1
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Huang Y, Liu X, Li S, Li C, Wang HY, Liu Q, Chen JY, Zhang Y, Li Y, Zhang X, Wang Q, Liu K, Liu YY, Pang Y, Liu S, Fan G, Shao C. Discovery of an unconventional lamprey lymphocyte lineage highlights divergent features in vertebrate adaptive immune system evolution. Nat Commun 2024; 15:7626. [PMID: 39227584 DOI: 10.1038/s41467-024-51763-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 08/16/2024] [Indexed: 09/05/2024] Open
Abstract
Lymphocyte receptors independently evolved in both jawed and jawless vertebrates with similar adaptive immune responses. However, the diversity of functional subtypes and molecular architecture in jawless vertebrate lymphocytes, comparable to jawed species, is not well defined. Here, we profile the gills, intestines, and blood of the lamprey, Lampetra morii, with single-cell RNA sequencing, using a full-length transcriptome as a reference. Our findings reveal higher tissue-specific heterogeneity among T-like cells in contrast to B-like cells. Notably, we identify a unique T-like cell subtype expressing a homolog of the nonlymphoid hematopoietic growth factor receptor, MPL-like (MPL-L). These MPL-L+ T-like cells exhibit features distinct from T cells of jawed vertebrates, particularly in their elevated expression of hematopoietic genes. We further discovered that MPL-L+ VLRA+ T-like cells are widely present in the typhlosole, gill, liver, kidney, and skin of lamprey and they proliferate in response to both a T cell mitogen and recombinant human thrombopoietin. These findings provide new insights into the adaptive immune response in jawless vertebrates, shedding new light on the evolution of adaptive immunity.
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Affiliation(s)
- Yingyi Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Xiang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | - Shuo Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Chen Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Qun Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jian-Yang Chen
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, China
| | - Yingying Zhang
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, China
| | - Yanan Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Xianghui Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Qian Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Kaiqiang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Yu-Yan Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China
| | - Yue Pang
- College of Life Sciences, Liaoning Normal University, Dalian, China
| | - Shanshan Liu
- BGI Research, Shenzhen, China
- MGI Tech, Shenzhen, China
| | - Guangyi Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China.
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2
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Ran L, Yue Z, Ran M, Liu Q, Su X, Wang L, Wen S, Xu L, Lei S, Ou Z, Hu J, Zhang Y, Qin C, Wang Y, He Q, Chen Y, Liu W, Ye L, Huang Q, Xu L. The transcription regulator ID3 maintains tumor-specific memory CD8 + T cells in draining lymph nodes during tumorigenesis. Cell Rep 2024; 43:114690. [PMID: 39216001 DOI: 10.1016/j.celrep.2024.114690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/10/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
During tumorigenesis, the recently identified tumor-specific memory T cells in draining lymph nodes (TdLN-TTSM cells) play a pivotal role in tumor repression that gives rise to progenitor exhausted T (TPEX) cells and further replenishes tumor-specific CD8+ T cells residing in the tumor microenvironment (TME). However, how TTSM cells are maintained in TdLN is largely unknown. Here, we show that the transcription regulator ID3 (inhibitor of DNA binding 3) is highly expressed by TTSM cells compared with other CD8+ T cell subsets. The deficiency of ID3 significantly interrupts the maintenance of TTSM and TPEX cells, resulting in decreased tumor-infiltrating CD8+ T cells and impaired tumor control. Consistent with this, overexpression of ID3 in CD8+ T cells increases the TTSM cell population and enhances the anti-tumor immune response.
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Affiliation(s)
- Ling Ran
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhengliang Yue
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Mengqu Ran
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China
| | - Qiao Liu
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xingxing Su
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Lisha Wang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Shuqiong Wen
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Luming Xu
- Medical Laboratory Technology, Southern Medical University, Guangzhou, China
| | - Shun Lei
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhanpeng Ou
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Jianjun Hu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Yan Zhang
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China; Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing Medical University, Chongqing, China
| | - Chenxi Qin
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Yuzhu Wang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qinyi He
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Yezi Chen
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China
| | - Wen Liu
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, China.
| | - Qizhao Huang
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China.
| | - Lifan Xu
- Institute of Immunology, Third Military Medical University, Chongqing, China.
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3
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Sadria M, Layton A, Goyal S, Bader GD. Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation. CELL REPORTS METHODS 2024; 4:100819. [PMID: 38986613 PMCID: PMC11294839 DOI: 10.1016/j.crmeth.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 11/20/2023] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
Cell reprogramming, which guides the conversion between cell states, is a promising technology for tissue repair and regeneration, with the ultimate goal of accelerating recovery from diseases or injuries. To accomplish this, regulators must be identified and manipulated to control cell fate. We propose Fatecode, a computational method that predicts cell fate regulators based only on single-cell RNA sequencing (scRNA-seq) data. Fatecode learns a latent representation of the scRNA-seq data using a deep learning-based classification-supervised autoencoder and then performs in silico perturbation experiments on the latent representation to predict genes that, when perturbed, would alter the original cell type distribution to increase or decrease the population size of a cell type of interest. We assessed Fatecode's performance using simulations from a mechanistic gene-regulatory network model and scRNA-seq data mapping blood and brain development of different organisms. Our results suggest that Fatecode can detect known cell fate regulators from single-cell transcriptomics datasets.
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Affiliation(s)
- Mehrshad Sadria
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada.
| | - Anita Layton
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada; Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada; Department of Biology, University of Waterloo, Waterloo, ON, Canada; School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
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4
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Huang F, Lin Y, Qiao Y, Yuan Y, Zhong Z, Luo B, Wu Y, Liu J, Chen J, Zhang W, Zhang H, Liu B. BRD7 as key factor in PBAF complex assembly and CD8+ T cell differentiation. JCI Insight 2024; 9:e171605. [PMID: 38954484 DOI: 10.1172/jci.insight.171605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
Upon infection, naive CD8+ T cells differentiate into cytotoxic effector cells to eliminate the pathogen-infected cells. Although many mechanisms underlying this process have been demonstrated, the regulatory role of chromatin remodeling system in this process remains largely unknown. Here we show that BRD7, a component of the polybromo-associated BAF complex (PBAF), was required for naive CD8+ T cells to differentiate into functional short-lived effector cells (SLECs) in response to acute infections caused by influenza virus or lymphocytic choriomeningitis virus (LCMV). BRD7 deficiency in CD8+ T cells resulted in profound defects in effector population and functions, thereby impairing viral clearance and host recovery. Further mechanical studies indicate that the expression of BRD7 significantly turned to high from naive CD8+ T cells to effector cells, which bridged BRG1 and PBRM1 to the core module of PBAF complex, consequently facilitating the assembly of PBAF complex rather than BAF complex in the effector cells. The PBAF complex changed the chromatin accessibility at the loci of Tbx21 gene and upregulated its expression, leading to the maturation of effector T cells. Our research demonstrates that BRD7 and the PBAF complex are key in CD8+ T cell development and present a significant target for advancing immune therapies.
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Affiliation(s)
- Feng Huang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangzhou Laboratory, Guangzhou, China
| | - Yingtong Lin
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yidan Qiao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yaochang Yuan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhihan Zhong
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baohong Luo
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yating Wu
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Jun Liu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jingliang Chen
- Infectious Diseases Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wanying Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bingfeng Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
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5
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Sankaran DG, Zhu H, Maymi VI, Forlastro IM, Jiang Y, Laniewski N, Scheible KM, Rudd BD, Grimson AW. Gene Regulatory Programs that Specify Age-Related Differences during Thymocyte Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599011. [PMID: 38948840 PMCID: PMC11212896 DOI: 10.1101/2024.06.14.599011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
T cell development is fundamental to immune system establishment, yet how this development changes with age remains poorly understood. Here, we construct a transcriptional and epigenetic atlas of T cell developmental programs in neonatal and adult mice, revealing the ontogeny of divergent gene regulatory programs and their link to age-related differences in phenotype and function. Specifically, we identify a gene module that diverges with age from the earliest stages of genesis and includes programs that govern effector response and cell cycle regulation. Moreover, we reveal that neonates possess more accessible chromatin during early thymocyte development, likely establishing poised gene expression programs that manifest later in thymocyte development. Finally, we leverage this atlas, employing a CRISPR-based perturbation approach coupled with single-cell RNA sequencing as a readout to uncover a conserved transcriptional regulator, Zbtb20, that contributes to age-dependent differences in T cell development. Altogether, our study defines transcriptional and epigenetic programs that regulate age-specific differences in T cell development.
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6
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Gray JI, Caron DP, Wells SB, Guyer R, Szabo P, Rainbow D, Ergen C, Rybkina K, Bradley MC, Matsumoto R, Pethe K, Kubota M, Teichmann S, Jones J, Yosef N, Atkinson M, Brusko M, Brusko TM, Connors TJ, Sims PA, Farber DL. Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span. Sci Immunol 2024; 9:eadn3954. [PMID: 38848342 DOI: 10.1126/sciimmunol.adn3954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
During ontogeny, γδ T cells emerge from the thymus and directly seed peripheral tissues for in situ immunity. However, their functional role in humans has largely been defined from blood. Here, we analyzed the phenotype, transcriptome, function, and repertoire of human γδ T cells in blood and mucosal and lymphoid tissues from 176 donors across the life span, revealing distinct profiles in children compared with adults. In early life, clonally diverse Vδ1 subsets predominate across blood and tissues, comprising naïve and differentiated effector and tissue repair functions, whereas cytolytic Vδ2 subsets populate blood, spleen, and lungs. With age, Vδ1 and Vδ2 subsets exhibit clonal expansions and elevated cytolytic signatures, which are disseminated across sites. In adults, Vδ2 cells predominate in blood, whereas Vδ1 cells are enriched across tissues and express residency profiles. Thus, antigenic exposures over childhood drive the functional evolution and tissue compartmentalization of γδ T cells, leading to age-dependent roles in immunity.
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Affiliation(s)
- Joshua I Gray
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Daniel P Caron
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Steven B Wells
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Rebecca Guyer
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Peter Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Daniel Rainbow
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Can Ergen
- Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ksenia Rybkina
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Marissa C Bradley
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032 USA
| | - Rei Matsumoto
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Kalpana Pethe
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032 USA
| | - Masaru Kubota
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Sarah Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joanne Jones
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Systems Immunology, Weizmann Institute, Rehovot, Israel
| | - Mark Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Maigan Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Todd M Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Thomas J Connors
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032 USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032 USA
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7
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Chen ACY, Jaiswal S, Martinez D, Yerinde C, Ji K, Miranda V, Fung ME, Weiss SA, Zschummel M, Taguchi K, Garris CS, Mempel TR, Hacohen N, Sen DR. The aged tumor microenvironment limits T cell control of cancer. Nat Immunol 2024; 25:1033-1045. [PMID: 38745085 DOI: 10.1038/s41590-024-01828-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024]
Abstract
The etiology and effect of age-related immune dysfunction in cancer is not completely understood. Here we show that limited priming of CD8+ T cells in the aged tumor microenvironment (TME) outweighs cell-intrinsic defects in limiting tumor control. Increased tumor growth in aging is associated with reduced CD8+ T cell infiltration and function. Transfer of T cells from young mice does not restore tumor control in aged mice owing to rapid induction of T cell dysfunction. Cell-extrinsic signals in the aged TME drive a tumor-infiltrating age-associated dysfunctional (TTAD) cell state that is functionally, transcriptionally and epigenetically distinct from canonical T cell exhaustion. Altered natural killer cell-dendritic cell-CD8+ T cell cross-talk in aged tumors impairs T cell priming by conventional type 1 dendritic cells and promotes TTAD cell formation. Aged mice are thereby unable to benefit from therapeutic tumor vaccination. Critically, myeloid-targeted therapy to reinvigorate conventional type 1 dendritic cells can improve tumor control and restore CD8+ T cell immunity in aging.
