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Cerovic V, Pabst O, Mowat AM. The renaissance of oral tolerance: merging tradition and new insights. Nat Rev Immunol 2024:10.1038/s41577-024-01077-7. [PMID: 39242920 DOI: 10.1038/s41577-024-01077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2024] [Indexed: 09/09/2024]
Abstract
Oral tolerance is the process by which feeding of soluble proteins induces antigen-specific systemic immune unresponsiveness. Oral tolerance is thought to have a central role in suppressing immune responses to 'harmless' food antigens, and its failure can lead to development of pathologies such as food allergies or coeliac disease. However, on the basis of long-standing experimental observations, the relevance of oral tolerance in human health has achieved new prominence recently following the discovery that oral administration of peanut proteins prevents the development of peanut allergy in at-risk human infants. In this Review, we summarize the new mechanistic insights into three key processes necessary for the induction of tolerance to oral antigens: antigen uptake and transport across the small intestinal epithelial barrier to the underlying immune cells; the processing, transport and presentation of fed antigen by different populations of antigen-presenting cells; and the development of immunosuppressive T cell populations that mediate antigen-specific tolerance. In addition, we consider how related but distinct processes maintain tolerance to bacterial antigens in the large intestine. Finally, we outline the molecular mechanisms and functional consequences of failure of oral tolerance and how these may be modulated to enhance clinical outcomes and prevent disease.
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Affiliation(s)
- Vuk Cerovic
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany.
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Allan McI Mowat
- School of Infection and Immunity, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, UK.
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2
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Ignacio A, Czyz S, McCoy KD. Early life microbiome influences on development of the mucosal innate immune system. Semin Immunol 2024; 73:101885. [PMID: 38788491 DOI: 10.1016/j.smim.2024.101885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024]
Abstract
The gut microbiota is well known to possess immunomodulatory capacities, influencing a multitude of cellular signalling pathways to maintain host homeostasis. Although the formation of the immune system initiates before birth in a sterile environment, an emerging body of literature indicates that the neonatal immune system is influenced by a first wave of external stimuli that includes signals from the maternal microbiota. A second wave of stimulus begins after birth and must be tightly regulated during the neonatal period when colonization of the host occurs concomitantly with the maturation of the immune system, requiring a fine adjustment between establishing tolerance towards the commensal microbiota and preserving inflammatory responses against pathogenic invaders. Besides integrating cues from commensal microbes, the neonatal immune system must also regulate responses triggered by other environmental signals, such as dietary antigens, which become more complex with the introduction of solid food during the weaning period. This "window of opportunity" in early life is thought to be crucial for the proper development of the immune system, setting the tone of subsequent immune responses in adulthood and modulating the risk of developing chronic and metabolic inflammatory diseases. Here we review the importance of host-microbiota interactions for the development and maturation of the immune system, particularly in the early-life period, highlighting the known mechanisms involved in such communication. This discussion is focused on recent data demonstrating microbiota-mediated education of innate immune cells and its role in the development of lymphoid tissues.
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Affiliation(s)
- Aline Ignacio
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sonia Czyz
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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3
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Paucar Iza YA, Brown CC. Early life imprinting of intestinal immune tolerance and tissue homeostasis. Immunol Rev 2024; 323:303-315. [PMID: 38501766 PMCID: PMC11102293 DOI: 10.1111/imr.13321] [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: 02/16/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024]
Abstract
Besides its canonical role in protecting the host from pathogens, the immune system plays an arguably equally important role in maintaining tissue homeostasis. Within barrier tissues that interface with the external microenvironment, induction of immune tolerance to innocuous antigens, such as commensal, dietary, and environmental antigens, is key to establishing immune homeostasis. The early postnatal period represents a critical window of opportunity in which parallel development of the tissue, immune cells, and microbiota allows for reciprocal regulation that shapes the long-term immunological tone of the tissue and subsequent risk of immune-mediated diseases. During early infancy, the immune system appears to sacrifice pro-inflammatory functions, prioritizing the establishment of tissue tolerance. In this review, we discuss mechanisms underlying early life windows for intestinal tolerance with a focus on newly identified RORγt+ antigen-presenting cells-Thetis cells-and highlight the role of the intestinal microenvironment in shaping intestinal immune system development and tolerance.
