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

Overview

Journal Immunity

Publisher Cell Press

Specialty Allergy & Immunology

Date 2020 Jul 9

PMID 32640256

Citations 59

Authors

Chin-San Loo

Jovylyn Gatchalian

Yuqiong Liang

Mathias Leblanc

Mingjun Xie

Josephine Ho

Bhargav Venkatraghavan

Diana C Hargreaves

Ye Zheng

Affiliations

Soon will be listed here.

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.

Citing Articles

PPARδ restrains the suppression function of intra-tumoral Tregs by limiting CIITA-MHC II expression.

Yang Q, Liang Y, Inoue-Hatanaka T, Koh Z, Ilkenhans N, Suman E bioRxiv. 2025; .

PMID: 39763816 PMC: 11702609. DOI: 10.1101/2024.12.16.628819.

Cullin-5 deficiency promotes chimeric antigen receptor T cell effector functions potentially via the modulation of JAK/STAT signaling pathway.

Adachi Y, Terakura S, Osaki M, Okuno Y, Sato Y, Sagou K Nat Commun. 2024; 15(1):10376.

PMID: 39658572 PMC: 11631977. DOI: 10.1038/s41467-024-54794-x.

High-throughput screening for optimizing adoptive T cell therapies.

Zhang Y, Xu Q, Gao Z, Zhang H, Xie X, Li M Exp Hematol Oncol. 2024; 13(1):113.

PMID: 39538305 PMC: 11562648. DOI: 10.1186/s40164-024-00580-w.

SWItch/Sucrose Nonfermentable complex-deficient pulmonary neoplasms: clinicopathologic characteristics and outcomes to radiotherapy and immunotherapy.

Gu Y, Lai S, Yang J, Zhang J, Fan X, Zheng Q Transl Lung Cancer Res. 2024; 13(10):2660-2672.

PMID: 39507018 PMC: 11535837. DOI: 10.21037/tlcr-24-339.

Glut3 promotes cellular O-GlcNAcylation as a distinctive tumor-supportive feature in Treg cells.

Sharma A, Sharma G, Gao Z, Li K, Li M, Wu M Cell Mol Immunol. 2024; 21(12):1474-1490.

PMID: 39468304 PMC: 11606946. DOI: 10.1038/s41423-024-01229-8.

References

Shalem O, Sanjana N, Hartenian E, Shi X, Scott D, Mikkelson T . Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2013; 343(6166):84-87. PMC: 4089965. DOI: 10.1126/science.1247005. View

Polansky J, Kretschmer K, Freyer J, Floess S, Garbe A, Baron U . DNA methylation controls Foxp3 gene expression. Eur J Immunol. 2008; 38(6):1654-63. DOI: 10.1002/eji.200838105. View

Burchill M, Yang J, Vogtenhuber C, Blazar B, Farrar M . IL-2 receptor beta-dependent STAT5 activation is required for the development of Foxp3+ regulatory T cells. J Immunol. 2006; 178(1):280-90. DOI: 10.4049/jimmunol.178.1.280. View

Li X, Liang Y, Leblanc M, Benner C, Zheng Y . Function of a Foxp3 cis-element in protecting regulatory T cell identity. Cell. 2014; 158(4):734-748. PMC: 4151505. DOI: 10.1016/j.cell.2014.07.030. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

Josefowicz S, Lu L, Rudensky A . Regulatory T cells: mechanisms of differentiation and function. Annu Rev Immunol. 2012; 30:531-64. PMC: 6066374. DOI: 10.1146/annurev.immunol.25.022106.141623. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Chaiyachati B, Jani A, Wan Y, Huang H, Flavell R, Chi T . BRG1-mediated immune tolerance: facilitation of Treg activation and partial independence of chromatin remodelling. EMBO J. 2013; 32(3):395-408. PMC: 3567501. DOI: 10.1038/emboj.2012.350. View

10.

Gatchalian J, Malik S, Ho J, Lee D, Kelso T, Shokhirev M . A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells. Nat Commun. 2018; 9(1):5139. PMC: 6277444. DOI: 10.1038/s41467-018-07528-9. View

11.

Rudra D, Egawa T, Chong M, Treuting P, Littman D, Rudensky A . Runx-CBFbeta complexes control expression of the transcription factor Foxp3 in regulatory T cells. Nat Immunol. 2009; 10(11):1170-7. PMC: 2764816. DOI: 10.1038/ni.1795. View

12.

Feng Y, Arvey A, Chinen T, van der Veeken J, Gasteiger G, Rudensky A . Control of the inheritance of regulatory T cell identity by a cis element in the Foxp3 locus. Cell. 2014; 158(4):749-763. PMC: 4151558. DOI: 10.1016/j.cell.2014.07.031. View

13.

Michel B, DAvino A, Cassel S, Mashtalir N, McKenzie Z, McBride M . A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat Cell Biol. 2018; 20(12):1410-1420. PMC: 6698386. DOI: 10.1038/s41556-018-0221-1. View

14.

Kim H, Leonard W . CREB/ATF-dependent T cell receptor-induced FoxP3 gene expression: a role for DNA methylation. J Exp Med. 2007; 204(7):1543-51. PMC: 2118651. DOI: 10.1084/jem.20070109. View

15.

Yang X, Nurieva R, Martinez G, Kang H, Chung Y, Pappu B . Molecular antagonism and plasticity of regulatory and inflammatory T cell programs. Immunity. 2008; 29(1):44-56. PMC: 2630532. DOI: 10.1016/j.immuni.2008.05.007. View

16.

Doench J, Fusi N, Sullender M, Hegde M, Vaimberg E, Donovan K . Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016; 34(2):184-191. PMC: 4744125. DOI: 10.1038/nbt.3437. View

17.

van Loosdregt J, Fleskens V, Fu J, Brenkman A, Bekker C, Pals C . Stabilization of the transcription factor Foxp3 by the deubiquitinase USP7 increases Treg-cell-suppressive capacity. Immunity. 2013; 39(2):259-71. PMC: 4133784. DOI: 10.1016/j.immuni.2013.05.018. View

18.

Tanaka A, Sakaguchi S . Regulatory T cells in cancer immunotherapy. Cell Res. 2016; 27(1):109-118. PMC: 5223231. DOI: 10.1038/cr.2016.151. View

19.

Delgoffe G, Woo S, Turnis M, Gravano D, Guy C, Overacre A . Stability and function of regulatory T cells is maintained by a neuropilin-1-semaphorin-4a axis. Nature. 2013; 501(7466):252-6. PMC: 3867145. DOI: 10.1038/nature12428. View

20.

Spahn P, Bath T, Weiss R, Kim J, Esko J, Lewis N . PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep. 2017; 7(1):15854. PMC: 5696473. DOI: 10.1038/s41598-017-16193-9. View