1
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Vardam-Kaur T, Banuelos A, Gabaldon-Parish M, Macedo BG, Salgado CL, Wanhainen KM, Zhou MH, van Dijk S, Santiago-Carvalho I, Beniwal AS, Leff CL, Peng C, Tran NL, Jameson SC, Borges da Silva H. The ATP-exporting channel Pannexin 1 promotes CD8 + T cell effector and memory responses. iScience 2024; 27:110290. [PMID: 39045105 PMCID: PMC11263643 DOI: 10.1016/j.isci.2024.110290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Sensing of extracellular ATP (eATP) controls CD8+ T cell function. Their accumulation can occur through export by specialized molecules, such as the release channel Pannexin 1 (Panx1). Whether Panx1 controls CD8+ T cell immune responses in vivo, however, has not been previously addressed. Here, we report that T-cell-specific Panx1 is needed for CD8+ T cell responses to viral infections and cancer. We found that CD8-specific Panx1 promotes both effector and memory CD8+ T cell responses. Panx1 favors initial effector CD8+ T cell activation through extracellular ATP (eATP) export and subsequent P2RX4 activation, which helps promote full effector differentiation through extracellular lactate accumulation and its subsequent recycling. In contrast, Panx1 promotes memory CD8+ T cell survival primarily through ATP export and subsequent P2RX7 engagement, leading to improved mitochondrial metabolism. In summary, Panx1-mediated eATP export regulates effector and memory CD8+ T cells through distinct purinergic receptors and different metabolic and signaling pathways.
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Affiliation(s)
- Trupti Vardam-Kaur
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | - Alma Banuelos
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | | | - Bruna Gois Macedo
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | | | | | - Maggie Hanqi Zhou
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | - Sarah van Dijk
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | | | - Angad S. Beniwal
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | - Chloe L. Leff
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | - Changwei Peng
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nhan L. Tran
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
| | - Stephen C. Jameson
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Henrique Borges da Silva
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85255, USA
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2
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Lucas ED, Huggins MA, Peng C, O'Connor C, Gress AR, Thefaine CE, Dehm EM, Kubota Y, Jameson SC, Hamilton SE. Circulating KLRG1 + long-lived effector memory T cells retain the flexibility to become tissue resident. Sci Immunol 2024; 9:eadj8356. [PMID: 38941479 DOI: 10.1126/sciimmunol.adj8356] [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: 07/24/2023] [Accepted: 05/30/2024] [Indexed: 06/30/2024]
Abstract
KLRG1+ CD8 T cells persist for months after clearance of acute infections and maintain high levels of effector molecules, contributing protective immunity against systemic pathogens. Upon secondary infection, these long-lived effector cells (LLECs) are incapable of forming other circulating KLRG1- memory subsets such as central and effector memory T cells. Thus, KLRG1+ memory T cells are frequently referred to as a terminally differentiated population that is relatively short lived. Here, we show that after viral infection of mice, effector cells derived from LLECs rapidly enter nonlymphoid tissues and reduce pathogen burden but are largely dependent on receiving antigen cues from vascular endothelial cells. Single-cell RNA sequencing reveals that secondary memory cells in nonlymphoid tissues arising from either KLRG1+ or KLRG1- memory precursors develop a similar resident memory transcriptional signature. Thus, although LLECs cannot differentiate into other circulating memory populations, they still retain the flexibility to enter tissues and establish residency.
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Affiliation(s)
- Erin D Lucas
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew A Huggins
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Changwei Peng
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christine O'Connor
- Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Abigail R Gress
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Claire E Thefaine
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emma M Dehm
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sara E Hamilton
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
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3
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Wang L, Mishra S, Fan KKH, Quon S, Li G, Yu B, Liao W, Liu Y, Zhang X, Qiu Y, Li Y, Goldrath AW, Ma C, Zhang N. T-bet deficiency and Hic1 induction override TGF-β-dependency in the formation of CD103 + intestine-resident memory CD8 + T cells. Cell Rep 2024; 43:114258. [PMID: 38781073 PMCID: PMC11240284 DOI: 10.1016/j.celrep.2024.114258] [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: 02/28/2023] [Revised: 03/01/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Transforming growth factor β (TGF-β) represents a well-established signal required for tissue-resident memory T cell (TRM) formation at intestinal surfaces, regulating the expression of a large collection of genes coordinately promoting intestinal TRM differentiation. The functional contribution from each TGF-β-controlled transcription factor is not entirely known. Here, we find that TGF-β-induced T-bet downregulation and Hic1 induction represent two critical events during intestinal TRM differentiation. Importantly, T-bet deficiency significantly rescues intestinal TRM formation in the absence of the TGF-β receptor. Hic1 induction further strengthens TRM maturation in the absence of TGF-β and T-bet. Our results reveal that provision of certain TGF-β-induced molecular events can partially replace TGF-β signaling to promote the establishment of intestinal TRMs, which allows the functional dissection of TGF-β-induced transcriptional targets and molecular mechanisms for TRM differentiation.
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Affiliation(s)
- Liwen Wang
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Shruti Mishra
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kenneth Ka-Ho Fan
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Sara Quon
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Guo Li
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bingfei Yu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Liao
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yong Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanzheng Qiu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Clinical Research Center for Laryngopharyngeal and Voice Disorders in Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yue Li
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Chaoyu Ma
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Nu Zhang
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; South Texas Veterans Health Care System, San Antonio, TX 78229, USA.
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4
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Setoguchi R, Sengiku T, Kono H, Kawakami E, Kubo M, Yamamoto T, Hori S. Memory CD8 T cells are vulnerable to chronic IFN-γ signals but not to CD4 T cell deficiency in MHCII-deficient mice. Nat Commun 2024; 15:4418. [PMID: 38806459 PMCID: PMC11133459 DOI: 10.1038/s41467-024-48704-4] [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: 07/18/2023] [Accepted: 05/10/2024] [Indexed: 05/30/2024] Open
Abstract
The mechanisms by which the number of memory CD8 T cells is stably maintained remains incompletely understood. It has been postulated that maintaining them requires help from CD4 T cells, because adoptively transferred memory CD8 T cells persist poorly in MHC class II (MHCII)-deficient mice. Here we show that chronic interferon-γ signals, not CD4 T cell-deficiency, are responsible for their attrition in MHCII-deficient environments. Excess IFN-γ is produced primarily by endogenous colonic CD8 T cells in MHCII-deficient mice. IFN-γ neutralization restores the number of memory CD8 T cells in MHCII-deficient mice, whereas repeated IFN-γ administration or transduction of a gain-of-function STAT1 mutant reduces their number in wild-type mice. CD127high memory cells proliferate actively in response to IFN-γ signals, but are more susceptible to attrition than CD127low terminally differentiated effector memory cells. Furthermore, single-cell RNA-sequencing of memory CD8 T cells reveals proliferating cells that resemble short-lived, terminal effector cells and documents global downregulation of gene signatures of long-lived memory cells in MHCII-deficient environments. We propose that chronic IFN-γ signals deplete memory CD8 T cells by compromising their long-term survival and by diverting self-renewing CD127high cells toward terminal differentiation.
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Affiliation(s)
- Ruka Setoguchi
- Formerly Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, 230-0045, Japan.
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Tomoya Sengiku
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroki Kono
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Eiryo Kawakami
- Advanced Data Science Project (ADSP), RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama City, Kanagawa, 230-0045, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, 260-8670, Japan
- Chiba University Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Chiba University, Chiba, 260-8670, Japan
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, 2669 Yamazaki, Noda-shi, Chiba, 278-0022, Japan
- Laboratory for Cytokine Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, 230-0045, Japan
| | - Tadashi Yamamoto
- Formerly Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, 230-0045, Japan
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, 904-0495, Japan
| | - Shohei Hori
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Formerly Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, 230-0045, Japan
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5
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Vardam-Kaur T, Banuelos A, Gabaldon-Parish M, Macedo BG, Salgado CL, Wanhainen KM, Zhou MH, van Dijk S, Santiago-Carvalho I, Beniwal AS, Leff CL, Peng C, Tran NL, Jameson SC, da Silva HB. The ATP-exporting channel Pannexin-1 promotes CD8 + T cell effector and memory responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.19.537580. [PMID: 37131831 PMCID: PMC10153284 DOI: 10.1101/2023.04.19.537580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Sensing of extracellular ATP (eATP) controls CD8+ T cell function. Their accumulation can occur through export by specialized molecules, such as the release channel Pannexin-1 (Panx1). Whether Panx1 controls CD8+ T cell immune responses in vivo, however, has not been previously addressed. Here, we report that T cell-specific Panx1 is needed for CD8+ T cell responses to viral infections and cancer. We found that CD8-specific Panx1 promotes both effector and memory CD8+ T cell responses. Panx1 favors initial effector CD8+ T cell activation through extracellular ATP (eATP) export and subsequent P2RX4 activation, which helps promote full effector differentiation through extracellular lactate accumulation and its subsequent recycling. In contrast, Panx1 promotes memory CD8+ T cell survival primarily through ATP export and subsequent P2RX7 engagement, leading to improved mitochondrial metabolism. In summary, Panx1-mediated eATP export regulates effector and memory CD8+ T cells through distinct purinergic receptors and different metabolic and signaling pathways.