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Affiliation(s)
- Yoselin A. Paucar Iza
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, New York, USA
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chrysothemis C. Brown
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, New York, USA
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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4
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Cruz de Casas P, Knöpper K, Dey Sarkar R, Kastenmüller W. Same yet different - how lymph node heterogeneity affects immune responses. Nat Rev Immunol 2024; 24:358-374. [PMID: 38097778 DOI: 10.1038/s41577-023-00965-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 05/04/2024]
Abstract
Lymph nodes are secondary lymphoid organs in which immune responses of the adaptive immune system are initiated and regulated. Distributed throughout the body and embedded in the lymphatic system, local lymph nodes are continuously informed about the state of the organs owing to a constant drainage of lymph. The tissue-derived lymph carries products of cell metabolism, proteins, carbohydrates, lipids, pathogens and circulating immune cells. Notably, there is a growing body of evidence that individual lymph nodes differ from each other in their capacity to generate immune responses. Here, we review the structure and function of the lymphatic system and then focus on the factors that lead to functional heterogeneity among different lymph nodes. We will discuss how lymph node heterogeneity impacts on cellular and humoral immune responses and the implications for vaccination, tumour development and tumour control by immunotherapy.
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Affiliation(s)
- Paulina Cruz de Casas
- Max Planck Research Group, Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Konrad Knöpper
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Rupak Dey Sarkar
- Max Planck Research Group, Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Wolfgang Kastenmüller
- Max Planck Research Group, Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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5
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Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [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: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
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Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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6
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Filipp D, Manning J, Petrusová J. Extrathymic AIRE-Expressing Cells: A Historical Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:33-49. [PMID: 38467971 DOI: 10.1007/978-981-99-9781-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Since its discovery, Aire has been the topic of numerous studies in its role as a transcriptional regulator in the thymus where it promotes the "promiscuous" expression of a large repertoire of tissue-restricted antigens (TRAs) that are normally expressed only in the immune periphery. This process occurs in specialized medullary thymic epithelial cells (mTECs) and mediates the elimination of self-reactive T cells or promotes their conversion to the Foxp3+ regulatory T cell lineage, both of which are required for the prevention of autoimmunity. In recent years, there has been increasing interest in the role of extrathymic Aire expression in peripheral organs. The focus has primarily been on the identification of the cellular source(s) and mechanism(s) by which extrathymic AIRE affects tolerance-related or other physiological processes. A cadre of OMICs tools including single cell RNA sequencing and novel transgenic models to trace Aire expression to perform lineage tracing experiments have shed light on a phenomenon that is more complex than previously thought. In this chapter, we provide a deeper analysis of how extrathymic Aire research has developed and progressed, how cellular sources were identified, and how the function of AIRE was determined. Current data suggests that extrathymic AIRE fulfills a function that differs from what has been observed in the thymus and strongly argues that its main purpose is to regulate transcriptional programs in a cell content-dependent manner. Surprisingly, there is data that also suggests a non-transcriptional role of extrathymic AIRE in the cytoplasm. We have arrived at a potential turning point that will take the field from the classical understanding of AIRE as a transcription factor in control of TRA expression to its role in immunological and non-immunological processes in the periphery.
