1
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Liu Y, Lin Y, Liao S, Feng W, Liu J, Luo X, Wei Q, Tang H. Single-cell RNA sequencing reveals the immune microenvironment landscape of osteosarcoma before and after chemotherapy. Heliyon 2024; 10:e23601. [PMID: 38332885 PMCID: PMC10851305 DOI: 10.1016/j.heliyon.2023.e23601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 02/10/2024] Open
Abstract
Chemotherapy, a primary treatment for osteosarcoma (OS), has limited knowledge regarding its impact on tumor immune microenvironment (TIME). Here, tissues from 6 chemotherapy-naive OS patients underwent single-cell RNA sequencing (scRNA-seq) and were analyzed alongside public dataset (GSE152048) containing 7 post-chemotherapy OS tissues. CD45+ (PTPRC+) cells were used for cell clustering and annotation. Changes in immune cell composition pre- and post-chemotherapy were characterized. Totally, 28,636 high-quality CD45+ (PTPRC+) cells were extracted. Following chemotherapy, the proportions of regulatory T cells (Tregs) and activated CD8 T cells decreased, while CD8 effector T cells increased. GO analysis indicated that differentially expressed genes (DEGs) in T cells were associated with cell activation, adaptive immune response, and immune response to tumor cells. Furthermore, the proportions of plasma cells increased, while naive B cells decreased. B cell surface receptors expression was upregulated, and GO analysis revealed DEGs of B cells were mainly enriched in B cell-mediated immunity and B cell activation. Moreover, M2 polarization of macrophages was suppressed post-chemotherapy. Overall, this study elucidates chemotherapy remodels the OS TIME landscape, triggering immune heterogeneity and enhancing anti-tumor properties.
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Affiliation(s)
- Yun Liu
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yunhua Lin
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shijie Liao
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Feng
- Department of Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jianhong Liu
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoting Luo
- Department of Pharmacy, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qingjun Wei
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haijun Tang
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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2
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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3
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Fu Y, Wang J, Liu C, Liao K, Gao X, Tang R, Fan B, Hong Y, Xiao N, Xiao C, Liu WH. Glycogen synthase kinase 3 controls T-cell exhaustion by regulating NFAT activation. Cell Mol Immunol 2023; 20:1127-1139. [PMID: 37553428 PMCID: PMC10541428 DOI: 10.1038/s41423-023-01075-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Cellular immunity mediated by CD8+ T cells plays an indispensable role in bacterial and viral clearance and cancers. However, persistent antigen stimulation of CD8+ T cells leads to an exhausted or dysfunctional cellular state characterized by the loss of effector function and high expression of inhibitory receptors during chronic viral infection and in tumors. Numerous studies have shown that glycogen synthase kinase 3 (GSK3) controls the function and development of immune cells, but whether GSK3 affects CD8+ T cells is not clearly elucidated. Here, we demonstrate that mice with deletion of Gsk3α and Gsk3β in activated CD8+ T cells (DKO) exhibited decreased CTL differentiation and effector function during acute and chronic viral infection. In addition, DKO mice failed to control tumor growth due to the upregulated expression of inhibitory receptors and augmented T-cell exhaustion in tumor-infiltrating CD8+ T cells. Strikingly, anti-PD-1 immunotherapy substantially restored tumor rejection in DKO mice. Mechanistically, GSK3 regulates T-cell exhaustion by suppressing TCR-induced nuclear import of NFAT, thereby in turn dampening NFAT-mediated exhaustion-related gene expression, including TOX/TOX2 and PD-1. Thus, we uncovered the molecular mechanisms underlying GSK3 regulation of CTL differentiation and T-cell exhaustion in anti-tumor immune responses.
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Affiliation(s)
- Yubing Fu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Jinjia Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Chenfeng Liu
- Department of Cell Biology, School of Life Science, Anhui Medical University, Hefei, 230031, Anhui, China
| | - Kunyu Liao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xianjun Gao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ronghan Tang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Binbin Fan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yazhen Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Changchun Xiao
- Sanofi Institute for Biomedical Research, Suzhou, Jiangsu, 215123, China
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Science, Xiamen University, Xiamen, 361102, Fujian, China.
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4
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Wu T, Tan JHL, Sin W, Luah YH, Tan SY, Goh M, Birnbaum ME, Chen Q, Cheow LF. Cell Granularity Reflects Immune Cell Function and Enables Selection of Lymphocytes with Superior Attributes for Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302175. [PMID: 37544893 PMCID: PMC10558660 DOI: 10.1002/advs.202302175] [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: 04/04/2023] [Revised: 07/20/2023] [Indexed: 08/08/2023]
Abstract
In keeping with the rule of "form follows function", morphological aspects of a cell can reflect its role. Here, it is shown that the cellular granularity of a lymphocyte, represented by its intrinsic side scatter (SSC), is a potent indicator of its cell state and function. The granularity of a lymphocyte increases from naïve to terminal effector state. High-throughput cell-sorting yields a SSChigh population that can mediate immediate effector functions, and a highly prolific SSClow population that can give rise to the replenishment of the memory pool. CAR-T cells derived from the younger SSClow population possess desirable attributes for immunotherapy, manifested by increased naïve-like cells and stem cell memory (TSCM )-like cells together with a balanced CD4/CD8 ratio, as well as enhanced target-killing in vitro and in vivo. Altogether, lymphocyte segregation based on biophysical properties is an effective approach for label-free selection of cells that share collective functions and can have important applications for cell-based immunotherapies.
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Affiliation(s)
- Tongjin Wu
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
| | - Joel Heng Loong Tan
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Wei‐Xiang Sin
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
| | - Yen Hoon Luah
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
| | - Sue Yee Tan
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Myra Goh
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Michael E. Birnbaum
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB)Agency for ScienceTechnology and Research (A*STAR)Singapore138673Singapore
| | - Lih Feng Cheow
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Critical Analytics for Manufacturing of Personalized MedicineSingapore‐MIT Alliance for Research and TechnologySingapore138602Singapore
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5
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Russ BE, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, Barugahare A, See M, Nussing S, Morey AE, Udupa VA, Bennett T.J, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naïvety through regulation of global genome architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530139. [PMID: 36909629 PMCID: PMC10002700 DOI: 10.1101/2023.02.26.530139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The differentiation of naïve CD8+ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naïve, effector and memory virus-specific CD8+ T cells. We observed that the architecture of the naive CD8+ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naïve chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naïve CD8+ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naïve chromatin state.
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Affiliation(s)
- Brendan E. Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
- Department of Molecular Biology, University of California, San Diego, USA
| | - Jason K. C. Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, USA
| | - Paul F. Harrison
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Michael See
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | | | - Alison E. Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Vibha A. Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Taylah .J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics platform, Biomedical Discovery Institute, Monash University, Australia
| | - Ananda W. Goldrath
- Department of Biological Sciences, University of California, San Diego, USA
| | - Stephen J. Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University
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6
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Perdomo-Celis F, Passaes C, Monceaux V, Volant S, Boufassa F, de Truchis P, Marcou M, Bourdic K, Weiss L, Jung C, Bourgeois C, Goujard C, Meyer L, Müller-Trutwin M, Lambotte O, Sáez-Cirión A. Reprogramming dysfunctional CD8+ T cells to promote properties associated with natural HIV control. J Clin Invest 2022; 132:e157549. [PMID: 35380989 PMCID: PMC9151687 DOI: 10.1172/jci157549] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/29/2022] [Indexed: 01/21/2023] Open
Abstract
Virus-specific CD8+ T cells play a central role in HIV-1 natural controllers to maintain suppressed viremia in the absence of antiretroviral therapy. These cells display a memory program that confers them stemness properties, high survival, polyfunctionality, proliferative capacity, metabolic plasticity, and antiviral potential. The development and maintenance of such qualities by memory CD8+ T cells appear crucial to achieving natural HIV-1 control. Here, we show that targeting the signaling pathways Wnt/transcription factor T cell factor 1 (Wnt/TCF-1) and mTORC through GSK3 inhibition to reprogram HIV-specific CD8+ T cells from noncontrollers promoted functional capacities associated with natural control of infection. Features of such reprogrammed cells included enrichment in TCF-1+ less-differentiated subsets, a superior response to antigen, enhanced survival, polyfunctionality, metabolic plasticity, less mTORC1 dependency, an improved response to γ-chain cytokines, and a stronger HIV-suppressive capacity. Thus, such CD8+ T cell reprogramming, combined with other available immunomodulators, might represent a promising strategy for adoptive cell therapy in the search for an HIV-1 cure.