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Affiliation(s)
- Trupti Vardam-Kaur
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
- Current address: Omeros Corporation, Seattle, Washington, United States
| | - Alma Banuelos
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
| | - Maria Gabaldon-Parish
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
- Current address: University of New Mexico, Albuquerque, New Mexico, United States
| | - Bruna Gois Macedo
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
| | | | | | - Maggie Hanqi Zhou
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
| | - Sarah van Dijk
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
- Current address: Biomedical Sciences Graduate Program, University of California, San Diego, California, United States
| | | | - Angad S. Beniwal
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
| | - Chloe L. Leff
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
| | - Changwei Peng
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States
- Current address: Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, Massachusetts, United States
| | - Nhan L. Tran
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
| | - Stephen C. Jameson
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States
| | - Henrique Borges da Silva
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona, United States
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6
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Niu L, Jang E, Chin AL, Huo Z, Wang W, Cai W, Tong R. Noncovalently particle-anchored cytokines with prolonged tumor retention safely elicit potent antitumor immunity. SCIENCE ADVANCES 2024; 10:eadk7695. [PMID: 38640236 PMCID: PMC11029804 DOI: 10.1126/sciadv.adk7695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
Preclinical studies have shown that immunostimulatory cytokines elicit antitumor immune responses but their clinical use is limited by severe immune-related adverse events upon systemic administration. Here, we report a facile and versatile strategy for noncovalently anchoring potent Fc-fused cytokine molecules to the surface of size-discrete particles decorated with Fc-binding peptide for local administration. Following intratumoral injection, particle-anchored Fc cytokines exhibit size-dependent intratumoral retention. The 1-micrometer particle prolongs intratumoral retention of Fc cytokine for over a week and has minimal systemic exposure, thereby eliciting antitumor immunity while eliminating systemic toxicity caused by circulating cytokines. In addition, the combination of these particle-anchored cytokines with immune checkpoint blockade antibodies safely promotes tumor regression in various syngeneic tumor models and genetically engineered murine tumor models and elicits systemic antitumor immunity against tumor rechallenge. Our formulation strategy renders a safe and tumor-agnostic approach that uncouples cytokines' immunostimulatory properties from their systemic toxicities for potential clinical application.
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Affiliation(s)
- Liqian Niu
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Eungyo Jang
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Ai Lin Chin
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Ziyu Huo
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
| | - Wenbo Wang
- Department of Materials Science and Engineering, Virginia Polytechnic Institute and State University, 445 Old Turner Street, Blacksburg, VA, 24061, USA
| | - Wenjun Cai
- Department of Materials Science and Engineering, Virginia Polytechnic Institute and State University, 445 Old Turner Street, Blacksburg, VA, 24061, USA
| | - Rong Tong
- Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 635 Prices Fork Road, Blacksburg, VA, 24061, USA
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7
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Ranek JS, Stallaert W, Milner JJ, Redick M, Wolff SC, Beltran AS, Stanley N, Purvis JE. DELVE: feature selection for preserving biological trajectories in single-cell data. Nat Commun 2024; 15:2765. [PMID: 38553455 PMCID: PMC10980758 DOI: 10.1038/s41467-024-46773-z] [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: 05/18/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Single-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package: https://github.com/jranek/delve .
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Affiliation(s)
- Jolene S Ranek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Margaret Redick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Wolff
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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8
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Sanchez S, Dangi T, Awakoaiye B, Irani N, Fourati S, Richner J, Penaloza-MacMaster P. Time-dependent enhancement of mRNA vaccines by 4-1BB costimulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582992. [PMID: 38496467 PMCID: PMC10942304 DOI: 10.1101/2024.03.01.582992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
mRNA vaccines have demonstrated efficacy against COVID-19. However, concerns regarding waning immunity and breakthrough infections have motivated the development of next-generation vaccines with enhanced efficacy. In this study, we investigated the impact of 4-1BB costimulation on immune responses elicited by mRNA vaccines in mice. We first vaccinated mice with an mRNA vaccine encoding the SARS-CoV-2 spike antigen like the Moderna and Pfizer-BioNTech vaccines, followed by administration of 4-1BB costimulatory antibodies at various times post-vaccination. Administering 4-1BB costimulatory antibodies during the priming phase did not enhance immune responses. However, administering 4-1BB costimulatory antibodies after 96 hours elicited a significant improvement in CD8 T cell responses, leading to enhanced protection against breakthrough infections. A similar improvement in immune responses was observed with multiple mRNA vaccines, including vaccines against common cold coronavirus, human immunodeficiency virus (HIV), and arenavirus. These findings demonstrate a time-dependent effect by 4-1BB costimulation and provide insights for developing improved mRNA vaccines.
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Affiliation(s)
- Sarah Sanchez
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tanushree Dangi
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bakare Awakoaiye
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nahid Irani
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Slim Fourati
- Department of Medicine, Division of Allergy and Immunology, Feinberg School of Medicine and Center for Human Immunobiology, Northwestern University, Chicago, IL 60611, USA
| | - Justin Richner
- Department of Microbiology & Immunology, University of Illinois Chicago College of Medicine, Chicago, IL 60612, USA
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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9
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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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10
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Gibson A, Ram R, Gangula R, Li Y, Mukherjee E, Palubinsky AM, Campbell CN, Thorne M, Konvinse KC, Choshi P, Deshpande P, Pedretti S, O’Neil RT, Wanjalla CN, Kalams SA, Gaudieri S, Lehloenya RJ, Bailin SS, Chopra A, Mallal SA, Phillips EJ. Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.26.568771. [PMID: 38405793 PMCID: PMC10888802 DOI: 10.1101/2023.11.26.568771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCRαβ clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.
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Affiliation(s)
- Andrew Gibson
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Rama Gangula
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Yueran Li
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Eric Mukherjee
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Amy M Palubinsky
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Chelsea N Campbell
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Michael Thorne
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Katherine C Konvinse
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Phuti Choshi
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Pooja Deshpande
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Sarah Pedretti
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Richard T O’Neil
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center and Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Spyros A Kalams
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
- School of Human Sciences, The University of Western Australia, Western Australia, Australia
| | - Rannakoe J Lehloenya
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
- Division of Dermatology, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Samuel S Bailin
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Jason A Trubiano on behalf of the AUS-SCAR study group
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Victoria, Australia
| | | | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
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11
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Loredan DG, Devlin JC, Khanna KM, Loke P. Recruitment and Maintenance of CX3CR1+CD4+ T Cells during Helminth Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:632-644. [PMID: 38180236 PMCID: PMC10954162 DOI: 10.4049/jimmunol.2300451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
Distinct subsets of T lymphocytes express CX3CR1 under inflammatory conditions, but little is known about CX3CR1+CD4+ T cells during type 2 inflammation in helminth infections. In this study, we used a fate-mapping mouse model to characterize CX3CR1+CD4+ T cells during both acute Nippostrongylus brasiliensis and chronic Schistosoma mansoni murine models of helminth infections, revealing CX3CR1+CD4+ T cells to be an activated tissue-homing subset with varying capacity for cytokine production. Tracking these cells over time revealed that maintenance of CX3CR1 itself along with a TH2 phenotype conferred a survival advantage in the inflamed tissue. Single-cell RNA sequencing analysis of fate-mapped CX3CR1+CD4+ T cells from both the peripheral tissue and the spleen revealed a considerable level of diversity and identified a distinct population of BCL6+TCF-1+PD1+CD4+ T cells in the spleen during helminth infections. Conditional deletion of BCL6 in CX3CR1+ cells resulted in fewer CX3CR1+CD4+ T cells during infection, indicating a role in sustaining CD4+ T cell responses to helminth infections. Overall, our studies revealed the behavior and heterogeneity of CX3CR1+CD4+ T cells during type 2 inflammation in helminth infections and identified BCL6 to be important in their maintenance.
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Affiliation(s)
- Denis G. Loredan
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Joseph C. Devlin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kamal M. Khanna
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - P’ng Loke
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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12
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van der Heide V, Davenport B, Cubitt B, Roudko V, Choo D, Humblin E, Jhun K, Angeliadis K, Dawson T, Furtado G, Kamphorst A, Ahmed R, de la Torre JC, Homann D. Functional impairment of "helpless" CD8 + memory T cells is transient and driven by prolonged but finite cognate antigen presentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576725. [PMID: 38328184 PMCID: PMC10849538 DOI: 10.1101/2024.01.22.576725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Generation of functional CD8 + T cell memory typically requires engagement of CD4 + T cells. However, in certain scenarios, such as acutely-resolving viral infections, effector (T E ) and subsequent memory (T M ) CD8 + T cell formation appear impervious to a lack of CD4 + T cell help during priming. Nonetheless, such "helpless" CD8 + T M respond poorly to pathogen rechallenge. At present, the origin and long-term evolution of helpless CD8 + T cell memory remain incompletely understood. Here, we demonstrate that helpless CD8 + T E differentiation is largely normal but a multiplicity of helpless CD8 T M defects, consistent with impaired memory maturation, emerge as a consequence of prolonged yet finite exposure to cognate antigen. Importantly, these defects resolve over time leading to full restoration of CD8 + T M potential and recall capacity. Our findings provide a unified explanation for helpless CD8 + T cell memory and emphasize an unexpected CD8 + T M plasticity with implications for vaccination strategies and beyond.
