Deciphering regulation of FOXP3 expression in human conventional T cells.

Autor:	Umhoefer JM; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Arce MM; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Dajani R; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA., Belk JA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA., Mowery CT; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Nguyen V; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.; Department of Surgery, University of California, San Francisco, San Francisco, CA, USA.; UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA., Gowen BG; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA., Simeonov DR; Department of Medicine, University of California, San Francisco, CA, USA.; Biomedical Sciences graduate program, University of California, San Francisco, CA, USA., Curie GL; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA., Corn JE; Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Switzerland., Chang HY; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Marson A; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.; Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.; Institute for Human Genetics, University of California, San Francisco, CA, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Sep 02. Date of Electronic Publication: 2024 Sep 02.
DOI:	10.1101/2024.08.30.610436
Abstrakt:	FOXP3 is a lineage-defining transcription factor that controls differentiation and maintenance of suppressive function of regulatory T cells (Tregs). Foxp3 is exclusively expressed in Tregs in mice. However, in humans, FOXP3 is not only constitutively expressed in Tregs; it is also transiently expressed in stimulated CD4+CD25- conventional T cells (Tconvs) 1-3 . Mechanisms governing the expression of FOXP3 in human Tconvs are not understood. Here, we performed CRISPR interference (CRISPRi) screens using a 15K-member gRNA library tiling 39 kb downstream of the FOXP3 transcriptional start site (TSS) to 85 kb upstream of the TSS in Treg and Tconvs. The FOXP3 promoter and conserved non-coding sequences (CNS0, CNS1, CNS2 and CNS3), characterized as enhancer elements in murine Tregs, were required for maintenance of FOXP3 in human Tregs. In contrast, FOXP3 in human Tconvs depended on regulation at CNS0 and a novel Tconv-specific noncoding sequence (TcNS+) located upstream of CNS0. Arrayed validations of these sites identified an additional repressive cis-element overlapping with the PPP1R3F promoter (TcNS-). Pooled CRISPR knockouts revealed multiple transcription factors required for proper expression of FOXP3 in Tconvs, including GATA3, STAT5, IRF4, ETS1 and DNA methylation-associated regulators DNMT1 and MBD2. Analysis of ChIP-seq and ATAC-seq paired with knock-out (KO) of GATA3, STAT5, IRF4, and ETS1 revealed regulation of CNS0 and TcNS+ accessibility. Collectively, this work identified Treg-shared and Tconv-specific cis-elements and the trans-factors that interact with them, building a network of regulators controlling FOXP3 expression in human Tconvs. Competing Interests: Competing Interests Declaration A.M. is a cofounder of Site Tx, Arsenal Biosciences, Spotlight Therapeutics and Survey Genomics, serves on the boards of directors at Site Tx, Spotlight Therapeutics and Survey Genomics, is a member of the scientific advisory boards of Site Tx, Arsenal Biosciences, Cellanome, Spotlight Therapeutics, Survey Genomics, NewLimit, Amgen, and Tenaya, owns stock in Arsenal Biosciences, Site Tx, Cellanome, Spotlight Therapeutics, NewLimit, Survey Genomics, Tenaya and Lightcast and has received fees from Site Tx, Arsenal Biosciences, Cellanome, Spotlight Therapeutics, NewLimit, Gilead, Pfizer, 23andMe, PACT Pharma, Juno Therapeutics, Tenaya, Lightcast, Trizell, Vertex, Merck, Amgen, Genentech, GLG, ClearView Healthcare, AlphaSights, Rupert Case Management, Bernstein and ALDA. A.M. is an investor in and informal advisor to Offline Ventures and a client of EPIQ. The Marson laboratory has received research support from the Parker Institute for Cancer Immunotherapy, the Emerson Collective, Arc Institute, Juno Therapeutics, Epinomics, Sanofi, GlaxoSmithKline, Gilead and Anthem and reagents from Genscript and Illumina. C.T.M. is a Bio+Health Venture Fellow at Andreessen Horowitz. J.E.C. is a co-founder and SAB member of Serac Biosciences and an SAB member of Mission Therapeutics, Relation Therapeutics, Hornet Bio, and Kano Therapeutics. The lab of J.E.C. has funded collaborations with Allogene, Cimeio, and Serac. H.Y.C. is a cofounder of Accent Therapeutics, Boundless Bio, Cartography Biosciences, and Orbital Therapeutics, and is an advisor of 10x Genomics, Arsenal Bio, Chroma Medicine, Exai Bio, and Spring Discovery.
Databáze:	MEDLINE
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