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Affiliation(s)
- Alex C Y Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sneha Jaiswal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniela Martinez
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Cansu Yerinde
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Keely Ji
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Velita Miranda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Megan E Fung
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah A Weiss
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Zschummel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kazuhiro Taguchi
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Garris
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Thorsten R Mempel
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Debattama R Sen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
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8
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Chan JD, Scheffler CM, Munoz I, Sek K, Lee JN, Huang YK, Yap KM, Saw NYL, Li J, Chen AXY, Chan CW, Derrick EB, Todd KL, Tong J, Dunbar PA, Li J, Hoang TX, de Menezes MN, Petley EV, Kim JS, Nguyen D, Leung PSK, So J, Deguit C, Zhu J, House IG, Kats LM, Scott AM, Solomon BJ, Harrison SJ, Oliaro J, Parish IA, Quinn KM, Neeson PJ, Slaney CY, Lai J, Beavis PA, Darcy PK. FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy. Nature 2024; 629:201-210. [PMID: 38600376 PMCID: PMC11062918 DOI: 10.1038/s41586-024-07242-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/27/2024] [Indexed: 04/12/2024]
Abstract
Chimeric antigen receptor (CAR) T cell therapy has transformed the treatment of haematological malignancies such as acute lymphoblastic leukaemia, B cell lymphoma and multiple myeloma1-4, but the efficacy of CAR T cell therapy in solid tumours has been limited5. This is owing to a number of factors, including the immunosuppressive tumour microenvironment that gives rise to poorly persisting and metabolically dysfunctional T cells. Analysis of anti-CD19 CAR T cells used clinically has shown that positive treatment outcomes are associated with a more 'stem-like' phenotype and increased mitochondrial mass6-8. We therefore sought to identify transcription factors that could enhance CAR T cell fitness and efficacy against solid tumours. Here we show that overexpression of FOXO1 promotes a stem-like phenotype in CAR T cells derived from either healthy human donors or patients, which correlates with improved mitochondrial fitness, persistence and therapeutic efficacy in vivo. This work thus reveals an engineering approach to genetically enforce a favourable metabolic phenotype that has high translational potential to improve the efficacy of CAR T cells against solid tumours.
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Affiliation(s)
- Jack D Chan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Christina M Scheffler
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Isabelle Munoz
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kevin Sek
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joel N Lee
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Yu-Kuan Huang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kah Min Yap
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicole Y L Saw
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jasmine Li
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Amanda X Y Chen
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Cheok Weng Chan
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Emily B Derrick
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kirsten L Todd
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Junming Tong
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Phoebe A Dunbar
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jiawen Li
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thang X Hoang
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Maria N de Menezes
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Emma V Petley
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joelle S Kim
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Dat Nguyen
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Patrick S K Leung
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Joan So
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Christian Deguit
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joe Zhu
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Imran G House
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Lev M Kats
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Faculty of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Benjamin J Solomon
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Simon J Harrison
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Clinical Haematology and Centre of Excellence for Cellular Immunotherapies, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Jane Oliaro
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kylie M Quinn
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Paul J Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Clare Y Slaney
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Junyun Lai
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Phillip K Darcy
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
- Clinical Haematology and Centre of Excellence for Cellular Immunotherapies, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Department of Immunology, Monash University, Clayton, Victoria, Australia.
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9
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Li F, Dang W, Du Y, Xu X, He P, Zhou Y, Zhu B. Tuberculosis Vaccines and T Cell Immune Memory. Vaccines (Basel) 2024; 12:483. [PMID: 38793734 PMCID: PMC11125691 DOI: 10.3390/vaccines12050483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Tuberculosis (TB) remains a major infectious disease partly due to the lack of an effective vaccine. Therefore, developing new and more effective TB vaccines is crucial for controlling TB. Mycobacterium tuberculosis (M. tuberculosis) usually parasitizes in macrophages; therefore, cell-mediated immunity plays an important role. The maintenance of memory T cells following M. tuberculosis infection or vaccination is a hallmark of immune protection. This review analyzes the development of memory T cells during M. tuberculosis infection and vaccine immunization, especially on immune memory induced by BCG and subunit vaccines. Furthermore, the factors affecting the development of memory T cells are discussed in detail. The understanding of the development of memory T cells should contribute to designing more effective TB vaccines and optimizing vaccination strategies.
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Affiliation(s)
- Fei Li
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
| | - Wenrui Dang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
| | - Yunjie Du
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
| | - Xiaonan Xu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
| | - Pu He
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
| | - Yuhe Zhou
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
| | - Bingdong Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Center for Tuberculosis Research, Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; (F.L.); (W.D.); (Y.D.); (X.X.); (P.H.); (Y.Z.)
- College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China
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10
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Shouse AN, LaPorte KM, Malek TR. Interleukin-2 signaling in the regulation of T cell biology in autoimmunity and cancer. Immunity 2024; 57:414-428. [PMID: 38479359 PMCID: PMC11126276 DOI: 10.1016/j.immuni.2024.02.001] [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: 11/22/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 05/26/2024]
Abstract
Interleukin-2 (IL-2) is a critical cytokine for T cell peripheral tolerance and immunity. Here, we review how IL-2 interaction with the high-affinity IL-2 receptor (IL-2R) supports the development and homeostasis of regulatory T cells and contributes to the differentiation of helper, cytotoxic, and memory T cells. A critical element for each T cell population is the expression of CD25 (Il2rα), which heightens the receptor affinity for IL-2. Signaling through the high-affinity IL-2R also reinvigorates CD8+ exhausted T (Tex) cells in response to checkpoint blockade. We consider the molecular underpinnings reflecting how IL-2R signaling impacts these various T cell subsets and the implications for enhancing IL-2-dependent immunotherapy of autoimmunity, other inflammatory disorders, and cancer.
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Affiliation(s)
- Acacia N Shouse
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kathryn M LaPorte
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Thomas R Malek
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
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11
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Yang Y, Wang Y, Wang Z, Yan H, Gong Y, Hu Y, Jiang Y, Wen S, Xu F, Wang B, Humphries F, Chen Y, Wang X, Yang S. ECSIT facilitates memory CD8 + T cell development by mediating fumarate synthesis during viral infection and tumorigenesis. Nat Cell Biol 2024; 26:450-463. [PMID: 38326554 DOI: 10.1038/s41556-024-01351-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 01/07/2024] [Indexed: 02/09/2024]
Abstract
Memory CD8+ T cells play a crucial role in infection and cancer and mount rapid responses to repeat antigen exposure. Although memory cell transcriptional programmes have been previously identified, the regulatory mechanisms that control the formation of CD8+ T cells have not been resolved. Here we report ECSIT as an essential mediator of memory CD8+ T cell differentiation. Ablation of ECSIT in T cells resulted in loss of fumarate synthesis and abrogated TCF-1 expression via demethylation of the TCF-1 promoter by the histone demethylase KDM5, thereby impairing memory CD8+ T cell development in a cell-intrinsic manner. In addition, ECSIT expression correlated positively with stem-like memory progenitor exhausted CD8+ T cells and the survival of patients with cancer. Our study demonstrates that ECSIT-mediated fumarate synthesis stimulates TCF-1 activity and memory CD8+ T cell development during viral infection and tumorigenesis and highlights the utility of therapeutic fumarate analogues and PD-L1 inhibition for tumour immunotherapy.
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Affiliation(s)
- Yongbing Yang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University, Wuxi, China
| | - Yanan Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Huanyu Yan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Gong
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yingchao Hu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuying Jiang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Shuang Wen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Bingwei Wang
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fiachra Humphries
- Division of Innate Immunity, Department of Medicine, UMass Chan Medical School, Worcester, MA, USA.
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, China.
| | - Xi Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.
| | - Shuo Yang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Gusu School, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.
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12
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Li Y, Han M, Wei H, Huang W, Chen Z, Zhang T, Qian M, Jing L, Nan G, Sun X, Dai S, Wang K, Jiang J, Zhu P, Chen L. Id2 epigenetically controls CD8 + T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex. Cell Mol Immunol 2024; 21:292-308. [PMID: 38287103 PMCID: PMC10902300 DOI: 10.1038/s41423-023-01118-6] [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: 07/31/2022] [Accepted: 12/01/2023] [Indexed: 01/31/2024] Open
Abstract
CD8+ T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6+ progenitor exhausted (Texprog) and Tim-3+ terminally exhausted (Texterm) subpopulations. Inhibitor of DNA binding protein 2 (Id2) has been shown to play important roles in T-cell development and CD8+ T-cell immunity. However, the role of Id2 in CD8+ T-cell exhaustion is unclear. Here, we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm cells. Genetic deletion of Id2 dampens CD8+ T-cell-mediated immune responses and the maintenance of stem-like CD8+ T-cell subpopulations, suppresses PD-1 blockade and increases tumor susceptibility. Mechanistically, through its HLH domain, Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex, and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase LSD1. Therefore, Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter, modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+ Texprog cells. An LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing mice. Inhibition of LSD1 increases the abundance of Slamf6+Tim-3- Texprog cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+ T cells. This study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8+ T-cell exhaustion, and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.
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Affiliation(s)
- Yiming Li
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Mingwei Han
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Haolin Wei
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Wan Huang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Zhinan Chen
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Tianjiao Zhang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Meirui Qian
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Lin Jing
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Gang Nan
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Xiuxuan Sun
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Shuhui Dai
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Kun Wang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Jianli Jiang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China.
| | - Ping Zhu
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China.
| | - Liang Chen
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China.
- School of Medicine, Shanghai University, Shanghai, 200444, China.
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13
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Liu Z, Zhao Z, Xie H, Lu N, Liu J, Jiao Q. CXCR5 +TIM-3 -PD-1 + stem-like cytotoxic CD8 + T cells: elevated in chronic rhinosinusitis and associated with disease severity. Front Immunol 2024; 15:1295309. [PMID: 38426098 PMCID: PMC10902131 DOI: 10.3389/fimmu.2024.1295309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 01/25/2024] [Indexed: 03/02/2024] Open
Abstract
Background Chronic rhinosinusitis (CRS) is a chronic inflammatory disease with an autoimmune background. Altered expression levels of T cell immunoglobulin and mucin-domain containing-3 (TIM-3), C-X-C chemokine receptor type 5 (CXCR5), and programmed cell death protein 1 (PD-1) are implicated in the progression of inflammatory and autoimmune diseases. Moreover, CXCR5+TIM-3-PD-1+ stem-like cytotoxic T cells function as memory stem cells during chronic disease processes and retain cytotoxicity-related gene networks. Objectives To explore the expressions of CXCR5, TIM-3, and PD-1 on T cells and their correlation with clinical parameters in CRS. Methods Flow cytometry was used to assess the expressions and co-expressions of CXCR5, TIM-3, and PD-1 on T cells in the tissues of the paranasal sinus and peripheral blood of patients with CRS as well as healthy controls. Immunofluorescence was used to assess the co-localization of TIM-3, CXCR5, and PD-1 with T cells. The disease severity of our patients with CRS was evaluated using the Lund-Mackay score. A complete blood count was also performed for the patients with CRS. Results Expression levels of CXCR5 and PD-1 on T cells were significantly increased in the nasal tissues of patients with CRS. Compared with those in healthy controls, patients with CRS had high percentages of CXCR5+TIM-3-PD-1+ CD8+ and CD4+ T cells in nasal tissues, while no significant difference was observed in peripheral blood levels. Patients with CRS had a higher density of nasal CXCR5+TIM-3-PD-1+ T cells than that in healthy controls. CXCR5+TIM-3-PD-1+ CD8+ T cell levels in the nasal polyps of patients with CRS were negatively correlated with the patients' Lund-Mackay scores. The levels of CXCR5+TIM-3-PD-1+ T cells in nasal tissues were also negatively associated with disease duration and positively associated with the chronic inflammatory state of CRS. Conclusions The level of CXCR5+TIM-3-PD-1+ stem cell-like T cells, especially CXCR5+TIM-3-PD-1+ CD8+ T cells, is increased in CRS. Therefore, inducing CXCR5+TIM-3-PD-1+ T cell exhaustion may be an effective immunotherapy for CRS.