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Affiliation(s)
- Federico Perdomo-Celis
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Valérie Monceaux
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Université Paris Cité, Hub Bioinformatique et Biostatistique, Paris, France
| | - Faroudy Boufassa
- Université Paris Saclay, INSERM Centre de Recherche en Épidémiologie et Santé des Populations (CESP) U1018, Assistance Publique–Hôpitaux de Paris (AP-HP), Department of Public Health, Bicêtre Hospital, Paris, France
| | - Pierre de Truchis
- Université Paris-Saclay, AP-HP Hôpital Raymond Poincaré, Garches, France
| | - Morgane Marcou
- Université Paris-Saclay, AP-HP Hôpital Raymond Poincaré, Garches, France
| | - Katia Bourdic
- Université Paris-Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Le Kremlin Bicêtre, France
| | - Laurence Weiss
- Université de Paris Cité, AP-HP, Paris Centre, Hôtel Dieu, Paris, France
| | - Corinne Jung
- Université de Paris Cité, AP-HP, Paris Centre, Hôtel Dieu, Paris, France
| | - Christine Bourgeois
- Université Paris-Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Le Kremlin Bicêtre, France
| | - Cécile Goujard
- Université Paris-Saclay, AP-HP, Hôpital Bicêtre, Départements Médico-Universitaires (DMU) 7, INSERM U1018, CESP, Le Kremlin Bicêtre, France
| | - Laurence Meyer
- Université Paris Saclay, INSERM Centre de Recherche en Épidémiologie et Santé des Populations (CESP) U1018, Assistance Publique–Hôpitaux de Paris (AP-HP), Department of Public Health, Bicêtre Hospital, Paris, France
| | - Michaela Müller-Trutwin
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Olivier Lambotte
- Université Paris-Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Le Kremlin Bicêtre, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
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7
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van Aalderen MC, van Lier RAW, Hombrink P. How to Reliably Define Human CD8 + T-Cell Subsets: Markers Playing Tricks. Cold Spring Harb Perspect Biol 2021; 13:a037747. [PMID: 33782028 PMCID: PMC8559543 DOI: 10.1101/cshperspect.a037747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In recent years, our understanding about the functional complexity of CD8+ T-cell populations has increased tremendously. The immunology field is now facing challenges to translate these insights into phenotypic definitions that correlate reliably with distinct functional traits. This is key to adequately monitor and understand compound immune responses including vaccination and immunotherapy regimens. Here we will summarize our understanding of the current state in the human CD8+ T-cell subset characterization field. We will address how reliably the currently used cell surface markers are connected to differentiation status and function of particular subsets. By restricting ourselves to CD8+ αβ T cells, we will focus mostly on major histocompatibility complex (MHC) class I-restricted virus- and tumor-specific T cells. This comes with a major advantage as fluorescently labeled peptide-loaded MHC class I multimers have been widely used to identify and characterize these cells.
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Affiliation(s)
- Michiel C van Aalderen
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centre (AUMC), Amsterdam 1105 AZ, The Netherlands
| | - Rene A W van Lier
- Adaptive Immunity Laboratory and Landsteiner Laboratory of the AUMC at Sanquin Blood Supply Foundation, Amsterdam 1066 CX, The Netherlands
| | - Pleun Hombrink
- Adaptive Immunity Laboratory and Landsteiner Laboratory of the AUMC at Sanquin Blood Supply Foundation, Amsterdam 1066 CX, The Netherlands
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8
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Cohen CA, Li APY, Hachim A, Hui DSC, Kwan MYW, Tsang OTY, Chiu SS, Chan WH, Yau YS, Kavian N, Ma FNL, Lau EHY, Cheng SMS, Poon LLM, Peiris M, Valkenburg SA. SARS-CoV-2 specific T cell responses are lower in children and increase with age and time after infection. Nat Commun 2021; 12:4678. [PMID: 34326343 PMCID: PMC8322064 DOI: 10.1038/s41467-021-24938-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 infection of children leads to a mild illness and the immunological differences with adults are unclear. Here, we report SARS-CoV-2 specific T cell responses in infected adults and children and find that the acute and memory CD4+ T cell responses to structural SARS-CoV-2 proteins increase with age, whereas CD8+ T cell responses increase with time post-infection. Infected children have lower CD4+ and CD8+ T cell responses to SARS-CoV-2 structural and ORF1ab proteins when compared with infected adults, comparable T cell polyfunctionality and reduced CD4+ T cell effector memory. Compared with adults, children have lower levels of antibodies to β-coronaviruses, indicating differing baseline immunity. Total T follicular helper responses are increased, whilst monocyte numbers are reduced, indicating rapid adaptive co-ordination of the T and B cell responses and differing levels of inflammation. Therefore, reduced prior β-coronavirus immunity and reduced T cell activation in children might drive milder COVID-19 pathogenesis.
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Affiliation(s)
- Carolyn A Cohen
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Athena P Y Li
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - David S C Hui
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Mike Y W Kwan
- Department of Paediatric and Adolescent Medicine, Hong Kong Hospital Authority Infectious Disease Center, Princess Margaret Hospital, Hong Kong, SAR, China
| | - Owen T Y Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Susan S Chiu
- Department of Paediatric and Adolescent Medicine, The University of Hong Kong and Queen Mary Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Wai Hung Chan
- Department of Paediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Yat Sun Yau
- Department of Paediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Fionn N L Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Leo L M Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
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9
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Zhao C, Zhang Y, Zheng H. The Effects of Interferons on Allogeneic T Cell Response in GVHD: The Multifaced Biology and Epigenetic Regulations. Front Immunol 2021; 12:717540. [PMID: 34305954 PMCID: PMC8297501 DOI: 10.3389/fimmu.2021.717540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potentially curative therapy for hematological malignancies. This beneficial effect is derived mainly from graft-versus-leukemia (GVL) effects mediated by alloreactive T cells. However, these alloreactive T cells can also induce graft-versus-host disease (GVHD), a life-threatening complication after allo-HSCT. Significant progress has been made in the dissociation of GVL effects from GVHD by modulating alloreactive T cell immunity. However, many factors may influence alloreactive T cell responses in the host undergoing allo-HSCT, including the interaction of alloreactive T cells with both donor and recipient hematopoietic cells and host non-hematopoietic tissues, cytokines, chemokines and inflammatory mediators. Interferons (IFNs), including type I IFNs and IFN-γ, primarily produced by monocytes, dendritic cells and T cells, play essential roles in regulating alloreactive T cell differentiation and function. Many studies have shown pleiotropic effects of IFNs on allogeneic T cell responses during GVH reaction. Epigenetic mechanisms, such as DNA methylation and histone modifications, are important to regulate IFNs’ production and function during GVHD. In this review, we discuss recent findings from preclinical models and clinical studies that characterize T cell responses regulated by IFNs and epigenetic mechanisms, and further discuss pharmacological approaches that modulate epigenetic effects in the setting of allo-HSCT.
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Affiliation(s)
- Chenchen Zhao
- Penn State Cancer Institute, Penn State University College of Medicine, Hershey, PA, United States
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, United States
| | - Hong Zheng
- Penn State Cancer Institute, Penn State University College of Medicine, Hershey, PA, United States
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10
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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11
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Turner SJ, Bennett TJ, Gruta NLL. CD8 + T-Cell Memory: The Why, the When, and the How. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a038661. [PMID: 33648987 PMCID: PMC8091951 DOI: 10.1101/cshperspect.a038661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The generation of effective adaptive T-cell memory is a cardinal feature of the adaptive immune system. The establishment of protective T-cell immunity requires the differentiation of CD8+ T cells from a naive state to one where pathogen-specific memory CD8+ T cells are capable of responding to a secondary infection more rapidly and robustly without the need for further differentiation. The study of factors that determine the fate of activated CD8+ T cells into either effector or memory subsets has a long history. The advent of new technologies is now providing new insights into how epigenetic regulation not only impacts acquisition and maintenance of effector function, but also the maintenance of the quiescent yet primed memory state. There is growing appreciation that rather than distinct subsets, memory T-cell populations may reflect different points on a spectrum between the starting naive T-cell population and a terminally differentiated effector CD8+ T-cell population. Interestingly, there is growing evidence that the molecular mechanisms that underpin the rapid effector function of memory T cells are also observed in innate immune cells such as macrophages and natural killer (NK) cells. This raises an interesting hypothesis that the memory/effector T-cell state represents a default innate-like response to antigen recognition, and that it is the naive state that is the defining feature of adaptive immunity. These issues are discussed.
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Affiliation(s)
- Stephen J Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Taylah J Bennett
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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12
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Li J, Hardy K, Olshansky M, Barugahare A, Gearing LJ, Prier JE, Sng XYX, Nguyen MLT, Piovesan D, Russ BE, La Gruta NL, Hertzog PJ, Rao S, Turner SJ. KDM6B-dependent chromatin remodeling underpins effective virus-specific CD8 + T cell differentiation. Cell Rep 2021; 34:108839. [PMID: 33730567 DOI: 10.1016/j.celrep.2021.108839] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 11/24/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Naive CD8+ T cell activation results in an autonomous program of cellular proliferation and differentiation. However, the mechanisms that underpin this process are unclear. Here, we profile genome-wide changes in chromatin accessibility, gene transcription, and the deposition of a key chromatin modification (H3K27me3) early after naive CD8+ T cell activation. Rapid upregulation of the histone demethylase KDM6B prior to the first cell division is required for initiating H3K27me3 removal at genes essential for subsequent T cell differentiation and proliferation. Inhibition of KDM6B-dependent H3K27me3 demethylation limits the magnitude of an effective primary virus-specific CD8+ T cell response and the formation of memory CD8+ T cell populations. Accordingly, we define the early spatiotemporal events underpinning early lineage-specific chromatin reprogramming that are necessary for autonomous CD8+ T cell proliferation and differentiation.
