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Yu Z, Sasidharan-Nair V, Buchta T, Bonifacius A, Khan F, Pietzsch B, Ahmadi H, Beckstette M, Niemz J, Hilgendorf P, Mausberg P, Keller A, Falk C, Busch DH, Schober K, Cicin-Sain L, Müller F, Brinkmann MM, Eiz-Vesper B, Floess S, Huehn J. DNA methylation profiling identifies TBKBP1 as potent amplifier of cytotoxic activity in CMV-specific human CD8+ T cells. PLoS Pathog 2024; 20:e1012581. [PMID: 39325839 DOI: 10.1371/journal.ppat.1012581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Epigenetic mechanisms stabilize gene expression patterns during CD8+ T cell differentiation. Although adoptive transfer of virus-specific T cells is clinically applied to reduce the risk of virus infection or reactivation in immunocompromised individuals, the DNA methylation pattern of virus-specific CD8+ T cells is largely unknown. Hence, we here performed whole-genome bisulfite sequencing of cytomegalovirus-specific human CD8+ T cells and found that they display a unique DNA methylation pattern consisting of 79 differentially methylated regions (DMRs) when compared to memory CD8+ T cells. Among the top demethylated DMRs in cytomegalovirus-specific CD8+ T cells was TBKBP1, coding for TBK-binding protein 1 that can interact with TANK-binding kinase 1 (TBK1) and mediate pro-inflammatory responses in innate immune cells downstream of intracellular virus sensing. Since TBKBP1 has not yet been reported in T cells, we aimed to unravel its role in virus-specific CD8+ T cells. TBKBP1 demethylation in terminal effector CD8+ T cells correlated with higher TBKBP1 expression at both mRNA and protein level, independent of alternative splicing of TBKBP1 transcripts. Notably, the distinct DNA methylation patterns in CD8+ T cell subsets was stable upon long-term in vitro culture. TBKBP1 overexpression resulted in enhanced TBK1 phosphorylation upon stimulation of CD8+ T cells and significantly improved their virus neutralization capacity. Collectively, our data demonstrate that TBKBP1 modulates virus-specific CD8+ T cell responses and could be exploited as therapeutic target to improve adoptive T cell therapies.
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Affiliation(s)
- Zheng Yu
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Varun Sasidharan-Nair
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thalea Buchta
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Research Group Virology and Innate Immunity, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Thematical Translation Unit-Immunocompromised Host (TTU-IICH), partner site Hannover-Braunschweig, Germany
| | - Fawad Khan
- Department Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CIIM), a joint venture of HZI and Hannover Medical School, Hannover, Germany
| | - Beate Pietzsch
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hosein Ahmadi
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Beckstette
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jana Niemz
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Philipp Hilgendorf
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Philip Mausberg
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University, Saarbrücken, Germany
| | - Christine Falk
- German Center for Infection Research (DZIF), Thematical Translation Unit-Immunocompromised Host (TTU-IICH), partner site Hannover-Braunschweig, Germany
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University Munich (TUM), Munich, Germany
- German Center for Infection Research (DZIF), Thematical Translation Unit-Immunocompromised Host (TTU-IICH), partner site Munich, Germany
| | - Kilian Schober
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- FAU Profile Center Immunomedicine, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Luka Cicin-Sain
- German Center for Infection Research (DZIF), Thematical Translation Unit-Immunocompromised Host (TTU-IICH), partner site Hannover-Braunschweig, Germany
- Department Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Centre for Individualized Infection Medicine (CIIM), a joint venture of HZI and Hannover Medical School, Hannover, Germany
| | - Fabian Müller
- Integrative Cellular Biology and Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Melanie M Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Research Group Virology and Innate Immunity, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Thematical Translation Unit-Immunocompromised Host (TTU-IICH), partner site Hannover-Braunschweig, Germany
| | - Stefan Floess
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jochen Huehn
- Department Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence Resolving Infection Susceptibility (RESIST; EXC 2155), Hannover Medical School, Hannover, Germany
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Melo GA, Xu T, Calôba C, Schutte A, Passos TO, Neto MAN, Brum G, Vieira BM, Higa L, Monteiro FLL, Berbet L, Gonçalves AN, Tanuri A, Viola JP, Werneck MBF, Nakaya HI, Pipkin ME, Martinez GJ, Pereira RM. Cutting Edge: Polycomb Repressive Complex 1 Subunit Cbx4 Positively Regulates Effector Responses in CD8 T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:721-726. [PMID: 37486206 PMCID: PMC10528949 DOI: 10.4049/jimmunol.2200757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
CTL differentiation is controlled by the crosstalk of various transcription factors and epigenetic modulators. Uncovering this process is fundamental to improving immunotherapy and designing novel therapeutic approaches. In this study, we show that polycomb repressive complex 1 subunit chromobox (Cbx)4 favors effector CTL differentiation in a murine model. Cbx4 deficiency in CTLs induced a transcriptional signature of memory cells and increased the memory CTL population during acute viral infection. It has previously been shown that besides binding to H3K27me3 through its chromodomain, Cbx4 functions as a small ubiquitin-like modifier (SUMO) E3 ligase in a SUMO-interacting motifs (SIM)-dependent way. Overexpression of Cbx4 mutants in distinct domains showed that this protein regulates CTL differentiation primarily in an SIM-dependent way and partially through its chromodomain. Our data suggest a novel role of a polycomb group protein Cbx4 controlling CTL differentiation and indicated SUMOylation as a key molecular mechanism connected to chromatin modification in this process.