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Affiliation(s)
- Dominik Filipp
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Jasper Manning
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Petrusová
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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7
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Abramson J, Dobeš J, Lyu M, Sonnenberg GF. The emerging family of RORγt + antigen-presenting cells. Nat Rev Immunol 2024; 24:64-77. [PMID: 37479834 PMCID: PMC10844842 DOI: 10.1038/s41577-023-00906-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2023] [Indexed: 07/23/2023]
Abstract
Antigen-presenting cells (APCs) are master regulators of the immune response by directly interacting with T cells to orchestrate distinct functional outcomes. Several types of professional APC exist, including conventional dendritic cells, B cells and macrophages, and numerous other cell types have non-classical roles in antigen presentation, such as thymic epithelial cells, endothelial cells and granulocytes. Accumulating evidence indicates the presence of a new family of APCs marked by the lineage-specifying transcription factor retinoic acid receptor-related orphan receptor-γt (RORγt) and demonstrates that these APCs have key roles in shaping immunity, inflammation and tolerance, particularly in the context of host-microorganism interactions. These RORγt+ APCs include subsets of group 3 innate lymphoid cells, extrathymic autoimmune regulator-expressing cells and, potentially, other emerging populations. Here, we summarize the major findings that led to the discovery of these RORγt+ APCs and their associated functions. We discuss discordance in recent reports and identify gaps in our knowledge in this burgeoning field, which has tremendous potential to advance our understanding of fundamental immune concepts.
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Affiliation(s)
- Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jan Dobeš
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Mengze Lyu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory F Sonnenberg
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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8
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Matsumoto M, Matsumoto M. Learning the Autoimmune Pathogenesis Through the Study of Aire. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:19-32. [PMID: 38467970 DOI: 10.1007/978-981-99-9781-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
One of the difficulties in studying the pathogenesis of autoimmune diseases is that the disease is multifactorial involving sex, age, MHC, environment, and some genetic factors. Because deficiency of Aire, a transcriptional regulator, is an autoimmune disease caused by a single gene abnormality, Aire is an ideal research target for approaching the enigma of autoimmunity, e.g., the mechanisms underlying Aire deficiency can be studied using genetically modified animals. Nevertheless, the exact mechanisms of the breakdown of self-tolerance due to Aire's dysfunction have not yet been fully clarified. This is due, at least in part, to the lack of information on the exact target genes controlled by Aire. State-of-the-art research infrastructures such as single-cell analysis are now in place to elucidate the essential function of Aire. The knowledge gained through the study of Aire-mediated tolerance should help our understanding of the pathogenesis of autoimmune disease in general.
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Affiliation(s)
| | - Minoru Matsumoto
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
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9
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Ulezko Antonova A, Lonardi S, Monti M, Missale F, Fan C, Coates ML, Bugatti M, Jaeger N, Fernandes Rodrigues P, Brioschi S, Trsan T, Fachi JL, Nguyen KM, Nunley RM, Moratto D, Zini S, Kong L, Deguine J, Peeples ME, Xavier RJ, Clatworthy MR, Wang T, Cella M, Vermi W, Colonna M. A distinct human cell type expressing MHCII and RORγt with dual characteristics of dendritic cells and type 3 innate lymphoid cells. Proc Natl Acad Sci U S A 2023; 120:e2318710120. [PMID: 38109523 PMCID: PMC10756205 DOI: 10.1073/pnas.2318710120] [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: 10/27/2023] [Accepted: 11/14/2023] [Indexed: 12/20/2023] Open
Abstract
Recent studies have characterized various mouse antigen-presenting cells (APCs) expressing the lymphoid-lineage transcription factor RORγt (Retinoid-related orphan receptor gamma t), which exhibit distinct phenotypic features and are implicated in the induction of peripheral regulatory T cells (Tregs) and immune tolerance to microbiota and self-antigens. These APCs encompass Janus cells and Thetis cell subsets, some of which express the AutoImmune REgulator (AIRE). RORγt+ MHCII+ type 3 innate lymphoid cells (ILC3) have also been implicated in the instruction of microbiota-specific Tregs. While RORγt+ APCs have been actively investigated in mice, the identity and function of these cell subsets in humans remain elusive. Herein, we identify a rare subset of RORγt+ cells with dendritic cell (DC) features through integrated single-cell RNA sequencing and single-cell ATAC sequencing. These cells, which we term RORγt+ DC-like cells (R-DC-like), exhibit DC morphology, express the MHC class II machinery, and are distinct from all previously reported DC and ILC3 subsets, but share transcriptional and epigenetic similarities with DC2 and ILC3. We have developed procedures to isolate and expand them in vitro, enabling their functional characterization. R-DC-like cells proliferate in vitro, continue to express RORγt, and differentiate into CD1c+ DC2-like cells. They stimulate the proliferation of allogeneic T cells. The identification of human R-DC-like cells with proliferative potential and plasticity toward CD1c+ DC2-like cells will prompt further investigation into their impact on immune homeostasis, inflammation, and autoimmunity.