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Affiliation(s)
- Jasmine Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kristine Hardy
- Epigenetics and Transcription Laboratory Melanie Swan Memorial Translational Centre, Sci-Tech, University of Canberra, Bruce, ACT 2617, Australia
| | - Moshe Olshansky
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Adele Barugahare
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Ly Thai Nguyen
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Dana Piovesan
- Department of Microbiology and Immunology, the Doherty Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Brendan E Russ
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Sudha Rao
- QIMR Berghofer Gene Regulation and Translational Medicine Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Hudson Institute for Medical Research, Clayton, VIC 3168, Australia.
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13
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Frias AB, Boi SK, Lan X, Youngblood B. Epigenetic regulation of T cell adaptive immunity. Immunol Rev 2021; 300:9-21. [PMID: 33644866 DOI: 10.1111/imr.12943] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022]
Abstract
The conceptualization of adaptive immunity, founded on the observation of immunological memory, has served as the basis for modern vaccination and immunotherapy approaches. This fundamental concept has allowed immunologists to explore mechanisms that enable humoral and cellular lymphocytes to tailor immune response functions to a wide array of environmental insults and remain poised for future pathogenic encounters. Until recently, for T cells it has remained unclear how memory differentiation acquires and sustains a gene expression program that grants a cell with a capacity for a heightened recall response. Recent investigations into this critical question have identified epigenetic programs as a causal molecular mechanism governing T cell subset specification and immunological memory. Here, we outline the studies that have illustrated this concept and posit on how insights into T cell adaptive immunity can be applied to improve upon existing immunotherapies.
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Affiliation(s)
- Adolfo B Frias
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon K Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Lan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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14
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Cohen CA, Li APY, Hachim A, Hui DSC, Kwan MYW, Tsang OTY, Chiu SS, Chan WH, Yau YS, Kavian N, Ma FNL, Lau EHY, Cheng SMS, Poon LLM, Peiris JSM, Valkenburg SA. SARS-CoV-2 specific T cell responses are lower in children and increase with age and time after infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.02.21250988. [PMID: 33564773 PMCID: PMC7872365 DOI: 10.1101/2021.02.02.21250988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 infection of children leads to a mild illness and the immunological differences with adults remains unclear. We quantified the SARS-CoV-2 specific T cell responses in adults and children (<13 years of age) with RT-PCR confirmed asymptomatic and symptomatic infection for long-term memory, phenotype and polyfunctional cytokines. Acute and memory CD4+ T cell responses to structural SARS-CoV-2 proteins significantly increased with age, whilst CD8+ T cell responses increased with time post infection. Infected children had significantly lower CD4+ and CD8+ T cell responses to SARS-CoV-2 structural and ORF1ab proteins compared to infected adults. SARS-CoV-2-specific CD8+ T cell responses were comparable in magnitude to uninfected negative adult controls. In infected adults CD4+ T cell specificity was skewed towards structural peptides, whilst children had increased contribution of ORF1ab responses. This may reflect differing T cell compartmentalisation for antigen processing during antigen exposure or lower recruitment of memory populations. T cell polyfunctional cytokine production was comparable between children and adults, but children had a lower proportion of SARS-CoV-2 CD4+ T cell effector memory. Compared to adults, children had significantly lower levels of antibodies to β-coronaviruses, indicating differing baseline immunity. Total T follicular helper responses was increased in children during acute infection indicating rapid co-ordination of the T and B cell responses. However total monocyte responses were reduced in children which may be reflective of differing levels of inflammation between children and adults. Therefore, reduced prior β-coronavirus immunity and reduced activation and recruitment of de novo responses in children may drive milder COVID-19 pathogenesis.
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Affiliation(s)
- Carolyn A Cohen
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Athena PY Li
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - David SC Hui
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mike YW Kwan
- Department of Paediatric and Adolescent Medicine, Hong Kong Hospital Authority Infectious Disease Center, Princess Margaret Hospital, Special Administrative Region of Hong Kong, China
| | - Owen TY Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Special Administrative Region of Hong Kong, China
| | - Susan S Chiu
- Department of Paediatric and Adolescent Medicine, The University of Hong Kong and Queen Mary Hospital, Hospital Authority of Hong Kong, Special Administrative Region of Hong Kong, China
| | - Wai Hung Chan
- Department of Paediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Special Administrative Region of Hong Kong, China
| | - Yat Sun Yau
- Department of Paediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Special Administrative Region of Hong Kong, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fionn NL Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Eric HY Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel MS Cheng
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo LM Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - JS Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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15
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Running to Stand Still: Naive CD8 + T Cells Actively Maintain a Program of Quiescence. Int J Mol Sci 2020; 21:ijms21249773. [PMID: 33371448 PMCID: PMC7767439 DOI: 10.3390/ijms21249773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
CD8+ T cells play a pivotal role in clearing intracellular pathogens and combatting tumours. Upon infection, naïve CD8+ T cells differentiate into effector and memory cells, and this program is underscored by large-scale and coordinated changes in the chromatin architecture and gene expression. Importantly, recent evidence demonstrates that the epigenetic mechanisms that regulate the capacity for rapid effector function of memory T cells are shared by innate immune cells such as natural killer (NK) cells. Thus, it appears that the crucial difference between innate and adaptive immunity is the presence of the naïve state. This important distinction raises an intriguing new hypothesis, that the naïve state was evolutionary installed to restrain a default program of effector and memory differentiation in response to antigen recognition. We argue that the hallmark of adaptive T immunity is therefore the naïve program, which actively maintains CD8+ T cell quiescence until receipt of appropriate activation signals. In this review, we examine the mechanistic control of naïve CD8+ T cell quiescence and summarise the multiple levels of restraint imposed in naïve cells in to limit spontaneous and inappropriate activation. This includes epigenetic mechanisms and transcription factor (TF) regulation of gene expression, in addition to novel inhibitory receptors, abundance of RNA, and protein degradation.
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16
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Rezinciuc S, Tian Z, Wu S, Hengel S, Pasa-Tolic L, Smallwood HS. Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells. Viruses 2020; 12:v12121409. [PMID: 33302437 PMCID: PMC7762524 DOI: 10.3390/v12121409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Zhixin Tian
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Shawna Hengel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
- Children’s Foundation Research Institute, Memphis, TN 38105, USA
- Correspondence: ; Tel.: +1-(901)-448–3068
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17
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Verdon DJ, Mulazzani M, Jenkins MR. Cellular and Molecular Mechanisms of CD8 + T Cell Differentiation, Dysfunction and Exhaustion. Int J Mol Sci 2020; 21:ijms21197357. [PMID: 33027962 PMCID: PMC7582856 DOI: 10.3390/ijms21197357] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
T cells follow a triphasic distinct pathway of activation, proliferation and differentiation before becoming functionally and phenotypically “exhausted” in settings of chronic infection, autoimmunity and in cancer. Exhausted T cells progressively lose canonical effector functions, exhibit altered transcriptional networks and epigenetic signatures and gain constitutive expression of a broad coinhibitory receptor suite. This review outlines recent advances in our understanding of exhausted T cell biology and examines cellular and molecular mechanisms by which a state of dysfunction or exhaustion is established, and mechanisms by which exhausted T cells may still contribute to pathogen or tumour control. Further, this review describes our understanding of exhausted T cell heterogeneity and outlines the mechanisms by which checkpoint blockade differentially engages exhausted T cell subsets to overcome exhaustion and recover T cell function.
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Affiliation(s)
- Daniel J. Verdon
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (D.J.V.); (M.M.)
| | - Matthias Mulazzani
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (D.J.V.); (M.M.)
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (D.J.V.); (M.M.)
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
- Institute of Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Correspondence:
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18
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Wang Z, Guan D, Wang S, Chai LYA, Xu S, Lam KP. Glycolysis and Oxidative Phosphorylation Play Critical Roles in Natural Killer Cell Receptor-Mediated Natural Killer Cell Functions. Front Immunol 2020; 11:202. [PMID: 32153568 PMCID: PMC7045049 DOI: 10.3389/fimmu.2020.00202] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/27/2020] [Indexed: 12/28/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that directly kill tumor and pathogen-infected cells upon activation by cytokines and NK cell receptors (NKRs) without previous sensitization. It is known that cell metabolism affects the differentiation and effector functions of immune cells. For instance, interleukin−2 and interleukin−15 treatment increases glycolysis and oxidative phosphorylation (OXPHOS) in NK cells to support their effector functions. However, little is known about the metabolic reprogramming of human NK cells upon their activation by NKRs. In this study, we investigated the metabolism of NK cells stimulated via NKRs. We found that NK cells upregulated glycolysis and OXPHOS in response to anti-CD16 antibody or NKG2D ligand engagement. Inhibition of either glycolysis or OXPHOS impaired NK cell production of interferon-γ. Interestingly, inhibition of glycolysis but not OXPHOS decreased NK cell killing and dampened NK cell degranulation and Fas ligand expression, suggesting that glycolysis is more critical for NKR-activated cell cytotoxicity. Thus, our study provides insight into understanding the metabolic requirements underlying different effector functions of human NK cells.