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13
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Wang Y, Mei X, Lin Z, Yang X, Cao J, Zhong J, Wang J, Cheng L, Wang Z. Virus infection pattern imprinted and diversified the differentiation of T-cell memory in transcription and function. Front Immunol 2024; 14:1334597. [PMID: 38264657 PMCID: PMC10803622 DOI: 10.3389/fimmu.2023.1334597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Memory T (Tm) cells are a subpopulation of immune cells with great heterogeneity. Part of this diversity came from T cells that were primed with different viruses. Understanding the differences among different viral-specific Tms will help develop new therapeutic strategies for viral infections. Methods In this study, we compared the transcriptome of Tm cells that primed with CMV, EBV and SARS-CoV-2 with single-cell sequencing and studied the similarities and differences in terms of subpopulation composition, activation, metabolism and transcriptional regulation. Results We found that CMV is marked by plentiful cytotoxic Temra cells, while EBV is more abundant in functional Tem cells. More importantly, we found that CD28 and CTLA4 can be used as continuous indicators to interrogate the antiviral ability of T cells. Furthermore, we proposed that REL is a main regulatory factor for CMV-specific T cells producing cytokines and plays an antiviral role. Discussion Our data gives deep insight into molecular characteristics of Tm subsets from different viral infection, which is important to understand T cell immunization. Furthermore, our results provide basic background knowledges for T cell based vaccine development in future.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Bioland, Guangzhou, Guangdong, China
| | - Xinyue Mei
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhengfang Lin
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoyun Yang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Bioland, Guangzhou, Guangdong, China
| | - Jinpeng Cao
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Bioland, Guangzhou, Guangdong, China
| | - Jiaying Zhong
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Cheng
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhongfang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Bioland, Guangzhou, Guangdong, China
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14
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Hu Z, Zuo C, Mao C, Shi C, Xu Y. Peripheral immune markers and amyotrophic lateral sclerosis: a Mendelian randomization study. Front Neurosci 2023; 17:1269354. [PMID: 38188028 PMCID: PMC10768049 DOI: 10.3389/fnins.2023.1269354] [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: 07/29/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The peripheral immune system changes in amyotrophic lateral sclerosis (ALS), but the causal relationship between the two is still controversial. Methods In this study, we aimed to estimate the causal relationship between peripheral immune markers and ALS using a two-sample Mendelian randomization method. Genome-wide association study (GWAS) data on peripheral blood immune traits from European populations were used for exposure, and ALS summary statistics were used as the outcome. The causal relationship was evaluated by inverse variance weighting, MR-Egger, and weighted median methods and verified by multiple sensitivity analysis. Results We found that the increase of one standard deviation of lymphocyte count is related to reducing ALS risk. CD3 on effector memory CD4+ T cell, HLA DR+ CD4+ T cell, effector memory CD8+ T cell, terminally differentiated CD8+ T cell and CD28- CD8+ T cell is also a protective factor for ALS. Among the circulating immune protein, the increase of one standard deviation of α-2-macroglobulin receptor-associated protein (α-2-MRAP) and C4b showed associated with low risk of ALS, while Interleukin-21 (IL-21) increases the risk of ALS. Discussion Our study further reveals the important role of peripheral immune activity in ALS.
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Affiliation(s)
- Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Chunyan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
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15
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Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, DeBarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 inhibits miR-15/16 to enhance cytotoxic T cell activation and memory cell formation. eLife 2023; 12:RP87900. [PMID: 38127070 PMCID: PMC10735224 DOI: 10.7554/elife.87900] [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] [Indexed: 12/23/2023] Open
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, intracellular bacteria, and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and memory. Comparative Argonaute-2 high-throughput sequencing of crosslinking immunoprecipitation (AHC) combined with gene expression profiling in normal and miR-15/16-deficient mouse T cells revealed a large network of hundreds of direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak. This binding site was among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16-binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of interleukin 2 (IL-2) and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence in mice following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long non-coding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
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Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Dimitre S Simeonov
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
| | - Rachel DeBarge
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
- Parker Institute for Cancer Immunotherapy, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Medicine, University of California San FranciscoLexingtonUnited States
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
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16
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Kos FJ, Frankel P, Cristea M, Eng M, Tinsley R, Dempsey S, Ruel N, Stewart D, Dellinger TH, Diamond DJ. Immunologic Signatures of Peripheral Blood T Cells Reveal the Outcome of p53MVA Vaccine and Pembrolizumab Treatment in Patients with Advanced Ovarian Cancer. CANCER RESEARCH COMMUNICATIONS 2023; 3:2585-2595. [PMID: 38032111 PMCID: PMC10732002 DOI: 10.1158/2767-9764.crc-23-0394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
PURPOSE Our previous studies indicated that p53-reactive T cells were associated with clinical benefit in patients with advanced ovarian cancer who were treated with p53-expressing modified vaccinia Ankara (p53MVA) vaccine and gemcitabine chemotherapy. To replace chemotherapy with an approach that will enhance vaccine efficacy and antitumor immunity, we treated patients with p53MVA in combination with PD-1 checkpoint blocker, pembrolizumab. We also attempted to further characterize the activation status of T cells prior to vaccination and during treatment. EXPERIMENTAL DESIGN Patients received up to three triweekly vaccinations concurrent with pembrolizumab, followed by pembrolizumab monotherapy at 3-week intervals. Correlative studies analyzed peripheral blood T-cell phenotypes and profiles of immune function gene expression. RESULTS We observed 6/28 (21%) patients with a clinical benefit to therapy, including 3 partial responses (PR) and 3 patients with stable disease (SD) for 6+ months. The median progression-free survival was 1.8 months (95% confidence interval: 1.7-3.8) and median overall survival was 15.1 months (9.4-30.4). Two patients remain progression-free at 28 and 33 months. Of the 18 patients evaluable in correlative studies, 6 were immunologic responders of whom 5 had clinical benefit (3 PR, 2 SD). Immunologic non-responders expressed in pretreatment peripheral blood mononuclear cell samples high levels of mRNA for multiple molecules associated with terminally differentiated T cells. CONCLUSIONS p53MVA/pembrolizumab immunotherapy showed promising antitumor activity in patients who demonstrated functionally competent peripheral blood T cells. Detection of markers of terminally differentiated T cells before treatment may identify patients unlikely to respond to p53MVA/pembrolizumab. SIGNIFICANCE The activity of a combination immunotherapy of p53 vaccine and PD-1 checkpoint blockade in patients with platinum-resistant ovarian cancer was evaluated in a phase II trial. Clinical benefit was correlated with the responsive immune status of patients before and during the treatment, defining potential predictive markers for immune therapy.
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Affiliation(s)
- Ferdynand J. Kos
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, California
| | - Paul Frankel
- Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, California
| | - Mihaela Cristea
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Melissa Eng
- Clinical Trials Office, City of Hope National Medical Center, Duarte, California
| | - Raechelle Tinsley
- Clinical Trials Office, City of Hope National Medical Center, Duarte, California
| | - Shannon Dempsey
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, California
| | - Nora Ruel
- Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, California
| | - Daphne Stewart
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Thanh H. Dellinger
- Department of Surgery, City of Hope National Medical Center, Duarte, California
| | - Don J. Diamond
- Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, California
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17
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Vantourout P, Eum J, Conde Poole M, Hayday TS, Laing AG, Hussain K, Nuamah R, Kannambath S, Moisan J, Stoop A, Battaglia S, Servattalab R, Hsu J, Bayliffe A, Katragadda M, Hayday AC. Innate TCRβ-chain engagement drives human T cells toward distinct memory-like effector phenotypes with immunotherapeutic potentials. SCIENCE ADVANCES 2023; 9:eadj6174. [PMID: 38055824 DOI: 10.1126/sciadv.adj6174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Clonotypic αβ T cell responses to cargoes presented by major histocompatibility complex (MHC), MR1, or CD1 proteins underpin adaptive immunity. Those responses are mostly mediated by complementarity-determining region 3 motifs created by quasi-random T cell receptor (TCR) gene rearrangements, with diversity being highest for TCRγδ. Nonetheless, TCRγδ also displays nonclonotypic innate responsiveness following engagement of germline-encoded Vγ-specific residues by butyrophilin (BTN) or BTN-like (BTNL) proteins that uniquely mediate γδ T cell subset selection. We now report that nonclonotypic TCR engagement likewise induces distinct phenotypes in TCRαβ+ cells. Specifically, antibodies to germline-encoded human TCRVβ motifs consistently activated naïve or memory T cells toward core states distinct from those induced by anti-CD3 or superantigens and from others commonly reported. Those states combined selective proliferation and effector function with activation-induced inhibitory receptors and memory differentiation. Thus, nonclonotypic TCRVβ targeting broadens our perspectives on human T cell response modes and might offer ways to induce clinically beneficial phenotypes in defined T cell subsets.
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Affiliation(s)
- Pierre Vantourout
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Josephine Eum
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - María Conde Poole
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Thomas S Hayday
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Adam G Laing
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Khiyam Hussain
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Rosamond Nuamah
- NIHR BRC Genomics Research Platform, Guy's and St Thomas' NHS Foundation Trust, King's College London School of Medicine, Guy's Hospital, London, SE1 9RT, UK
| | - Shichina Kannambath
- NIHR BRC Genomics Research Platform, Guy's and St Thomas' NHS Foundation Trust, King's College London School of Medicine, Guy's Hospital, London, SE1 9RT, UK
| | | | | | | | | | | | | | | | - Adrian C Hayday
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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18
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Ulibarri MR, Lin Y, Ramprashad JR, Han G, Hasan MH, Mithila FJ, Ma C, Gopinath S, Zhang N, Milner JJ, Beura LK. Epithelial organoid supports resident memory CD8 T cell differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569395. [PMID: 38076957 PMCID: PMC10705482 DOI: 10.1101/2023.12.01.569395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Resident Memory T cells (TRM) play a vital role in regional immune defense in barrier organs. Although laboratory rodents have been extensively used to study fundamental TRM biology, poor isolation efficiency, sampling bias and low cell survival rates have limited our ability to conduct TRM-focused high-throughput assays. Here, we engineered a murine vaginal epithelial organoid (VEO)-CD8 T cell co-culture system that supports CD8 TRM differentiation in vitro. The three-dimensional VEOs established from murine adult stem cells resembled stratified squamous vaginal epithelium and induced gradual differentiation of activated CD8 T cells into epithelial TRM. These in vitro generated TRM were phenotypically and transcriptionally similar to in vivo TRM, and key tissue residency features were reinforced with a second cognate-antigen exposure during co-culture. TRM differentiation was not affected even when VEOs and CD8 T cells were separated by a semipermeable barrier, indicating soluble factors' involvement. Pharmacological and genetic approaches showed that TGF-β signaling played a crucial role in their differentiation. We found that the VEOs in our model remained susceptible to viral infections and the CD8 T cells were amenable to genetic manipulation; both of which will allow detailed interrogation of antiviral CD8 T cell biology in a reductionist setting. In summary, we established a robust model which captures bonafide TRM differentiation that is scalable, open to iterative sampling, and can be subjected to high throughput assays that will rapidly add to our understanding of TRM.
