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Kim HJ, Nakagawa H, Choi JY, Che X, Divris A, Liu Q, Wight AE, Zhang H, Saad A, Solhjou Z, Deban C, Azzi JR, Cantor H. A narrow T cell receptor repertoire instructs thymic differentiation of MHC class Ib-restricted CD8+ regulatory T cells. J Clin Invest 2024; 134:e170512. [PMID: 37934601 PMCID: PMC10760956 DOI: 10.1172/jci170512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Although most CD8+ T cells are equipped to kill infected or transformed cells, a subset may regulate immune responses and preserve self-tolerance. Here, we describe a CD8 lineage that is instructed to differentiate into CD8 T regulatory cells (Tregs) by a surprisingly restricted set of T cell receptors (TCRs) that recognize MHC-E (mouse Qa-1) and several dominant self-peptides. Recognition and elimination of pathogenic target cells that express these Qa-1-self-peptide complexes selectively inhibits pathogenic antibody responses without generalized immune suppression. Immunization with synthetic agonist peptides that mobilize CD8 Tregs in vivo efficiently inhibit antigraft antibody responses and markedly prolong heart and kidney organ graft survival. Definition of TCR-dependent differentiation and target recognition by this lineage of CD8 Tregs may open the way to new therapeutic approaches to inhibit pathogenic antibody responses.
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Affiliation(s)
- Hye-Jung Kim
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology and
| | - Hidetoshi Nakagawa
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology and
| | - John Y. Choi
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Transplant Research Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Xuchun Che
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Andrew Divris
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Qingshi Liu
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Andrew E. Wight
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology and
| | - Hengcheng Zhang
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Transplant Research Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Anis Saad
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Transplant Research Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Zhabiz Solhjou
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Transplant Research Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Christa Deban
- Transplant Research Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jamil R. Azzi
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Transplant Research Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Harvey Cantor
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Immunology and
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2
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Guan J, Peske JD, Manoharan Valerio M, Park C, Robey EA, Sadegh-Nasseri S. Commensal bacteria maintain a Qa-1 b-restricted unconventional CD8 + T population in gut epithelium. eLife 2023; 12:RP90466. [PMID: 38127067 PMCID: PMC10735220 DOI: 10.7554/elife.90466] [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
Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+ T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+ T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigens, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Moreover, monocolonization with Pediococcus pentosaceus, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.
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Affiliation(s)
- Jian Guan
- Department of Pathology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Institute of Cell Engineering, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - J David Peske
- Department of Pathology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Institute of Cell Engineering, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Michael Manoharan Valerio
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Chansu Park
- Department of Pathology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Institute of Cell Engineering, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Ellen A Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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3
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Manoharan Valerio M, Arana K, Guan J, Chan SW, Yang X, Kurd N, Lee A, Shastri N, Coscoy L, Robey EA. The promiscuous development of an unconventional Qa1b-restricted T cell population. Front Immunol 2023; 14:1250316. [PMID: 38022509 PMCID: PMC10644506 DOI: 10.3389/fimmu.2023.1250316] [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: 06/29/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
MHC-E restricted CD8 T cells show promise in vaccine settings, but their development and specificity remain poorly understood. Here we focus on a CD8 T cell population reactive to a self-peptide (FL9) bound to mouse MHC-E (Qa-1b) that is presented in response to loss of the MHC I processing enzyme ERAAP, termed QFL T cells. We find that mature QFL thymocytes are predominantly CD8αβ+CD4-, show signs of agonist selection, and give rise to both CD8αα and CD8αβ intraepithelial lymphocytes (IEL), as well as memory phenotype CD8αβ T cells. QFL T cells require the MHC I subunit β-2 microglobulin (β2m), but do not require Qa1b or classical MHC I for positive selection. However, QFL thymocytes do require Qa1b for agonist selection and full functionality. Our data highlight the relaxed requirements for positive selection of an MHC-E restricted T cell population and suggest a CD8αβ+CD4- pathway for development of CD8αα IELs.
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Affiliation(s)
- Michael Manoharan Valerio
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Kathya Arana
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Jian Guan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Shiao Wei Chan
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Xiaokun Yang
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Nadia Kurd
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Angus Lee
- Gene Targeting Facility Cancer Research Laboratory, University of California Berkeley, Berkeley, CA, United States
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Laurent Coscoy
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Ellen A. Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
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4
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Guan J, Peske JD, Valerio MM, Park C, Robey EA, Sadegh-Nasseri S. Commensal Bacteria Maintain a Qa-1 b -restricted Unconventional CD8 + T Population in Gut Epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530600. [PMID: 36909616 PMCID: PMC10002720 DOI: 10.1101/2023.03.01.530600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8 + T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1 b -restricted CD8 + T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1 b -dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigen, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Moreover, monocolonization with Pediococcus pentosaceus, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1 b -restricted IEL landscape.