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Affiliation(s)
- Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Silvia Lonardi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Matilde Monti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Francesco Missale
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
- Department of Head & Neck Oncology & Surgery Otorhinolaryngology, Antoni Van Leeuwenhoek Nederlands Kanker Instituut, Amsterdam1066, The Netherlands
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO63110
| | - Matthew L. Coates
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, United Kingdom
- Cambridge University Hospitals National Health Service Foundation Trust, CambridgeCB2 0QQ, United Kingdom
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | | | - Simone Brioschi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - José L. Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Khai M. Nguyen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Ryan M. Nunley
- Washington University Orthopedics, Barnes Jewish Hospital, Saint Louis, MO63110
| | - Daniele Moratto
- Department of Lab Diagnostics, Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia25100, Italy
| | - Stefania Zini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Lingjia Kong
- Immunology Program, Broad Institute of Massachussets Institute of Technology and Harvard, Cambridge, MA02142
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
| | - Jacques Deguine
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
| | - Mark E. Peeples
- Infectious Diseases Institute, The Ohio State University, Columbus, OH43210
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH43205
- Department of Pediatrics, The Ohio State University, Columbus, OH43210
| | - Ramnik J. Xavier
- Immunology Program, Broad Institute of Massachussets Institute of Technology and Harvard, Cambridge, MA02142
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA02114
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, CambridgeCB10 1SA, United Kingdom
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO63110
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - William Vermi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
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10
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Ramanan D, Pratama A, Zhu Y, Venezia O, Sassone-Corsi M, Chowdhary K, Galván-Peña S, Sefik E, Brown C, Gélineau A, Mathis D, Benoist C. Regulatory T cells in the face of the intestinal microbiota. Nat Rev Immunol 2023; 23:749-762. [PMID: 37316560 DOI: 10.1038/s41577-023-00890-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
Regulatory T cells (Treg cells) are key players in ensuring a peaceful coexistence with microorganisms and food antigens at intestinal borders. Startling new information has appeared in recent years on their diversity, the importance of the transcription factor FOXP3, how T cell receptors influence their fate and the unexpected and varied cellular partners that influence Treg cell homeostatic setpoints. We also revisit some tenets, maintained by the echo chambers of Reviews, that rest on uncertain foundations or are a subject of debate.
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Affiliation(s)
| | - Alvin Pratama
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Yangyang Zhu
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Olivia Venezia
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Esen Sefik
- Department of Immunology, Yale University, New Haven, CT, USA
| | - Chrysothemis Brown
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Paediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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11
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Feng Y, Yao S, Li S, Peng Z, Feng G, Ma Y, Guo B, Liu H. Autoimmune regulator (Aire) deficiency results in reduced memory CD8 + T cells after Listeria monocytogenes infection in a murine model. FEBS Lett 2023; 597:2185-2195. [PMID: 37418594 DOI: 10.1002/1873-3468.14696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
Homozygous mutations in the autoimmune regulator (AIRE) gene that cripple thymic negative selection of autoreactive T cells result in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). However, how AIRE regulates the T-cell response against foreign pathogens is not well understood. Here, we observed comparable primary CD8+ T cells but a markedly reduced memory T-cell population and protective function in Aire-/- mice compared with wild-type after infection with a strain of recombinant Listeria monocytogenes. In adoptive transfer models, exogenous congenic CD8+ T cells transferred into Aire-/- mice also showed a reduction in the memory T-cell population, indicating an important role for extrathymic Aire-expressing cells in shaping or sustaining memory T cells. Moreover, using a bone marrow chimeric model, we found that Aire expressed in radioresistant cells plays an important role in maintaining the memory phenotype. These results provide important insights into the role of extrathymic Aire in the T-cell response to infection.