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Affiliation(s)
- Max R. Ulibarri
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Ying Lin
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
- Pathobiology Graduate Program, Brown University, Providence, RI, 02912
| | - Julian R. Ramprashad
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Geongoo Han
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Mohammad H. Hasan
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Farha J. Mithila
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
- Molecular Biology, Cell Biology and Biochemistry Graduate Program, Brown University, Providence, RI, 02912
| | - Chaoyu Ma
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, 78229
| | - Smita Gopinath
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Cambridge, MA, 02115
| | - Nu Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, 78229
- South Texas Veterans Health Care System, San Antonio, TX, 78229
| | - J. Justin Milner
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599
| | - Lalit K. Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
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19
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Al Saihati HA, Hussein HAM, Thabet AA, Wardany AA, Mahmoud SY, Farrag ES, Mohamed TIA, Fathy SM, Elnosary ME, Sobhy A, Ahmed AE, El-Adly AM, El-Shenawy FS, Elsadek AA, Rayan A, Zahran ZAM, El-Badawy O, El-Naggar MGM, Afifi MM, Zahran AM. Memory T Cells Discrepancies in COVID-19 Patients. Microorganisms 2023; 11:2737. [PMID: 38004749 PMCID: PMC10673271 DOI: 10.3390/microorganisms11112737] [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: 09/18/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The immune response implicated in Coronavirus disease 2019 (COVID-19) pathogenesis remains to be fully understood. The present study aimed to clarify the alterations in CD4+ and CD8+ memory T cells' compartments in SARS-CoV-2-infected patients, with an emphasis on various comorbidities affecting COVID-19 patients. Peripheral blood samples were collected from 35 COVID-19 patients, 16 recovered individuals, and 25 healthy controls, and analyzed using flow cytometry. Significant alterations were detected in the percentage of CD8+ T cells and effector memory-expressing CD45RA CD8+ T cells (TEMRA) in COVID-19 patients compared to healthy controls. Interestingly, altered percentages of CD4+ T cells, CD8+ T cells, T effector (TEff), T naïve cells (TNs), T central memory (TCM), T effector memory (TEM), T stem cell memory (TSCM), and TEMRA T cells were significantly associated with the disease severity. Male patients had more CD8+ TSCMs and CD4+ TNs cells, while female patients had a significantly higher percentage of effector CD8+CD45RA+ T cells. Moreover, altered percentages of CD8+ TNs and memory CD8+CD45RO+ T cells were detected in diabetic and non-diabetic COVID-19 patients, respectively. In summary, this study identified alterations in memory T cells among COVID-19 patients, revealing a sex bias in the percentage of memory T cells. Moreover, COVID-19 severity and comorbidities have been linked to specific subsets of T memory cells which could be used as therapeutic, diagnostic, and protective targets for severe COVID-19.
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Affiliation(s)
- Hajir A. Al Saihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
| | - Hosni A. M. Hussein
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Ali A. Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt;
| | - Ahmed A. Wardany
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Sabry Y. Mahmoud
- Biology Department, College of Sciences, University of Hafr Al-Batin, Hafr Al-Batin 31991, Saudi Arabia;
- Department of Microbiology, Sohag University, Sohag 82524, Egypt
| | - Eman S. Farrag
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
- Department of Microbiology, South Valley University, Qena 83523, Egypt
| | - Taha I. A. Mohamed
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Samah M. Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum 63514, Egypt;
| | - Mohamed E. Elnosary
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Abdelazeem E. Ahmed
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Ahmed M. El-Adly
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Fareed S. El-Shenawy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | | | - Amal Rayan
- Department of Clinical Oncology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | | | - Omnia El-Badawy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Mohamed G. M. El-Naggar
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
| | - Magdy M. Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Asmaa M. Zahran
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
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20
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Neubert EN, DeRogatis JM, Lewis SA, Viramontes KM, Ortega P, Henriquez ML, Buisson R, Messaoudi I, Tinoco R. HMGB2 regulates the differentiation and stemness of exhausted CD8 + T cells during chronic viral infection and cancer. Nat Commun 2023; 14:5631. [PMID: 37704621 PMCID: PMC10499904 DOI: 10.1038/s41467-023-41352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Chronic infections and cancers evade the host immune system through mechanisms that induce T cell exhaustion. The heterogeneity within the exhausted CD8+ T cell pool has revealed the importance of stem-like progenitor (Tpex) and terminal (Tex) exhausted T cells, although the mechanisms underlying their development are not fully known. Here we report High Mobility Group Box 2 (HMGB2) protein expression is upregulated and sustained in exhausted CD8+ T cells, and HMGB2 expression is critical for their differentiation. Through epigenetic and transcriptional programming, we identify HMGB2 as a cell-intrinsic regulator of the differentiation and maintenance of Tpex cells during chronic viral infection and in tumors. Despite Hmgb2-/- CD8+ T cells expressing TCF-1 and TOX, these master regulators were unable to sustain Tpex differentiation and long-term survival during persistent antigen. Furthermore, HMGB2 also had a cell-intrinsic function in the differentiation and function of memory CD8+ T cells after acute viral infection. Our findings show that HMGB2 is a key regulator of CD8+ T cells and may be an important molecular target for future T cell-based immunotherapies.
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Affiliation(s)
- Emily N Neubert
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
- Center for Virus Research, University of California Irvine, Irvine, CA, 92697, USA
| | - Julia M DeRogatis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Sloan A Lewis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Karla M Viramontes
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, 92697, USA
| | - Monique L Henriquez
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Rémi Buisson
- Center for Virus Research, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, 92697, USA
| | - Ilhem Messaoudi
- Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, 40536, USA
| | - Roberto Tinoco
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
- Center for Virus Research, University of California Irvine, Irvine, CA, 92697, USA.
- Institute for Immunology, University of California, Irvine, Irvine, CA, 92697, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.
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21
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Reina-Campos M, Heeg M, Kennewick K, Mathews IT, Galletti G, Luna V, Nguyen Q, Huang H, Milner JJ, Hu KH, Vichaidit A, Santillano N, Boland BS, Chang JT, Jain M, Sharma S, Krummel MF, Chi H, Bensinger SJ, Goldrath AW. Metabolic programs of T cell tissue residency empower tumour immunity. Nature 2023; 621:179-187. [PMID: 37648857 PMCID: PMC11238873 DOI: 10.1038/s41586-023-06483-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Tissue resident memory CD8+ T (TRM) cells offer rapid and long-term protection at sites of reinfection1. Tumour-infiltrating lymphocytes with characteristics of TRM cells maintain enhanced effector functions, predict responses to immunotherapy and accompany better prognoses2,3. Thus, an improved understanding of the metabolic strategies that enable tissue residency by T cells could inform new approaches to empower immune responses in tissues and solid tumours. Here, to systematically define the basis for the metabolic reprogramming supporting TRM cell differentiation, survival and function, we leveraged in vivo functional genomics, untargeted metabolomics and transcriptomics of virus-specific memory CD8+ T cell populations. We found that memory CD8+ T cells deployed a range of adaptations to tissue residency, including reliance on non-steroidal products of the mevalonate-cholesterol pathway, such as coenzyme Q, driven by increased activity of the transcription factor SREBP2. This metabolic adaptation was most pronounced in the small intestine, where TRM cells interface with dietary cholesterol and maintain a heightened state of activation4, and was shared by functional tumour-infiltrating lymphocytes in diverse tumour types in mice and humans. Enforcing synthesis of coenzyme Q through deletion of Fdft1 or overexpression of PDSS2 promoted mitochondrial respiration, memory T cell formation following viral infection and enhanced antitumour immunity. In sum, through a systematic exploration of TRM cell metabolism, we reveal how these programs can be leveraged to fuel memory CD8+ T cell formation in the context of acute infections and enhance antitumour immunity.
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Affiliation(s)
- Miguel Reina-Campos
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Kelly Kennewick
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ian T Mathews
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Giovanni Galletti
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Vida Luna
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Quynhanh Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Hongling Huang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J Justin Milner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kenneth H Hu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Amy Vichaidit
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Natalie Santillano
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sonia Sharma
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steven J Bensinger
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA.
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22
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Cohen GS, Kallarakal MA, Jayaraman S, Ibukun FI, Tong KP, Orzolek LD, Larman HB, Krummey SM. Transplantation elicits a clonally diverse CD8 + T cell response that is comprised of potent CD43 + effectors. Cell Rep 2023; 42:112993. [PMID: 37590141 PMCID: PMC10727118 DOI: 10.1016/j.celrep.2023.112993] [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: 06/09/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
CD8+ T cells mediate acute rejection of allografts, which threatens the long-term survival of transplanted organs. Using MHC class I tetramers, we find that allogeneic CD8+ T cells are present at an elevated naive precursor frequency relative to other epitopes, only modestly increase in number after grafting, and maintain high T cell receptor diversity throughout the immune response. While antigen-specific effector CD8+ T cells poorly express the canonical effector marker KLRG-1, expression of the activated glycoform of CD43 defines potent effectors after transplantation. Activated CD43+ effector T cells maintain high expression of the coreceptor induced T cell costimulator (ICOS) in the presence of CTLA-4 immunoglobulin (Ig), and dual CTLA-4 Ig/anti-ICOS treatment prolongs graft survival. These data demonstrate that graft-specific CD8+ T cells have a distinct response profile relative to anti-pathogen CD8+ T cells and that CD43 and ICOS are critical surface receptors that define potent effector CD8+ T cell populations that form after transplantation.
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Affiliation(s)
- Gregory S Cohen
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Melissa A Kallarakal
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sahana Jayaraman
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Francis I Ibukun
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Katherine P Tong
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Linda D Orzolek
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - H Benjamin Larman
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Scott M Krummey
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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23
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Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DR, Li Z, Debarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536843. [PMID: 37547023 PMCID: PMC10401941 DOI: 10.1101/2023.04.14.536843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, many intracellular bacteria and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 also play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and T cell memory. Comparative Argonaute-2 high throughput sequencing of crosslinking immunoprecipitation (Ago2 HITS-CLIP, or AHC) combined with gene expression profiling in normal and miR-15/16-deficient T cells revealed a large network of several hundred direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, the long non-coding RNA Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak in T cells. This binding site was also among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16 binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of IL-2 and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long noncoding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
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Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Dimitre R Simeonov
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Rachel Debarge
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
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24
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Louis TL, Wong WH, Yao P, Kurd NS, Tysl T, Indralingam CS, Ma S, Huang WJM, Chang JT. Regulation of CD8 T Cell Differentiation by the RNA-Binding Protein DDX5. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:241-251. [PMID: 37265401 PMCID: PMC10373580 DOI: 10.4049/jimmunol.2200778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
The RNA-binding protein DEAD-box protein 5 (DDX5) is a polyfunctional regulator of gene expression, but its role in CD8+ T cell biology has not been extensively investigated. In this study, we demonstrate that deletion of DDX5 in murine CD8+ T cells reduced the differentiation of terminal effector, effector memory T, and terminal effector memory cells while increasing the generation of central memory T cells, whereas forced expression of DDX5 elicited the opposite phenotype. DDX5-deficient CD8+ T cells exhibited increased expression of genes that promote central memory T cell differentiation, including Tcf7 and Eomes. Taken together, these findings reveal a role for DDX5 in regulating the differentiation of effector and memory CD8+ T cell subsets in response to microbial infection.