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Affiliation(s)
- Guilherme A. Melo
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Tianhao Xu
- Center for Cancer Cell Biology, Immunology, and Infection; Discipline of Microbiology and Immunology. Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Carolina Calôba
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Alexander Schutte
- Center for Cancer Cell Biology, Immunology, and Infection; Discipline of Microbiology and Immunology. Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Thaís O. Passos
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Moisés A. N. Neto
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Gabrielle Brum
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Bárbara M. Vieira
- Programa de Imunologia e Biologia Tumoral, Instituto Nacional do Câncer, 20231-050, Rio de Janeiro, RJ, Brazil
| | - Luiza Higa
- Departamento de Genética. Instituto de Biologia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Fábio L. L. Monteiro
- Departamento de Genética. Instituto de Biologia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Luiz Berbet
- Coordenação de Atividade com Modelos Biológicos Experimentais (CAMBE), Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - André N.A. Gonçalves
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Amilcar Tanuri
- Departamento de Genética. Instituto de Biologia, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - João P.B. Viola
- Programa de Imunologia e Biologia Tumoral, Instituto Nacional do Câncer, 20231-050, Rio de Janeiro, RJ, Brazil
| | - Miriam B. F. Werneck
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Helder I. Nakaya
- Hospital Israelita Albert Einstein, 05652-900, São Paulo, SP, Brazil
| | - Matthew E. Pipkin
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | - Gustavo J. Martinez
- Center for Cancer Cell Biology, Immunology, and Infection; Discipline of Microbiology and Immunology. Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Renata M. Pereira
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
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3
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Rose JR, Akdogan-Ozdilek B, Rahmberg AR, Powell MD, Hicks SL, Scharer CD, Boss JM. Distinct transcriptomic and epigenomic modalities underpin human memory T cell subsets and their activation potential. Commun Biol 2023; 6:363. [PMID: 37012418 PMCID: PMC10070634 DOI: 10.1038/s42003-023-04747-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Human memory T cells (MTC) are poised to rapidly respond to antigen re-exposure. Here, we derived the transcriptional and epigenetic programs of resting and ex vivo activated, circulating CD4+ and CD8+ MTC subsets. A progressive gradient of gene expression from naïve to TCM to TEM is observed, which is accompanied by corresponding changes in chromatin accessibility. Transcriptional changes suggest adaptations of metabolism that are reflected in altered metabolic capacity. Other differences involve regulatory modalities comprised of discrete accessible chromatin patterns, transcription factor binding motif enrichment, and evidence of epigenetic priming. Basic-helix-loop-helix factor motifs for AHR and HIF1A distinguish subsets and predict transcription networks to sense environmental changes. Following stimulation, primed accessible chromatin correlate with an augmentation of MTC gene expression as well as effector transcription factor gene expression. These results identify coordinated epigenetic remodeling, metabolic, and transcriptional changes that enable MTC subsets to ultimately respond to antigen re-encounters more efficiently.
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Affiliation(s)
- James R Rose
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bagdeser Akdogan-Ozdilek
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Michael D Powell
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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4
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Cassioli C, Baldari CT. The Expanding Arsenal of Cytotoxic T Cells. Front Immunol 2022; 13:883010. [PMID: 35514977 PMCID: PMC9065447 DOI: 10.3389/fimmu.2022.883010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Cytotoxic T cells (CTLs) are the main cellular mediators of the adaptive immune defenses against intracellular pathogens and malignant cells. Upon recognition of specific antigen on their cellular target, CTLs assemble an immunological synapse where they mobilise their killing machinery that is released into the synaptic cleft to orchestrate the demise of their cell target. The arsenal of CTLs is stored in lysosome-like organelles that undergo exocytosis in response to signals triggered by the T cell antigen receptor following antigen recognition. These organelles include lytic granules carrying a cargo of cytotoxic proteins packed on a proteoglycan scaffold, multivesicular bodies carrying the death receptor ligand FasL, and the recently discovered supramolecular attack particles that carry a core of cytotoxic proteins encased in a non-membranous glycoprotein shell. Here we will briefly review the main features of these killing entities and discuss their interrelationship and interplay in CTL-mediated killing.
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Affiliation(s)
- Chiara Cassioli
- Department of Life Sciences, University of Siena, Siena, Italy
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5
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Melo GA, Calôba C, Brum G, Passos TO, Martinez GJ, Pereira RM. Epigenetic regulation of T cells by Polycomb group proteins. J Leukoc Biol 2022; 111:1253-1267. [DOI: 10.1002/jlb.2ri0122-039r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Guilherme A. Melo
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Carolina Calôba
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Gabrielle Brum
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Thaís O. Passos
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Gustavo J. Martinez
- Center for Cancer Cell Biology, Immunology and Infection, Discipline of Microbiology and Immunology Rosalind Franklin University of Medicine and Science Chicago Illinois USA
| | - Renata M. Pereira
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
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