Connectivity Map 100k

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DESCRIPTION (provided by applicant): PROJECT SUMMARY: The Connectivity Map 100k project aims to forge a path toward a comprehensive 'functional look-up table' that that links disease biology, genome function and small-molecule action. Such a Connectivity Map would enable researchers worldwide to generate testable hypotheses that might otherwise remain undiscovered. By using genomic signatures as a common language with which to describe different cellular states, a broad range of research applications would be enabled. We propose here an ambitious plan to generate 100,000 Connectivity Map profiles of genetic and pharmacologic perturbation that will serve two important purposes. First, it will generate an expanded Connectivity Map database that will further support biological discovery. Second, it will establish the parameters for a future, larger scale Connectivity Map resource that might include, for example, profiles of perturbation of all human and mouse genes plus hundreds of thousands of small-molecules in a large number of cell types. In Aim 1, we will extend our pilot pharmacologic Connectivity Map data to genetic perturbations. Specifically, we will use lentiviral shRNAs to knock down the expression of 1,000 human genes in 10 diverse cell types. These experiments will establish the feasibility of developing large-scale signatures of genetic perturbation, and will establish the extent of cellular context-dependence of the observed connections. In Aim 2, we will generate profiles of 1,500 small-molecules (a blend of FDA-approved drugs and tool compounds being studied in NIH-sponsored chemical biology programs), again in 10 diverse cell types. By the end of this 2-year project, we expect a) to have generated 100,000 perturbational profiles made publicly accessible via a user-friendly web interface, and b) to have laid the foundation for the creation of a future, community-based, large-scale Connectivity Map public resource. RELEVANCE The proposed project is expected to have significant impact on a broad range of the biomedical research community. It has the potential to yield new approaches to genome functional annotation, to provide a path toward the elucidation of mechanism-of-action of small-molecule compounds, and to facilitate the discovery of drugs with unanticipated therapeutic effects on disease biology. PUBLIC HEALTH RELEVANCE: NARRATIVE: The Connectivity Map 100k project aims to forge a path toward a comprehensive 'functional look-up table' that links disease biology, genome function and small-molecule action. Through the generation of a database of 100,000 gene expression profiles of genetic and pharmacologic perturbation, the Connectivity Map will enable the biomedical community with a set of tools that facilitate systematic discoveries that link disease biology, genome biology and chemical biology. The proposed project will lay the groundwork for a future, large-scale, community-wide effort to create a public Connectivity Map resource that spans diverse perturbational profiles across a large number of cell types.