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

Parnas, Oren, Jovanovic, Marko, Eisenhaure, Thomas M., Herbst, Rebecca H., Dixit, Atray, Ye, Chun Jimmie, Przybylski, Dariusz, Platt, Randall J., Tirosh, Itay, Sanjana, Neville E., Shalem, Ophir, Satija, Rahul, Raychowdhury, Raktima, Mertins, Philipp, Carr, Steven A., Zhang, Feng, Hacohen, Nir, Regev, Aviv
Cell 2015 v.162 pp. 675-686
dendritic cells, genes, lipopolysaccharides, mammals, messenger RNA, pathogens, tumor necrosis factors
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.