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5
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Geiger KM, Manoharan M, Coombs R, Arana K, Park CS, Lee AY, Shastri N, Robey EA, Coscoy L. Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self. Cell Rep 2023; 42:112317. [PMID: 36995940 PMCID: PMC10539480 DOI: 10.1016/j.celrep.2023.112317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/02/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP) plays a crucial role in shaping the peptide-major histocompatibility complex (MHC) class I repertoire and maintaining immune surveillance. While murine cytomegalovirus (MCMV) has multiple strategies for manipulating the antigen processing pathway to evade immune responses, the host has also developed ways to counter viral immune evasion. In this study, we find that MCMV modulates ERAAP and induces an interferon γ (IFN-γ)-producing CD8+ T cell effector response that targets uninfected ERAAP-deficient cells. We observe that ERAAP downregulation during infection leads to the presentation of the self-peptide FL9 on non-classical Qa-1b, thereby eliciting Qa-1b-restricted QFL T cells to proliferate in the liver and spleen of infected mice. QFL T cells upregulate effector markers upon MCMV infection and are sufficient to reduce viral load after transfer to immunodeficient mice. Our study highlights the consequences of ERAAP dysfunction during viral infection and provides potential targets for anti-viral therapies.
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Affiliation(s)
- Kristina M Geiger
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Manoharan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel Coombs
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kathya Arana
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chan-Su Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Angus Y Lee
- Cancer Research Lab, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ellen A Robey
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Laurent Coscoy
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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6
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Vargas-Zapata V, Geiger KM, Tran D, Ma J, Mao X, Puschnik AS, Coscoy L. SARS-CoV-2 Envelope-mediated Golgi pH dysregulation interferes with ERAAP retention in cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.29.518257. [PMID: 36482965 PMCID: PMC9727756 DOI: 10.1101/2022.11.29.518257] [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: 12/02/2022]
Abstract
Endoplasmic reticulum (ER) aminopeptidase associated with antigen processing (ERAAP) trims peptide precursors in the ER for presentation by major histocompatibility (MHC)-I molecules to surveying CD8+ T-cells. This function allows ERAAP to regulate the nature and quality of the peptide repertoire and, accordingly, the resulting immune responses. We recently showed that infection with murine cytomegalovirus leads to a dramatic loss of ERAAP levels in infected cells. In mice, this loss is associated with the activation of QFL T-cells, a subset of T-cells that monitor ERAAP integrity and eliminate cells experiencing ERAAP dysfunction. In this study, we aimed to identify host factors that regulate ERAAP expression level and determine whether these could be manipulated during viral infections. We performed a CRISPR knockout screen and identified ERp44 as a factor promoting ERAAP retention in the ER. ERp44's interaction with ERAAP is dependent on the pH gradient between the ER and Golgi. We hypothesized that viruses that disrupt the pH of the secretory pathway interfere with ERAAP retention. Here, we demonstrate that expression of the Envelope (E) protein from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) leads to Golgi pH neutralization and consequently decrease of ERAAP intracellular levels. Furthermore, SARS-CoV-2-induced ERAAP loss correlates with its release into the extracellular environment. ERAAP's reliance on ERp44 and a functioning ER/Golgi pH gradient for proper localization and function led us to propose that ERAAP serves as a sensor of disturbances in the secretory pathway during infection and disease.
