A Genome-wide CRISPR Screen Reveals a Role for the Non-canonical Nucleosome-Remodeling BAF Complex in Foxp3 Expression and Regulatory T Cell Function

Immunity. 2020 Jul 14;53(1):143-157.e8. doi: 10.1016/j.immuni.2020.06.011. Epub 2020 Jul 7.

Abstract

Regulatory T (Treg) cells play a pivotal role in suppressing auto-reactive T cells and maintaining immune homeostasis. Treg cell development and function are dependent on the transcription factor Foxp3. Here, we performed a genome-wide CRISPR loss-of-function screen to identify Foxp3 regulators in mouse primary Treg cells. Foxp3 regulators were enriched in genes encoding subunits of the SWI/SNF nucleosome-remodeling and SAGA chromatin-modifying complexes. Among the three SWI/SNF-related complexes, the Brd9-containing non-canonical (nc) BAF complex promoted Foxp3 expression, whereas the PBAF complex was repressive. Chemical-induced degradation of Brd9 led to reduced Foxp3 expression and reduced Treg cell function in vitro. Brd9 ablation compromised Treg cell function in inflammatory disease and tumor immunity in vivo. Furthermore, Brd9 promoted Foxp3 binding and expression of a subset of Foxp3 target genes. Our findings provide an unbiased analysis of the genetic networks regulating Foxp3 and reveal ncBAF as a target for therapeutic manipulation of Treg cell function.

Keywords: Brd9; CRISPR; Foxp3; GBAF; SWI/SNF; Treg; ncBAF; screen.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Autoimmunity / immunology
  • CRISPR-Cas Systems / genetics*
  • Cell Line, Tumor
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Disease Models, Animal
  • Forkhead Transcription Factors / genetics
  • Forkhead Transcription Factors / metabolism*
  • Gene Expression Regulation / genetics
  • HEK293 Cells
  • Humans
  • Mice, Inbred C57BL
  • Mice, Knockout
  • Neoplasms / immunology*
  • Nucleosomes / immunology
  • RNA, Guide / genetics
  • T-Lymphocytes, Regulatory / cytology
  • T-Lymphocytes, Regulatory / immunology
  • T-Lymphocytes, Regulatory / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*

Substances

  • Brd9 protein, mouse
  • Forkhead Transcription Factors
  • Foxp3 protein, mouse
  • Nucleosomes
  • RNA, Guide
  • Transcription Factors