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Digital Course: microRNA Identification, Profiling and Validation Techniques


CONFERENCE SERIES: Informatics & IT
Recorded at: microRNA as Biomarkers and Diagnostics
 

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Digital Course: microRNA Identification, Profiling and Validation Techniques

March 22, 2010


About this Product:
The role of microRNA in regulating mammalian development and disease is now well established. miRNAs represent a novel class of targets for therapeutic and diagnostic development, currently not fully exploited by the pharmaceutical and biotechnology industries. This digital course features expert speakers in the pre-conference short course from CHI’s microRNA in Human Disease and Development 2010 meeting addressing technologies used for miRNA identification, profiling and validation involving microarrays, PCR, informatics, etc.

About the Conference:
CHI’s microRNA conference covers progress in identifying human miRNA and the latest research in linking miRNA to human disease. Opportunities for using miRNA as diagnostic biomarkers and a novel class of targets for therapeutic development are explored. Topics covered at this conference include, miRNA pathways and mechanisms, miRNA role in development and disease (special focus on cancer), miRNA and stem cells, miRNA biomarkers for diagnostic development, miRNA targets for therapeutic development, microRNA polymorphisms, and more.

Agenda at a Glance: 

 Direct, Electronic microRNA Profiling on a Multiplexed Chip
Shana O. Kelley, Ph.D., Professor, Biochemistry, University of Toronto
We have developed an electronic chip featuring nanostructured microelectrodes (NMEs) that enables the analysis of microRNA expression profiles in 30 minutes in small RNA samples without enzymatic amplification or sequence labeling. The multiplexed chip detects the hybridization of microRNA targets to NME surfaces and provides large electrocatalytic gain through the use of an ultrasensitive redox reporter system. Using this device, we identified several microRNA sequences that are overexpressed in cancer cells. This technology has the potential to enable the high-throughput identification of microRNAs for biomarker identification or cancer diagnosis.

Biography: After earning her Ph.D. at the California Institute of Technology in 1999, Dr. Kelley completed an NIH post-doctoral fellowship at Scripps Research Institute.  She was later a professor of Biology at Boston University from 2000-2006, until she joined the faculty of the University of Toronto.  Since 2008, she has been Director of the Division of Biomolecular Sciences, Faculty of Pharmacy, Medicine and Biochemistry at the University of Toronto, where she also heads up the Kelley Laboratory for Cellular and Molecular Sensors.  She has won numerous honors and awards, and authored and co-authored numerous publications in her field, most recently for ACS Nano and Nature Nanotechnology. The papers appearing in ACS Nano and Nature Nanotechnology received extensive media coverage and were featured by the National Post, Scientific American, and CBC National News/Mansbrisge One on One.

 The Regulation of microRNA Biogenesis in Cancer and Development
J. Michael Thomson, Ph.D., Assistant Professor, Department of Cancer Biology, Vanderbilt-Ingram Cancer Center
microRNA expression is highly tissue-specific and is tightly regulated, both spatially and temporally, in normal development. Additionally, microRNA dysregulation has proven to play a pivotal role in the initiation and progression of a wide variety of human cancers. It was long assumed that the strict control of microRNA expression was attributable to transcriptional regulation, but it’s become increasingly clear that, at least for a subset of microRNAs, expression is regulated at a post-transcriptional level via differential processing. Our lab has developed novel tools to address the post-transcriptional regulation of microRNA biogenesis.

Biography: Dr. J. Michael Thomson is an Assistant Professor of Cancer Biology in the Department of Cancer Biology at Vanderbilt University Medical Center. He received his B.S. and M.S. degrees from the University of Georgia at Athens followed by a Ph.D. from the University of Florida working with Dr. Steven Benner. After his Ph.D., he did his postdoctoral research work with Dr. Scott Hammond at the University of North Carolina School of Medicine at Chapel Hill.

 Nuclear miRNAs and Cytoplasmic miRNAs
Clark Jeffries, Ph.D., Research Professor, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
We report discovery of two classes of miRNAs relative to one cell system, namely, miRNAs that preferentially accumulate in the nucleus or in the cytoplasm of human embryonic neural progenitor cells. While it is known that many miRNAs appear in both nucleus and cytoplasm, we used TaqMan® technology to yield accurate measurements showing that certain miRNAs have preferred localization. Remarkably, if one miRNA is localized, then other miRNAs that have both similar 5’ end patterns and similar 3’ end patterns tend also to be localized in the same way. If nuclear import of mature miRNAs is part of a feedback mechanism that regulates miRNA levels, then importation dysregulation might correlate with disease.