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Affiliation(s)
- Valerie Vargas-Zapata
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kristina M Geiger
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dan Tran
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jessica Ma
- Division of Microbial Biology, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaowen Mao
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Laurent Coscoy
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
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7
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Dunnick JK, Pandiri AR, Shockley KR, Herbert R, Mav D, Phadke D, Shah RR, Merrick BA. Single nucleotide polymorphism patterns associated with a cancer resistant phenotype. Exp Mol Pathol 2022; 128:104812. [PMID: 35872013 PMCID: PMC10463559 DOI: 10.1016/j.yexmp.2022.104812] [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: 04/27/2022] [Revised: 06/14/2022] [Accepted: 07/16/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS In this study ten mouse strains representing ~90% of genetic diversity in laboratory mice (B6C3F1/J, C57BL/6J, C3H/HeJ, A/J, NOD.B1oSnH2/J, NZO/HILtJ, 129S1/SvImJ, WSB/EiJ, PWK/PhJ, CAST/EiJ) were examined to identify the mouse strain with the lowest incidence of cancer. The unique single polymorphisms (SNPs) associated with this low cancer incidence are reported. METHODS Evaluations of cancer incidence in the 10 mouse strains were based on gross and microscopic diagnosis of tumors. Single nucleotide polymorphisms (SNPs) in the coding regions of the genome were derived from the respective mouse strains located in the Sanger mouse sequencing database and the B6C3F1/N genome from the National Toxicology Program (NTP). RESULTS The WSB strain had an overall lower incidence of both benign and malignant tumors compared to the other mouse strains. At 2 years, the incidence of total malignant tumors (Poly-3 incidence rate) ranged from 2% (WSB) to 92% (C3H) in males, and 14% (WSB) to 93% (NZO) in females, and the total incidence of benign and malignant tumor incidence ranged from 13% (WSB) to 99% (C3H) in males and 25% (WSB) to 96% (NOD) in females. Single nucleotide polymorphism (SNP) patterns were examined in the following strains: B6C3F1/N, C57BL/6J, C3H/HeJ, 129S1/SvImJ, A/J, NZO/HILtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ. We identified 7519 SNPs (involving 5751 Ensembl transcripts of 3453 Ensembl Genes) that resulted in a unique amino acid change in the coding region of the WSB strain. CONCLUSIONS The inherited genetic patterns in the WSB cancer-resistant mouse strain occurred in genes involved in multiple cell functions including mitochondria, metabolic, immune, and membrane-related cell functions. The unique SNP patterns in a cancer resistant mouse strain provides insights for understanding and developing strategies for cancer prevention.
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Affiliation(s)
- June K Dunnick
- Systemic Toxicology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| | - Arun R Pandiri
- Comparative and Molecular Pathogenesis Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Keith R Shockley
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ronald Herbert
- Comparative and Molecular Pathogenesis Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Deepak Mav
- Sciome, LLC, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Dhiral Phadke
- Sciome, LLC, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ruchir R Shah
- Sciome, LLC, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - B Alex Merrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC 27709, USA
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Van Kaer L, Postoak JL, Song W, Wu L. Innate and Innate-like Effector Lymphocytes in Health and Disease. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:199-207. [PMID: 35821102 PMCID: PMC9285656 DOI: 10.4049/jimmunol.2200074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 04/20/2023]
Abstract
Lymphocytes can be functionally partitioned into subsets belonging to the innate or adaptive arms of the immune system. Subsets of innate and innate-like lymphocytes may or may not express Ag-specific receptors of the adaptive immune system, yet they are poised to respond with innate-like speed to pathogenic insults but lack the capacity to develop classical immunological memory. These lymphocyte subsets display a number of common properties that permit them to integrate danger and stress signals dispatched by innate sensor cells to facilitate the generation of specialized effector immune responses tailored toward specific pathogens or other insults. In this review, we discuss the functions of distinct subsets of innate and innate-like lymphocytes. A better understanding of the mechanisms by which these cells are activated in different contexts, their interactions with other immune cells, and their role in health and disease may inform the development of new or improved immunotherapies.
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Affiliation(s)
- Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - J Luke Postoak
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Wenqiang Song
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Lan Wu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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The nonclassical immune surveillance for ERAAP function. Curr Opin Immunol 2021; 70:105-111. [PMID: 34098489 DOI: 10.1016/j.coi.2021.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023]
Abstract
The peptide repertoire presented by MHC class I molecules on the cell surface is essential for the immune surveillance of intracellular pathogens and transformed cells. The generation of this peptide repertoire is critically dependent on the endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP). Loss of ERAAP function leads to the generation of a profoundly disrupted peptide repertoire including many novel and immunogenic peptides. Strikingly, a large fraction of these novel peptides on ERAAP-KO cells are presented by the nonclassical MHC Ib molecule, Qa-1b. One immunodominant Qa-1b-restricted novel peptide is recognized by a unique CD8+ T cell population showing features of both conventional cytotoxic T cells and unconventional innate-like T cells. While much remains to be uncovered, here we summarize the latest discoveries of our lab on the important immune surveillance of ERAAP function mediated by nonclassical MHC Ib molecules and their unusual cognate T cells.
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11
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Abstract
Modulating unconventional antigen presentation could treat infections and cancer
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Affiliation(s)
- Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands.