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Affiliation(s)
- Zhichen Liu
- Department of Ear, Nose, and Throat, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zixuan Zhao
- The First Clinical Medicine School, Suzhou Medical College, Suzhou University, Suzhou, China
| | - Huanxia Xie
- Department of Ear, Nose, and Throat, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ning Lu
- Department of Ear, Nose, and Throat, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jisheng Liu
- Department of Ear, Nose, and Throat, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qingqing Jiao
- Department of Dermatology, The First Affiliated Hospital of Soochow University, Suzhou, China
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14
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McManus DT, Valanparambil RM, Medina CB, Hu Y, Scharer CD, Sobierajska E, Chang DY, Wieland A, Lee J, Nasti TH, Hashimoto M, Ross JL, Prokhnevska N, Cardenas MA, Gill AL, Clark EC, Abadie K, Kueh HY, Kaye J, Au-Yeung BB, Kissick HT, Ahmed R. Early generation of a precursor CD8 T cell that can adapt to acute or chronic viral infection. RESEARCH SQUARE 2024:rs.3.rs-3922168. [PMID: 38410458 PMCID: PMC10896375 DOI: 10.21203/rs.3.rs-3922168/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Virus specific PD-1+ TCF-1+ TOX+ stem-like CD8+ T cells are essential for maintaining T cell responses during chronic infection and are also critical for PD-1 directed immunotherapy. In this study we have used the mouse model of chronic LCMV infection to examine when these virus specific stem-like CD8+ T cells are generated during the course of chronic infection and what is the role of antigen in maintaining the stem-like program. We found that these stem-like CD8+ T cells are generated early (day 5) during chronic infection and that antigen is essential for maintaining their stem-like program. This early generation of stem-like CD8+ T cells suggested that the fate commitment to this cell population was agnostic to the eventual outcome of infection and the immune system prepares a priori for a potential chronic infection. Indeed, we found that an identical virus specific stem-cell like CD8+ T cell population was also generated during acute LCMV infection but these cells were lost once the virus was cleared. To determine the fate of these early PD-1+TCF-1+TOX+ stem-like CD8+ T cells that are generated during both acute and chronic LCMV infection we set up two reciprocal adoptive transfer experiments. In the first experiment we transferred day 5 stem-like CD8+ T cells from chronically infected into acutely infected mice and examined their differentiation after viral clearance. We found that these early stem-like CD8+ T cells downregulated canonical markers of the chronic stem-like CD8+ T cells and expressed markers (CD127 and CD62L) associated with central memory CD8+ T cells. In the second experiment, we transferred day 5 stem-like cells from acutely infected mice into chronically infected mice and found that these CD8+ T cells could function like resource cells after transfer into a chronic environment by generating effector CD8+ T cells in both lymphoid and non-lymphoid tissues while also maintaining the number of stem-like CD8+ T cells. These findings provide insight into the generation and maintenance of virus specific stem-like CD8+ T cells that play a critical role in chronic viral infection. In particular, our study highlights the early generation of stem-like CD8+ T cells and their ability to adapt to either an acute or chronic infection. These findings are of broad significance since these novel stem-like CD8+ T cells play an important role in not only viral infections but also in cancer and autoimmunity.
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Affiliation(s)
- Daniel T. McManus
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- These authors contributed equally
| | - Rajesh M. Valanparambil
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- These authors contributed equally
| | - Christopher B. Medina
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Yinghong Hu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ewelina Sobierajska
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Y. Chang
- Department of Pathology, Mass General Brigham, Harvard Medical School, Boston, MA, USA
| | - Andreas Wieland
- Department of Otolaryngology, The Ohio State University College of Medicine, Columbus, OH
| | - Judong Lee
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Tahseen H. Nasti
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Masao Hashimoto
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - James L. Ross
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nataliya Prokhnevska
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria A. Cardenas
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Amanda L. Gill
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Elisa C. Clark
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Kathleen Abadie
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jonathan Kaye
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Byron B. Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Haydn T. Kissick
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
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15
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Marchesini Tovar G, Gallen C, Bergsbaken T. CD8+ Tissue-Resident Memory T Cells: Versatile Guardians of the Tissue. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:361-368. [PMID: 38227907 PMCID: PMC10794029 DOI: 10.4049/jimmunol.2300399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/07/2023] [Indexed: 01/18/2024]
Abstract
Tissue-resident memory T (Trm) cells are a subset of T cells maintained throughout life within nonlymphoid tissues without significant contribution from circulating memory T cells. CD8+ Trm cells contribute to both tissue surveillance and direct elimination of pathogens through a variety of mechanisms. Reactivation of these Trm cells during infection drives systematic changes within the tissue, including altering the state of the epithelium, activating local immune cells, and contributing to the permissiveness of the tissue for circulating immune cell entry. Trm cells can be further classified by their functional outputs, which can be either subset- or tissue-specific, and include proliferation, tissue egress, and modulation of tissue physiology. These functional outputs of Trm cells are linked to the heterogeneity and plasticity of this population, and uncovering the unique responses of different Trm cell subsets and their role in immunity will allow us to modulate Trm cell responses for optimal control of disease.
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Affiliation(s)
- Giuseppina Marchesini Tovar
- Center for Immunity and Inflammation, Department of Pathology, Immunology, and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, NJ
| | - Corey Gallen
- Center for Immunity and Inflammation, Department of Pathology, Immunology, and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, NJ
| | - Tessa Bergsbaken
- Center for Immunity and Inflammation, Department of Pathology, Immunology, and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, NJ
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16
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Wang Y, He S, Calendo G, Bui T, Tian Y, Lee CY, Zhou Y, Zhao X, Abraham C, Mo W, Chen M, Sanders-Braggs R, Madzo J, Issa JP, Hexner EO, Wiest DL, Reshef R, Xue HH, Zhang Y. Tissue-infiltrating alloreactive T cells require Id3 to deflect PD-1-mediated immune suppression during GVHD. Blood 2024; 143:166-177. [PMID: 37871574 PMCID: PMC10797551 DOI: 10.1182/blood.2023021126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/25/2023] Open
Abstract
ABSTRACT Persisting alloreactive donor T cells in target tissues are a determinant of graft-versus-host disease (GVHD), but the transcriptional regulators that control the persistence and function of tissue-infiltrating T cells remain elusive. We demonstrate here that Id3, a DNA-binding inhibitor, is critical for sustaining T-cell responses in GVHD target tissues in mice, including the liver and intestine. Id3 loss results in aberrantly expressed PD-1 in polyfunctional T helper 1 (Th1) cells, decreased tissue-infiltrating PD-1+ polyfunctional Th1 cell numbers, impaired maintenance of liver TCF-1+ progenitor-like T cells, and inhibition of GVHD. PD-1 blockade restores the capacity of Id3-ablated donor T cells to mediate GVHD. Single-cell RNA-sequencing analysis revealed that Id3 loss leads to significantly decreased CD28- and PI3K/AKT-signaling activity in tissue-infiltrating polyfunctional Th1 cells, an indicator of active PD-1/PD-L1 effects. Id3 is also required for protecting CD8+ T cells from the PD-1 pathway-mediated suppression during GVHD. Genome-wide RNA-sequencing analysis reveals that Id3 represses transcription factors (e.g., Nfatc2, Fos, Jun, Ets1, and Prdm1) that are critical for PD-1 transcription, exuberant effector differentiation, and interferon responses and dysfunction of activated T cells. Id3 achieves these effects by restraining the chromatin accessibility for these transcription factors. Id3 ablation in donor T cells preserved their graft vs tumor effects in mice undergoing allogeneic hematopoietic stem cell transplantation. Furthermore, CRISPR/Cas9 knockout of ID3 in human CD19-directed chimeric antigen receptor T cells retained their antitumor activity in NOD/SCID/IL2Rg-/- mice early after administration. These findings identify that ID3 is an important target to reduce GVHD, and the gene-editing program of ID3 may have broad implications in T-cell-based immunotherapy.
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Affiliation(s)
- Ying Wang
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Shan He
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Tien Bui
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yuanyuan Tian
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Che Young Lee
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yan Zhou
- Fox Chase Cancer Center, Temple University, Philadelphia, PA
| | - Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Ciril Abraham
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Wenbin Mo
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Mimi Chen
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | | | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, NJ
| | | | - Elizabeth O. Hexner
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David L. Wiest
- Fox Chase Cancer Center, Temple University, Philadelphia, PA
| | - Ran Reshef
- Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yi Zhang
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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17
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Bernardi C, Simonetta F. Id3 keeps the PD-1 checkpoint in check in GVHD. Blood 2024; 143:103-104. [PMID: 38206642 DOI: 10.1182/blood.2023022712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
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18
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Zhu S, Liu J, Patel V, Zhao X, Peng W, Xue HH. Antigen exposure reshapes chromatin architecture in central memory CD8 + T cells and imprints enhanced recall capacity. Proc Natl Acad Sci U S A 2023; 120:e2313476120. [PMID: 38085779 PMCID: PMC10742382 DOI: 10.1073/pnas.2313476120] [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: 08/05/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
CD62L+ central memory CD8+ T (TCM) cells provide enhanced protection than naive cells; however, the underlying mechanism, especially the contribution of higher-order genomic organization, remains unclear. Systematic Hi-C analyses reveal that antigen-experienced CD8+ T cells undergo extensive rewiring of chromatin interactions (ChrInt), with TCM cells harboring specific interaction hubs compared with naive CD8+ T cells, as observed at cytotoxic effector genes such as Ifng and Tbx21. TCM cells also acquire de novo CTCF (CCCTC-binding factor) binding sites, which are not only strongly associated with TCM-specific hubs but also linked to increased activities of local gene promoters and enhancers. Specific ablation of CTCF in TCM cells impairs rapid induction of genes in cytotoxic program, energy supplies, transcription, and translation by recall stimulation. Therefore, acquisition of CTCF binding and ChrInt hubs by TCM cells serves as a chromatin architectural basis for their transcriptomic dynamics in primary response and for imprinting the code of "recall readiness" against secondary challenge.
