title: Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
abstract: Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.
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: 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: Biyu
authors.initials: B
authors.lastname: Li
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: Jenny
authors.initials: J
authors.lastname: Chen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Charles P
authors.initials: CP
authors.lastname: Fulco
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Livnat
authors.initials: L
authors.lastname: Jerby-Arnon
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
authors.forename: Nemanja D
authors.initials: ND
authors.lastname: Marjanovic
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Dionne
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Tyler
authors.initials: T
authors.lastname: Burks
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Raktima
authors.initials: R
authors.lastname: Raychowdhury
authors.affiliation: Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Britt
authors.initials: B
authors.lastname: Adamson
authors.affiliation: Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Norman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Weissman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; School of Engineering and Computer Science and Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: aregev@broadinstitute.org.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D002453:Cell Cycle; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D005246:Feedback; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D006801:Humans; D020014:K562 Cells; D051379:Mice; D008822:Mice, Transgenic; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors
keywords: CRISPR; epistasis; genetic interactions; pooled screen; single-cell RNA-seq