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Affiliation(s)
- Tiani L. Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA, USA
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25
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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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26
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Evrard M, Becht E, Fonseca R, Obers A, Park SL, Ghabdan-Zanluqui N, Schroeder J, Christo SN, Schienstock D, Lai J, Burn TN, Clatch A, House IG, Beavis P, Kallies A, Ginhoux F, Mueller SN, Gottardo R, Newell EW, Mackay LK. Single-cell protein expression profiling resolves circulating and resident memory T cell diversity across tissues and infection contexts. Immunity 2023:S1074-7613(23)00262-5. [PMID: 37392736 DOI: 10.1016/j.immuni.2023.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/08/2023] [Accepted: 06/07/2023] [Indexed: 07/03/2023]
Abstract
Memory CD8+ T cells can be broadly divided into circulating (TCIRCM) and tissue-resident memory T (TRM) populations. Despite well-defined migratory and transcriptional differences, the phenotypic and functional delineation of TCIRCM and TRM cells, particularly across tissues, remains elusive. Here, we utilized an antibody screening platform and machine learning prediction pipeline (InfinityFlow) to profile >200 proteins in TCIRCM and TRM cells in solid organs and barrier locations. High-dimensional analyses revealed unappreciated heterogeneity within TCIRCM and TRM cell lineages across nine different organs after either local or systemic murine infection models. Additionally, we demonstrated the relative effectiveness of strategies allowing for the selective ablation of TCIRCM or TRM populations across organs and identified CD55, KLRG1, CXCR6, and CD38 as stable markers for characterizing memory T cell function during inflammation. Together, these data and analytical framework provide an in-depth resource for memory T cell classification in both steady-state and inflammatory conditions.
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Affiliation(s)
- Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia.
| | - Etienne Becht
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Simone L Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Nagela Ghabdan-Zanluqui
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Jan Schroeder
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Susan N Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Dominik Schienstock
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Junyun Lai
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Thomas N Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Imran G House
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Paul Beavis
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Scott N Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre Hospitalier Universitaire du Vaud and University of Lausanne, Lausanne 1011, Switzerland
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia.
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27
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Buggert M, Price DA, Mackay LK, Betts MR. Human circulating and tissue-resident memory CD8 + T cells. Nat Immunol 2023:10.1038/s41590-023-01538-6. [PMID: 37349380 DOI: 10.1038/s41590-023-01538-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/04/2023] [Indexed: 06/24/2023]
Abstract
Our current knowledge of human memory CD8+ T cells is derived largely from studies of the intravascular space. However, emerging data are starting to challenge some of the dogmas based on this work, suggesting that a conceptual revision may be necessary. In this review, we provide a brief history of the field and summarize the biology of circulating and tissue-resident memory CD8+ T cells, which are ultimately responsible for effective immune surveillance. We also incorporate recent findings into a biologically integrated model of human memory CD8+ T cell differentiation. Finally, we address how future innovative human studies could improve our understanding of anatomically localized CD8+ T cells to inform the development of more effective immunotherapies and vaccines, the need for which has been emphasized by the global struggle to contain severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael R Betts
- Institute for Immunology and Center for AIDS Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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28
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McDonald B, Chick BY, Ahmed NS, Burns M, Ma S, Casillas E, Chen D, Mann TH, O'Connor C, Hah N, Hargreaves DC, Kaech SM. Canonical BAF complex activity shapes the enhancer landscape that licenses CD8 + T cell effector and memory fates. Immunity 2023; 56:1303-1319.e5. [PMID: 37315534 PMCID: PMC10281564 DOI: 10.1016/j.immuni.2023.05.005] [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: 08/09/2022] [Revised: 02/08/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cells provide host protection against pathogens by differentiating into distinct effector and memory cell subsets, but how chromatin is site-specifically remodeled during their differentiation is unclear. Due to its critical role in regulating chromatin and enhancer accessibility through its nucleosome remodeling activities, we investigated the role of the canonical BAF (cBAF) chromatin remodeling complex in antiviral CD8+ T cells during infection. ARID1A, a subunit of cBAF, was recruited early after activation and established de novo open chromatin regions (OCRs) at enhancers. Arid1a deficiency impaired the opening of thousands of activation-induced enhancers, leading to loss of TF binding, dysregulated proliferation and gene expression, and failure to undergo terminal effector differentiation. Although Arid1a was dispensable for circulating memory cell formation, tissue-resident memory (Trm) formation was strongly impaired. Thus, cBAF governs the enhancer landscape of activated CD8+ T cells that orchestrates TF recruitment and activity and the acquisition of specific effector and memory differentiation states.
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Affiliation(s)
- Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Brent Y Chick
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Nasiha S Ahmed
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mannix Burns
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shixin Ma
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eduardo Casillas
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Dan Chen
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Thomas H Mann
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Carolyn O'Connor
- Flow Cytometry Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nasun Hah
- Chapman Charitable Foundations Genomic Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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29
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Riffelmacher T, Paynich Murray M, Wientjens C, Chandra S, Cedillo-Castelán V, Chou TF, McArdle S, Dillingham C, Devereaux J, Nilsen A, Brunel S, Lewinsohn DM, Hasty J, Seumois G, Benedict CA, Vijayanand P, Kronenberg M. Divergent metabolic programmes control two populations of MAIT cells that protect the lung. Nat Cell Biol 2023; 25:877-891. [PMID: 37231163 PMCID: PMC10264248 DOI: 10.1038/s41556-023-01152-6] [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: 09/07/2022] [Accepted: 04/18/2023] [Indexed: 05/27/2023]
Abstract
Although mucosal-associated invariant T (MAIT) cells provide rapid, innate-like responses, they are not pre-set, and memory-like responses have been described for MAIT cells following infections. The importance of metabolism for controlling these responses, however, is unknown. Here, following pulmonary immunization with a Salmonella vaccine strain, mouse MAIT cells expanded as separate CD127-Klrg1+ and CD127+Klrg1- antigen-adapted populations that differed in terms of their transcriptome, function and localization in lung tissue. These populations remained altered from steady state for months as stable, separate MAIT cell lineages with enhanced effector programmes and divergent metabolism. CD127+ MAIT cells engaged in an energetic, mitochondrial metabolic programme, which was critical for their maintenance and IL-17A synthesis. This programme was supported by high fatty acid uptake and mitochondrial oxidation and relied on highly polarized mitochondria and autophagy. After vaccination, CD127+ MAIT cells protected mice against Streptococcus pneumoniae infection. In contrast, Klrg1+ MAIT cells had dormant but ready-to-respond mitochondria and depended instead on Hif1a-driven glycolysis to survive and produce IFN-γ. They responded antigen independently and participated in protection from influenza virus. These metabolic dependencies may enable tuning of memory-like MAIT cell responses for vaccination and immunotherapies.
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Affiliation(s)
- Thomas Riffelmacher
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
| | | | | | | | | | | | - Sara McArdle
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | | | - Aaron Nilsen
- Oregon Health and Science University, Portland, OR, USA
| | - Simon Brunel
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Jeff Hasty
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Mitchell Kronenberg
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
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30
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Nuñez NG, Schmid J, Power L, Alberti C, Krishnarajah S, Kreutmair S, Unger S, Blanco S, Konigheim B, Marín C, Onofrio L, Kienzler JC, Costa-Pereira S, Ingelfinger F, Pasinovich ME, Castelli JM, Vizzotti C, Schaefer M, Villar-Vesga J, Mundt S, Merten CH, Sethi A, Wertheimer T, Lutz M, Vanoaica D, Sotomayor C, Gruppi A, Münz C, Cardozo D, Barbás G, Lopez L, Carreño P, Castro G, Raboy E, Gallego S, Morón G, Cervi L, Acosta Rodriguez EV, Maletto BA, Maccioni M, Becher B. High-dimensional analysis of 16 SARS-CoV-2 vaccine combinations reveals lymphocyte signatures correlating with immunogenicity. Nat Immunol 2023; 24:941-954. [PMID: 37095378 PMCID: PMC10232362 DOI: 10.1038/s41590-023-01499-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023]
Abstract
The range of vaccines developed against severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) provides a unique opportunity to study immunization across different platforms. In a single-center cohort, we analyzed the humoral and cellular immune compartments following five coronavirus disease 2019 (COVID-19) vaccines spanning three technologies (adenoviral, mRNA and inactivated virus) administered in 16 combinations. For adenoviral and inactivated-virus vaccines, heterologous combinations were generally more immunogenic compared to homologous regimens. The mRNA vaccine as the second dose resulted in the strongest antibody response and induced the highest frequency of spike-binding memory B cells irrespective of the priming vaccine. Priming with the inactivated-virus vaccine increased the SARS-CoV-2-specific T cell response, whereas boosting did not. Distinct immune signatures were elicited by the different vaccine combinations, demonstrating that the immune response is shaped by the type of vaccines applied and the order in which they are delivered. These data provide a framework for improving future vaccine strategies against pathogens and cancer.