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Affiliation(s)
- Shaoqi Zhu
- Department of Physics, The George Washington University, Washington, DC20052
| | - Jia Liu
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - Vanita Patel
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - Xiuyi Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
- Solon High School, Solon, OH44139
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC20052
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
- New Jersey Veterans Affairs Health Care System, East Orange, NJ07018
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19
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Evangelous TD, Berry M, Venkatayogi S, LeMaster C, Geanes ES, De Naeyer N, DeMarco T, Shen X, Li H, Hora B, Solomonis N, Misamore J, Lewis MG, Denny TN, Montefiori D, Shaw GM, Wiehe K, Bradley T, Williams WB. Host immunity associated with spontaneous suppression of viremia in therapy-naïve young rhesus macaques following neonatal SHIV infection. J Virol 2023; 97:e0109423. [PMID: 37874153 PMCID: PMC10688376 DOI: 10.1128/jvi.01094-23] [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: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Despite the advent of highly active anti-retroviral therapy, people are still dying from HIV-related causes, many of whom are children, and a protective vaccine or cure is needed to end the HIV pandemic. Understanding the nature and activation states of immune cell subsets during infection will provide insights into the immunologic milieu associated with viremia suppression that can be harnessed via therapeutic strategies to achieve a functional cure, but these are understudied in pediatric subjects. We evaluated humoral and adaptive host immunity associated with suppression of viremia in rhesus macaques infected soon after birth with a pathogenic SHIV. The results from our study provide insights into the immune cell subsets and functions associated with viremia control in young macaques that may translate to pediatric subjects for the design of future anti-viral strategies in HIV-1-infected infants and children and contribute to an understudied area of HIV-1 pathogenesis in pediatric subjects.
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Affiliation(s)
- Tyler D. Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Cas LeMaster
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Eric S. Geanes
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Nicole De Naeyer
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Todd DeMarco
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | | | | | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Todd Bradley
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, Missouri, USA
- Departments of Pediatrics and Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
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20
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Capelle CM, Ciré S, Hedin F, Hansen M, Pavelka L, Grzyb K, Kyriakis D, Hunewald O, Konstantinou M, Revets D, Tslaf V, Marques TM, Gomes CPC, Baron A, Domingues O, Gomez M, Zeng N, Betsou F, May P, Skupin A, Cosma A, Balling R, Krüger R, Ollert M, Hefeng FQ. Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females. Nat Commun 2023; 14:7461. [PMID: 37985656 PMCID: PMC10662447 DOI: 10.1038/s41467-023-43053-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Neuroinflammation in the brain contributes to the pathogenesis of Parkinson's disease (PD), but the potential dysregulation of peripheral immunity has not been systematically investigated for idiopathic PD (iPD). Here we showed an elevated peripheral cytotoxic immune milieu, with more terminally-differentiated effector memory (TEMRA) CD8 T, CD8+ NKT cells and circulating cytotoxic molecules in fresh blood of patients with early-to-mid iPD, especially females, after analyzing > 700 innate and adaptive immune features. This profile, also reflected by fewer CD8+FOXP3+ T cells, was confirmed in another subcohort. Co-expression between cytotoxic molecules was selectively enhanced in CD8 TEMRA and effector memory (TEM) cells. Single-cell RNA-sequencing analysis demonstrated the accelerated differentiation within CD8 compartments, enhanced cytotoxic pathways in CD8 TEMRA and TEM cells, while CD8 central memory (TCM) and naïve cells were already more-active and transcriptionally-reprogrammed. Our work provides a comprehensive map of dysregulated peripheral immunity in iPD, proposing candidates for early diagnosis and treatments.
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Affiliation(s)
- Christophe M Capelle
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de Université, L-4365, Esch-sur-Alzette, Luxembourg
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8049, Zurich, Switzerland
| | - Séverine Ciré
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Eligo Bioscience, 111 Av. de France, 75013, Paris, France
| | - Fanny Hedin
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Maxime Hansen
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 4 Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 4 Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
| | - Dimitrios Kyriakis
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Maria Konstantinou
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Dominique Revets
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Vera Tslaf
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de Université, L-4365, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Tainá M Marques
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Clarissa P C Gomes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
| | - Alexandre Baron
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Olivia Domingues
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Mario Gomez
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Ni Zeng
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de Université, L-4365, Esch-sur-Alzette, Luxembourg
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1 Rue Louis Rech, L-3555, Dudelange, Luxembourg
- CRBIP, Institut Pasteur, Université Paris Cité, Paris, France
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Department of Physics and Material Science, University of Luxembourg, 162a Av. de la Faïencerie, L-1511, Luxembourg, Luxembourg
- Department of Neurosciences, University California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093-0662, USA
| | - Antonio Cosma
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Institute of Molecular Psychiatry, University of Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 4 Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis (ORCA), University of Southern Denmark, Odense, 5000C, Denmark.
| | - Feng Q Hefeng
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.
- Data Integration and Analysis Unit, Luxembourg Institute of Health (LIH), L-1445, Strassen, Luxembourg.
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21
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Vizcarra EA, Ulu A, Landrith TA, Qiu X, Godzik A, Wilson EH. Group 1 metabotropic glutamate receptor expression defines a T cell memory population during chronic Toxoplasma infection that enhances IFN-gamma and perforin production in the CNS. Brain Behav Immun 2023; 114:131-143. [PMID: 37604212 DOI: 10.1016/j.bbi.2023.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
Within the brain, a pro-inflammatory response is essential to prevent clinical disease due to Toxoplasma gondii reactivation. Infection in the immunocompromised leads to lethal Toxoplasmic encephalitis while in the immunocompetent, there is persistent low-grade inflammation which is devoid of clinical symptoms. This signifies that there is a well-balanced and regulated inflammatory response to T. gondii in the brain. T cells are the dominant immune cells that prevent clinical disease, and this is mediated through the secretion of effector molecules such as perforins and IFN-γ. The presence of cognate antigen, the expression of survival cytokines, and the alteration of the epigenetic landscape drive the development of memory T cells. However, specific extrinsic signals that promote the formation and maintenance of memory T cells within tissue are poorly understood. During chronic infection, there is an increase in extracellular glutamate that, due to its function as an excitatory neurotransmitter, is normally tightly controlled in the CNS. Here we demonstrate that CD8+ T cells from the T. gondii-infected brain parenchyma are enriched for metabotropic glutamate receptors (mGluR's). Characterization studies determined that mGluR+ expression by CD8+ T cells defines a distinct memory population at the transcriptional and protein level. Finally, using receptor antagonists and agonists we demonstrate mGluR signaling is required for optimal CD8+ T cell production of the effector cytokine IFNγ. This work suggests that glutamate is an important environmental signal of inflammation that promotes T cell function. Understanding glutamate's influence on T cells in the brain can provide insights into the mechanisms that govern protective immunity against CNS-infiltrating pathogens and neuroinflammation.
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Affiliation(s)
- Edward A Vizcarra
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Arzu Ulu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Tyler A Landrith
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Xinru Qiu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Adam Godzik
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States
| | - Emma H Wilson
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, United States.
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22
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Santosa EK, Sun JC. Cardinal features of immune memory in innate lymphocytes. Nat Immunol 2023; 24:1803-1812. [PMID: 37828377 PMCID: PMC10998651 DOI: 10.1038/s41590-023-01607-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/28/2023] [Indexed: 10/14/2023]
Abstract
The ability of vertebrates to 'remember' previous infections had once been attributed exclusively to adaptive immunity. We now appreciate that innate lymphocytes also possess memory properties akin to those of adaptive immune cells. In this Review, we draw parallels from T cell biology to explore the key features of immune memory in innate lymphocytes, including quantity, quality, and location. We discuss the signals that trigger clonal or clonal-like expansion in innate lymphocytes, and highlight recent studies that shed light on the complex cellular and molecular crosstalk between metabolism, epigenetics, and transcription responsible for differentiating innate lymphocyte responses towards a memory fate. Additionally, we explore emerging evidence that activated innate lymphocytes relocate and establish themselves in specific peripheral tissues during infection, which may facilitate an accelerated response program akin to those of tissue-resident memory T cells.
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Affiliation(s)
- Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA.
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23
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Smith NP, Yan Y, Pan Y, Williams JB, Manakongtreecheep K, Pant S, Zhao J, Tian T, Pan T, Stingley C, Wu K, Zhang J, Kley AL, Sorger PK, Villani AC, Kupper TS. Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560006. [PMID: 37873428 PMCID: PMC10592877 DOI: 10.1101/2023.09.29.560006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Tissue-resident memory T (T RM ) cells play a central role in immune responses to pathogens across all barrier tissues after infection. However, the underlying mechanisms that drive T RM differentiation and priming for their recall effector function remains unclear. In this study, we leveraged both newly generated and publicly available single-cell RNA-sequencing (scRNAseq) data generated across 10 developmental time points to define features of CD8 T RM across both skin and small-intestine intraepithelial lymphocytes (siIEL). We employed linear modeling to capture temporally-associated gene programs that increase their expression levels in T cell subsets transitioning from an effector to a memory T cell state. In addition to capturing tissue-specific gene programs, we defined a consensus T RM signature of 60 genes across skin and siIEL that can effectively distinguish T RM from circulating T cell populations, providing a more specific T RM signature than what was previously generated by comparing bulk T RM to naïve or non-tissue resident memory populations. This updated T RM signature included the AP-1 transcription factor family members Fos, Fosb and Fosl2 . Moreover, ATACseq analysis detected an enrichment of AP-1-specific motifs at open chromatin sites in mature T RM . CyCIF tissue imaging detected nuclear co-localization of AP-1 members Fosb and Junb in resting CD8 T RM >100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in T RM biology and suggests a novel mechanism for rapid reactivation of resting T RM in tissue upon antigen encounter.
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24
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Xie L, Fang J, Yu J, Zhang W, He Z, Ye L, Wang H. The role of CD4 + T cells in tumor and chronic viral immune responses. MedComm (Beijing) 2023; 4:e390. [PMID: 37829505 PMCID: PMC10565399 DOI: 10.1002/mco2.390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Immunotherapies are mainly aimed to promote a CD8+ T cell response rather than a CD4+ T cell response as cytotoxic T lymphocytes (CTLs) can directly kill target cells. Recently, CD4+ T cells have received more attention due to their diverse roles in tumors and chronic viral infections. In antitumor and antichronic viral responses, CD4+ T cells relay help signals through dendritic cells to indirectly regulate CD8+ T cell response, interact with B cells or macrophages to indirectly modulate humoral immunity or macrophage polarization, and inhibit tumor blood vessel formation. Additionally, CD4+ T cells can also exhibit direct cytotoxicity toward target cells. However, regulatory T cells exhibit immunosuppression and CD4+ T cells become exhausted, which promote tumor progression and chronic viral persistence. Finally, we also outline immunotherapies based on CD4+ T cells, including adoptive cell transfer, vaccines, and immune checkpoint blockade. Overall, this review summarizes diverse roles of CD4+ T cells in the antitumor or protumor and chronic viral responses, and also highlights the immunotherapies based on CD4+ T cells, giving a better understanding of their roles in tumors and chronic viral infections.
