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Zhu F, McMonigle RJ, Schroeder AR, Xia X, Figge D, Greer BD, González-Avalos E, Sialer DO, Wang YH, Chandler KM, Getzler AJ, Brown ER, Xiao C, Kutsch O, Harada Y, Pipkin ME, Hu H. Spatiotemporal resolution of germinal center Tfh cell differentiation and divergence from central memory CD4 + T cell fate. Nat Commun 2023; 14:3611. [PMID: 37330549 PMCID: PMC10276816 DOI: 10.1038/s41467-023-39299-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/27/2023] [Indexed: 06/19/2023] Open
Abstract
Follicular helper T (Tfh) cells are essential for germinal center (GC) B cell responses. However, it is not clear which PD-1+CXCR5+Bcl6+CD4+ T cells will differentiate into PD-1hiCXCR5hiBcl6hi GC-Tfh cells and how GC-Tfh cell differentiation is regulated. Here, we report that the sustained Tigit expression in PD-1+CXCR5+CD4+ T cells marks the precursor Tfh (pre-Tfh) to GC-Tfh transition, whereas Tigit-PD-1+CXCR5+CD4+ T cells upregulate IL-7Rα to become CXCR5+CD4+ T memory cells with or without CCR7. We demonstrate that pre-Tfh cells undergo substantial further differentiation at the transcriptome and chromatin accessibility levels to become GC-Tfh cells. The transcription factor c-Maf appears critical in governing the pre-Tfh to GC-Tfh transition, and we identify Plekho1 as a stage-specific downstream factor regulating the GC-Tfh competitive fitness. In summary, our work identifies an important marker and regulatory mechanism of PD-1+CXCR5+CD4+ T cells during their developmental choice between memory T cell fate and GC-Tfh cell differentiation.
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Affiliation(s)
- Fangming Zhu
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Ryan J McMonigle
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Andrew R Schroeder
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Xianyou Xia
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - David Figge
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Braxton D Greer
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Diego O Sialer
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yin-Hu Wang
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Kelly M Chandler
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Adam J Getzler
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Emily R Brown
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Changchun Xiao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Olaf Kutsch
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yohsuke Harada
- Faculty of Pharmaceutical Sciences, Tokyo, University of Science, Chiba, 278-8510, Japan
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Hui Hu
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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2
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Zhu C, Dixon KO, Newcomer K, Gu G, Xiao S, Zaghouani S, Schramm MA, Wang C, Zhang H, Goto K, Christian E, Rangachari M, Rosenblatt-Rosen O, Okada H, Mak T, Singer M, Regev A, Kuchroo V. Tim-3 adaptor protein Bat3 is a molecular checkpoint of T cell terminal differentiation and exhaustion. SCIENCE ADVANCES 2021; 7:eabd2710. [PMID: 33931442 PMCID: PMC8087420 DOI: 10.1126/sciadv.abd2710] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/10/2021] [Indexed: 05/03/2023]
Abstract
T cell exhaustion has been associated with poor prognosis in persistent viral infection and cancer. Conversely, in the context of autoimmunity, T cell exhaustion has been favorably correlated with long-term clinical outcome. Understanding the development of exhaustion in autoimmune settings may provide underlying principles that can be exploited to quell autoreactive T cells. Here, we demonstrate that the adaptor molecule Bat3 acts as a molecular checkpoint of T cell exhaustion, with deficiency of Bat3 promoting a profound exhaustion phenotype, suppressing autoreactive T cell-mediated neuroinflammation. Mechanistically, Bat3 acts as a critical mTORC2 inhibitor to suppress Akt function. As a result, Bat3 deficiency leads to increased Akt activity and FoxO1 phosphorylation, indirectly promoting Prdm1 expression. Transcriptional analysis of Bat3 -/- T cells revealed up-regulation of dysfunction-associated genes, concomitant with down-regulation of genes associated with T cell effector function, suggesting that absence of Bat3 can trigger T cell dysfunction even under highly proinflammatory autoimmune conditions.
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Affiliation(s)
- Chen Zhu
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Karen O Dixon
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathleen Newcomer
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Data Sciences, DFCI, Boston, MA 02215, USA
| | - Guangxiang Gu
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sheng Xiao
- Celsius Therapeutics, Cambridge, MA 02139, USA
| | - Sarah Zaghouani
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Markus A Schramm
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Chao Wang
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Huiyuan Zhang
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kouichiro Goto
- The Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University of Health Network, Toronto, Ontario M5G 2M9, Canada
| | | | - Manu Rangachari
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, QC, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC, Canada
| | | | - Hitoshi Okada
- Department of Biochemistry, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Tak Mak
- The Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University of Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Meromit Singer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Data Sciences, DFCI, Boston, MA 02215, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Koch Institute and Ludwig Center, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vijay Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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3
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Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R, Teichmann SA. Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell 2019; 176:882-896.e18. [PMID: 30639098 PMCID: PMC6370901 DOI: 10.1016/j.cell.2018.11.044] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.
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Affiliation(s)
- Johan Henriksson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo Miragaia
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK.
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4
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Arojo OA, Ouyang X, Liu D, Meng T, Kaech SM, Pereira JP, Su B. Active mTORC2 Signaling in Naive T Cells Suppresses Bone Marrow Homing by Inhibiting CXCR4 Expression. THE JOURNAL OF IMMUNOLOGY 2018; 201:908-915. [DOI: 10.4049/jimmunol.1800529] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/25/2018] [Indexed: 01/03/2023]
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