A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Abstract

Finding the components of cellular circuits and determining their functions systematically remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled CRISPR-Cas9 libraries into dendritic cells (DCs) to identify genes that control the induction of tumor necrosis factor (Tnf) by bacterial lipopolysaccharide (LPS), a key process in the host response to pathogens, mediated by the Tlr4 pathway. We found many of the known regulators of Tlr4 signaling, as well as dozens of previously unknown candidates that we validated. By measuring protein markers and mRNA profiles in DCs that are deficient in known or candidate genes, we classified the genes into three functional modules with distinct effects on the canonical responses to LPS and highlighted functions for the PAF complex and oligosaccharyltransferase (OST) complex. Our findings uncover new facets of innate immune circuits in primary cells and provide a genetic approach for dissection of mammalian cell circuits.Broad InstituteNational Institutes of Health (U.S.) (NIMH: 5DP1-MH100706)National Institutes of Health (U.S.) (NIDDK: 5R01-DK097768)National Science Foundation (U.S.) (Waterman Award)W. M. Keck FoundationNew York Stem Cell FoundationDamon Runyon Cancer Research FoundationSearle Scholars ProgramVallee FoundationRobert MetcalfeMassachusetts Institute of Technology. Simons Center for the Social BrainNational Human Genome Research Institute (U.S.) (K99- HG008171)National Science Foundation (U.S.). Graduate Research Fellowship Program (grant number 1122374)Human Frontier Science Program (Strasbourg, France