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Affiliation(s)
- Luoyingzi Xie
- Institute of Hepatopancreatobiliary SurgeryChongqing General HospitalChongqingChina
- The Institute of ImmunologyThird Military Medical University (Army Medical University)ChongqingChina
| | - Jingyi Fang
- The Institute of ImmunologyThird Military Medical University (Army Medical University)ChongqingChina
| | - Juncheng Yu
- Department of Thoracic SurgeryXinqiao Hospital Third Military Medical University (Army Medical University)ChongqingChina
| | - Weinan Zhang
- Department of Plastic & Cosmetic SurgeryArmy Medical Center of PLAAmy Medical UniversityChongqingChina
| | - Zhiqiang He
- Department of Plastic & Cosmetic SurgeryArmy Medical Center of PLAAmy Medical UniversityChongqingChina
| | - Lilin Ye
- The Institute of ImmunologyThird Military Medical University (Army Medical University)ChongqingChina
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary SurgeryChongqing General HospitalChongqingChina
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25
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Santosa EK, Kim H, Rückert T, Le Luduec JB, Abbasi AJ, Wingert CK, Peters L, Frost JN, Hsu KC, Romagnani C, Sun JC. Control of nutrient uptake by IRF4 orchestrates innate immune memory. Nat Immunol 2023; 24:1685-1697. [PMID: 37697097 PMCID: PMC11098052 DOI: 10.1038/s41590-023-01620-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Natural killer (NK) cells are innate cytotoxic lymphocytes with adaptive immune features, including antigen specificity, clonal expansion and memory. As such, NK cells share many transcriptional and epigenetic programs with their adaptive CD8+ T cell siblings. Various signals ranging from antigen, co-stimulation and proinflammatory cytokines are required for optimal NK cell responses in mice and humans during virus infection; however, the integration of these signals remains unclear. In this study, we identified that the transcription factor IRF4 integrates signals to coordinate the NK cell response during mouse cytomegalovirus infection. Loss of IRF4 was detrimental to the expansion and differentiation of virus-specific NK cells. This defect was partially attributed to the inability of IRF4-deficient NK cells to uptake nutrients required for survival and memory generation. Altogether, these data suggest that IRF4 is a signal integrator that acts as a secondary metabolic checkpoint to orchestrate the adaptive response of NK cells during viral infection.
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Affiliation(s)
- Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Hyunu Kim
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
| | | | - Aamna J Abbasi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lila Peters
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe N Frost
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katharine C Hsu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Leibniz-Science Campus Chronic Inflammation, Berlin, Germany
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA.
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26
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Kang H, Sun H, Yang Y, Tuong ZK, Shu M, Wei Y, Zhang Y, Yu D, Tao Y. Autoimmune uveitis in Behçet's disease and Vogt-Koyanagi-Harada disease differ in tissue immune infiltration and T cell clonality. Clin Transl Immunology 2023; 12:e1461. [PMID: 37720629 PMCID: PMC10503407 DOI: 10.1002/cti2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/16/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023] Open
Abstract
Objectives Non-infectious uveitis is often secondary to systemic autoimmune diseases, with Behçet's disease (BD) and Vogt-Koyanagi-Harada disease (VKHD) as the two most common causes. Uveitis in BD and VKHD can show similar clinical manifestations, but the underlying immunopathogenesis remains unclear. Methods To understand immune landscapes in inflammatory eye tissues, we performed single-cell RNA paired with T cell receptor (TCR) sequencing of immune cell infiltrates in aqueous humour from six patients with BD (N = 3) and VKHD (N = 3) uveitis patients. Results Although T cells strongly infiltrated in both types of autoimmune uveitis, myeloid cells only significantly presented in BD uveitis but not in VKHD uveitis. Conversely, VKHD uveitis but not BD uveitis showed an overwhelming dominance by CD4+ T cells (> 80%) within the T cell population due to expansion of CD4+ T cell clusters with effector memory (Tem) phenotypes. Correspondingly, VKHD uveitis demonstrated a selective expansion of CD4+ T cell clones which were enriched in pro-inflammatory Granzyme H+ CD4+ Tem cluster and showed TCR and Th1 pathway activation. In contrast, BD uveitis showed a preferential expansion of CD8+ T cell clones in pro-inflammatory Granzyme H+ CD8+ Tem cluster, and pathway activation for cytoskeleton remodelling, cellular adhesion and cytotoxicity. Conclusion Single-cell analyses of ocular tissues reveal distinct landscapes of immune cell infiltration and T-cell clonal expansions between VKHD and BD uveitis. Preferential involvements of pro-inflammatory CD4+ Th1 cells in VKHD and cytotoxic CD8+ T cells in BD suggest a difference in disease immunopathogenesis and can guide precision disease management.
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Affiliation(s)
- Hao Kang
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
| | - Hongjian Sun
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yang Yang
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Zewen K Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Minglei Shu
- Shandong Artificial Intelligence InstituteQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yunbo Wei
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Yu Zhang
- School of Pharmaceutical Sciences, Laboratory of Immunology for Environment and Health, Shandong Analysis and Test CenterQilu University of Technology (Shandong Academy of Sciences)JinanChina
| | - Di Yu
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- Ian Frazer Centre for Children's Immunotherapy Research, Children's Health Research Centre, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang HospitalCapital Medical UniversityBeijingChina
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27
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Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M. Hallmarks of CD8 + T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat Immunol 2023; 24:1527-1539. [PMID: 37537361 PMCID: PMC10878719 DOI: 10.1038/s41590-023-01578-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
Tumor-specific CD8+ T cells (TST) in patients with cancer are dysfunctional and unable to halt cancer progression. TST dysfunction, also known as exhaustion, is thought to be driven by chronic T cell antigen receptor (TCR) stimulation over days to weeks. However, we know little about the interplay between CD8+ T cell function, cell division and epigenetic remodeling within hours of activation. Here, we assessed early CD8+ T cell differentiation, cell division, chromatin accessibility and transcription in tumor-bearing mice and acutely infected mice. Surprisingly, despite robust activation and proliferation, TST had near complete effector function impairment even before undergoing cell division and had acquired hallmark chromatin accessibility features previously associated with later dysfunction/exhaustion. Moreover, continued tumor/antigen exposure drove progressive epigenetic remodeling, 'imprinting' the dysfunctional state. Our study reveals the rapid divergence of T cell fate choice before cell division in the context of tumors versus infection.
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Affiliation(s)
- Michael W Rudloff
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Natalie R Favret
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Jessica J Roetman
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Carlos R Detrés Román
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Megan M Erwin
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Kristen A Murray
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Sriya T Jonnakuti
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Department of Pathology, Microbiology, and Immunology, Vanderbilt School of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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28
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Chen Y, Xu Z, Sun H, Ouyang X, Han Y, Yu H, Wu N, Xie Y, Su B. Regulation of CD8 + T memory and exhaustion by the mTOR signals. Cell Mol Immunol 2023; 20:1023-1039. [PMID: 37582972 PMCID: PMC10468538 DOI: 10.1038/s41423-023-01064-3] [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: 03/18/2023] [Accepted: 07/02/2023] [Indexed: 08/17/2023] Open
Abstract
CD8+ T cells are the key executioners of the adaptive immune arm, which mediates antitumor and antiviral immunity. Naïve CD8+ T cells develop in the thymus and are quickly activated in the periphery after encountering a cognate antigen, which induces these cells to proliferate and differentiate into effector cells that fight the initial infection. Simultaneously, a fraction of these cells become long-lived memory CD8+ T cells that combat future infections. Notably, the generation and maintenance of memory cells is profoundly affected by various in vivo conditions, such as the mode of primary activation (e.g., acute vs. chronic immunization) or fluctuations in host metabolic, inflammatory, or aging factors. Therefore, many T cells may be lost or become exhausted and no longer functional. Complicated intracellular signaling pathways, transcription factors, epigenetic modifications, and metabolic processes are involved in this process. Therefore, understanding the cellular and molecular basis for the generation and fate of memory and exhausted CD8+ cells is central for harnessing cellular immunity. In this review, we focus on mammalian target of rapamycin (mTOR), particularly signaling mediated by mTOR complex (mTORC) 2 in memory and exhausted CD8+ T cells at the molecular level.
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Affiliation(s)
- Yao Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziyang Xu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongxiang Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinxing Ouyang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Department of Tumor Biology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuheng Han
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Haihui Yu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ningbo Wu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yiting Xie
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, and The Ministry of Education Key Laboratory of Cell Death and Differentiation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Tumor Biology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.
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29
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Wang W, Garcia C, Shao F, Cohen JA, Bai Y, Fine A, Ai X. Lung dopaminergic nerves facilitate the establishment of T H2 resident memory cells in early life. J Allergy Clin Immunol 2023; 152:386-399. [PMID: 36841266 PMCID: PMC10440294 DOI: 10.1016/j.jaci.2023.02.011] [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: 08/31/2022] [Revised: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND Allergic asthma develops from allergen exposure in early childhood and progresses into adulthood. The central mediator of progressive allergic asthma is allergen-specific, TH2-resident memory cells (TRMs). Although the crosstalk between nerves and immune cells plays an established role in acute allergic inflammation, whether nerves facilitate the establishment of TH2-TRMs in the immature lung following early life allergen exposure is unknown. OBJECTIVES The aim of this study was to identify nerve-derived signals that act in TH2 effector cells to regulate the tissue residency in the immature lung. METHODS Following neonatal allergen exposure, allergen-specific TH2-TRMs were tracked temporally and spatially in relationship to developing sympathetic nerves in the lung. Functional mediators of dopamine signaling in the establishment of TH2-TRMs were identified by in vitro bulk RNA-sequencing of dopamine-treated TH2 cells followed by in vivo assessment of candidate genes using adoptive transfer of TH2 cells with viral gene knockdown. RESULTS This study found that sympathetic nerves produce dopamine and reside in proximity to TH2 effector cells during the contraction phase following neonatal allergen exposure. Dopamine signals via DRD4 on TH2 cells to elevate IL2RA and epigenetically facilitate type 2 cytokine expression. Blockade of dopamine-DRD4 signaling following neonatal allergen exposure impairs lung residence of TH2 cells and ameliorates anamnestic inflammation in adults. CONCLUSIONS These results demonstrate that maturing sympathetic nerves enable a dopamine-enriched lung environment in early life that promotes the establishment of allergen-specific TH2-TRMs. The dopamine-DRD4 axis may provide a therapeutic target to modify allergic asthma progression from childhood to adulthood.
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Affiliation(s)
- Wei Wang
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Boston, Mass.
| | - Carolyn Garcia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Mass
| | - Fengzhi Shao
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Jonathan A Cohen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Mass
| | - Yan Bai
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Boston, Mass
| | - Alan Fine
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Xingbin Ai
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Boston, Mass.
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30
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Kornberg A, Botella T, Moon CS, Rao S, Gelbs J, Cheng L, Miller J, Bacarella AM, García-Vilas JA, Vargas J, Yu X, Krupska I, Bush E, Garcia-Carrasquillo R, Lebwohl B, Krishnareddy S, Lewis S, Green PH, Bhagat G, Yan KS, Han A. Gluten induces rapid reprogramming of natural memory αβ and γδ intraepithelial T cells to induce cytotoxicity in celiac disease. Sci Immunol 2023; 8:eadf4312. [PMID: 37450575 PMCID: PMC10481382 DOI: 10.1126/sciimmunol.adf4312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/26/2023] [Indexed: 07/18/2023]
Abstract
Celiac disease (CD) is an autoimmune disease in which intestinal inflammation is induced by dietary gluten. The means through which gluten-specific CD4+ T cell activation culminates in intraepithelial T cell (T-IEL)-mediated intestinal damage remain unclear. Here, we performed multiplexed single-cell analysis of intestinal and gluten-induced peripheral blood T cells from patients in different CD states and healthy controls. Untreated, active, and potential CD were associated with an enrichment of activated intestinal T cell populations, including CD4+ follicular T helper (TFH) cells, regulatory T cells (Tregs), and natural CD8+ αβ and γδ T-IELs. Natural CD8+ αβ and γδ T-IELs expressing activating natural killer cell receptors (NKRs) exhibited a distinct TCR repertoire in CD and persisted in patients on a gluten-free diet without intestinal inflammation. Our data further show that NKR-expressing cytotoxic cells, which appear to mediate intestinal damage in CD, arise from a distinct NKR-expressing memory population of T-IELs. After gluten ingestion, both αβ and γδ T cell clones from this memory population of T-IELs circulated systemically along with gluten-specific CD4+ T cells and assumed a cytotoxic and activating NKR-expressing phenotype. Collectively, these findings suggest that cytotoxic T cells in CD are rapidly mobilized in parallel with gluten-specific CD4+ T cells after gluten ingestion.
