WEDNESDAY, NOVEMBER 18, 2009
7:30 am Breakfast Presentation (Sponsorship Opportunity) and Morning Coffee
8:10 Chairperson’s Remarks
Christopher Winrow, Ph.D., Director, Psychiatry, Merck Research Laboratories
FEATURED SPEAKER
8:15 New Approaches Towards Characterizing Non-Coding RNA’s and Their Role in Health and Disease
Allen Nicholson, Ph.D., Professor, Biology and Chemistry, Temple University
The diverse functions of non-coding (nc) RNAs in cellular and viral gene expression and regulation rival those of proteins. New technologies are addressing the challenging goals of identifying ncRNAs, determining their roles in health and disease, and suggesting new therapeutic approaches. Specific studies will be presented that either analyze the ncRNA component of cellular transcriptomes or that characterize diseases involving ncRNAs and their potential treatment strategies.
9:00 Application of Gene Expression Profiling in Discovery and Early Development to Identify and Characterize the Toxic Profiles of Compounds
Wayne Buck, Ph.D., Cellular Molecular & Exploratory Toxicology, Abbott Laboratories
Gene expression profiling can help predict the toxic properties of compounds and identify novel molecular biomarkers of toxicity early in the discovery process. However, the optimal implementation and positioning of these molecular techniques in an organization can be challenging. In this presentation, using specific examples, we will illustrate how these emerging techniques can be successfully used in vitro and in vivo to identify compounds with an acceptable toxicologic profile and novel biomarkers of toxicity.
9:30 Examining CNS Gene Expression in Isolated Sleep Circuits
Christopher Winrow, Ph.D., Director, Psychiatry, Merck Research Laboratories
A circuit-based analysis of brain regions is complicated by the spatial and cellular diversity of the CNS. Combining laser capture microdissection with transcriptome-wide profiling enabled detection of significant changes in sleep/wake regulating nuclei between night and day in preclinical species.
10:00 Networking Coffee Break, Poster & Exhibit Viewing
10:45 Genetic Tools to Study Gene Expression During Bacterial Pathogen Infection
Jay Zhu, Ph.D., Assistant Professor, Microbiology, University of Pennsylvania School of Medicine
The astonishing flexibility and adaptability of the bacterial cell has enabled many pathogenic species to freely transition between dramatically different environmental conditions. The transcriptional changes that underlie this ability can determine the success of the pathogen in the host. We will use Vibrio cholerae as a primary example to introduce a number of genetic techniques that have been devised to examine the transcriptional repertoire of bacteria in vivo during infection.
11:15 Evaluating Quality in a Multicenter Gene Expression Microarray Study
Kellie Archer, Ph.D., Assistant Professor, Department of Biostatistics, Virginia Commonwealth University
Multicenter microarray studies are increasing to ensure an adequate number of samples will be procured, particularly when the phenotype being studied is rare. The quality of hybridized microarrays is dependent upon the quality of the extracted RNA, which in turn is dependent upon the quality of the source tissue samples. In this presentation, procedures undertaken to evaluate quality of samples submitted for inclusion in a multicenter microarray study, from RNA isolation, to cDNA synthesis and IVT labeling, to hybridization will be described.
11:45 Increased Expression of Desmoglein 2 in Malignant Skin Carcinomas: A Tissue- and RNA-Microarray Based Study
M G. Mahoney, Ph.D., Associate Professor, Department of Dermatology and Cutaneous Biology, Thomas Jefferson University
Desmoglein 2 (Dsg2), a transmembrane cadherin of the desmosomal cell-cell adhesion structure, is downregulated with epithelial differentiation. We recently demonstrated that overexpression of Dsg2 in epidermal keratinocytes deregulates multiple signaling pathways associated with increased growth rate, anchorage-independent cell survival, and the development of skin tumors. Using tissue microarrays, we show a dramatic upregulation of Dsg2 expression in certain human epithelial malignancies including basal cell carcinomas, squamous cell carcinomas, carcinomas of sebaceous and sweat glands and adenocarcinomas. Dsg2 expression was completely absent in malignant fibrosarcomas and melanomas. Thus, we have identified Dsg2 as a potential novel marker for epithelial-derived malignancies.
12:15 pm Close of Morning Session
12:30 Lunch on Your Own
2:00 Chairperson’s Remarks
Allen Nicholson, Ph.D., Professor, Biology and Chemistry, Temple University
2:05 Mapping Transcriptome-wide Functional Protein-RNA Interactions in the Mouse Brain
Donny Licatalosi, Ph.D., Postdoctoral Associate, Laboratory of Molecular Neuro-oncology, Rockefeller University
2:35 Development and Validation of Molecular Signatures Predicting Risk of Recurrence and Survival of Human Breast Carcinoma Patients
Sarah A. Andres, Ph.D., Post-doctoral Research Associate, Department of Biochemistry & Molecular Biology, University of Louisville
The Human Genome Project provided opportunities to develop precise tests for cancer diagnostics, therapy selection and monitoring. From analyses of various microarray studies, genes expressed in human breast cancer cells procured from de-identified tissue sections by LCM and genes predicted in adjacent stromal cells were identified, whose expression appears related to clinical outcome. Molecular signatures consisting of subsets of candidate genes predicted breast cancer recurrence and overall survival in multivariate Cox proportional hazards models. Collectively, results suggest that these genes may form the basis for developing clinical laboratory tests to predict clinical outcome of breast cancer.
3:05 Networking Refreshment Break, Final Poster & Exhibit Viewing
3:30 Novel Gene Knockdown Models for Studying Reprogramming in the Early Embryo
Mylene W. M. Yao, M.D., Assistant Professor, Department of Obstetrics and Gynecology, Stanford University School of Medicine
Compared to the embryonic stem cell (ESC) gene regulatory network, little is known about the dynamic gene network that directs reprogramming in the early mammalian embryo. We have found that ESC pluripotency regulators, such as Oct4, have novel and critical functions in the first few days of development, when both maternal and embryonic transcripts may be present. We established models of gene-specific knockdown by microinjecting morpholinos and discovered novel Oct4 functions in post-transcriptional regulation by global gene expression profiling and large-scale semi-quantitative RT-PCR (RT-qPCR) at the level of the single-embryo. This experimental strategy is being applied to deconstruct the dynamic gene network that regulates development, reprogramming and cell fate decisions.
4:00 Single Molecule Sequencing for Unbiased Views of Gene Expression from Small Numbers of Cells
John Thompson, Ph.D., Senior Director, Genomic Research, Helicos Biosciences
Deep sequencing of cDNAs from a variety of biological systems has provided gene expression data that spans a much broader linear range than possible with hybridization-based methodologies as well as providing information about previously unannotated transcription units and splice sites. Though sequencing technologies are much better at quantitating the transcriptome than hybridization-based technologies, many still suffer from the need for ligation and amplification steps that can bias the quantitative outcomes. Single molecule sequencing, in contrast, is able to provide quantitative information without the need for either amplification or ligation and the concomitant biases they can introduce. Furthermore, the simple sample preparation and low sample needs allow the use of very small numbers of cells for starting material. Advances in reducing sample requirements and demonstrating the broad range of samples that can be addressed by single molecule sequencing will be described.
4:30 Current-Generation High-Throughput Sequencing: Deepening Insights into Mammalian Transcriptomes
Benjamin Blencowe, Ph.D., Professor, Banting and Best Department of Medical Research, Molecular Genetics, Center for Cellular and Biomolecular Research, University of Toronto
5:00 Close of Meeting