Open AccessFunctional CRISPR dissection of gene networks controlling human regulatory T cell identity
Author(s) -
Kathrin Schumann,
Siddharth S. Raju,
Michael Lauber,
Saskia Kolb,
Eric Shifrut,
Jessica T Cortez,
Nikolaos Skartsis,
Vinh Nguyen,
Jonathan M. Woo,
Theodore L. Roth,
Ruby Yu,
Michelle Nguyen,
Dimitre R. Simeonov,
David N. Nguyen,
Sasha Targ,
Rachel E. Gate,
Qizhi Tang,
Jeffrey A. Bluestone,
Matthew H. Spitzer,
Chun Jimmie Ye,
Alexander Marson
Publication year - 2020
Publication title -
nature immunology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.074
H-Index - 388
eISSN - 1529-2916
pISSN - 1529-2908
DOI - 10.1038/s41590-020-0784-4
Subject(s) - biology , transcription factor , gene regulatory network , foxp3 , gene , irf4 , regulation of gene expression , crispr , microbiology and biotechnology , genetics , computational biology , immune system , gene expression
Human regulatory T (T reg ) cells are essential for immune homeostasis. The transcription factor FOXP3 maintains T reg cell identity, yet the complete set of key transcription factors that control T reg cell gene expression remains unknown. Here, we used pooled and arrayed Cas9 ribonucleoprotein screens to identify transcription factors that regulate critical proteins in primary human T reg cells under basal and proinflammatory conditions. We then generated 54,424 single-cell transcriptomes from T reg cells subjected to genetic perturbations and cytokine stimulation, which revealed distinct gene networks individually regulated by FOXP3 and PRDM1, in addition to a network coregulated by FOXO1 and IRF4. We also discovered that HIVEP2, to our knowledge not previously implicated in T reg cell function, coregulates another gene network with SATB1 and is important for T reg cell-mediated immunosuppression. By integrating CRISPR screens and single-cell RNA-sequencing profiling, we have uncovered transcriptional regulators and downstream gene networks in human T reg cells that could be targeted for immunotherapies.