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Affiliation(s)
- Adam Kornberg
- Columbia Center for Translational Immunology, Columbia University; New York, NY
- Department of Microbiology and Immunology, Columbia University; New York, NY
| | - Theo Botella
- Columbia Center for Human Development, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Department of Genetics and Development, Columbia University; New York, NY
| | - Christine S. Moon
- Columbia Center for Translational Immunology, Columbia University; New York, NY
- Columbia Center for Human Development, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Department of Genetics and Development, Columbia University; New York, NY
| | - Samhita Rao
- Columbia Center for Translational Immunology, Columbia University; New York, NY
- Department of Microbiology and Immunology, Columbia University; New York, NY
| | - Jared Gelbs
- Columbia Center for Translational Immunology, Columbia University; New York, NY
- Department of Pediatrics, Columbia University; New York, NY
| | - Liang Cheng
- Columbia Center for Human Development, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Department of Genetics and Development, Columbia University; New York, NY
| | - Jonathan Miller
- Columbia Center for Human Development, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Department of Genetics and Development, Columbia University; New York, NY
| | | | - Javier A. García-Vilas
- Columbia Center for Translational Immunology, Columbia University; New York, NY
- Department of Microbiology and Immunology, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
| | - Justin Vargas
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Celiac Disease Center, Columbia University; New York, NY
| | - Xuechen Yu
- Celiac Disease Center, Columbia University; New York, NY
| | - Izabela Krupska
- Department of Systems Biology, Columbia University; New York, NY
| | - Erin Bush
- Department of Systems Biology, Columbia University; New York, NY
| | | | - Benjamin Lebwohl
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Celiac Disease Center, Columbia University; New York, NY
| | - Suneeta Krishnareddy
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Celiac Disease Center, Columbia University; New York, NY
| | - Suzanne Lewis
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Celiac Disease Center, Columbia University; New York, NY
| | - Peter H.R. Green
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Celiac Disease Center, Columbia University; New York, NY
| | - Govind Bhagat
- Celiac Disease Center, Columbia University; New York, NY
- Department of Pathology and Cell Biology, Columbia University; New York, NY
| | - Kelley S. Yan
- Columbia Center for Human Development, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Department of Genetics and Development, Columbia University; New York, NY
| | - Arnold Han
- Columbia Center for Translational Immunology, Columbia University; New York, NY
- Department of Microbiology and Immunology, Columbia University; New York, NY
- Department of Medicine, Digestive and Liver Diseases, Columbia University; New York, NY
- Celiac Disease Center, Columbia University; New York, NY
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Abstract
Cytotoxic CD8+ T cells recognize and eliminate infected or cancerous cells. A subset of CD8+ memory T cells called tissue-resident memory T cells (TRM ) resides in peripheral tissues, monitors the periphery for pathogen invasion, and offers a rapid and potent first line of defense at potential sites of re-infection. TRM cells are found in almost all tissues and are transcriptionally and epigenetically distinct from circulating memory populations, which shows their ability to acclimate to the tissue environment to allow for long-term survival. Recent work and the broader availability of single-cell profiling have highlighted TRM heterogeneity among different tissues, as well as identified specialized subsets within individual tissues, that are time and infection dependent. TRM cell phenotypic and transcriptional heterogeneity has implications for understanding TRM function and longevity. This review aims to summarize and discuss the latest findings on CD8+ TRM heterogeneity using single-cell molecular profiling and explore the potential implications for immune protection and the design of immune therapies.
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Affiliation(s)
- Maximilian Heeg
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Ananda W Goldrath
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
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32
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Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ. The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8 + T cells. Immunity 2023; 56:1320-1340.e10. [PMID: 37315535 DOI: 10.1016/j.immuni.2023.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cell exhaustion (Tex) limits disease control during chronic viral infections and cancer. Here, we investigated the epigenetic factors mediating major chromatin-remodeling events in Tex-cell development. A protein-domain-focused in vivo CRISPR screen identified distinct functions for two versions of the SWI/SNF chromatin-remodeling complex in Tex-cell differentiation. Depletion of the canonical SWI/SNF form, BAF, impaired initial CD8+ T cell responses in acute and chronic infection. In contrast, disruption of PBAF enhanced Tex-cell proliferation and survival. Mechanistically, PBAF regulated the epigenetic and transcriptional transition from TCF-1+ progenitor Tex cells to more differentiated TCF-1- Tex subsets. Whereas PBAF acted to preserve Tex progenitor biology, BAF was required to generate effector-like Tex cells, suggesting that the balance of these factors coordinates Tex-cell subset differentiation. Targeting PBAF improved tumor control both alone and in combination with anti-PD-L1 immunotherapy. Thus, PBAF may present a therapeutic target in cancer immunotherapy.
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Affiliation(s)
- Amy E Baxter
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer E Wu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sydney Drury
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Katherine Dalton
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Simone L Park
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leonel Torres
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brandon W Simone
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Max Klapholz
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elizabeth Freilich
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Victor Alcalde
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Viktoriya Ekshyyan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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33
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Nguyen QP, Takehara KK, Deng TZ, O’Shea S, Heeg M, Omilusik KD, Milner JJ, Quon S, Pipkin ME, Choi J, Crotty S, Goldrath AW. Transcriptional programming of CD4 + T RM differentiation in viral infection balances effector- and memory-associated gene expression. Sci Immunol 2023; 8:eabq7486. [PMID: 37172104 PMCID: PMC10350289 DOI: 10.1126/sciimmunol.abq7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 04/19/2023] [Indexed: 05/14/2023]
Abstract
After resolution of infection, T cells differentiate into long-lived memory cells that recirculate through secondary lymphoid organs or establish residence in tissues. In contrast to CD8+ tissue-resident memory T cells (TRM), the developmental origins and transcriptional regulation of CD4+ TRM remain largely undefined. Here, we investigated the phenotypic, functional, and transcriptional profiles of CD4+ TRM in the small intestine (SI) responding to acute viral infection, revealing a shared gene expression program and chromatin accessibility profile with circulating TH1 and the progressive acquisition of a mature TRM program. Single-cell RNA sequencing identified heterogeneity among established CD4+ TRM, which were predominantly located in the lamina propria, and revealed a population of cells that coexpressed both effector- and memory-associated genes, including the transcriptional regulators Blimp1, Id2, and Bcl6. TH1-associated Blimp1 and Id2 and TFH-associated Bcl6 were required for early TRM formation and development of a mature TRM population in the SI. These results demonstrate a developmental relationship between TH1 effector cells and the establishment of early TRM, as well as highlighted differences in CD4+ versus CD8+ TRM populations, providing insights into the mechanisms underlying the origins, differentiation, and persistence of CD4+ TRM in response to viral infection.
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Affiliation(s)
- Quynh P Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kennidy K Takehara
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Tianda Z Deng
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Shannon O’Shea
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kyla D Omilusik
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - J Justin Milner
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Sara Quon
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida
| | - Jinyong Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
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34
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Mutascio S, Mota T, Franchitti L, Sharma AA, Willemse A, Bergstresser SN, Wang H, Statzu M, Tharp GK, Weiler J, Sékaly RP, Bosinger SE, Paiardini M, Silvestri G, Jones RB, Kulpa DA. CD8 + T cells promote HIV latency by remodeling CD4 + T cell metabolism to enhance their survival, quiescence, and stemness. Immunity 2023; 56:1132-1147.e6. [PMID: 37030290 PMCID: PMC10880039 DOI: 10.1016/j.immuni.2023.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/16/2022] [Accepted: 03/15/2023] [Indexed: 04/10/2023]
Abstract
HIV infection persists during antiretroviral therapy (ART) due to a reservoir of latently infected cells that harbor replication-competent virus and evade immunity. Previous ex vivo studies suggested that CD8+ T cells from people with HIV may suppress HIV expression via non-cytolytic mechanisms, but the mechanisms responsible for this effect remain unclear. Here, we used a primary cell-based in vitro latency model and demonstrated that co-culture of autologous activated CD8+ T cells with HIV-infected memory CD4+ T cells promoted specific changes in metabolic and/or signaling pathways resulting in increased CD4+ T cell survival, quiescence, and stemness. Collectively, these pathways negatively regulated HIV expression and ultimately promoted the establishment of latency. As shown previously, we observed that macrophages, but not B cells, promoted latency in CD4+ T cells. The identification of CD8-specific mechanisms of pro-latency activity may favor the development of approaches to eliminate the viral reservoir in people with HIV.
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Affiliation(s)
- Simona Mutascio
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Talia Mota
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ashish A Sharma
- Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Abigail Willemse
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | - Hong Wang
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maura Statzu
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K Tharp
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jared Weiler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rafick-Pierre Sékaly
- Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Deanna A Kulpa
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
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35
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Duong HG, Choi EJ, Hsu P, Chiang NR, Patel SA, Olvera JG, Liu YC, Lin YH, Yao P, Wong WH, Indralingam CS, Tsai MS, Boland BS, Wang W, Chang JT. Identification of CD8 + T-Cell-Immune Cell Communications in Ileal Crohn's Disease. Clin Transl Gastroenterol 2023; 14:e00576. [PMID: 36854061 PMCID: PMC10208704 DOI: 10.14309/ctg.0000000000000576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
INTRODUCTION Crohn's disease (CD) is a major subtype of inflammatory bowel disease (IBD), a spectrum of chronic intestinal disorders caused by dysregulated immune responses to gut microbiota. Although transcriptional and functional changes in a number of immune cell types have been implicated in the pathogenesis of IBD, the cellular interactions and signals that drive these changes have been less well-studied. METHODS We performed Cellular Indexing of Transcriptomes and Epitopes by sequencing on peripheral blood, colon, and ileal immune cells derived from healthy subjects and patients with CD. We applied a previously published computational approach, NicheNet, to predict immune cell types interacting with CD8 + T-cell subsets, revealing putative ligand-receptor pairs and key transcriptional changes downstream of these cell-cell communications. RESULTS As a number of recent studies have revealed a potential role for CD8 + T-cell subsets in the pathogenesis of IBD, we focused our analyses on identifying the interactions of CD8 + T-cell subsets with other immune cells in the intestinal tissue microenvironment. We identified ligands and signaling pathways that have implicated in IBD, such as interleukin-1β, supporting the validity of the approach, along with unexpected ligands, such as granzyme B, which may play previously unappreciated roles in IBD. DISCUSSION Overall, these findings suggest that future efforts focused on elucidating cell-cell communications among immune and nonimmune cell types may further our understanding of IBD pathogenesis.