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Affiliation(s)
- Yi Feng
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Shu Yao
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Shan Li
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Zuxiang Peng
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Guoying Feng
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Yan Ma
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Bo Guo
- Maternal & Child Health Research Institute, Baoan Womens's and Children's Hospital, Jinan University, Shenzhen, China
| | - Hongming Liu
- Department of Hepatobiliary Surgery, Daping Hospital, Army Medical University, Chongqing, China
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12
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Seo SK, Kwon B. Immune regulation through tryptophan metabolism. Exp Mol Med 2023:10.1038/s12276-023-01028-7. [PMID: 37394584 PMCID: PMC10394086 DOI: 10.1038/s12276-023-01028-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 07/04/2023] Open
Abstract
Amino acids are fundamental units of molecular components that are essential for sustaining life; however, their metabolism is closely interconnected to the control systems of cell function. Tryptophan (Trp) is an essential amino acid catabolized by complex metabolic pathways. Several of the resulting Trp metabolites are bioactive and play central roles in physiology and pathophysiology. Additionally, various physiological functions of Trp metabolites are mutually regulated by the gut microbiota and intestine to coordinately maintain intestinal homeostasis and symbiosis under steady state conditions and during the immune response to pathogens and xenotoxins. Cancer and inflammatory diseases are associated with dysbiosis- and host-related aberrant Trp metabolism and inactivation of the aryl hydrocarbon receptor (AHR), which is a receptor of several Trp metabolites. In this review, we focus on the mechanisms through which Trp metabolism converges to AHR activation for the modulation of immune function and restoration of tissue homeostasis and how these processes can be targeted using therapeutic approaches for cancer and inflammatory and autoimmune diseases.
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Affiliation(s)
- Su-Kil Seo
- Department of Microbiology and Immunology, College of Medicine Inje University, Busan, 47392, Republic of Korea.
- Parenchyma Biotech, Busan, 47392, Republic of Korea.
| | - Byungsuk Kwon
- Parenchyma Biotech, Busan, 47392, Republic of Korea.
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Republic of Korea.
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13
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Torow N, Li R, Hitch TCA, Mingels C, Al Bounny S, van Best N, Stange EL, Simons B, Maié T, Rüttger L, Gubbi NMKP, Abbott DA, Benabid A, Gadermayr M, Runge S, Treichel N, Merhof D, Rosshart SP, Jehmlich N, Hand TW, von Bergen M, Heymann F, Pabst O, Clavel T, Tacke F, Lelouard H, Costa IG, Hornef MW. M cell maturation and cDC activation determine the onset of adaptive immune priming in the neonatal Peyer's patch. Immunity 2023; 56:1220-1238.e7. [PMID: 37130522 PMCID: PMC10262694 DOI: 10.1016/j.immuni.2023.04.002] [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: 01/02/2023] [Revised: 03/03/2023] [Accepted: 04/06/2023] [Indexed: 05/04/2023]
Abstract
Early-life immune development is critical to long-term host health. However, the mechanisms that determine the pace of postnatal immune maturation are not fully resolved. Here, we analyzed mononuclear phagocytes (MNPs) in small intestinal Peyer's patches (PPs), the primary inductive site of intestinal immunity. Conventional type 1 and 2 dendritic cells (cDC1 and cDC2) and RORgt+ antigen-presenting cells (RORgt+ APC) exhibited significant age-dependent changes in subset composition, tissue distribution, and reduced cell maturation, subsequently resulting in a lack in CD4+ T cell priming during the postnatal period. Microbial cues contributed but could not fully explain the discrepancies in MNP maturation. Type I interferon (IFN) accelerated MNP maturation but IFN signaling did not represent the physiological stimulus. Instead, follicle-associated epithelium (FAE) M cell differentiation was required and sufficient to drive postweaning PP MNP maturation. Together, our results highlight the role of FAE M cell differentiation and MNP maturation in postnatal immune development.