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Affiliation(s)
- Nicolás Gonzalo Nuñez
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina.
| | - Jonas Schmid
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Laura Power
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Chiara Alberti
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Stefanie Kreutmair
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sebastián Blanco
- Facultad de Ciencias Médicas, Instituto de Virología 'Dr. J. M. Vanella' Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Brenda Konigheim
- Facultad de Ciencias Médicas, Instituto de Virología 'Dr. J. M. Vanella' Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Constanza Marín
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Luisina Onofrio
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | | | - Sara Costa-Pereira
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Florian Ingelfinger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | | | - Carla Vizzotti
- Ministerio de Salud de la Nación, Buenos Aires, Argentina
| | - Maximilian Schaefer
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Juan Villar-Vesga
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sarah Mundt
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Carla Helena Merten
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Aakriti Sethi
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Tobias Wertheimer
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Mirjam Lutz
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Danusia Vanoaica
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Claudia Sotomayor
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Adriana Gruppi
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Christian Münz
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Diego Cardozo
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Gabriela Barbás
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Laura Lopez
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Paula Carreño
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Gonzalo Castro
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Elias Raboy
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Sandra Gallego
- Facultad de Ciencias Médicas, Instituto de Virología 'Dr. J. M. Vanella' Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriel Morón
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Laura Cervi
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Eva V Acosta Rodriguez
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Belkys A Maletto
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina
| | - Mariana Maccioni
- Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Córdoba, Argentina.
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
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31
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Ranek JS, Stallaert W, Milner J, Stanley N, Purvis JE. Feature selection for preserving biological trajectories in single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540043. [PMID: 37214963 PMCID: PMC10197710 DOI: 10.1101/2023.05.09.540043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Single-cell technologies can readily measure the expression of thousands of molecular features from individual cells undergoing dynamic biological processes, such as cellular differentiation, immune response, and disease progression. While examining cells along a computationally ordered pseudotime offers the potential to study how subtle changes in gene or protein expression impact cell fate decision-making, identifying characteristic features that drive continuous biological processes remains difficult to detect from unenriched and noisy single-cell data. Given that all profiled sources of feature variation contribute to the cell-to-cell distances that define an inferred cellular trajectory, including confounding sources of biological variation (e.g. cell cycle or metabolic state) or noisy and irrelevant features (e.g. measurements with low signal-to-noise ratio) can mask the underlying trajectory of study and hinder inference. Here, we present DELVE (dynamic selection of locally covarying features), an unsupervised feature selection method for identifying a representative subset of dynamically-expressed molecular features that recapitulates cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effect of unwanted sources of variation confounding inference, and instead models cell states from dynamic feature modules that constitute core regulatory complexes. Using simulations, single-cell RNA sequencing data, and iterative immunofluorescence imaging data in the context of the cell cycle and cellular differentiation, we demonstrate that DELVE selects features that more accurately characterize cell populations and improve the recovery of cell type transitions. This feature selection framework provides an alternative approach for improving trajectory inference and uncovering co-variation amongst features along a biological trajectory. DELVE is implemented as an open-source python package and is publicly available at: https://github.com/jranek/delve.
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Affiliation(s)
- Jolene S. Ranek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E. Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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32
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Quon S, Yu B, Russ BE, Tsyganov K, Nguyen H, Toma C, Heeg M, Hocker JD, Milner JJ, Crotty S, Pipkin ME, Turner SJ, Goldrath AW. DNA architectural protein CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8 + T cells. Immunity 2023; 56:959-978.e10. [PMID: 37040762 PMCID: PMC10265493 DOI: 10.1016/j.immuni.2023.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 04/13/2023]
Abstract
Although the importance of genome organization for transcriptional regulation of cell-fate decisions and function is clear, the changes in chromatin architecture and how these impact effector and memory CD8+ T cell differentiation remain unknown. Using Hi-C, we studied how genome configuration is integrated with CD8+ T cell differentiation during infection and investigated the role of CTCF, a key chromatin remodeler, in modulating CD8+ T cell fates through CTCF knockdown approaches and perturbation of specific CTCF-binding sites. We observed subset-specific changes in chromatin organization and CTCF binding and revealed that weak-affinity CTCF binding promotes terminal differentiation of CD8+ T cells through the regulation of transcriptional programs. Further, patients with de novo CTCF mutations had reduced expression of the terminal-effector genes in peripheral blood lymphocytes. Therefore, in addition to establishing genome architecture, CTCF regulates effector CD8+ T cell heterogeneity through altering interactions that regulate the transcription factor landscape and transcriptome.
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Affiliation(s)
- Sara Quon
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bingfei Yu
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kirill Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hongtuyet Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Toma
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - James D Hocker
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - J Justin Milner
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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33
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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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Hodgson R, Crockford TL, Bhandari A, Kepple JD, Back J, Cawthorne E, Abeler-Dörner L, Laing AG, Clare S, Speak A, Adams DJ, Dougan G, Hayday AC, Deobagkar-Lele M, Cornall RJ, Bull KR. Prolidase Deficiency Causes Spontaneous T Cell Activation and Lupus-like Autoimmunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:547-557. [PMID: 36637239 PMCID: PMC9946897 DOI: 10.4049/jimmunol.2200212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/10/2022] [Indexed: 01/14/2023]
Abstract
Prolidase deficiency (PD) is a multisystem disorder caused by mutations in the PEPD gene, which encodes a ubiquitously expressed metallopeptidase essential for the hydrolysis of dipeptides containing C-terminal proline or hydroxyproline. PD typically presents in childhood with developmental delay, skin ulcers, recurrent infections, and, in some patients, autoimmune features that can mimic systemic lupus erythematosus. The basis for the autoimmune association is uncertain, but might be due to self-antigen exposure with tissue damage, or indirectly driven by chronic infection and microbial burden. In this study, we address the question of causation and show that Pepd-null mice have increased antinuclear autoantibodies and raised serum IgA, accompanied by kidney immune complex deposition, consistent with a systemic lupus erythematosus-like disease. These features are associated with an accumulation of CD4 and CD8 effector T cells in the spleen and liver. Pepd deficiency leads to spontaneous T cell activation and proliferation into the effector subset, which is cell intrinsic and independent of Ag receptor specificity or antigenic stimulation. However, an increase in KLRG1+ effector CD8 cells is not observed in mixed chimeras, in which the autoimmune phenotype is also absent. Our findings link autoimmune susceptibility in PD to spontaneous T cell dysfunction, likely to be acting in combination with immune activators that lie outside the hemopoietic system but result from the abnormal metabolism or loss of nonenzymatic prolidase function. This knowledge provides insight into the role of prolidase in the maintenance of self-tolerance and highlights the importance of treatment to control T cell activation.
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Affiliation(s)
- Rose Hodgson
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tanya L. Crockford
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Aneesha Bhandari
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jessica D. Kepple
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer Back
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eleanor Cawthorne
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Adam G. Laing
- Department of Immunobiology, King’s College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom; and
| | - Simon Clare
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | - Adrian C. Hayday
- Department of Immunobiology, King’s College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom; and
| | - Mukta Deobagkar-Lele
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard J. Cornall
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Katherine R. Bull
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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35
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Dean JW, Helm EY, Fu Z, Xiong L, Sun N, Oliff KN, Muehlbauer M, Avram D, Zhou L. The aryl hydrocarbon receptor cell intrinsically promotes resident memory CD8 + T cell differentiation and function. Cell Rep 2023; 42:111963. [PMID: 36640340 PMCID: PMC9940759 DOI: 10.1016/j.celrep.2022.111963] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
The Aryl hydrocarbon receptor (Ahr) regulates the differentiation and function of CD4+ T cells; however, its cell-intrinsic role in CD8+ T cells remains elusive. Herein we show that Ahr acts as a promoter of resident memory CD8+ T cell (TRM) differentiation and function. Genetic ablation of Ahr in mouse CD8+ T cells leads to increased CD127-KLRG1+ short-lived effector cells and CD44+CD62L+ T central memory cells but reduced granzyme-B-producing CD69+CD103+ TRM cells. Genome-wide analyses reveal that Ahr suppresses the circulating while promoting the resident memory core gene program. A tumor resident polyfunctional CD8+ T cell population, revealed by single-cell RNA-seq, is diminished upon Ahr deletion, compromising anti-tumor immunity. Human intestinal intraepithelial CD8+ T cells also highly express AHR that regulates in vitro TRM differentiation and granzyme B production. Collectively, these data suggest that Ahr is an important cell-intrinsic factor for CD8+ T cell immunity.
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Affiliation(s)
- Joseph W Dean
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Eric Y Helm
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Zheng Fu
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Lifeng Xiong
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Na Sun
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Kristen N Oliff
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Marcus Muehlbauer
- Division of Gastroenterology, Hepatology and Nutrition, College of Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Dorina Avram
- Department of Immunology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA.
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36
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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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37
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Lin YH, Duong HG, Limary AE, Kim ES, Hsu P, Patel SA, Wong WH, Indralingam CS, Liu YC, Yao P, Chiang NR, Vandenburgh SA, Anderson TR, Olvera JG, Ferry A, Takehara KK, Jin W, Tsai MS, Yeo GW, Goldrath AW, Chang JT. Small intestine and colon tissue-resident memory CD8 + T cells exhibit molecular heterogeneity and differential dependence on Eomes. Immunity 2023; 56:207-223.e8. [PMID: 36580919 PMCID: PMC9904390 DOI: 10.1016/j.immuni.2022.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022]
Abstract
Tissue-resident memory CD8+ T (TRM) cells are a subset of memory T cells that play a critical role in limiting early pathogen spread and controlling infection. TRM cells exhibit differences across tissues, but their potential heterogeneity among distinct anatomic compartments within the small intestine and colon has not been well recognized. Here, by analyzing TRM cells from the lamina propria and epithelial compartments of the small intestine and colon, we showed that intestinal TRM cells exhibited distinctive patterns of cytokine and granzyme expression along with substantial transcriptional, epigenetic, and functional heterogeneity. The T-box transcription factor Eomes, which represses TRM cell formation in some tissues, exhibited unexpected context-specific regulatory roles in supporting the maintenance of established TRM cells in the small intestine, but not in the colon. Taken together, these data provide previously unappreciated insights into the heterogeneity and differential requirements for the formation vs. maintenance of intestinal TRM cells.