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Affiliation(s)
- Han G. Duong
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Eunice J. Choi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA;
| | - Paul Hsu
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Natalie R. Chiang
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Shefali A. Patel
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Jocelyn G. Olvera
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Yun Hsuan Lin
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | | | - Matthew S. Tsai
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, California, USA
| | - Brigid S. Boland
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, California, USA
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36
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Getzler AJ, Frederick MA, Milner JJ, Venables T, Diao H, Toma C, Nagaraja SD, Albao DS, Bélanger S, Tsuda SM, Kim J, Crotty S, Goldrath AW, Pipkin ME. Mll1 pioneers histone H3K4me3 deposition and promotes formation of CD8 + T stem cell memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524461. [PMID: 37090503 PMCID: PMC10120707 DOI: 10.1101/2023.01.18.524461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
CD8 + T cells with stem cell-like properties (T SCM ) sustain adaptive immunity to intracellular pathogens and tumors. However, the developmental origins and chromatin regulatory factors (CRFs) that establish their differentiation are unclear. Using an RNA interference screen of all CRFs we discovered the histone methylase Mll1 was required during T cell receptor (TCR) stimulation for development of a T SCM precursor state and mature memory (T MEM ) cells, but not short-lived or transitory effector cell-like states, in response to viral infections and tumors. Mll1 was essential for widespread de novo deposition of histone H3 lysine 4 trimethylation (H3K4me3) upon TCR stimulation, which accounted for 70% of all activation-induced sites in mature T MEM cells. Mll1 promoted both H3K4me3 deposition and reduced TCR-induced Pol II pausing at genes whose single-cell transcriptional dynamics explained trajectories into nascent T SCM precursor states during viral infection. Our results suggest Mll1-dependent control of Pol II elongation and H3K4me3 establishes and maintains differentiation of CD8 + T SCM cell states.
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37
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Chronic lymphocytic leukemia presence impairs antigen-specific CD8 + T-cell responses through epigenetic reprogramming towards short-lived effectors. Leukemia 2023; 37:606-616. [PMID: 36658390 PMCID: PMC9851097 DOI: 10.1038/s41375-023-01817-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/22/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023]
Abstract
T-cell dysregulation in chronic lymphocytic leukemia (CLL) associates with low response rates to autologous T cell-based therapies. How CLL affects antigen-specific T-cell responses remains largely unknown. We investigated (epi)genetic and functional consequences of antigen-specific T-cell responses in presence of CLL in vitro and in an adoptive-transfer murine model. Already at steady-state, antigen-experienced patient-derived T cells were skewed towards short-lived effector cells (SLEC) at the expense of memory-precursor effector cells (MPEC). Stimulation of these T cells in vitro showed rapid induction of effector genes and suppression of key memory transcription factors only in presence of CLL cells, indicating epigenetic regulation. This was investigated in vivo by following antigen-specific responses of naïve OT-I CD8+ cells to mCMV-OVA in presence/absence of TCL1 B-cell leukemia. Presence of leukemia resulted in increased SLEC formation, with disturbed inflammatory cytokine production. Chromatin and transcriptome profiling revealed strong epigenetic modifications, leading to activation of an effector and silencing of a memory profile through presence of CLL cells. Secondary challenge in vivo confirmed dysfunctional memory responses by antigen-experienced OT-I cells generated in presence of CLL. Altogether, we show that presence of CLL induces a short-lived effector phenotype and impaired memory responses by epigenetic reprogramming during primary responses.
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38
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Pyrimidine de novo synthesis inhibition selectively blocks effector but not memory T cell development. Nat Immunol 2023; 24:501-515. [PMID: 36797499 DOI: 10.1038/s41590-023-01436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/13/2023] [Indexed: 02/18/2023]
Abstract
Blocking pyrimidine de novo synthesis by inhibiting dihydroorotate dehydrogenase is used to treat autoimmunity and prevent expansion of rapidly dividing cell populations including activated T cells. Here we show memory T cell precursors are resistant to pyrimidine starvation. Although the treatment effectively blocked effector T cells, the number, function and transcriptional profile of memory T cells and their precursors were unaffected. This effect occurred in a narrow time window in the early T cell expansion phase when developing effector, but not memory precursor, T cells are vulnerable to pyrimidine starvation. This vulnerability stems from a higher proliferative rate of early effector T cells as well as lower pyrimidine synthesis capacity when compared with memory precursors. This differential sensitivity is a drug-targetable checkpoint that efficiently diminishes effector T cells without affecting the memory compartment. This cell fate checkpoint might therefore lead to new methods to safely manipulate effector T cell responses.
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39
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Vanni A, Carnasciali A, Mazzoni A, Russo E, Farahvachi P, Gloria LD, Ramazzotti M, Lamacchia G, Capone M, Salvati L, Calosi L, Bani D, Liotta F, Cosmi L, Amedei A, Ballerini C, Maggi L, Annunziato F. Musculin does not modulate the disease course of Experimental Autoimmune Encephalomyelitis and DSS colitis. Immunol Lett 2023; 255:21-31. [PMID: 36848960 DOI: 10.1016/j.imlet.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Previous evidences show that Musculin (Msc), a repressor member of basic helix-loop-helix transcription factors, is responsible in vitro for the low responsiveness of human Th17 cells to the growth factor IL-2, providing an explanation for Th17 cells rarity in inflammatory tissue. However, how and to what extent Musculin gene can regulate the immune response in vivo in an inflammatory context is still unknown. Here, exploiting two animal models of inflammatory diseases, the Experimental Autoimmune Encephalomyelitis (EAE) and the dextran sodium sulfate (DSS)-induced colitis, we evaluated the effect of Musculin gene knock-out on clinical course, performing also a deep immune phenotypical analysis on T cells compartment and an extended microbiota analysis in colitis-sick mice. We found that, at least during the early phase, Musculin gene has a very marginal role in modulating both the diseases. Indeed, the clinical course and the histological analysis showed no differences between wild type and Msc knock-out mice, whereas immune system appeared to give rise to a regulatory milieu in lymph nodes of EAE mice and in the spleen of DSS colitis-sick mice. Moreover, in the microbiota analysis, we found irrelevant differences between wild type and Musculin knock-out colitis-sick mice, with a similar bacterial strains' frequency and diversity after the DSS treatment. This work strengthened the idea of a negligible Msc gene involvement in these models.
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Affiliation(s)
- Anna Vanni
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Alberto Carnasciali
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Edda Russo
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Parham Farahvachi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Leandro Di Gloria
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence 50139, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence 50139, Italy
| | - Giulia Lamacchia
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Manuela Capone
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Lorenzo Salvati
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Laura Calosi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Daniele Bani
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Clara Ballerini
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy.
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
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40
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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41
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Heidarian M, Griffith TS, Badovinac VP. Sepsis-induced changes in differentiation, maintenance, and function of memory CD8 T cell subsets. Front Immunol 2023; 14:1130009. [PMID: 36756117 PMCID: PMC9899844 DOI: 10.3389/fimmu.2023.1130009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Formation of long-lasting memory lymphocytes is one of the foundational characteristics of adaptive immunity and the basis of many vaccination strategies. Following the rapid expansion and contraction of effector CD8 T cells, the surviving antigen (Ag)-specific cells give rise to the memory CD8 T cells that persist for a long time and are phenotypically and functionally distinct from their naïve counterparts. Significant heterogeneity exists within the memory CD8 T cell pool, as different subsets display distinct tissue localization preferences, cytotoxic ability, and proliferative capacity, but all memory CD8 T cells are equipped to mount an enhanced immune response upon Ag re-encounter. Memory CD8 T cells demonstrate numerical stability under homeostatic conditions, but sepsis causes a significant decline in the number of memory CD8 T cells and diminishes their Ag-dependent and -independent functions. Sepsis also rewires the transcriptional profile of memory CD8 T cells, which profoundly impacts memory CD8 T cell differentiation and, ultimately, the protective capacity of memory CD8 T cells upon subsequent stimulation. This review delves into different aspects of memory CD8 T cell subsets as well as the immediate and long-term impact of sepsis on memory CD8 T cell biology.
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Affiliation(s)
| | - Thomas S. Griffith
- Department of Urology, University of Minnesota, Minneapolis, MN, United States,Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, United States
| | - Vladimir P. Badovinac
- Department of Pathology, University of Iowa, Iowa, IA, United States,Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa, IA, United States,*Correspondence: Vladimir P. Badovinac,
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42
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Kenney D, Harly C. Purification of Bone Marrow Precursors to T Cells and ILCs. Methods Mol Biol 2023; 2580:211-232. [PMID: 36374460 DOI: 10.1007/978-1-0716-2740-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
T cells and innate lymphoid cells (ILCs) share expression of many key transcription factors during development and at mature stage, resulting in striking functional similarities between these lineages. Taking into account ILC contribution is thus necessary to appreciate T cell functions during immune responses. Furthermore, understanding ILC development and functions helps to understand T cells. Here we provide methods and protocols to isolate pure populations of multipotent precursors to T cells and innate lymphoid cells (ILCs) from adult mouse bone marrow, using flow cytometric sorting. These include precursors to all lymphocytes (viz., LMPPs and ALPs) and multipotent precursors to ILCs that have been recently refined (viz., specified EILPs, committed EILPs, and ILCPs).
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Affiliation(s)
- Devin Kenney
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Christelle Harly
- Nantes Université, INSERM UMR 1307, CNRS UMR 6075, Université d'Angers, CRCI2NA, Nantes, France.
- LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.
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43
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Oladipo OO, Adedeji BO, Adedokun SP, Gbadamosi JA, Salaudeen M. Regulation of effector and memory CD8 + T cell differentiation: a focus on orphan nuclear receptor NR4A family, transcription factor, and metabolism. Immunol Res 2022; 71:314-327. [PMID: 36571657 DOI: 10.1007/s12026-022-09353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022]
Abstract
CD8 + T cells undergo rapid expansion followed by contraction and the development of memory cells after their receptors are activated. The development of immunological memory following acute infection is a complex phenomenon that involves several molecular, transcriptional, and metabolic mechanisms. As memory cells confer long-term protection and respond to secondary stimulation with strong effector function, understanding the mechanisms that influence their development is of great importance. Orphan nuclear receptors, NR4As, are immediate early genes that function as transcription factors and bind with the NBRE region of chromatin. Interestingly, the NBRE region of activated CD8 + T cells is highly accessible at the same time the expression of NR4As is induced. This suggests a potential role of NR4As in the early events post T cell activation that determines cell fate decisions. In this review, we will discuss the influence of NR4As on the differentiation of CD8 + T cells during the immune response to acute infection and the development of immunological memory. We will also discuss the signals, transcription factors, and metabolic mechanisms that control cell fate decisions. HIGHLIGHTS: Memory CD8 + T cells are an essential subset that mediates long-term protection after pathogen encounters. Some specific environmental cues, transcriptional factors, and metabolic pathways regulate the differentiation of CD8 + T cells and the development of memory cells. Orphan nuclear receptor NR4As are early genes that act as transcription factors and are highly expressed post-T cell receptor activation. NR4As influence the effector function and differentiation of CD8 + T cells and also control the development of immunological memory following acute infection.