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Affiliation(s)
- Natalia Torow
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany.
| | - Ronghui Li
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Thomas Charles Adrian Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Clemens Mingels
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Shahed Al Bounny
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Niels van Best
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany; Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht 6200, the Netherlands
| | - Eva-Lena Stange
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Britta Simons
- Institute of Molecular Medicine, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Tiago Maié
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Lennart Rüttger
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | | | - Darryl Adelaide Abbott
- Pediatrics Department, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Adam Benabid
- Institute for Cell and Tumor Biology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Michael Gadermayr
- Institute of Imaging & Computer Vision, RWTH Aachen University, Aachen 52056, Germany
| | - Solveig Runge
- Department of Microbiome Research, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen 91054, Germany; Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Nicole Treichel
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Dorit Merhof
- Institute of Imaging & Computer Vision, RWTH Aachen University, Aachen 52056, Germany
| | - Stephan Patrick Rosshart
- Department of Microbiome Research, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen 91054, Germany; Department of Medicine II, University of Freiburg, Freiburg im Breisgau, Germany
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Department of Molecular Systems Biology, Leipzig 04318, Germany
| | - Timothy Wesley Hand
- Pediatrics Department, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Department of Molecular Systems Biology, Leipzig 04318, Germany; German Centre for Integrative Biodiversity Research (iDiv), Leipzig 04103, Germany; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig 04103, Germany
| | - Felix Heymann
- Department of Hepatology & Gastroenterology, Charité University Hospital, Berlin 13353, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Frank Tacke
- Department of Hepatology & Gastroenterology, Charité University Hospital, Berlin 13353, Germany
| | - Hugues Lelouard
- Aix Marseille University, CNRS, INSERM, CIML, Marseille 13288, France
| | - Ivan Gesteira Costa
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Mathias Walter Hornef
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen 52074, Germany.
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14
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Weckel A, Dhariwala MO, Ly K, Tran VM, Ojewumi OT, Riggs JB, Gonzalez JR, Dwyer LR, Okoro JN, Leech JM, Bacino MS, Cho GD, Merana G, Anandasabapathy N, Kumamoto Y, Scharschmidt TC. Long-term tolerance to skin commensals is established neonatally through a specialized dendritic cell subgroup. Immunity 2023; 56:1239-1254.e7. [PMID: 37028427 PMCID: PMC10330031 DOI: 10.1016/j.immuni.2023.03.008] [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: 06/30/2022] [Revised: 11/29/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023]
Abstract
Early-life establishment of tolerance to commensal bacteria at barrier surfaces carries enduring implications for immune health but remains poorly understood. Here, we showed that tolerance in skin was controlled by microbial interaction with a specialized subset of antigen-presenting cells. More particularly, CD301b+ type 2 conventional dendritic cells (DCs) in neonatal skin were specifically capable of uptake and presentation of commensal antigens for the generation of regulatory T (Treg) cells. CD301b+ DC2 were enriched for phagocytosis and maturation programs, while also expressing tolerogenic markers. In both human and murine skin, these signatures were reinforced by microbial uptake. In contrast to their adult counterparts or other early-life DC subsets, neonatal CD301b+ DC2 highly expressed the retinoic-acid-producing enzyme, RALDH2, the deletion of which limited commensal-specific Treg cell generation. Thus, synergistic interactions between bacteria and a specialized DC subset critically support early-life tolerance at the cutaneous interface.