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Affiliation(s)
- Yun Hsuan Lin
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Han G Duong
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Abigail E Limary
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleanor S Kim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Shefali A Patel
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - William H Wong
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Natalie R Chiang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sara A Vandenburgh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Taylor R Anderson
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amir Ferry
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kennidy K Takehara
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA 92161, USA.
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38
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Geginat J, Granucci F. Regulatory T-cell-derived interleukin-15 shapes cytotoxic T cell memory. Eur J Immunol 2023; 53:e2250238. [PMID: 36398486 DOI: 10.1002/eji.202250238] [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: 11/07/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
It is well known that regulatory T-cells (Tregs) are required to prevent autoimmunity, but they may also have some less-well understood immune-stimulatory effects. In particular, in CD8+ T-cell responses Tregs select high-affinity clones upon priming and promote memory by inhibiting inflammation-dependent generation of short-lived effector cells. In the current issue of the European Journal of Immunology [Eur. J. Immunol. 2023. 53: 2149400], Madi et al. report the surprising finding that human and murine FOXP3+ Tregs are a physiologically relevant source of IL-15, a homeostatic cytokine that promotes antigen-independent maintenance of CD8+ memory T-cells. In mice that lack IL-15 selectively in FOXP3+ Tregs the authors show that the composition of the CD8+ T-cell memory pool is altered in the absence of Treg-derived IL-15, since a subset of terminally effector memory cells is drastically reduced. Otherwise Treg-derived IL-15 is dispensable for antiviral immune responses and the generation of anti-viral CD8+ memory T-cells. These findings add to our understanding of the multifaceted role of Tregs in immune responses, and how IL-15 derived from different cellular sources maintains anti-viral T-cell memory.
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Affiliation(s)
- Jens Geginat
- University of Milan, Department of Clinical Sciences and Community Health, Milan, Italy.,Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Francesca Granucci
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
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39
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Madi A, Wu J, Ma S, Weisshaar N, Mieg A, Hering M, Ming Y, Zettl F, Mohr K, Ten Bosch N, Schlimbach T, Hertel F, Cui G. Regulatory T cell-derived interleukin-15 promotes the diversity of immunological memory. Eur J Immunol 2023; 53:e2149400. [PMID: 36263815 DOI: 10.1002/eji.202149400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/07/2022] [Accepted: 10/18/2022] [Indexed: 02/02/2023]
Abstract
While the immunosuppressive function of regulatory T (Treg) cells has been extensively studied, their immune-supportive roles have been less well investigated. Using a lymphocytic choriomeningitis virus (LCMV) Armstrong infection mouse model, we found that Treg cell-derived interleukin (IL)-15 is required for long-term maintenance of the KLRG1+ IL-7Rα- CD62L- terminal effector memory CD8+ T (tTEM) cell subset, but dispensable for the suppressive function of Treg cells themselves. In contrast, deletion of Il15 from other sources, including myeloid cells and muscles, did not affect the composition of the memory CD8+ T cell pool. Our findings identify Treg cells as an essential IL-15 source maintaining tTEM cells and suggest that Treg cells promote the diversity of immunological memory.
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Affiliation(s)
- Alaa Madi
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Jingxia Wu
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sicong Ma
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Nina Weisshaar
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alessa Mieg
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Marvin Hering
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Yanan Ming
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ferdinand Zettl
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Kerstin Mohr
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Nora Ten Bosch
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany
| | - Tilo Schlimbach
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Franziska Hertel
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Guoliang Cui
- T Cell Metabolism Group (D192), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany.,Helmholtz Institute for Translational Oncology (HI-TRON), Mainz, Germany
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40
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Daniel B, Yost KE, Hsiung S, Sandor K, Xia Y, Qi Y, Hiam-Galvez KJ, Black M, J Raposo C, Shi Q, Meier SL, Belk JA, Giles JR, Wherry EJ, Chang HY, Egawa T, Satpathy AT. Divergent clonal differentiation trajectories of T cell exhaustion. Nat Immunol 2022; 23:1614-1627. [PMID: 36289450 PMCID: PMC11225711 DOI: 10.1038/s41590-022-01337-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
Chronic antigen exposure during viral infection or cancer promotes an exhausted T cell (Tex) state with reduced effector function. However, whether all antigen-specific T cell clones follow the same Tex differentiation trajectory remains unclear. Here, we generate a single-cell multiomic atlas of T cell exhaustion in murine chronic viral infection that redefines Tex phenotypic diversity, including two late-stage Tex subsets with either a terminal exhaustion (Texterm) or a killer cell lectin-like receptor-expressing cytotoxic (TexKLR) phenotype. We use paired single-cell RNA and T cell receptor sequencing to uncover clonal differentiation trajectories of Texterm-biased, TexKLR-biased or divergent clones that acquire both phenotypes. We show that high T cell receptor signaling avidity correlates with Texterm, whereas low avidity correlates with effector-like TexKLR fate. Finally, we identify similar clonal differentiation trajectories in human tumor-infiltrating lymphocytes. These findings reveal clonal heterogeneity in the T cell response to chronic antigen that influences Tex fates and persistence.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Sunnie Hsiung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Yu Xia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kamir J Hiam-Galvez
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mollie Black
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Colin J Raposo
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Quanming Shi
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Stefanie L Meier
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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41
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Demery-Poulos C, Romero R, Xu Y, Arenas-Hernandez M, Miller D, Tao L, Galaz J, Farias-Jofre M, Bhatti G, Garcia-Flores V, Seyerle M, Tarca AL, Gomez-Lopez N. Pregnancy imparts distinct systemic adaptive immune function. Am J Reprod Immunol 2022; 88:e13606. [PMID: 35989229 PMCID: PMC9648024 DOI: 10.1111/aji.13606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/05/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
PROBLEM Pregnancy represents a state of systemic immune activation that is primarily driven by alterations in circulating innate immune cells. Recent studies have suggested that cellular adaptive immune components, T cells and B cells, also undergo changes throughout gestation. However, the phenotypes and functions of such adaptive immune cells are poorly understood. Herein, we utilized high-dimensional flow cytometry and functional assays to characterize T-cell and B-cell responses in pregnant and non-pregnant women. METHODS Peripheral blood mononuclear cells from pregnant (n = 20) and non-pregnant (n = 25) women were used for phenotyping of T-cell and B-cell subsets. T-cell proliferation and B-cell activation were assessed by flow cytometry after in vitro stimulation, and lymphocyte cytotoxicity was evaluated by using a cell-based assay. Statistical comparisons were performed with linear mixed-effects models. RESULTS Pregnancy was associated with modestly enhanced basal activation of peripheral CD4+ T cells. Both CD4+ and CD8+ T cells from pregnant women showed increased activation-induced proliferation; yet, a reduced proportion of these cells expressed activation markers compared to non-pregnant women. There were no differences in peripheral lymphocyte cytotoxicity between study groups. A greater proportion of B cells from pregnant women displayed memory-like and activated phenotypes, and such cells exhibited higher activation following stimulation. CONCLUSION Maternal circulating T cells and B cells display distinct responses during pregnancy. The former may reflect the unique capacity of T cells to respond to potential threats without undergoing aberrant activation, thereby preventing systemic inflammatory responses that can lead to adverse perinatal consequences.
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Affiliation(s)
- Catherine Demery-Poulos
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Centerfor Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
- Detroit Medical Center, Detroit, Michigan, USA
| | - Yi Xu
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Marcia Arenas-Hernandez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Derek Miller
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Li Tao
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Division of Obstetrics and Gynecology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcelo Farias-Jofre
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Division of Obstetrics and Gynecology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gaurav Bhatti
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Valeria Garcia-Flores
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Megan Seyerle
- Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Adi L. Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS), Bethesda, Maryland, and Detroit, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
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42
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Responsiveness to interleukin-15 therapy is shared between tissue-resident and circulating memory CD8 + T cell subsets. Proc Natl Acad Sci U S A 2022; 119:e2209021119. [PMID: 36260745 PMCID: PMC9618124 DOI: 10.1073/pnas.2209021119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interleukin-15 (IL-15) is often considered a central regulator of memory CD8+ T cells, based primarily on studies of recirculating subsets. However, recent work identified IL-15-independent CD8+ T cell memory populations, including tissue-resident memory CD8+ T cells (TRM) in some nonlymphoid tissues (NLTs). Whether this reflects the existence of IL-15-insensitive memory CD8+ T cells is unclear. We report that IL-15 complexes (IL-15c) stimulate rapid proliferation and expansion of both tissue-resident and circulating memory CD8+ T cell subsets across lymphoid and nonlymphoid tissues with varying magnitude by tissue and memory subset, in some sites correlating with differing levels of the IL-2Rβ. This was conserved for memory CD8+ T cells recognizing distinct antigens and elicited by different pathogens. Following IL-15c-induced expansion, divided cells contracted to baseline numbers and only slowly returned to basal proliferation, suggesting a mechanism to transiently amplify memory populations. Through parabiosis, we showed that IL-15c drive local proliferation of TRM, with a degree of recruitment of circulating cells to some NLTs. Hence, irrespective of homeostatic IL-15 dependence, IL-15 sensitivity is a defining feature of memory CD8+ T cell populations, with therapeutic potential for expansion of TRM and other memory subsets in an antigen-agnostic and temporally controlled fashion.