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Affiliation(s)
- Zixi Wang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Di Guan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.,NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, Singapore, Singapore
| | - Shu Wang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, University Medicine Cluster, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shengli Xu
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kong-Peng Lam
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
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19
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Wang H, Luo H, Wan X, Fu X, Mao Q, Xiang X, Zhou Y, He W, Zhang J, Guo Y, Tan W, Deng G. TNF-α/IFN-γ profile of HBV-specific CD4 T cells is associated with liver damage and viral clearance in chronic HBV infection. J Hepatol 2020; 72:45-56. [PMID: 31499130 DOI: 10.1016/j.jhep.2019.08.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS The role of hepatitis B virus (HBV)-specific CD4 T cells in patients with chronic HBV infection is not clear. Thus, we aimed to elucidate this in patients with chronic infection, and those with hepatitis B flares. METHODS Through intracellular IFN-γ and TNF-α staining, HBV-specific CD4 T cells were analyzed in 68 patients with chronic HBV infection and alanine aminotransferase (ALT) <2x the upper limit of normal (ULN), and 28 patients with a hepatitis B flare. HBV-specific HLA-DRB1*0803/HLA-DRB1*1202-restricted CD4 T cell epitopes were identified. RESULTS TNF-α producing cells were the dominant population in patients' HBV-specific CD4 T cells. In patients with ALT <2xULN, both the frequency and the dominance of HBV-specific IFN-γ producing CD4 T cells increased sequentially in patients with elevated levels of viral clearance: HBV e antigen (HBeAg) positive, HBeAg negative, and HBV surface antigen (HBsAg) negative. In patients with a hepatitis B flare, the frequency of HBV core-specific TNF-α producing CD4 T cells was positively correlated with patients' ALT and total bilirubin levels, and the frequency of those cells changed in parallel with the severity of liver damage. Patients with HBeAg/HBsAg loss after flare showed higher frequency and dominance of HBV-specific IFN-γ producing CD4 T cells, compared to patients without HBeAg/HBsAg loss. Both the frequency and the dominance of HBV S-specific IFN-γ producing CD4 T cells were positively correlated with the decrease of HBsAg during flare. A differentiation process from TNF-α producing cells to IFN-γ producing cells in HBV-specific CD4 T cells was observed during flare. Eight and 9 HBV-derived peptides/pairs were identified as HLA-DRB1*0803 restricted epitopes and HLA-DRB1*1202 restricted epitopes, respectively. CONCLUSIONS HBV-specific TNF-α producing CD4 T cells are associated with liver damage, while HBV-specific IFN-γ producing CD4 T cells are associated with viral clearance in patients with chronic HBV infection. LAY SUMMARY TNF-α producing cells are the dominant population of hepatitis B virus (HBV)-specific CD4 T cells in patients with chronic HBV infection. This population of cells might contribute to the aggravation of liver damage in patients with a hepatitis B flare. HBV-specific IFN-γ producing CD4 T cells are associated with HBV viral clearance. Differentiation from HBV-specific TNF-α producing CD4 T cells into HBV-specific IFN-γ producing CD4 T cells might favor HBV viral clearance.
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Affiliation(s)
- Haoliang Wang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Heng Luo
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xing Wan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiaolan Fu
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Qing Mao
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiaomei Xiang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yi Zhou
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Weiwei He
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Juan Zhang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yanzhi Guo
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Wenting Tan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
| | - Guohong Deng
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
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20
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Freen-van Heeren JJ, Nicolet BP, Wolkers MC. Combined Single-Cell Measurement of Cytokine mRNA and Protein in Immune Cells. Methods Mol Biol 2020; 2108:259-271. [PMID: 31939187 DOI: 10.1007/978-1-0716-0247-8_22] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A key feature of immune cells, such as T cells, is their rapid responsiveness to activation. The response rate of T cells depends on the signal strength, and the type of signals they receive. Studying the underlying mechanisms that define responsiveness, however, is confounded by the fact that immune cells do not uniformly respond to activation. Tools that measure gene products on a single-cell level therefore provide additional insights in T cell biology. Here we describe flow cytometry-based fluorescence in situ hybridization (Flow-FISH), a high-throughput assay that allows for the simultaneous measurement of cytokine mRNA and protein levels of the gene(s) of interest by flow cytometry. We present several possible applications of Flow-FISH in human and murine T cells that-with minor adjustments-should also be applicable for other cell types.
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Affiliation(s)
- Julian J Freen-van Heeren
- Department of Hematopoiesis, Sanquin Research-Amsterdam UMC Landsteiner Laboratory and Oncode Institute, Amsterdam, The Netherlands
| | - Benoit P Nicolet
- Department of Hematopoiesis, Sanquin Research-Amsterdam UMC Landsteiner Laboratory and Oncode Institute, Amsterdam, The Netherlands
| | - Monika C Wolkers
- Department of Hematopoiesis, Sanquin Research-Amsterdam UMC Landsteiner Laboratory and Oncode Institute, Amsterdam, The Netherlands.
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21
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Ibáñez-Cabellos JS, Seco-Cervera M, Osca-Verdegal R, Pallardó FV, García-Giménez JL. Epigenetic Regulation in the Pathogenesis of Sjögren Syndrome and Rheumatoid Arthritis. Front Genet 2019; 10:1104. [PMID: 31798626 PMCID: PMC6863924 DOI: 10.3389/fgene.2019.01104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 01/01/2023] Open
Abstract
Autoimmune rheumatic diseases, such as Sjögren syndrome (SS) and rheumatoid arthritis (RA), are characterized by chronic inflammation and autoimmunity, which cause joint tissue damage and destruction by triggering reduced mobility and debilitation in patients with these diseases. Initiation and maintenance of chronic inflammatory stages account for several mechanisms that involve immune cells as key players and the interaction of the immune cells with other tissues. Indeed, the overlapping of certain clinical and serologic manifestations between SS and RA may indicate that numerous immunologic-related mechanisms are involved in the physiopathology of both these diseases. It is widely accepted that epigenetic pathways play an essential role in the development and function of the immune system. Although many published studies have attempted to elucidate the relation between epigenetic modifications (e.g. DNA methylation, histone post-translational modifications, miRNAs) and autoimmune disorders, the contribution of epigenetic regulation to the pathogenesis of SS and RA is at present poorly understood. This review attempts to shed light from a critical point of view on the identification of the most relevant epigenetic mechanisms related to RA and SS by explaining intricate regulatory processes and phenotypic features of both autoimmune diseases. Moreover, we point out some epigenetic markers which can be used to monitor the inflammation status and the dysregulated immunity in SS and RA. Finally, we discuss the inconvenience of using epigenetic data obtained from bulk immune cell populations instead specific immune cell subpopulations.
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Affiliation(s)
- José Santiago Ibáñez-Cabellos
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Marta Seco-Cervera
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Health Research Institute, Mixed Unit for rare diseases INCLIVA-CIPF, Valencia, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
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22
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Prier JE, Li J, Gearing LJ, Olshansky M, Sng XYX, Hertzog PJ, Turner SJ. Early T-BET Expression Ensures an Appropriate CD8 + Lineage-Specific Transcriptional Landscape after Influenza A Virus Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:1044-1054. [PMID: 31227580 DOI: 10.4049/jimmunol.1801431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/31/2019] [Indexed: 01/12/2023]
Abstract
Virus infection triggers large-scale changes in the phenotype and function of naive CD8+ T cells, resulting in the generation of effector and memory T cells that are then critical for immune clearance. The T-BOX family of transcription factors (TFs) are known to play a key role in T cell differentiation, with mice deficient for the TF T-BET (encoded by Tbx21) unable to generate optimal virus-specific effector responses. Although the importance of T-BET in directing optimal virus-specific T cell responses is accepted, the precise timing and molecular mechanism of action remains unclear. Using a mouse model of influenza A virus infection, we demonstrate that although T-BET is not required for early CD8+ T cell activation and cellular division, it is essential for early acquisition of virus-specific CD8+ T cell function and sustained differentiation and expansion. Whole transcriptome analysis at this early time point showed that Tbx21 deficiency resulted in global dysregulation in early programming events with inappropriate lineage-specific signatures apparent with alterations in the potential TF binding landscape. Assessment of histone posttranslational modifications within the Ifng locus demonstrated that Tbx21 -/- CD8+ T cells were unable to activate "poised" enhancer elements compared with wild-type CD8+ T cells, correlating with diminished Ifng transcription. In all, these data support a model whereby T-BET serves to promote appropriate chromatin remodeling at specific gene loci that underpins appropriate CD8+ T cell lineage-specific commitment and differentiation.