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Affiliation(s)
- Antonin Weckel
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Miqdad O Dhariwala
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Kevin Ly
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Victoria M Tran
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Oluwasunmisola T Ojewumi
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Julianne B Riggs
- University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Jeanmarie R Gonzalez
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Laura R Dwyer
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, San Francisco, Biomedical Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Joy N Okoro
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - John M Leech
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Margot S Bacino
- University of California, San Francisco, Oral and Craniofacial Sciences Graduate Program, San Francisco, CA 94143, USA
| | - Grace D Cho
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA; University of California, Los Angeles, Department of Infectious Diseases, Los Angeles, CA 90095, USA
| | - Geil Merana
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA
| | - Niroshana Anandasabapathy
- Department of Dermatology, Meyer Cancer Center, Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medical College, New York, NY, USA
| | - Yosuke Kumamoto
- Department of Pathology, Immunology and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Tiffany C Scharschmidt
- University of California, San Francisco, Department of Dermatology, San Francisco, CA 94143, USA.
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15
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Li JH, Hepworth MR, O'Sullivan TE. Regulation of systemic metabolism by tissue-resident immune cell circuits. Immunity 2023; 56:1168-1186. [PMID: 37315533 PMCID: PMC10321269 DOI: 10.1016/j.immuni.2023.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/11/2023] [Accepted: 05/02/2023] [Indexed: 06/16/2023]
Abstract
Recent studies have demonstrated that tissue homeostasis and metabolic function are dependent on distinct tissue-resident immune cells that form functional cell circuits with structural cells. Within these cell circuits, immune cells integrate cues from dietary contents and commensal microbes in addition to endocrine and neuronal signals present in the tissue microenvironment to regulate structural cell metabolism. These tissue-resident immune circuits can become dysregulated during inflammation and dietary overnutrition, contributing to metabolic diseases. Here, we review the evidence describing key cellular networks within and between the liver, gastrointestinal tract, and adipose tissue that control systemic metabolism and how these cell circuits become dysregulated during certain metabolic diseases. We also identify open questions in the field that have the potential to enhance our understanding of metabolic health and disease.
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Affiliation(s)
- Joey H Li
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 900953, USA; Medical Scientist Training Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Matthew R Hepworth
- Division of Immunology, Immunity to Infection and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Collaborative Centre for Inflammation Research, Lydia Becker Institute of Immunology and Inflammation, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Timothy E O'Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 900953, USA.
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16
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Jiang S, Zheng Y, Lv B, He S, Yang W, Wang B, Zhou J, Liu S, Li D, Lin J. Single-cell landscape dissecting the transcription and heterogeneity of innate lymphoid cells in ischemic heart. Front Immunol 2023; 14:1129007. [PMID: 37228603 PMCID: PMC10203554 DOI: 10.3389/fimmu.2023.1129007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Background Until now, few articles have revealed the potential roles of innate lymphoid cells (ILCs) in cardiovascular diseases. However, the infiltration of ILC subsets in ischemic myocardium, the roles of ILC subsets in myocardial infarction (MI) and myocardial ischemia-reperfusion injury (MIRI) and the related cellular and molecular mechanisms have not been described with a sufficient level of detail. Method In the current study, 8-week-old male C57BL/6J mice were divided into three groups: MI, MIRI and sham group. Single-cell sequencing technology was used to perform dimensionality reduction clustering of ILC to analyze the ILC subset landscape at a single-cell resolution, and finally flow cytometry was used to confirm the existence of the new ILC subsets in different disease groups. Results Five ILC subsets were found, including ILC1, ILC2a, ILC2b, ILCdc and ILCt. It is worth noting that ILCdc, ILC2b and ILCt were identified as new ILC subclusters in the heart. The cellular landscapes of ILCs were revealed and signal pathways were predicted. Furthermore, pseudotime trajectory analysis exhibited different ILC statuses and traced related gene expression in normal and ischemic conditions. In addition, we established a ligand-receptor-transcription factor-target gene regulatory network to disclose cell communications among ILC clusters. Moreover, we further revealed the transcriptional features of the ILCdc and ILC2a subsets. Finally, the existence of ILCdc was confirmed by flow cytometry. Conclusion Collectively, by characterizing the spectrums of ILC subclusters, our results provide a new blueprint for understanding ILC subclusters' roles in myocardial ischemia diseases and further potential treatment targets.
