Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

TY - JOUR

T1 - Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

AU - Jaitin, Diego Adhemar

AU - Weiner, Assaf

AU - Yofe, Ido

AU - Lara-Astiaso, David

AU - Keren-Shaul, Hadas

AU - David, Eyal

AU - Salame, Tomer Meir

AU - Tanay, Amos

AU - van Oudenaarden, Alexander

AU - Amit, Ido

N1 - Copyright © 2016 Elsevier Inc. All rights reserved.

PY - 2016/12/15

Y1 - 2016/12/15

N2 - 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.

AB - 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.

U2 - 10.1016/j.cell.2016.11.039

DO - 10.1016/j.cell.2016.11.039

M3 - Article

C2 - 27984734

SN - 0092-8674

VL - 167

SP - 1883-1896.e15

JO - Cell

JF - Cell

IS - 7

ER -