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Affiliation(s)
- Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Linden J Gearing
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Moshe Olshansky
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Paul J Hertzog
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia; .,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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23
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CD4 + T help promotes influenza virus-specific CD8 + T cell memory by limiting metabolic dysfunction. Proc Natl Acad Sci U S A 2019; 116:4481-4488. [PMID: 30787194 DOI: 10.1073/pnas.1808849116] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is continued interest in developing novel vaccine strategies that induce establish optimal CD8+ cytotoxic T lymphocyte (CTL) memory for pathogens like the influenza A viruses (IAVs), where the recall of IAV-specific T cell immunity is able to protect against serologically distinct IAV infection. While it is well established that CD4+ T cell help is required for optimal CTL responses and the establishment of memory, when and how CD4+ T cell help contributes to determining the ideal memory phenotype remains unclear. We assessed the quality of IAV-specific CD8+ T cell memory established in the presence or absence of a concurrent CD4+ T cell response. We demonstrate that CD4+ T cell help appears to be required at the initial priming phase of infection for the maintenance of IAV-specific CTL memory, with "unhelped" memory CTL exhibiting intrinsic dysfunction. High-throughput RNA-sequencing established that distinct transcriptional signatures characterize the helped vs. unhelped IAV-specific memory CTL phenotype, with the unhelped set showing a more "exhausted T cell" transcriptional profile. Moreover, we identify that unhelped memory CTLs exhibit defects in a variety of energetic pathways, leading to diminished spare respiratory capacity and diminished capacity to engage glycolysis upon reactivation. Hence, CD4+ T help at the time of initial priming promotes molecular pathways that limit exhaustion by channeling metabolic processes essential for the rapid recall of memory CD8+ T cells.
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24
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Kartikasari AER, Prakash MD, Cox M, Wilson K, Boer JC, Cauchi JA, Plebanski M. Therapeutic Cancer Vaccines-T Cell Responses and Epigenetic Modulation. Front Immunol 2019; 9:3109. [PMID: 30740111 PMCID: PMC6357987 DOI: 10.3389/fimmu.2018.03109] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022] Open
Abstract
There is great interest in developing efficient therapeutic cancer vaccines, as this type of therapy allows targeted killing of tumor cells as well as long-lasting immune protection. High levels of tumor-infiltrating CD8+ T cells are associated with better prognosis in many cancers, and it is expected that new generation vaccines will induce effective production of these cells. Epigenetic mechanisms can promote changes in host immune responses, as well as mediate immune evasion by cancer cells. Here, we focus on epigenetic modifications involved in both vaccine-adjuvant-generated T cell immunity and cancer immune escape mechanisms. We propose that vaccine-adjuvant systems may be utilized to induce beneficial epigenetic modifications and discuss how epigenetic interventions could improve vaccine-based therapies. Additionally, we speculate on how, given the unique nature of individual epigenetic landscapes, epigenetic mapping of cancer progression and specific subsequent immune responses, could be harnessed to tailor therapeutic vaccines to each patient.
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Affiliation(s)
- Apriliana E R Kartikasari
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Monica D Prakash
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Momodou Cox
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Kirsty Wilson
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia.,Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
| | - Jennifer C Boer
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Jennifer A Cauchi
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Magdalena Plebanski
- Translational Immunology and Nanotechnology Unit, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
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25
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Chen Y, Zander R, Khatun A, Schauder DM, Cui W. Transcriptional and Epigenetic Regulation of Effector and Memory CD8 T Cell Differentiation. Front Immunol 2018; 9:2826. [PMID: 30581433 PMCID: PMC6292868 DOI: 10.3389/fimmu.2018.02826] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/15/2018] [Indexed: 12/25/2022] Open
Abstract
Immune protection and lasting memory are accomplished through the generation of phenotypically and functionally distinct CD8 T cell subsets. Understanding how these effector and memory T cells are formed is the first step in eventually manipulating the immune system for therapeutic benefit. In this review, we will summarize the current understanding of CD8 T cell differentiation upon acute infection, with a focus on the transcriptional and epigenetic regulation of cell fate decision and memory formation. Moreover, we will highlight the importance of high throughput sequencing approaches and single cell technologies in providing insight into genome-wide investigations and the heterogeneity of individual CD8 T cells.
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Affiliation(s)
- Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ryan Zander
- Blood Center of Wisconsin, Blood Research Institute, Milwaukee, WI, United States
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - David M Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States.,Blood Center of Wisconsin, Blood Research Institute, Milwaukee, WI, United States
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26
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Salerno F, Guislain A, Freen-Van Heeren JJ, Nicolet BP, Young HA, Wolkers MC. Critical role of post-transcriptional regulation for IFN-γ in tumor-infiltrating T cells. Oncoimmunology 2018; 8:e1532762. [PMID: 30713785 DOI: 10.1080/2162402x.2018.1532762] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022] Open
Abstract
Protective T cell responses against tumors require the production of Interferon gamma (IFN-γ). However, tumor-infiltrating T cells (TILs) gradually lose their capacity to produce IFN-γ and therefore fail to clear malignant cells. Dissecting the underlying mechanisms that block cytokine production is thus key for improving T cell products. Here we show that although TILs express substantial levels of Ifng mRNA, post-transcriptional mechanisms impede the production of IFN-γ protein due to loss of mRNA stability. CD28 triggering, but not PD1 blocking antibodies, effectively restores the stability of Ifng mRNA. Intriguingly, TILs devoid of AU-rich elements within the 3'untranslated region maintain stabilized Ifng mRNA and produce more IFN-γ protein than wild-type TILs. This sustained IFN-γ production translates into effective suppression of tumor outgrowth, which is almost exclusively mediated by direct effects on the tumor cells. We therefore conclude that post-transcriptional mechanisms could be modulated to potentiate effective T cell therapies in cancer.
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Affiliation(s)
- Fiamma Salerno
- Department of Hematopoiesis, Sanquin Research/AMC Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Aurelie Guislain
- Department of Hematopoiesis, Sanquin Research/AMC Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Julian J Freen-Van Heeren
- Department of Hematopoiesis, Sanquin Research/AMC Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Benoit P Nicolet
- Department of Hematopoiesis, Sanquin Research/AMC Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Howard A Young
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, MD, USA
| | - Monika C Wolkers
- Department of Hematopoiesis, Sanquin Research/AMC Landsteiner Laboratory, Amsterdam, The Netherlands
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27
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Regulation of H3K4me3 at Transcriptional Enhancers Characterizes Acquisition of Virus-Specific CD8 + T Cell-Lineage-Specific Function. Cell Rep 2018; 21:3624-3636. [PMID: 29262339 DOI: 10.1016/j.celrep.2017.11.097] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 08/08/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022] Open
Abstract
Infection triggers large-scale changes in the phenotype and function of T cells that are critical for immune clearance, yet the gene regulatory mechanisms that control these changes are largely unknown. Using ChIP-seq for specific histone post-translational modifications (PTMs), we mapped the dynamics of ∼25,000 putative CD8+ T cell transcriptional enhancers (TEs) differentially utilized during virus-specific T cell differentiation. Interestingly, we identified a subset of dynamically regulated TEs that exhibited acquisition of a non-canonical (H3K4me3+) chromatin signature upon differentiation. This unique TE subset exhibited characteristics of poised enhancers in the naive CD8+ T cell subset and demonstrated enrichment for transcription factor binding motifs known to be important for virus-specific CD8+ T cell differentiation. These data provide insights into the establishment and maintenance of the gene transcription profiles that define each stage of virus-specific T cell differentiation.
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28
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Abstract
Upon stimulation, small numbers of naive CD8+ T cells proliferate and differentiate into a variety of memory and effector cell types. CD8+ T cells can persist for years and kill tumour cells and virally infected cells. The functional and phenotypic changes that occur during CD8+ T cell differentiation are well characterized, but the epigenetic states that underlie these changes are incompletely understood. Here, we review the epigenetic processes that direct CD8+ T cell differentiation and function. We focus on epigenetic modification of DNA and associated histones at genes and their regulatory elements. We also describe structural changes in chromatin organization that affect gene expression. Finally, we examine the translational potential of epigenetic interventions to improve CD8+ T cell function in individuals with chronic infections and cancer.
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Affiliation(s)
- Amanda N Henning
- Center for Cell-Based Therapy, National Cancer Institute (NCI)
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Nicholas P Restifo
- Center for Cell-Based Therapy, National Cancer Institute (NCI)
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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29
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Abdelsamed HA, Zebley CC, Youngblood B. Epigenetic Maintenance of Acquired Gene Expression Programs during Memory CD8 T Cell Homeostasis. Front Immunol 2018; 9:6. [PMID: 29403491 PMCID: PMC5778141 DOI: 10.3389/fimmu.2018.00006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/03/2018] [Indexed: 12/15/2022] Open
Abstract
Memory CD8 T cells have a unique ability to provide lifelong immunity against pathogens containing their cognate epitope. Because of their ability to provide lifelong protection, the generation of memory T cells is now a major focus for current vaccination or adoptive cell therapy approaches to treat chronic viral infections and cancer. It is now clear that maintenance of memory CD8 T cells occurs through a process of antigen-independent homeostatic proliferation, which is regulated in part by the gamma chain cytokines IL-7 and IL-15. Here, we will describe the role of these cytokines in the survival and self-renewal of memory CD8 T cells. Further, we will describe the role of epigenetics in the maintenance of acquired functions among memory CD8 T cells during homeostatic proliferation.
