title: 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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Oren
authors.initials: O
authors.lastname: Parnas
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Marko
authors.initials: M
authors.lastname: Jovanovic
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Eisenhaure
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Rebecca H
authors.initials: RH
authors.lastname: Herbst
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
authors.forename: Atray
authors.initials: A
authors.lastname: Dixit
authors.affiliation: Institute for Human Genetics, Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Chun Jimmie
authors.initials: CJ
authors.lastname: Ye
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Dariusz
authors.initials: D
authors.lastname: Przybylski
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Randall J
authors.initials: RJ
authors.lastname: Platt
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Itay
authors.initials: I
authors.lastname: Tirosh
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Neville E
authors.initials: NE
authors.lastname: Sanjana
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Ophir
authors.initials: O
authors.lastname: Shalem
authors.affiliation: New York Genome Center, New York, NY 10013, USA; New York University, Center for Genomics and Systems Biology, New York, NY 10012, USA.
authors.forename: Rahul
authors.initials: R
authors.lastname: Satija
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Raktima
authors.initials: R
authors.lastname: Raychowdhury
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Philipp
authors.initials: P
authors.lastname: Mertins
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston MA 02114. Electronic address: nhacohen@broadinstitute.org.
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02140, USA. Electronic address: aregev@broadinstitute.org.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D001854:Bone Marrow Cells / Q000276:immunology; D064113:CRISPR-Cas Systems; D002454:Cell Differentiation; D002470:Cell Survival; D003713:Dendritic Cells / Q000166:cytology / Q000276:immunology; D055786:Gene Knockout Techniques; D053263:Gene Regulatory Networks; D005821:Genetic Techniques; D006602:Hexosyltransferases / Q000378:metabolism; D007113:Immunity, Innate; D008565:Membrane Proteins / Q000378:metabolism; D051379:Mice; D008822:Mice, Transgenic; D051197:Toll-Like Receptor 4 / Q000276:immunology; D014409:Tumor Necrosis Factor-alpha / Q000276:immunology
chemical_list: D008565:Membrane Proteins; C493487:Tlr4 protein, mouse; D051197:Toll-Like Receptor 4; D014409:Tumor Necrosis Factor-alpha; D006602:Hexosyltransferases; C025620:dolichyl-diphosphooligosaccharide - protein glycotransferase