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43
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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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Chandiran K, Suarez-Ramirez JE, Hu Y, Jellison ER, Ugur Z, Low JS, McDonald B, Kaech SM, Cauley LS. SMAD4 and TGFβ are architects of inverse genetic programs during fate-determination of antiviral CTLs. eLife 2022; 11:76457. [PMID: 35942952 PMCID: PMC9402230 DOI: 10.7554/elife.76457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Transforming growth factor β (TGFβ) is an important differentiation factor for cytotoxic T lymphocytes (CTLs) and alters the expression levels of several of homing receptors during infection. SMAD4 is part of the canonical signaling network used by members of the transforming growth factor family. For this study, genetically modified mice were used to determine how SMAD4 and TGFβ receptor II (TGFβRII) participate in transcriptional programming of pathogen-specific CTLs. We show that these molecules are essential components of opposing signaling mechanisms, and cooperatively regulate a collection of genes that determine whether specialized populations of pathogen-specific CTLs circulate around the body, or settle in peripheral tissues. TGFβ uses a canonical SMAD-dependent signaling pathway to downregulate Eomesodermin (EOMES), KLRG1, and CD62L, while CD103 is induced. Conversely, in vivo and in vitro data show that EOMES, KLRG1, CX3CR1, and CD62L are positively regulated via SMAD4, while CD103 and Hobit are downregulated. Intravascular staining also shows that signaling via SMAD4 promotes formation of long-lived terminally differentiated CTLs that localize in the vasculature. Our data show that inflammatory molecules play a key role in lineage determination of pathogen-specific CTLs, and use SMAD-dependent signaling to alter the expression levels of multiple homing receptors and transcription factors with known functions during memory formation.
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Affiliation(s)
- Karthik Chandiran
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Jenny E Suarez-Ramirez
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Yinghong Hu
- Department of Microbiology and Immunology, Emory University, Atlanta, United States
| | - Evan R Jellison
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Zenep Ugur
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
| | - Jun-Siong Low
- Department of Immunobiology, Yale University, Bellinzona, Switzerland
| | - Bryan McDonald
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, San Diego, United States
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, San Diego, United States
| | - Linda S Cauley
- Department of Immunology, University of Connecticut Health Center, Farmington, United States
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45
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Abstract
Memory CD4+ T cells play a pivotal role in mediating long-term protective immunity, positioning them as an important target in vaccine development. However, multiple functionally distinct helper CD4+ T-cell subsets can arise in response to a single invading pathogen, complicating the identification of rare populations of memory precursor cells during the effector phase of infection and memory CD4+ T cells following pathogen clearance and the contraction phase of infection. Furthermore, current literature remains unclear regarding whether a single CD4+ memory T-cell lineage gives rise to secondary CD4+ T helper subsets or if there are unique memory precursor cells within each helper lineage. A majority of T follicular helper (Tfh) cells, which have established memory potential, express Id3, an inhibitor of E protein transcription factors, following acute viral infection. We show that expression of Id3 definitively identified a subset of cells within both the CD4+ Tfh and T helper 1 (Th1) lineages at memory time points that exhibited memory potential, with the capacity for significant re-expansion in response to secondary infection. Notably, we demonstrate that a subset of Th1 cells that survive into the memory phase were marked by Id3 expression and possessed the potential for enhanced expansion and generation of both Th1 and Tfh secondary effector cell populations in a secondary response to pathogen. Additionally, these cells exhibited enrichment of key molecules associated with memory potential when compared with Id3lo Th1 cells. Therefore, we propose that Id3 expression serves as an important marker to indicate multipotent potential in memory CD4+ T cells.
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46
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Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4 + T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. eLife 2022; 11:e76339. [PMID: 35829695 PMCID: PMC9323004 DOI: 10.7554/elife.76339] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cells are critical orchestrators of immune responses against a large variety of pathogens, including viruses. While multiple CD4+ T cell subtypes and their key transcriptional regulators have been identified, there is a lack of consistent definition for CD4+ T cell transcriptional states. In addition, the progressive changes affecting CD4+ T cell subtypes during and after immune responses remain poorly defined. Using single-cell transcriptomics, we characterized the diversity of CD4+ T cells responding to self-resolving and chronic viral infections in mice. We built a comprehensive map of virus-specific CD4+ T cells and their evolution over time, and identified six major cell states consistently observed in acute and chronic infections. During the course of acute infections, T cell composition progressively changed from effector to memory states, with subtype-specific gene modules and kinetics. Conversely, in persistent infections T cells acquired distinct, chronicity-associated programs. By single-cell T cell receptor (TCR) analysis, we characterized the clonal structure of virus-specific CD4+ T cells across individuals. Virus-specific CD4+ T cell responses were essentially private across individuals and most T cells differentiated into both Tfh and Th1 subtypes irrespective of their TCR. Finally, we showed that our CD4+ T cell map can be used as a reference to accurately interpret cell states in external single-cell datasets across tissues and disease models. Overall, this study describes a previously unappreciated level of adaptation of the transcriptional states of CD4+ T cells responding to viruses and provides a new computational resource for CD4+ T cell analysis.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of LausanneLausanneSwitzerland
- Agora Cancer Research CenterLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Ariel Tjitropranoto
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
| | - Zachary Sherman
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
| | - Michael C Kelly
- Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research IncFrederickUnited States
| | - Thomas Ciucci
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Santiago J Carmona
- Department of Oncology, UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of LausanneLausanneSwitzerland
- Agora Cancer Research CenterLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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47
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Tissue-resident memory CD8 + T cells possess unique transcriptional, epigenetic and functional adaptations to different tissue environments. Nat Immunol 2022; 23:1121-1131. [PMID: 35761084 PMCID: PMC10041538 DOI: 10.1038/s41590-022-01229-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 04/26/2022] [Indexed: 11/08/2022]
Abstract
Tissue-resident memory T cells (TRM cells) provide protective immunity, but the contributions of specific tissue environments to TRM cell differentiation and homeostasis are not well understood. In the present study, the diversity of gene expression and genome accessibility by mouse CD8+ TRM cells from distinct organs that responded to viral infection revealed both shared and tissue-specific transcriptional and epigenetic signatures. TRM cells in the intestine and salivary glands expressed transforming growth factor (TGF)-β-induced genes and were maintained by ongoing TGF-β signaling, whereas those in the fat, kidney and liver were not. Constructing transcriptional-regulatory networks identified the transcriptional repressor Hic1 as a critical regulator of TRM cell differentiation in the small intestine and showed that Hic1 overexpression enhanced TRM cell differentiation and protection from infection. Provision of a framework for understanding how CD8+ TRM cells adapt to distinct tissue environments, and identification of tissue-specific transcriptional regulators mediating these adaptations, inform strategies to boost protective memory responses at sites most vulnerable to infection.
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48
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Kanbar JN, Ma S, Kim ES, Kurd NS, Tsai MS, Tysl T, Widjaja CE, Limary AE, Yee B, He Z, Hao Y, Fu XD, Yeo GW, Huang WJ, Chang JT. The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. J Exp Med 2022; 219:213232. [PMID: 35593887 DOI: 10.1084/jem.20211756] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/21/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-TEM) circulating memory subset. Evaluation of chromatin-enriched lncRNAs revealed that Malat1 grouped with trans lncRNAs that exhibit increased RNA interactions at gene promoters and gene bodies. Moreover, we observed that Malat1 was associated with increased H3K27me3 deposition at a number of memory cell-associated genes through a direct interaction with Ezh2, thereby promoting terminal effector and t-TEM cell differentiation. Our findings suggest an important functional role of Malat1 in regulating CD8+ T cell differentiation and broaden the knowledge base of lncRNAs in CD8+ T cell biology.
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Affiliation(s)
- Jad N Kanbar
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Eleanor S Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Nadia S Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Matthew S Tsai
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Tiffani Tysl
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | | | - Abigail E Limary
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Brian Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | - Wendy J Huang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA.,Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA
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49
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Vardam-Kaur T, van Dijk S, Peng C, Wanhainen KM, Jameson SC, Borges da Silva H. The Extracellular ATP Receptor P2RX7 Imprints a Promemory Transcriptional Signature in Effector CD8 + T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1686-1699. [PMID: 35264459 PMCID: PMC8976739 DOI: 10.4049/jimmunol.2100555] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Development of CD8+ central memory T (Tcm) and resident memory T (Trm) cells, which promote immunity in the circulation and in barrier tissues, respectively, is not completely understood. Tcm and Trm cells may arise from common precursors; however, their fate-inducing signals are elusive. We found that virus-specific effector CD8+ T cells display heterogeneous expression of the extracellular ATP sensor P2RX7. P2RX7-high expression is confined, at peak effector phase, to CD62L+ memory precursors, which preferentially form Tcm cells. Among early effector CD8+ T cells, asymmetrical P2RX7 distribution correlated with distinct transcriptional signatures, with P2RX7-high cells enriched for memory and tissue residency sets. P2RX7-high early effectors preferentially form both Tcm and Trm cells. Defective Tcm and Trm cell formation in P2RX7 deficiency is significantly reverted when the transcriptional repressor Zeb2 is ablated. Mechanistically, P2RX7 negatively regulates Zeb2 expression, at least partially through TGF-β sensing in early effector CD8+ T cells. Our study indicates that unequal P2RX7 upregulation in effector CD8+ T cells is a foundational element of the early Tcm/Trm fate.
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Affiliation(s)
| | - Sarah van Dijk
- Department of Immunology, Mayo Clinic Arizona, Scottsdale, AZ; and
| | - Changwei Peng
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Kelsey M Wanhainen
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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50
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Tsuda S, Pipkin ME. Transcriptional Control of Cell Fate Determination in Antigen-Experienced CD8 T Cells. Cold Spring Harb Perspect Biol 2022; 14:a037945. [PMID: 34127445 PMCID: PMC8805646 DOI: 10.1101/cshperspect.a037945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Robust immunity to intracellular infections is mediated by antigen-specific naive CD8 T cells that become activated and differentiate into phenotypically and functionally diverse subsets of effector cells, some of which terminally differentiate and others that give rise to memory cells that provide long-lived protection. This developmental system is an outstanding model with which to elucidate how regulation of chromatin structure and transcriptional control establish gene expression programs that govern cell fate determination, insights from which are likely to be useful for informing the design of immunotherapeutic approaches to engineer durable immunity to infections and tumors. A unifying framework that describes how naive CD8 T cells develop into memory cells is still outstanding. We propose a model that incorporates a common early linear path followed by divergent paths that slowly lose capacity to interconvert and discuss classical and contemporary observations that support these notions, focusing on insights from transcriptional control and chromatin regulation.
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Affiliation(s)
- Shanel Tsuda
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, USA
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