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Affiliation(s)
- Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Caitlin C Zebley
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
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30
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Bao XJ, Mao SQ, Gu TL, Zheng SY, Zhao JS, Zhang LN. Hypomethylation of the Interferon γ Gene as a Potential Risk Factor for Essential Hypertension: A Case-Control Study. TOHOKU J EXP MED 2018; 244:283-290. [DOI: 10.1620/tjem.244.283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Xing-Jie Bao
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University
| | - Shu-Qi Mao
- Beilun District Center for Disease Control and Prevention
| | - Tian-Lun Gu
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University
| | - Shu-Ying Zheng
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University
| | - Jin-Shun Zhao
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University
| | - Li-Na Zhang
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University
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31
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Extrinsically derived TNF is primarily responsible for limiting antiviral CD8+ T cell response magnitude. PLoS One 2017; 12:e0184732. [PMID: 28886201 PMCID: PMC5590991 DOI: 10.1371/journal.pone.0184732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/23/2017] [Indexed: 11/26/2022] Open
Abstract
TNF is a pro-inflammatory cytokine produced by both lymphoid and non-lymphoid cells. As a consequence of the widespread expression of its receptors (TNFR1 and 2), TNF plays a role in many important biological processes. In the context of influenza A virus (IAV) infection, TNF has variably been implicated in mediating immunopathology as well as suppression of the immune response. Although a number of cell types are able to produce TNF, the ability of CD8+ T cells to produce TNF following viral infection is a hallmark of their effector function. As such, the regulation and role of CD8+ T cell-derived TNF following viral infection is of great interest. Here, we show that the biphasic production of TNF by CD8+ T cells following in vitro stimulation corresponds to distinct patterns of epigenetic modifications. Further, we show that a global loss of TNF during IAV infection results in an augmentation of the peripheral virus-specific CD8+ T cell response. Subsequent adoptive transfer experiments demonstrated that this attenuation of the CD8+ T cell response was largely, but not exclusively, conferred by extrinsic TNF, with intrinsically-derived TNF making only modest contributions. In conclusion, TNF exerts an immunoregulatory role on CD8+ T cell responses following IAV infection, an effect that is largely mediated by extrinsically-derived TNF.
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32
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Gelfand EW, Joetham A, Wang M, Takeda K, Schedel M. Spectrum of T-lymphocyte activities regulating allergic lung inflammation. Immunol Rev 2017; 278:63-86. [PMID: 28658551 PMCID: PMC5501488 DOI: 10.1111/imr.12561] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Despite advances in the treatment of asthma, optimization of symptom control remains an unmet need in many patients. These patients, labeled severe asthma, are responsible for a substantial fraction of the disease burden. In these patients, research is needed to define the cellular and molecular pathways contributing to disease which in large part are refractory to corticosteroid treatment. The causes of steroid-resistant asthma are multifactorial and result from complex interactions of genetics, environmental factors, and innate and adaptive immunity. Adaptive immunity, addressed here, integrates the activities of distinct T-cell subsets and by definition is dynamic and responsive to an ever-changing environment and the influences of epigenetic modifications. These T-cell subsets exhibit different susceptibilities to the actions of corticosteroids and, in some, corticosteroids enhance their functional activation. Moreover, these subsets are not fixed in lineage differentiation but can undergo transcriptional reprogramming in a bidirectional manner between protective and pathogenic effector states. Together, these factors contribute to asthma heterogeneity between patients but also in the same patient at different stages of their disease. Only by carefully defining mechanistic pathways, delineating their sensitivity to corticosteroids, and determining the balance between regulatory and effector pathways will precision medicine become a reality with selective and effective application of targeted therapies.
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Affiliation(s)
- Erwin W Gelfand
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Anthony Joetham
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Meiqin Wang
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Katsuyuki Takeda
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Michaela Schedel
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
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33
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Dogra P, Ghoneim HE, Abdelsamed HA, Youngblood B. Generating long-lived CD8(+) T-cell memory: Insights from epigenetic programs. Eur J Immunol 2017; 46:1548-62. [PMID: 27230488 DOI: 10.1002/eji.201545550] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/28/2016] [Accepted: 05/24/2016] [Indexed: 12/13/2022]
Abstract
T-cell-based immunological memory has the potential to provide the host with life-long protection against pathogen reexposure and thus offers tremendous promise for the design of vaccines targeting chronic infections or cancer. In order to exploit this potential in the design of new vaccines, it is necessary to understand how and when memory T cells acquire their poised effector potential, and moreover, how they maintain these properties during homeostatic proliferation. To gain insight into the persistent nature of memory T-cell functions, investigators have turned their attention to epigenetic mechanisms. Recent efforts have revealed that many of the properties acquired among memory T cells are coupled to stable changes in DNA methylation and histone modifications. Furthermore, it has recently been reported that the delineating features among memory T cells subsets are also linked to distinct epigenetic events, such as permissive and repressive histone modifications and DNA methylation programs, providing exciting new hypotheses regarding their cellular ancestry. Here, we review recent studies focused on epigenetic programs acquired during effector and memory T-cell differentiation and discuss how these data may shed new light on the developmental path for generating long-lived CD8(+) T-cell memory.
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Affiliation(s)
- Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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34
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Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, Scott AC, Viale A, Lauer P, Merghoub T, Hellmann MD, Wolchok JD, Leslie CS, Schietinger A. Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature 2017. [PMID: 28514453 DOI: 10.1038/nature22367.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.
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Affiliation(s)
- Mary Philip
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lauren Fairchild
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ellen L Horste
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Steven Camara
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mojdeh Shakiba
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Andrew C Scott
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Peter Lauer
- Aduro Biotech, Inc., Berkeley, California 94720, USA
| | - Taha Merghoub
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Melanoma and Immunotherapeutics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Matthew D Hellmann
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jedd D Wolchok
- Weill Cornell Medical College, Cornell University, New York, New York 10065, USA.,Melanoma and Immunotherapeutics Service, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Weill Cornell Medical College, Cornell University, New York, New York 10065, USA
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35
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Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature 2017; 545:452-456. [PMID: 28514453 PMCID: PMC5693219 DOI: 10.1038/nature22367] [Citation(s) in RCA: 591] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/12/2017] [Indexed: 12/11/2022]
Abstract
Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.
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36
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Abdelsamed HA, Moustaki A, Fan Y, Dogra P, Ghoneim HE, Zebley CC, Triplett BM, Sekaly RP, Youngblood B. Human memory CD8 T cell effector potential is epigenetically preserved during in vivo homeostasis. J Exp Med 2017; 214:1593-1606. [PMID: 28490440 PMCID: PMC5461005 DOI: 10.1084/jem.20161760] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/16/2017] [Accepted: 04/04/2017] [Indexed: 12/15/2022] Open
Abstract
Abdelsamed et al. demonstrate that the poised effector potential of human memory CD8 T cells is coupled to maintenance of effector-associated DNA methylation programs during in vitro and in vivo homeostatic proliferation. Antigen-independent homeostasis of memory CD8 T cells is vital for sustaining long-lived T cell–mediated immunity. In this study, we report that maintenance of human memory CD8 T cell effector potential during in vitro and in vivo homeostatic proliferation is coupled to preservation of acquired DNA methylation programs. Whole-genome bisulfite sequencing of primary human naive, short-lived effector memory (TEM), and longer-lived central memory (TCM) and stem cell memory (TSCM) CD8 T cells identified effector molecules with demethylated promoters and poised for expression. Effector-loci demethylation was heritably preserved during IL-7– and IL-15–mediated in vitro cell proliferation. Conversely, cytokine-driven proliferation of TCM and TSCM memory cells resulted in phenotypic conversion into TEM cells and was coupled to increased methylation of the CCR7 and Tcf7 loci. Furthermore, haploidentical donor memory CD8 T cells undergoing in vivo proliferation in lymphodepleted recipients also maintained their effector-associated demethylated status but acquired TEM-associated programs. These data demonstrate that effector-associated epigenetic programs are preserved during cytokine-driven subset interconversion of human memory CD8 T cells.
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Affiliation(s)
- Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Ardiana Moustaki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Caitlin C Zebley
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Brandon M Triplett
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105
| | | | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
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37
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Hsp90 inhibition destabilizes Ezh2 protein in alloreactive T cells and reduces graft-versus-host disease in mice. Blood 2017; 129:2737-2748. [PMID: 28246193 DOI: 10.1182/blood-2016-08-735886] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 02/17/2017] [Indexed: 01/02/2023] Open
Abstract
Modulating T-cell alloreactivity has been a main strategy to reduce graft-versus-host disease (GVHD), a life-threatening complication after allogeneic hematopoietic stem-cell transplantation (HSCT). Genetic deletion of T-cell Ezh2, which catalyzes trimethylation of histone H3 at lysine 27 (H3K27me3), inhibits GVHD. Therefore, reducing Ezh2-mediated H3K27me3 is thought to be essential for inhibiting GVHD. We tested this hypothesis in mouse GVHD models. Unexpectedly, administration of the Ezh2 inhibitor GSK126, which specifically decreases H3K27me3 without affecting Ezh2 protein, failed to prevent the disease. In contrast, destabilizing T-cell Ezh2 protein by inhibiting Hsp90 using its specific inhibitor AUY922 reduced GVHD in mice undergoing allogeneic HSCT. In vivo administration of AUY922 selectively induced apoptosis of activated T cells and decreased the production of effector cells producing interferon γ and tumor necrosis factor α, similar to genetic deletion of Ezh2. Introduction of Ezh2 into alloreactive T cells restored their expansion and production of effector cytokines upon AUY922 treatment, suggesting that impaired T-cell alloreactivity by inhibiting Hsp90 is achieved mainly through depleting Ezh2. Mechanistic analysis revealed that the enzymatic SET domain of Ezh2 directly interacted with Hsp90 to prevent Ezh2 from rapid degradation in activated T cells. Importantly, pharmacological inhibition of Hsp90 preserved antileukemia activity of donor T cells, leading to improved overall survival of recipient mice after allogeneic HSCT. Our findings identify the Ezh2-Hsp90 interaction as a previously unrecognized mechanism essential for T-cell responses and an effective target for controlling GVHD.
