Overview

Sessions Include:
• Expression Profiling to Characterize Compound Activity,Mechanism of Action, and Selectivity
• Toxicogenomics
• Proteins as Toxicity and Pharmacodynamic Biomarkers
• Organ- or Mechanism-Specific Toxicity Biomarkers
• Systems Biology Approaches to Toxicology
• Genomic and Proteomic Data Analysis for Biomarker Discovery

Part of the Biomarker Discovery Summit
• Third Annual Protein Biomarkers
• Second Annual Toxicity Biomarkers
• Workshop: Mass Spectrometry for Protein Biomarker Discovery
• Workshop: Expression Profiling for Compound Characterization

Built on the solid track-record of Cambridge Healthtech Institute’s Biomarker Series

KEY FEATURES:
4 events  |  50+ speakers  |  400+ delegates  |  20+ exhibits  |  30+ posters

Monday, September 26th

7:30-8:30 Workshop Registration and Morning Coffee

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

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

8:40-9:20 Is There Any Value in Using Gene Expression Profiling for Compound Prioritization and Elucidating Possible Mechanism of Action?
Dr. Timothy Perera, Principal Scientist, Oncology Discovery Research, Johnson and Johnson Pharmaceutical Research and Development 
High-content data sources, such as gene expression profiling, are now commonly used in compound characterization and prioritization. However, the full value of this approach requires a systematic experimental design that is instigated from the start. Some of the issues and benefits of using such a ‘systems biology’ approach that unfolded in a study aimed at uncovering the mechanism of action of a multi-targeted kinase inhibitor will be presented. Further value of this data for identifying ‘responder’ and ‘non-responder’ signatures will also be discussed.

9:20-10:00 High-Throughput Screening, Lead Optimization and Development Candidate Selection Using Gene Expression Profiling
Dr. Jeffrey Strovel, Staff Scientist, Development, Avalon Pharmaceuticals, Inc.
Gene expression profiling enables us to describe both the target-specific pathway effects as well as the off-target effects that compounds have on disease cells. We have developed a suite of applications for multiparametric gene expression assays to screen compound libraries for novel pathway activities, discriminate amongst screening hits, and select lead compounds for optimization. Following lead selection, we use gene expression microarrays to identify a set of biomarkers that describes the most desired effects of the compound series, and use this core gene set to drive chemical optimization toward the identification of a development candidate. Additionally, gene expression biomarker sets are used in in vivo experiments that accelerate pharmacologic optimization and establish clinical biomarkers to 1) guide dose escalation 2) correlate patient responses with pre-clinical efficacy results, and 3) enrich for responsive patients.

10:00-10:30 Networking Coffee Break

10:30-11:10 Integrated Computational and Experimental Approach for Identifying Compound Mode-of-Action
Dr. Guillaume Cottarel, President, Systems Biology, Cellicon Biotechnologies Inc.
A major challenge in drug discovery is to distinguish the molecular targets of a bioactive compound from the hundreds to thousands of gene products that respond indirectly to changes in the activity of the targets. Here, we present an integrated computational and experimental approach for identifying the gene products and pathways that are targets of a compound. This is achieved by filtering the mRNA expression profile of compound-exposed cells using a reverse-engineered model of the cell’s gene regulatory network. Using this method, we successfully predicted the molecular targets of multiple compounds, including a potential new anticancer compound, PTSB. PTSB inhibits growth in human small lung carcinoma cells and in the test organism (baker’s yeast). In follow-up experiments, we verified that PTSB acts on thioredoxin and thioredoxin reductase, the molecular targets predicted by our algorithm. These findings have validated the algorithm’s capabilities and facilitated investigation of a novel class of therapeutic compounds.

11:10-11:50 Transcriptional Profiling for Drug Candidate Selection
Dr. Simon Plummer, Senior Scientist, Pre-Clinical, CXR Biosciences Ltd.
The assessment of risk using animals is limited by difficulties in data extrapolation to man. Integration of transcriptional profiling with conventional toxicity tests can provide mechanistic information enabling the design of in vitro studies in ‘target’ cells. This facilitates a comparison of toxic effects in rodent and human cells. The paradigm provides a basis for assessment of potential toxicity to man and the comparison/selection of drug candidates.

