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PMID: 27984732 Published · ppublish English Journal Article

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Cell ·Vol. 167 ·No. 7 ·2016-12-15 ·Pages 1853-1866.e17

Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A

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.

Keywords
CRISPR epistasis genetic interactions pooled screen single-cell RNA-seq
MeSH Terms
Animals Cell Cycle Clustered Regularly Interspaced Short Palindromic Repeats Feedback Gene Expression Profiling Gene Knockdown Techniques Humans K562 Cells Mice Mice, Transgenic Sequence Analysis, RNA/methods Single-Cell Analysis/methods Transcription Factors/metabolism
Chemicals
Transcription Factors
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Dixit Atray
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
Parnas Oren
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Li Biyu
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Chen Jenny
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
Fulco Charles P
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Jerby-Arnon Livnat
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Marjanovic Nemanja D
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
Dionne Danielle
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Burks Tyler
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Raychowdhury Raktima
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Adamson Britt
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.
Norman Thomas M
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.
Lander Eric S
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.
Weissman Jonathan S
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.
Friedman Nir
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.
Regev Aviv
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.
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Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
DOI
10.1016/j.cell.2016.11.038
Email
aregev@broadinstitute.org
Published
2016-12-15
Pages
1853-1866.e17
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC5181115
Subset
IM
Grants
NCI NIH HHS · P30 CA014051 · United States
NIDA NIH HHS · R01 DA036858 · United States
Howard Hughes Medical Institute · United States
NIA NIH HHS · R01 AG041826 · United States
NHGRI NIH HHS · P50 HG006193 · United States
NHGRI NIH HHS · RM1 HG006193 · United States
Corrections
CommentIn
PMID: 28096529
CommentIn
PMID: 28245215
CommentIn
PMID: 28398325
External Links
PubMed source DOI: 10.1016/j.cell.2016.11.038 PMC Full Text View journal details
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