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38
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Scharer CD, Bally APR, Gandham B, Boss JM. Cutting Edge: Chromatin Accessibility Programs CD8 T Cell Memory. THE JOURNAL OF IMMUNOLOGY 2017; 198:2238-2243. [PMID: 28179496 DOI: 10.4049/jimmunol.1602086] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022]
Abstract
CD8 T cell memory is characterized by rapid recall of effector function, increased proliferation, and reduced activation requirements. Despite the extensive functional characterization, the molecular mechanisms that facilitate these enhanced properties are not well characterized. In this study, the assay for transposase-accessible chromatin sequencing was employed to map the cis-regulatory elements in CD8 T cells responding to acute and chronic lymphocytic choriomeningitis virus infections. Integration of chromatin accessibility profiles with gene expression data identified unique regulatory modules that were enriched for distinct combinations of transcription factor-binding motifs. Memory CD8 T cells displayed a chromatin accessibility structure that was absent from other acute and exhausted cells types and included key effector and proliferative genes. Stimulation of memory cells revealed enhanced transcription of "memory-primed" genes compared with naive cells. Thus, memory CD8 T cells display a preprogrammed chromatin accessibility profile and maintain a molecular history of cis-element usage, thereby reducing the steps necessary to revive effector functions.
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Affiliation(s)
- Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322; and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
| | - Alexander P R Bally
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322; and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
| | - Bhanu Gandham
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322; and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322; and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
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39
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Nicolet BP, Guislain A, Wolkers MC. Combined Single-Cell Measurement of Cytokine mRNA and Protein Identifies T Cells with Persistent Effector Function. THE JOURNAL OF IMMUNOLOGY 2016; 198:962-970. [DOI: 10.4049/jimmunol.1601531] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/07/2016] [Indexed: 11/19/2022]
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40
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Liu M, Zhou J, Chen Z, Cheng ASL. Understanding the epigenetic regulation of tumours and their microenvironments: opportunities and problems for epigenetic therapy. J Pathol 2016; 241:10-24. [PMID: 27770445 DOI: 10.1002/path.4832] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022]
Abstract
The tumour microenvironment plays an instrumental role in cancer development, progression and treatment response/resistance. Accumulating evidence is underscoring the fundamental importance of epigenetic regulation in tumour immune evasion. Following many pioneering discoveries demonstrating malignant transformation through epigenetic anomalies ('epimutations'), there is also a growing emphasis on elucidating aberrant epigenetic mechanisms that reprogramme the milieu of tumour-associated immune and stromal cells towards an immunosuppressive state. Pharmacological inhibition of DNA methylation and histone modifications can augment the efficiency of immune checkpoint blockage, and unleash anti-tumour T-cell responses. However, these non-specific agents also represent a 'double-edged sword', as they can also reactivate gene transcription of checkpoint molecules, interrupting immune surveillance programmes. By understanding the impact of epigenetic control on the tumour microenvironment, rational combinatorial epigenetic and checkpoint blockage therapies have the potential to harness the immune system for the treatment of cancer. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Man Liu
- School of Biomedical Sciences and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Jingying Zhou
- School of Biomedical Sciences and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, PR China
| | - Alfred Sze-Lok Cheng
- School of Biomedical Sciences and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
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41
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Abstract
IFN-γ is a critical inflammatory cytokine that is closely regulated to cellular metabolic status and requires high rates of glycolysis. It has now been shown that a key mechanism to link these pathways is through maintenance of acetyl-CoA and epigenetic regulation of the IFNG locus.
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Affiliation(s)
- Peter J Siska
- Department of Pathology, Microbiology and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232-2363, USA.
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42
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Ghoneim HE, Zamora AE, Thomas PG, Youngblood BA. Cell-Intrinsic Barriers of T Cell-Based Immunotherapy. Trends Mol Med 2016; 22:1000-1011. [PMID: 27825667 DOI: 10.1016/j.molmed.2016.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
Prolonged exposure of CD8+ T cells to their cognate antigen can result in exhaustion of effector functions enabling the persistence of infected or transformed cells. Recent advances in strategies to rejuvenate host effector function using Immune Checkpoint Blockade have resulted in tremendous success towards the treatment of several cancers. However, it is unclear if T cell rejuvenation results in long-lived antitumor functions. Emerging evidence suggests that T cell exhaustion may also represent a significant impediment in sustaining long-lived antitumor activity by chimeric antigen receptor T cells. Here, we discuss current findings regarding transcriptional regulation during T cell exhaustion and address the hypothesis that epigenetics may be a potential barrier to achieving the maximum benefit of T cell-based immunotherapies.
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Affiliation(s)
- Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben A Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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43
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Li J, Hardy K, Phetsouphanh C, Tu WJ, Sutcliffe EL, McCuaig R, Sutton CR, Zafar A, Munier CML, Zaunders JJ, Xu Y, Theodoratos A, Tan A, Lim PS, Knaute T, Masch A, Zerweck J, Brezar V, Milburn PJ, Dunn J, Casarotto MG, Turner SJ, Seddiki N, Kelleher AD, Rao S. Nuclear PKC-θ facilitates rapid transcriptional responses in human memory CD4+ T cells through p65 and H2B phosphorylation. J Cell Sci 2016; 129:2448-61. [PMID: 27149922 PMCID: PMC4920249 DOI: 10.1242/jcs.181248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/21/2016] [Indexed: 12/14/2022] Open
Abstract
Memory T cells are characterized by their rapid transcriptional programs upon re-stimulation. This transcriptional memory response is facilitated by permissive chromatin, but exactly how the permissive epigenetic landscape in memory T cells integrates incoming stimulatory signals remains poorly understood. By genome-wide ChIP-sequencing ex vivo human CD4+ T cells, here, we show that the signaling enzyme, protein kinase C theta (PKC-θ) directly relays stimulatory signals to chromatin by binding to transcriptional-memory-responsive genes to induce transcriptional activation. Flanked by permissive histone modifications, these PKC-enriched regions are significantly enriched with NF-κB motifs in ex vivo bulk and vaccinia-responsive human memory CD4+ T cells. Within the nucleus, PKC-θ catalytic activity maintains the Ser536 phosphorylation on the p65 subunit of NF-κB (also known as RelA) and can directly influence chromatin accessibility at transcriptional memory genes by regulating H2B deposition through Ser32 phosphorylation. Furthermore, using a cytoplasm-restricted PKC-θ mutant, we highlight that chromatin-anchored PKC-θ integrates activating signals at the chromatin template to elicit transcriptional memory responses in human memory T cells. Summary: Memory T cells have a rapid transcriptional program upon re-stimulation. Chromatin-anchored PKC-θ integrates activating signals at the chromatin template to elicit this transcriptional memory in T cells.
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Affiliation(s)
- Jasmine Li
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia Department of Microbiology & Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kristine Hardy
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Chan Phetsouphanh
- The Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Wen Juan Tu
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Elissa L Sutcliffe
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Robert McCuaig
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Christopher R Sutton
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Anjum Zafar
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - C Mee Ling Munier
- The Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John J Zaunders
- The Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Yin Xu
- The Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Angelo Theodoratos
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Abel Tan
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Pek Siew Lim
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Tobias Knaute
- JPT Peptide Technologies Gmbh, Berlin 12489, Germany
| | - Antonia Masch
- Department of Enzymology, Institute of Biochemistry & Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle 06108, Germany
| | | | - Vedran Brezar
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Peter J Milburn
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Jenny Dunn
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Marco G Casarotto
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Stephen J Turner
- Department of Microbiology & Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nabila Seddiki
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Anthony D Kelleher
- The Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Sudha Rao
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
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44
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Urban SL, Berg LJ, Welsh RM. Type 1 interferon licenses naïve CD8 T cells to mediate anti-viral cytotoxicity. Virology 2016; 493:52-9. [PMID: 26999026 DOI: 10.1016/j.virol.2016.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/07/2016] [Indexed: 11/28/2022]
Abstract
Naïve T cells, unlike memory T cells, exhibit very limited effector function in response to cognate antigen, but exposure to type 1 interferon (IFN) prior to cognate antigen allows for rapid manifestation of effector functions. A full assessment of the functions of these IFN-sensitized otherwise naïve T cells has not been made, nor has their capacity to be effector cells in vivo. We describe here that IFN-sensitized naïve T cells in the absence of cognate antigen adopt a partial activated phenotype distinguished by the upregulation of the surface activation marker CD69, effector-associated transcription factors Eomes and IRF4, and cytotoxicity effector molecule granzyme B. IFN-sensitized naive T cells lysed target cells in vivo and responded to low concentrations and affinities of cognate ligands. We suggest that this rapid and sensitive effector function of IFN-conditioned naïve CD8 T cells may play a role in pathogen control and help ward off superinfections.