Biography: After earning a Ph.D. in mathematics, University of Toronto, Clark joined Mathematical Sciences at Clemson University in 1987 as a lecturer.  He rose to professor rank in six years.  Following a sabbatical involving algorithm design for networks, he was hired in 1998 by IBM Microelectronics Division in a 12-member core design team for a new product, a high-performance router with powerful security features on one, low-power chip. Consequently, he is listed today as an inventor on 86 issued US patents.  In 2005 he joined Renaissance Computing Institute and, as research professor, the Eshelman School of Pharmacy, University of North Carolina at Chapel Hill.  Five years of intense study of human molecular genetics including extensive wet lab work have resulted in collaborations, publications, and invited talks. "A lot more is on the way," he says, and, "I don’t plan to change careers ever again...I’ve found what I love to do."

 microRNAs and Breast Cancer Metastasis: The Power of Pleiotropy
Scott Valastyan, Ph.D., Laboratory of Robert A. Weinberg, Massachusetts Institute of Technology and Whitehead Institute for Biomedical Research
microRNAs are well-suited to regulate tumor metastasis due to their capacity to concomitantly inhibit numerous target genes, thereby potentially enabling their simultaneous intervention at multiple distinct steps of the metastatic process. We have identified a microRNA exemplifying these attributes, miR-31, whose expression levels correlated inversely with metastatic recurrence in human breast cancer patients. Ectopic expression of miR-31 in otherwise aggressive breast tumor cells impeded metastasis. We deployed a novel microRNA sponge strategy to stably inhibit miR-31 in vivo; this allowed otherwise non-aggressive breast cancer cells to metastasize. These effects were achieved via pleiotropic modulation of a cohort of clinically relevant motility- and metastasis-promoting genes, which were overrepresented among the >200 mRNAs computationally predicted to be direct downstream targets of miR-31. In fact, we discovered that miR-31-evoked concurrent regulation of three such effectors – integrin 5, radixin, and RhoA – which was sufficient to explain the full spectrum of this microRNA’s impacts on metastasis. Taken together, these findings provide mechanistic insights into tumor metastasis and have implications concerning the importance of pleiotropy for the biological actions of microRNAs.

Biography: Scott Valastyan earned his B.S from Cornell University in 2006, graduating summa cum laude with high honors in research. Since that time, he has been a graduate student at the Massachusetts Institute of Technology, working in the laboratory of Robert Weinberg. Scott will complete his Ph.D. in May of 2010, at which time he will begin a post-doctoral position in the laboratory of Joan Brugge at Harvard Medical School.

 Development and Validation of a miRNA-Based Laboratory Developed Test (LDT) for Pancreatic Cancer
Anna Szafranska-Schwarzbach, Ph.D., CLIA Laboratory Supervisor, Pharmacogenomics Services, Asuragen, Inc.We have previously reported a laboratory-developed test (LDT) based on differential expression of miR-196a and miR-217 that can distinguish pancreatic ductal adenocarcinoma (PDAC) from chronic pancreatitis with a sensitivity and specificity of ~95%. This test performs well on specimens with either large (=60%) tumor area or those that can be enriched to this tumor content. There is additional clinical interest in identifying small pancreatic malignancies in a background of pancreatitis, particularly as a step toward early detection in tissues. We will discuss the LDT validation and the identification of a new miRNA classifier that allows discrimination of PDAC in specimens with low suspected tumor content.

Biography: Anna E. (Szafranska) Schwarzbach, Ph.D., the CLIA Laboratory Supervisor at Asuragen, Inc., first joined the company in 2005 as a staff scientist.  She received her M.S. degree in Pharmacy at the Wroclaw University of Medicine in Poland, and her Ph.D. degree in Bio-Organic Chemistry & Enzymology at the University of Bristol.  She completed a postdoctoral fellowship in the Department of Medicinal Chemistry, College of Pharmacy at the University of Texas in Austin.  Dr. Szafranska-Schwarzbach has authored and co-authored many articles on microRNA expression, analysis and related topics in molecular pathology, which have been published in such journals as Clinical Chemistry, the Journal of Molecular Diagnostics, and Oncogene.  A member of the Association of Molecular Pathologists (AMP), she has filed a patent for differentially expressed microRNA in pancreatic diseases, and has presented her work at numerous scientific conferences around the world.

About this Product:
5 Presentations
Over 138 slides
114 minutes
Single Copy - $345.00
Site License - $1,380.00



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