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Affiliation(s)
- Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
- College of Health Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Bernard O Adedeji
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- College of Health Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Samson P Adedokun
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- College of Health Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Jibriil A Gbadamosi
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- College of Health Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Marzuq Salaudeen
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- College of Health Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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44
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Lv Y, Ricard L, Gaugler B, Huang H, Ye Y. Biology and clinical relevance of follicular cytotoxic T cells. Front Immunol 2022; 13:1036616. [PMID: 36591286 PMCID: PMC9794565 DOI: 10.3389/fimmu.2022.1036616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Follicular cytotoxic T (Tfc) cells are a newly identified subset of CD8+ T cells enriched in B cell follicles and their surroundings, which integrate multiple functions such as killing, memory, supporting and regulation. Tfc cells share similarities with follicular helper T (Tfh) cells, conventional cytotoxic CD8+ T (Tc cells)cells and follicular regulatory T (Tfr) cells, while they express distinct transcription factors, phenotype, and perform different functions. With the participation of cytokines and cell-cell interactions, Tfc cells modulate Tfh cells and B cells and play an essential role in regulating the humoral immunity. Furthermore, Tfc cells have been found to change in their frequencies and functions during the occurrence and progression of chronic infections, immune-mediated diseases and cancers. Strategies targeting Tfc cells are under investigations, bringing novel insights into control of these diseases. We summarize the characteristics of Tfc cells, and introduce the roles and potential targeting modalities of Tfc cells in different diseases.
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Affiliation(s)
- Yuqi Lv
- Bone Marrow Transplantation Center, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Liangzhu Laboratory of Zhejiang University Medical Center, Hangzhou, Zhejiang, China,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Province Stem Cell and Cellular Immunotherapy Engineering Laboratory, Hangzhou, Zhejiang, China
| | - Laure Ricard
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine (CRSA), Paris, France,AP-HP, Hôpital Saint-Antoine, Service d’Hématologie Clinique et Thérapie Cellulaire, Sorbonne Université, Paris, France
| | - Béatrice Gaugler
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine (CRSA), Paris, France,AP-HP, Hôpital Saint-Antoine, Service d’Hématologie Clinique et Thérapie Cellulaire, Sorbonne Université, Paris, France
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Liangzhu Laboratory of Zhejiang University Medical Center, Hangzhou, Zhejiang, China,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Province Stem Cell and Cellular Immunotherapy Engineering Laboratory, Hangzhou, Zhejiang, China,*Correspondence: Yishan Ye, ; He Huang,
| | - Yishan Ye
- Bone Marrow Transplantation Center, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Liangzhu Laboratory of Zhejiang University Medical Center, Hangzhou, Zhejiang, China,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China,Zhejiang Province Stem Cell and Cellular Immunotherapy Engineering Laboratory, Hangzhou, Zhejiang, China,*Correspondence: Yishan Ye, ; He Huang,
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45
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Sigvardsson M, Kee BL, Zúñiga-Pflücker JC, Anderson MK. Editorial: Molecular switches of the immune system: The E-protein/Id axis in hematopoietic development and function. Front Immunol 2022; 13:1062734. [DOI: 10.3389/fimmu.2022.1062734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
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46
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Jiang P, Zhang Z, Hu Y, Liang Z, Han Y, Li X, Zeng X, Zhang H, Zhu M, Dong J, Huang H, Qian P. Single-cell ATAC-seq maps the comprehensive and dynamic chromatin accessibility landscape of CAR-T cell dysfunction. Leukemia 2022; 36:2656-2668. [PMID: 35962059 DOI: 10.1038/s41375-022-01676-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/09/2022]
Abstract
Chimeric antigen receptor T cells (CAR-T) therapy has achieved remarkable therapeutic success in treating a variety of hematopoietic malignancies. However, the high relapse rate and poor in vivo persistence, partially caused by CAR-T cell exhaustion, are still important barriers against CAR-T therapy. It remains largely elusive on the mechanisms of CAR-T exhaustion and how to attenuate exhaustion to achieve better therapeutic efficacy. In this study, we initially observed that CAR-T cells showed rapid differentiation and increased exhaustion after co-culture with tumor cells in vitro, and then performed single-cell ATAC-seq to depict the comprehensive and dynamic landscape of chromatin accessibility of CAR-T cells during tumor cell stimulation. Analyses of differential chromatin accessible regions and motif accessibility revealed that TFs were distinct in each cell type and reconstituted a coordinated regulatory network to drive CAR-T exhaustion. Furthermore, we performed scATAC-seq in patient-derived CAR-T cells and identified BATF and IRF4 as pivotal regulators in CAR-T cell exhaustion. Finally, knockdown of BATF or IRF4 enhanced the killing ability, inhibited exhaustion, and prolonged the persistence of CAR-T cells in vivo. Together, our study unraveled the epigenetic regulatory mechanisms of CAR-T exhaustion and provided new insights into CAR-T engineering to achieve better clinical treatment benefits.
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Affiliation(s)
- Penglei Jiang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Zhaoru Zhang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Yongxian Hu
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China.,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Zuyu Liang
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China.,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Xia Li
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China.,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Xin Zeng
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Hao Zhang
- Department of Hematology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325200, Zhejiang, China
| | - Meng Zhu
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - Jian Dong
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China. .,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China. .,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China. .,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, 310058, China.
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47
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Zander R, Khatun A, Kasmani MY, Chen Y, Cui W. Delineating the transcriptional landscape and clonal diversity of virus-specific CD4 + T cells during chronic viral infection. eLife 2022; 11:e80079. [PMID: 36255051 PMCID: PMC9629829 DOI: 10.7554/elife.80079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
Although recent evidence indicates that CD4+ T cells responding to chronic viral infection are functionally heterogenous, our understanding of the developmental relationships between these subsets, and a determination of how their transcriptional landscape compares to their acute infection counterparts remains unclear. Additionally, whether cell-intrinsic factors such as TCR usage influence CD4+ T cell fate commitment during persistent infection has not previously been studied. Herein, we perform single-cell RNA sequencing (scRNA-seq) combined with single-cell T cell receptor sequencing (scTCR-seq) on virus-specific CD4+ T cells isolated from mice infected with chronic lymphocytic choriomeningitis virus (LCMV) infection. We identify several transcriptionally distinct states among the Th1, Tfh, and memory-like T cell subsets that form at the peak of infection, including the presence of a previously unrecognized Slamf7+ subset with cytolytic features. We further show that the relative distribution of these populations differs substantially between acute and persistent LCMV infection. Moreover, while the progeny of most T cell clones displays membership within each of these transcriptionally unique populations, overall supporting a one cell-multiple fate model, a small fraction of clones display a biased cell fate decision, suggesting that TCR usage may impact CD4+ T cell development during chronic infection. Importantly, comparative analyses further reveal both subset-specific and core gene expression programs that are differentially regulated between CD4+ T cells responding to acute and chronic LCMV infection. Together, these data may serve as a useful framework and allow for a detailed interrogation into the clonal distribution and transcriptional circuits underlying CD4+ T cell differentiation during chronic viral infection.
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Affiliation(s)
- Ryan Zander
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
| | - Achia Khatun
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Moujtaba Y Kasmani
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Yao Chen
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Weiguo Cui
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
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48
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Kaminskiy Y, Kuznetsova V, Kudriaeva A, Zmievskaya E, Bulatov E. Neglected, yet significant role of FOXP1 in T-cell quiescence, differentiation and exhaustion. Front Immunol 2022; 13:971045. [PMID: 36268015 PMCID: PMC9576946 DOI: 10.3389/fimmu.2022.971045] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
FOXP1 is ubiquitously expressed in the human body and is implicated in both physiological and pathological processes including cancer. However, despite its importance the role of FOXP1 in T-cells has not been extensively studied. Although relatively few phenotypic and mechanistic details are available, FOXP1 role in T-cell quiescence and differentiation of CD4+ subsets has recently been established. FOXP1 prevents spontaneous T-cell activation, preserves memory potential, and regulates the development of follicular helper and regulatory T-cells. Moreover, there is growing evidence that FOXP1 also regulates T-cell exhaustion. Altogether this makes FOXP1 a crucial and highly undervalued regulator of T-cell homeostasis. In this review, we discuss the biology of FOXP1 with a focus on discoveries made in T-cells in recent years.
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Affiliation(s)
- Yaroslav Kaminskiy
- Department of Oncology and Pathology, Karolinska Institutet, SciLifeLab, Solna, Sweden
- Laboratory of Transplantation Immunology, National Research Centre for Hematology, Moscow, Russia
| | - Varvara Kuznetsova
- Laboratory of Transplantation Immunology, National Research Centre for Hematology, Moscow, Russia
| | - Anna Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Zmievskaya
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Emil Bulatov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- *Correspondence: Emil Bulatov,
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49
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Suarez-Ramirez JE, Cauley LS, Chandiran K. CTLs Get SMAD When Pathogens Tell Them Where to Go. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1025-1032. [PMID: 36130123 PMCID: PMC9512391 DOI: 10.4049/jimmunol.2200345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 01/04/2023]
Abstract
Vaccines protect against infections by eliciting both Ab and T cell responses. Because the immunity wanes as protective epitopes get modified by accruing mutations, developing strategies for immunization against new variants is a major priority for vaccine development. CTLs eliminate cells that support viral replication and provide protection against new variants by targeting epitopes from internal viral proteins. This form of protection has received limited attention during vaccine development, partly because reliable methods for directing pathogen-specific memory CD8 T cells to vulnerable tissues are currently unavailable. In this review we examine how recent studies expand our knowledge of mechanisms that contribute to the functional diversity of CTLs as they respond to infection. We discuss the role of TGF-β and the SMAD signaling cascade during genetic programming of pathogen-specific CTLs and the pathways that promote formation of a newly identified subset of terminally differentiated memory CD8 T cells that localize in the vasculature.
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50
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Spath S, Roan F, Presnell SR, Höllbacher B, Ziegler SF. Profiling of Tregs across tissues reveals plasticity in ST2 expression and hierarchies in tissue-specific phenotypes. iScience 2022; 25:104998. [PMID: 36093048 PMCID: PMC9460833 DOI: 10.1016/j.isci.2022.104998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/03/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Foxp3+ regulatory T cells (Tregs) are critical mediators of peripheral tolerance and immune homeostasis and exert tissue-specific functions. In many nonlymphoid tissues, Tregs show enriched expression of the IL-33 receptor ST2. Through comprehensive profiling of murine ST2+ and ST2- Tregs, we found that Treg transcriptomes and phenotypes formed a hierarchical relationship across tissues. Only a small core signature distinguished ST2+ Tregs from ST2- Tregs across all tissues, and differences in transcriptional profiles were predominantly tissue-specific. We also identified unique, highly proliferative, circulating ST2+ Tregs with high migratory potential. In adoptive transfers, both ST2+ and ST2- Tregs seeded various host tissues and demonstrated plasticity in ST2 expression. Furthermore, Tregs from donor lungs were differentially recovered from host nonlymphoid tissues in an IL-33-dependent manner. In summary, our work identified tissue residency rather than ST2 expression as a primary driver of tissue Treg identity and highlights the unique, tissue-specific adaption of ST2+ Tregs. Tissue of residency rather than ST2 expression is a primary driver of Treg identity A small core signature distinguishes ST2+ Tregs from ST2- Tregs across tissues Circulating ST2+ Tregs have diverse chemokine receptor profiles Plasticity of ST2 expression on transferred Tregs occurs in a tissue-specific manner
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Affiliation(s)
- Sabine Spath
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Florence Roan
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Scott R. Presnell
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Barbara Höllbacher
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
- Institute of Computational Biology (ICB), Helmholtz Zentrum Muenchen (HMGU), 85764 Munich, Neuherberg, Germany
- Department of Informatics, TUM, 85748 Munich, Garching, Germany
| | - Steven F. Ziegler
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
- Corresponding author
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