Genetic and Pathway Analysis Core

Washington University, Saint Louis MO

Investigators

Linked publications & trials

Abstract

The process of autophagy in response to bacteria, viruses and other pathogens is a critical feature of innate immunity and the overall host response to potential pathogens. The overall goal of this CETR is to define the shared and distinct mechanisms of autophagy and autophagy-protein-dependent immune responses to different classes of pathogens. These include Sindbis virus and herpes simplex virus, intracellular bacteria that are degraded by classical autophagy (including Salmonella typhimurium and Listeria monocytogenes) as well as other viruses (murine norovirus) and the protozoan parasite, T. gondii, that are controlled by nondegradative functions of autophagy proteins. (For brevity, these distinct processes will be collectively referred to as pathogen-induced autophagy.) The goal of Core B is to provide the analytic and chemical biology capabilities that will be critical to all four Projects as they systematically identify pathway components important for pathogen-induced autophagy, and devise therapeutics that target host autophagy, and are active against a variety of unrelated pathogens. Core B will integrate complementary datasets from a systematic, forward genetic approach (genome-wide RNAi screen) as well as a more targeted chemical biology approach (cell perturbation by compounds with known targets). Core B will also perform Landmark 1000 analysis of promising RNAi knockdowns, and chemical compounds identified by the individual Projects through their screens. The Core Director and Co-Director have a record of collaboration and extensive experience performing the analyses that will be provided in order to extract mechanistic insights into pathogen-induced autophagy and derive functional connections between genes and chemical compounds that can modulate pathogen-induced autophagy. This Core leverages extensive chemical biology/chemical perturbation and analytic resources available at IVIGH and the Broad Institute. Equally important, the Core builds upon existing collaborations and a history of co-publication among the Project Pi's, the Core Director and Co-Director, team members at the Broad Institute, and the CETR Project Pis