assembling Protein Microarrays for Biomarker and Target Discovery

Joshua LaBaer, M.D., Ph.D., Director, Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University

Self assembling protein microarrays arrays can be used to study protein-protein interactions, protein-drug interactions, search for enzyme substrates, and as tools to search for disease biomarkers. In particular, recent experiments have focused on using these protein microarrays to search for autoantibody responses in autoimmune and cancer patients. Several bona fide autoantibody responses, such as responses to p53 in cancer and Gad and IA2 in type I diabetes, have been detected. More comprehensive searches for new autoantibodies using arrays with 7500 full length human proteins are yield promising results. These experiments show promise in finding antibody responses that appear in only patients.

3:20-3:30 Q&A with Speakers


3:30-4:30 Networking Refreshment Break with Poster and Exhibit Viewing


4:30-5:00 A Pipeline for Protein Biomarker Discovery and Development: Application to Disease Progression and Drug Treatment Studies

Daniel S. Spellman, Ph.D., Senior Research Biochemist, Proteomics, Merck Research Laboratories

Identification of protein biomarkers from accessible tissues and biofluids is important to drug discovery and development, with the goal of enabling decision making at critical stage gates during the development process. A general proteomic approach for the discovery and identification of protein biomarkers, differential mass spectrometry (dMS), based on the analysis of full scan mass spectrometry data, has been previously described. Examples of how such a quantitative label-free proteomics approach can be applied to characterize changes resulting from pharmacological intervention, disease state, and observed clinical characteristics will be described.  A workflow for translating protein markers from discovery to robust, quantitative triple-quadruple mass spectrometry assays that are more amenable to measuring large numbers of clinical samples will also be presented.

5:00-5:30 Single Cell Multiplexed Phosphoprotein Analysis for Inflammatory Disorders

Gary Means, Ph.D., Principal Scientist, Molecular Sciences Group, Amgen, Inc.

Phosphoproteins involved in signal transduction are being evaluated as biomarkers of effective inhibition by therapeutics. In these samples, the responses of individual cell subsets can be accurately determined by multi-parameter flow cytometry. One advantage of this approach is that the impact of a therapeutic is monitored on each cell subset expressing the signaling pathway. We have observed differential responses to cytokine induced receptor activation in selected cell subsets of patients with autoimmune disease which suggests that immune cells with altered signal transduction pathways are present in whole blood from these patients and that intrinsically different responses may be anticipated to some therapies.

5:30 Close of Day