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
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12
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Perdomo-Celis F, Feria MG, Taborda NA, Rugeles MT. Induction of Follicular-Like CXCR5 + CD8 + T Cells by TGF- β1/IL-23 Is Limited During HIV Infection. Viral Immunol 2019; 32:278-288. [PMID: 31274389 DOI: 10.1089/vim.2019.0029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Follicular CD4+ T cells are the main HIV reservoirs due to, among other factors, the low frequency of CD8+ T cells in lymphoid follicles. Follicular CXCR5+ CD8+ T cells are associated with HIV control, but their differentiation conditions are yet undefined. In this study, we explored the in vitro effect of transforming growth factor (TGF)-β1, interleukin (IL)-12, and IL-23 on the induction of CXCR5, the follicle homing receptor, in human circulating CD8+ T cells from seronegative, and treated HIV-infected individuals. The combination of TGF-β1 plus IL-23 induced the highest expression of CXCR5 in purified CD8+ T cells. These CXCR5+ CD8+ T cells also expressed a transcriptional and phenotypic profile similar to that of follicular CD4+ T cells, such as the upregulation of BCL6, inducible costimulator and CD40L, and downregulation of PRDM1. These cells responded in vitro to CXCL13 and had low expression of CCR7. In addition, after polyclonal stimulation, they produced IL-21, interferon-γ, and de novo perforin. However, in comparison with seronegative individuals, CD8+ T cells from HIV-infected patients had a lower response to TGF-β1/IL-23, a defect that was restored with the blockade of the programmed cell death 1 inhibitory receptor. Thus, TGF-β1 plus IL-23 induce follicular-like CXCR5+ CD8+ T cells in seronegative individuals, but in HIV-infected patients there is a limited response which could impair the generation of this cell population.
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Affiliation(s)
- Federico Perdomo-Celis
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Manuel G Feria
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín, Colombia.,Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - María T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín, Colombia
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Abstract
Most studies of T lymphocytes focus on recognition of classical major histocompatibility complex (MHC) class I or II molecules presenting oligopeptides, yet there are numerous variations and exceptions of biological significance based on recognition of a wide variety of nonclassical MHC molecules. These include αβ and γδ T cells that recognize different class Ib molecules (CD1, MR-1, HLA-E, G, F, et al.) that are nearly monomorphic within a given species. Collectively, these T cells can be considered “unconventional,” in part because they recognize lipids, metabolites, and modified peptides. Unlike classical MHC-specific cells, unconventional T cells generally exhibit limited T-cell antigen receptor (TCR) repertoires and often produce innate immune cell-like rapid effector responses. Exploiting this system in new generation vaccines for human immunodeficiency virus (HIV), tuberculosis (TB), other infectious agents, and cancer was the focus of a recent workshop, “Immune Surveillance by Non-classical MHC Molecules: Improving Diversity for Antigens,” sponsored by the National Institute of Allergy and Infectious Diseases. Here, we summarize salient points presented regarding the basic immunobiology of unconventional T cells, recent advances in methodologies to measure unconventional T-cell activity in diseases, and approaches to harness their considerable clinical potential.
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Doorduijn EM, Sluijter M, Querido BJ, Seidel UJE, Oliveira CC, van der Burg SH, van Hall T. T Cells Engaging the Conserved MHC Class Ib Molecule Qa-1 b with TAP-Independent Peptides Are Semi-Invariant Lymphocytes. Front Immunol 2018; 9:60. [PMID: 29422902 PMCID: PMC5788890 DOI: 10.3389/fimmu.2018.00060] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/10/2018] [Indexed: 12/12/2022] Open
Abstract
The HLA-E homolog in the mouse (Qa-1b) is a conserved MHC class Ib molecule presenting monomorphic peptides to germline-encoded natural killer receptor CD94/NKG2A. Previously, we demonstrated the replacement of this canonical peptide by a diverse peptidome upon deficiency of the TAP peptide transporter. Analysis of this Qa-1b-restricted T cell repertoire against these non-mutated neoantigens revealed characteristics of conventional hypervariable CD8+ T cells, but also of invariant T cell receptor (TCR)αβ T cells. A shared TCR Vα chain was used by this subset in combination with a variety of Vβ chains. The TCRs target peptide ligands that are conserved between mouse and man, like the identified peptide derived from the transcriptional cofactor Med15. The thymus selection was studied in a TCR-transgenic mouse and emerging naïve CD8+ T cells displayed a slightly activated phenotype, as witnessed by higher CD122 and Ly6C expression. Moreover, the Qa-1b protein was dispensable for thymus selection. Importantly, no self-reactivity was observed as reported for other MHC class Ib-restricted subsets. Naïve Qa-1b restricted T cells expanded, contracted, and formed memory cells in vivo upon peptide vaccination in a similar manner as conventional CD8+ T cells. Based on these data, the Qa-1b restricted T cell subset might be positioned closest to conventional CD8+ T cells of all MHC class Ib populations.
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Affiliation(s)
- Elien M Doorduijn
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Bianca J Querido
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Ursula J E Seidel
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Claudia C Oliveira
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Leiden University Medical Center (LUMC), Leiden, Netherlands
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