title: Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.
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 CRISP-seq, 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.
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
authors.forename: Diego Adhemar
authors.initials: DA
authors.lastname: Jaitin
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel; Hubrecht Institute-KNAW, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands.
authors.forename: Assaf
authors.initials: A
authors.lastname: Weiner
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
authors.forename: Ido
authors.initials: I
authors.lastname: Yofe
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
authors.forename: David
authors.initials: D
authors.lastname: Lara-Astiaso
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
authors.forename: Hadas
authors.initials: H
authors.lastname: Keren-Shaul
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
authors.forename: Eyal
authors.initials: E
authors.lastname: David
authors.affiliation: Flow Cytometry Unit, Department of Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Tomer Meir
authors.initials: TM
authors.lastname: Salame
authors.affiliation: Department of Computer Science and Applied Mathematics, Department of Biological Regulation, Weizmann Institute, Rehovot 76100, Israel.
authors.forename: Amos
authors.initials: A
authors.lastname: Tanay
authors.affiliation: Hubrecht Institute-KNAW, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands.
authors.forename: Alexander
authors.initials: A
authors.lastname: van Oudenaarden
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot 76100, Israel. Electronic address: ido.amit@weizmann.ac.il.
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
mesh_terms: D000818:Animals; D022782:CCAAT-Enhancer-Binding Protein-beta / Q000378:metabolism; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D003713:Dendritic Cells / Q000378:metabolism; D007249:Inflammation / Q000378:metabolism; D008264:Macrophages / Q000378:metabolism; D008810:Mice, Inbred C57BL; D009000:Monocytes / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D022782:CCAAT-Enhancer-Binding Protein-beta
keywords: CRISPR/Cas9; RNA-seq; functional genomics; gene networks; genetic screen; immune response; innate immunity; single-cell RNA-seq; transcriptomics