11:50-1:15 Lunch (on your own) 

1:15-1:45 Technology Solutions Showcase
(sponsorship available, contact Arnie Wolfson at awolfson@healthtech.com or 781-972-5431)

1:45-2:25 Exploring Compound Activities Through Pathway Analysis of Expression Profiling Data
Dr. Petra Ross-Macdonald, Senior Research Investigator, Applied Genomics, Bristol-Myers Squibb Co.
It seems that the more we look for drug selectivity, the less we find. Genomic technologies such as expression profiling should dramatically increase our ability to analyze the biological effects of compounds - if we can effectively use the large amounts of data that they produce. At some level, we need to understand the changes that occur. Databases and tools for interpreting profiling data have proliferated recently. To compare several such resources with the benefit of 20/20 hindsight, we applied them to an expression profiling data set from a well-characterized group of compounds. 

2:25-3:05 Activity-Based Profiling of Kinase Inhibitors on Substrate Microarrays
Dr. Jos Joore, VP Array Technologies, Peptide Microarrays, Pepscan Systems
We have developed a method to study the kinome of cells and tissues, meaning a fingerprint of kinase activity. This technology is studied for its usefulness in compound characterization by comparing activity profiles of different kinase inhibitors in a variety of cells and tissues. This method gives a far better insight in the complex interactions that influence the effects of signal transduction modulating compounds, as compared to classical kinase assays on panels of purified kinases.

3:05-3:55 Exhibit Hall Opening, Refreshment Break with Poster and Exhibit Viewing

3:55-4:35 Expression Profiling Revealed Novel Activities of Compounds
Dr. Yan Luo, Senior Group Leader, Cancer Research, Abbott Laboratories
Conventional assessment of compound selectivity is often limited to classes of closely related proteins. Even for the panel of selected proteins that we are able to test in vitro, these proteins may not be in the same physiological state as in cells. All of these factors could result in an inaccurate assessment of compound selectivity. In contrast, gene expression profile analysis could provide a physiological, as well as a thorough and unbiased snapshot of the gene expression changes resulting from compound treatment, and thus, a more accurate assessment of a compound selectivity in cells.

4:35-5:15 Panel Discussion with the Speakers

5:15-6:30 Reception in the Exhibit Hall

Second Annual Toxicity Biomarkers 2005

Tuesday, September 27th

7:00-8:30 Conference Registration

7:30-8:15 Technology Workshop (sponsorship available, contact Arnie Wolfson at awolfson@healthtech.com or 781-972-5431)

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

TOXICOGENOMICS

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

8:40-9:05 Toxicogenomics for Toxicity Evaluation and Marker Identification
Dr. Jing-Shan Hu, Research Leader, Toxicogenomics, Roche Palo Alto 
Earlier and sensitive safety evaluation of candidate drugs has been crucial for drug development.  Toxicogenomics is an approach of using genome-wide gene expression profiling to study molecular changes in cells and tissues in response to toxic compound exposure.  Compared with traditional approaches, this approach has the potential to us to detect toxic response more sensitively at earlier stages and to understand better the molecular mechanism of toxicity.  We will discuss the discoveries from our toxicogenomics study in this presentation.

9:05-9:30 Development of in Vitro Toxicogenomics Assay to Screen Compound for Potential Toxicity 
Dr. Yi Yang, Senior Research Biologist, Cellular and Molecular Toxicology, Abbott Laboratories
In vitro toxicogenomics can be a powerful tool for evaluating the toxic potential of compounds early in the drug discovery process because of the minimal amounts of compounds required. At Abbott, we developed an in vitro toxicogenomics assay by profiling over 100 reference compounds in isolated rat hepatocytes. This assay can identify compounds with the potential to induce a variety of toxic changes, including mitochondrial damage, phospholipidosis, microvesicular steatosis and peroxisome proliferation with a high degree of sensitivity and specificity. The assay was originally developed using microarray technology, but have since been transferred to a gene expression platform with higher throughput, lower cost, and amenable to customization. This presentation will highlight some of the workflow processes. 

9:30-9:55 Quality Analysis in Toxicogenomics
Ms. Susan Flood, Global Pharma Strategist, SAS Institute
Inherent in all toxicological studies is the ability to assess biomarkers (genomics or proteomics based) and their correlations with toxicological responses with confidence. This is a common challenge, regardless of the toxicological application- environmental, biodefense, or disease treatment related. We will discuss the requirements needed to establish quality analysis procedures that support toxicogenomic projects by pulling from case studies and best practices. These projects include environmental hazard studies with microarray and clinical data, identification of toxicity signatures, and qualifying biomarkers using mining techniques. Topics will include experimental design, data preparation, and incorporating pathway information to optimize results.

