Research Investigator I
Functional profiling is the study of gene function at the level of the genome. At GNF, we have pioneered a technological platform that enables high throughput gain-of-function and loss-of-function analyses of phenotypes in mammalian cells.
These cellular genetics methodologies draw on the extensive collection of full length cDNA, siRNA, and shRNA arrayed libraries compiled and constructed at the institute. Current estimates place the coverage of these libraries at more than 85% of the genome, thus enabling comprehensive genome-scale analyses. These nucleic acid collections can be transduced into cells through either a high throughput transfection methodology or large-scale lentiviral preparation and delivery. In a collaboration with the Engineering Group at GNF, the viral production anda screening process has been completely automated with a fully integrated robotic suite, enabling greater throughput and reproducibility while ensuring the safety of researchers.
Group members are currently pursuing additional methodologies that will facilitate the genome-level detection of protein-protein interactions, protein localization, and post-translational modifications. Our scientists are also using high throughput microscopy and automated image analysis technologies and instrumentation for the study of complex molecular and cellular phenotypes, such as subcellular ltrafficking, cellular migration, and chromatin dynamics. Taken together, these resources provide GNF researchers unparalleled opportunities for the discovery of novel gene function and therapeutic target identification.
In the Functional Profiling Group, we are taking advantage of our state-of-the-art facilities to elucidate novel gene activities at an unprecedented rate, build a comprehensive understanding of disease pathways and processes, and facilitate the validation of novel targets for therapeutic discovery.
We are focusing on exploiting novel functional genomics technologies to establish a global understanding of cancer, innate immunity, and viral infection. These genomics platforms include functional profiling of genome-scale cDNA and siRNA arrayed libraries, high throughput viral production methodologies, and automated microscopy and image analysis (HCS). Using these and other functional genomics platforms available at GNF, we are unraveling the intricate networks of gene activities involved in important disease processes, such as cancer, inflammation, and HIV/AIDS. For instance, we are cataloging cellular factors involved in proliferation and tumor promotion. By conducting genome-scale analysis of protein activities in the cancer-related AP-1 and p53 signaling pathways and of cellular growth and death, we have identified a significant number of novel signaling molecules and more than 15 new oncogenes. Finally, we are applying these technologies to identify host-pathogen interactions, specifically those that are required for the HIV life cycle. The elucidation of these proteins are lending insight into the cellular circuitry hijacked by the virus to establish pathogenesis, providing the basis for additional therapeutic strategies in combating multi-drug resistant viral strains.
These systems-level investigations are further complemented by intensive molecular, cellular, and mechanistic analysis of identified protein activities, including those critical for pro-inflammatory responses and HIV infection.
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- Mukherji M, Bell R, Supekova L, Wang Y, Orth AP, Batalov S, Miraglia L, Huesken D, Lange J, Martin C, et al. Genome-wide functional analysis of human cell-cycle regulators. Proc Natl Acad Sci U S A 2006;103(40):14819-24.
- Harada JN, Bower KE, Orth AP, Callaway S, Nelson CG, Laris C, Hogenesch JB, Vogt PK, Chanda SK. Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis. Genome Res 2005;15(8):1136-44.