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Affiliation(s)
- Stina L Urban
- Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, United States
| | - Leslie J Berg
- Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, United States
| | - Raymond M Welsh
- Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, United States.
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45
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Lissina A, Ambrozak DR, Boswell KL, Yang W, Boritz E, Wakabayashi Y, Iglesias MC, Hashimoto M, Takiguchi M, Haddad E, Douek DC, Zhu J, Koup RA, Yamamoto T, Appay V. Fine-tuning of CD8(+) T-cell effector functions by targeting the 2B4-CD48 interaction. Immunol Cell Biol 2016; 94:583-92. [PMID: 26860368 DOI: 10.1038/icb.2016.17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 01/08/2016] [Accepted: 01/24/2016] [Indexed: 12/22/2022]
Abstract
Polyfunctionality and cytotoxic activity dictate CD8(+) T-cell efficacy in the eradication of infected and malignant cells. The induction of these effector functions depends on the specific interaction between the T-cell receptor (TCR) and its cognate peptide-MHC class I complex, in addition to signals provided by co-stimulatory or co-inhibitory receptors, which can further regulate these functions. Among these receptors, the role of 2B4 is contested, as it has been described as either co-stimulatory or co-inhibitory in modulating T-cell functions. We therefore combined functional, transcriptional and epigenetic approaches to further characterize the impact of disrupting the interaction of 2B4 with its ligand CD48, on the activity of human effector CD8(+) T-cell clones. In this setting, we show that the 2B4-CD48 axis is involved in the fine-tuning of CD8(+) T-cell effector function upon antigenic stimulation. Blocking this interaction resulted in reduced CD8(+) T-cell clone-mediated cytolytic activity, together with a subtle drop in the expression of genes involved in effector function regulation. Our results also imply a variable contribution of the 2B4-CD48 interaction to the modulation of CD8(+) T-cell functional properties, potentially linked to intrinsic levels of T-bet expression and TCR avidity. The present study thus provides further insights into the role of the 2B4-CD48 interaction in the fine regulation of CD8(+) T-cell effector function upon antigenic stimulation.
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Affiliation(s)
- Anna Lissina
- Sorbonne Universités, UPMC Univ Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,INSERM U1135, CIMI-Paris, Paris, France
| | - David R Ambrozak
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kristin L Boswell
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wenjing Yang
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Eli Boritz
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Yoshiyuki Wakabayashi
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Maria C Iglesias
- Sorbonne Universités, UPMC Univ Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,INSERM U1135, CIMI-Paris, Paris, France
| | - Masao Hashimoto
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | - Elias Haddad
- Vaccine and Gene Therapy Institute of Florida, Lucie, FL, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Takuya Yamamoto
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Victor Appay
- Sorbonne Universités, UPMC Univ Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,INSERM U1135, CIMI-Paris, Paris, France
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46
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Baz A, Groves P, Buttigieg K, Apte SH, Kienzle N, Kelso A. Quantitative assessment of the functional plasticity of memory CD8(+) T cells. Eur J Immunol 2016; 46:863-73. [PMID: 26799367 DOI: 10.1002/eji.201545726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 11/29/2015] [Accepted: 01/15/2016] [Indexed: 01/28/2023]
Abstract
While the functional plasticity of memory CD4(+) T cells has been studied extensively, less is known about this property in memory CD8(+) T cells. Here, we report the direct measurement of plasticity by paired daughter analysis of effector and memory OT-I CD8(+) T cells primed in vivo with ovalbumin. Naïve, effector, and memory OT-I cells were isolated and activated in single-cell culture; then, after the first division, their daughter cells were transferred to new cultures with and without IL-4; expression of IFN-γ and IL-4 mRNAs was measured 5 days later in the resultant subclones. Approximately 40% of clonogenic memory CD8(+) T cells were bipotential in this assay, giving rise to an IL-4(-) subclone in the absence of IL-4 and an IL-4(+) subclone in the presence of IL-4. The frequency of bipotential cells was lower among memory cells than naïve cells but markedly higher than among 8-day effectors. Separation based on high or low expression of CD62L, CD122, CD127, or Ly6C did not identify a phenotypic marker of the bipotential cells. Functional plasticity in memory CD8(+) T-cell populations can therefore reflect modulation at the level of a single memory cell and its progeny.
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Affiliation(s)
- Adriana Baz
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Penny Groves
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Kathy Buttigieg
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Simon H Apte
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Norbert Kienzle
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Anne Kelso
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
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Burel JG, Apte SH, Doolan DL. Systems Approaches towards Molecular Profiling of Human Immunity. Trends Immunol 2016; 37:53-67. [DOI: 10.1016/j.it.2015.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022]
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Nguyen MLT, Hatton L, Li J, Olshansky M, Kelso A, Russ BE, Turner SJ. Dynamic regulation of permissive histone modifications and GATA3 binding underpin acquisition of granzyme A expression by virus-specific CD8(+) T cells. Eur J Immunol 2015; 46:307-18. [PMID: 26519105 DOI: 10.1002/eji.201545875] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/17/2015] [Accepted: 10/27/2015] [Indexed: 11/11/2022]
Abstract
Numerous studies have focused on the molecular regulation of perforin (PFP) and granzyme B (GZMB) expression by activated cytotoxic T lymphocytes (CTLs), but little is known about the molecular factors that underpin granzyme A (GZMA) expression. In vitro activation of naïve CD8(+) T cells, in the presence of IL-4, enhanced STAT6-dependent GZMA expression and was associated with GATA3 binding and enrichment of transcriptionally permissive histone posttranslational modifications (PTMs) across the Gzma gene locus. While GZMA expression by effector influenza A virus specific CTLs was also associated with a similar permissive epigenetic signature, memory CTL lacked enrichment of permissive histone PTMs at the Gzma locus, although this was restored within recalled secondary effector CTLs. Importantly, GZMA expression by virus-specific CTLs was associated with GATA3 binding at the Gzma locus, and independent of STAT6-mediated signaling. This suggests regulation of GZMA expression is underpinned by differentiation-dependent regulation of chromatin composition at the Gzma locus and that, given GATA3 is key for CTL differentiation in response to infection, GATA3 expression is regulated by a distinct, IL-4 independent, signaling pathway. Overall, this study provides insights into the molecular mechanisms that control transcription of Gzma during virus-induced CD8(+) T-cell differentiation.
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Affiliation(s)
- Michelle L T Nguyen
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lauren Hatton
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Moshe Olshansky
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Anne Kelso
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory; at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brendan E Russ
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Stephen J Turner
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Tserel L, Kolde R, Limbach M, Tretyakov K, Kasela S, Kisand K, Saare M, Vilo J, Metspalu A, Milani L, Peterson P. Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes. Sci Rep 2015; 5:13107. [PMID: 26286994 PMCID: PMC4541364 DOI: 10.1038/srep13107] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/14/2015] [Indexed: 12/25/2022] Open
Abstract
Human ageing affects the immune system resulting in an overall decline in immunocompetence. Although all immune cells are affected during aging, the functional capacity of T cells is most influenced and is linked to decreased responsiveness to infections and impaired differentiation. We studied age-related changes in DNA methylation and gene expression in CD4+ and CD8+ T cells from younger and older individuals. We observed marked difference between T cell subsets, with increased number of methylation changes and higher methylome variation in CD8+ T cells with age. The majority of age-related hypermethylated sites were located at CpG islands of silent genes and enriched for repressive histone marks. Specifically, in CD8+ T cell subset we identified strong inverse correlation between methylation and expression levels in genes associated with T cell mediated immune response (LGALS1, IFNG, CCL5, GZMH, CCR7, CD27 and CD248) and differentiation (SATB1, TCF7, BCL11B and RUNX3). Our results thus suggest the link between age-related epigenetic changes and impaired T cell function.
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Affiliation(s)
- Liina Tserel
- Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Raivo Kolde
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Maia Limbach
- Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia
| | | | - Silva Kasela
- 1] Estonian Genome Center, University of Tartu, Tartu, Estonia [2] Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kai Kisand
- Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Mario Saare
- Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- 1] Estonian Genome Center, University of Tartu, Tartu, Estonia [2] Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia
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Abstract
The multiple lineages and differentiation states that constitute the T-cell compartment all derive from a common thymic precursor. These distinct transcriptional states are maintained both in time and after multiple rounds of cell division by the concerted actions of a small set of lineage-defining transcription factors that act in conjunction with a suite of chromatin-modifying enzymes to activate, repress, and fine-tune gene expression. These chromatin modifications collectively provide an epigenetic code that allows the stable and heritable maintenance of the T-cell phenotype. Recently, it has become apparent that the epigenetic code represents a therapeutic target for a variety of immune cell disorders, including lymphoma and acute and chronic inflammatory diseases. Here, we review the recent advances in epigenetic regulation of gene expression, particularly as it relates to the T-cell differentiation and function.
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Affiliation(s)
- Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia; Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
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