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

ORGAN- OR MECHANISM-SPECIFIC
TOXICITY BIOMARKERS

10:45-11:10 A Mechanistic Biomarker of Mitochondrial Electron Transfer Inhibition in Toxicity Screening
Dr. Yankai Jia, Laboratory Manager, Medicinal Chemistry, University of Washington
Using DNA microarray we discovered a set of genomic responses, which are unique to mitochondrial respiratory chain inhibition. This will make an excellent biomarker for pre-clinical drug toxicity screening. The gene expression profile is from a mouse cell line and validated with an in vivo mouse model. It will provide a very useful tool for high-throughput toxicity screening.

11:10-11:35 Human Organ Specific in Vitro Assessment through Expression Profiling
Prof. Sisir Dutta, Professor Emeritus, Howard University
Our group has been working on this topic currently funded by NIH using human Liver (HepG2) and Kidney (HK2) cells in vitro. We have accumulated significant data on the specific polychlorinatedbiphenyl (PCB) induced toxicity and gene profiling. It appears that none of these organ specific cell lines dechlorinates PCBs. However, these cell lines differ significantly in PCB induced gene expression using total human oligoneucleotide Affymetrix Genechip microarrays, and in specific toxicity tests done such as DNA fragmentation and apoptotic studies.

11:35-12:00 Large-Scale Identification of Biomarkers of Drug Resistance by Enhanced DNA Repair
Prof. Dan Mercola, Director of Molecular Pathology, Sidney Kimmel Cancer Center
We have developed a “ChIP-on-chip” approach to identify genes that functionally mediate drug resistance to cancer chemotherapeutic agents. First, a model system of cisplatin-damaged DNA in breast cancer cells is used to examine genes induced by the DNA damage mediating Jun Kinase pathway via phsophorylation of c-Jun and ATF2. Second, we fabricated human array of 5,000 promoter sequences in order to identify the ChIP-products. In this case, 269 genes were shown to be bound and activated within 3 hours of DNA damage, the largest functional group of which were 26 DNA repair genes. These results and similar studies of the adrogen receptor in prostate cancer cells demonstrate that promoter arrays provide a high-throughput basis for the identification of biomarkers of toxicity and of genes likely mediating drug resistance.

12:00-1:30 Lunch (on your own) 

TECHNOLOGY SOLUTIONS SHOWCASE 

1:30-2:00 Technology Short Talks (sponsorship available, contact Arnie Wolfson at awolfson@healthtech.com or 781-972-5431)

SYSTEMS BIOLOGY APPROACHES TO TOXICOLOGY

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

2:05-2:30 Strategic Metabonomics Approach to Toxicity Biomarkers
Dr. Marielle Delnomdedieu, Metabonomics Team Leader, Worldwide Safety Sciences, Pfizer Global R&D 
As other members of the “Omics” family, metabonomics focuses on obtaining relevant metabolic profiles. Metabonomics is a combination of nuclear magnetic resonance (NMR), mass spectrometry (MS) and multivariate data analysis. Its applications in pharmaceutical R&D have been the subject of several publications. Metabonomics provides a snapshot of all small molecules present in a given sample, without “a priori” decisions on what to measure. This metabolic profile can be used to look for biomarkers of toxicity in pre-clinical and clinical studies, with a diagnostic potential as a way to assess drug safety.

2:30-2:55 Computational Models of Biological Pathways can Reveal Toxicity Mechanisms
Dr. Gordana Apic, CEO, Cambridge Cell Networks Ltd.
Systems biology promises to significantly impact biomarker identification. One of its ultimate goals is to provide an understanding of the complete set of molecular mechanisms describing an organism. Although this goal is a long way off, many useful insights can already come from currently available information and technology. One of the biggest challenges in drug discovery today is the high attrition rate: many promising candidates prove ineffective or toxic owing to a poor understanding of the molecular mechanisms of biological systems they target. A ‘‘systems’’ approach can help identify pathways related to a disease and can suggest secondary effects of drugs that might cause these problems and thus ultimately improve the drug discovery pipeline. Computational models of biological pathways are already starting to provide some useful insight into the mechanisms of toxicity.

2:55-3:20 Systems Toxicology
Dr. Yvonne P. Dragan, Director, Center for Hepatotoxicity and Director, Division of Systems Toxicology, National Center for Toxicological Research, FDA

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

BIOMARKER IDENTIFICATION FROM GENE AND PROTEIN EXPRESSION DATA:LIMITATIONS IN TECHNOLOGY AND DATA INTERPRETATION

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.

Wednesday, September 28th

7:30-8:15 Breakfast Technology Workshop Sponsored by Ventana Medical Systems

PROTEINS AS TOXICITY AND
PHARMACODYNAMIC BIOMARKERS

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