Journal article
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq
Cell, Vol.167(7), pp.1883-+
Dec/2016
Abstract
In multicellular organisms, dedicated regulatory circuits control cell type diversity and responses. The crosstalk and redundancies within these circuits and substantial cellular heterogeneity pose a major research challenge. Here, we present CRISPseq, an integrated method for massively parallel single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-pooled screens. We show that profiling the genomic perturbation and transcriptome in the same cell enables us to simultaneously elucidate the function of multiple factors and their interactions. We applied CRISP-seq to probe regulatory circuits of innate immunity. By sampling tens of thousands of perturbed cells in vitro and in mice, we identified interactions and redundancies between developmental and signaling-dependent factors. These include opposing effects of Cebpb and Irf8 in regulating the monocyte/macrophage versus dendritic cell lineages and differential functions for Rela and Stat1/2 in monocyte versus dendritic cell responses to pathogens. This study establishes CRISP-seq as a broadly applicable, comprehensive, and unbiased approach for elucidating mammalian regulatory circuits.
Details
- Title
- Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq
- Creators
- Diego Adhemar Jaitin (null) - 972WIS_INST___120Assaf Weiner (null) - 972WIS_INST___120Ido Yofe (null) - 972WIS_INST___120David Lara Astiaso (null) - 972WIS_INST___120Hadas Keren-Shaul (null) - 972WIS_INST___120Eyal David (null) - The Weizmann Institute of ScienceTomer Meir Salame (null) - 972WIS_INST___113Amos Tanay (null) - 972WIS_INST___83Alexander van Oudenaarden (null) - Royal Netherlands Academy of Arts and SciencesIdo Amit (null) - 972WIS_INST___120
- Resource Type
- Journal article
- Publication Details
- Cell, Vol.167(7), pp.1883-+; Dec/2016
- Number of pages
- 29
- Language
- English
- DOI
- https://doi.org/10.1016/j.cell.2016.11.039
- Grant note
- We thank Dana Peer for discussions on CRISP-seq analysis and Feng Zhang and Ophir Shalem for critical advice and reagents. We also thank Genia Brodsky for help with the artwork. A.v.O. is supported by European Research Council Advanced GrantERC-AdG 294325-GeneNoiseControl. I.A. is supported by the European Research Council Consolidator Grant (ERC-COG) 724471- HemTree2.0; the Israel Science Foundation; the Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine; the Helen and Martin Kimmel award for innovative investigation; a Minerva Stiftung research grant; the Israeli Ministry of Science, Technology, and Space; the David and Fela Shapell Family Foundation; and the Abramson Family Center for Young Scientists. I.A. is the incumbent of the Alan and Laraine Fischer Career Development Chair. A patent application has been filed related to this work, and the authors have made the CRISP-seq vectors widely available to the academic community through Addgene._ALMAME_DELIMITER_
- Record Identifier
- 993267274303596
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