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Affiliation(s)
- Shijiu Jiang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, The First Affiliated Hospital, Shihezi University, Shihezi, Xinjiang, China
| | - Yuqi Zheng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bingjie Lv
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaolin He
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenling Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Boyuan Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jin Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shangwei Liu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dazhu Li
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jibin Lin
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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Abstract
The incomplete removal of T cells that are reactive against self-proteins during their differentiation in the thymus requires mechanisms of tolerance that prevent their effector function within the periphery. A further challenge is imposed by the need to establish tolerance to the holobiont self, which comprises a highly complex community of commensal microorganisms. Here, we review recent advances in the investigation of peripheral T cell tolerance, focusing on new insights into mechanisms of tolerance to the gut microbiota, including tolerogenic antigen-presenting cell types and immunomodulatory lymphocytes, and their layered ontogeny that underlies developmental windows for establishing intestinal tolerance. While emphasizing the intestine as a model tissue for studying peripheral T cell tolerance, we highlight overlapping and distinct pathways that underlie tolerance to self-antigens versus commensal antigens within a broader framework for immune tolerance.
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18
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Matsumoto M, Yoshida H, Tsuneyama K, Oya T, Matsumoto M. Revisiting Aire and tissue-restricted antigens at single-cell resolution. Front Immunol 2023; 14:1176450. [PMID: 37207224 PMCID: PMC10191227 DOI: 10.3389/fimmu.2023.1176450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
The thymus is a highly specialized organ that plays an indispensable role in the establishment of self-tolerance, a process characterized by the "education" of developing T-cells. To provide competent T-cells tolerant to self-antigens, medullary thymic epithelial cells (mTECs) orchestrate negative selection by ectopically expressing a wide range of genes, including various tissue-restricted antigens (TRAs). Notably, recent advancements in the high-throughput single-cell analysis have revealed remarkable heterogeneity in mTECs, giving us important clues for dissecting the mechanisms underlying TRA expression. We overview how recent single-cell studies have furthered our understanding of mTECs, with a focus on the role of Aire in inducing mTEC heterogeneity to encompass TRAs.
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Affiliation(s)
- Minoru Matsumoto
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- *Correspondence: Minoru Matsumoto,
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
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19
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Schnell A, Littman DR, Kuchroo VK. T H17 cell heterogeneity and its role in tissue inflammation. Nat Immunol 2023; 24:19-29. [PMID: 36596896 PMCID: PMC10795475 DOI: 10.1038/s41590-022-01387-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/04/2022] [Indexed: 01/05/2023]
Abstract
Since their discovery almost two decades ago, interleukin-17-producing CD4+ T cells (TH17 cells) have been implicated in the pathogenesis of multiple autoimmune and inflammatory disorders. In addition, TH17 cells have been found to play an important role in tissue homeostasis, especially in the intestinal mucosa. Recently, the use of single-cell technologies, along with fate mapping and various mutant mouse models, has led to substantial progress in the understanding of TH17 cell heterogeneity in tissues and of TH17 cell plasticity leading to alternative T cell states and differing functions. In this Review, we discuss the heterogeneity of TH17 cells and the role of this heterogeneity in diverse functions of TH17 cells from homeostasis to tissue inflammation. In addition, we discuss TH17 cell plasticity and its incorporation into the current understanding of T cell subsets and alternative views on the role of TH17 cells in autoimmune and inflammatory diseases.
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Affiliation(s)
- Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan R Littman
- Department of Cell Biology and Regenerative Medicine, New York University School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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20
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Miyazawa R, Nagao JI, Arita-Morioka KI, Matsumoto M, Morimoto J, Yoshida M, Oya T, Tsuneyama K, Yoshida H, Tanaka Y, Matsumoto M. Dispensable Role of Aire in CD11c+ Conventional Dendritic Cells for Antigen Presentation and Shaping the Transcriptome. Immunohorizons 2023; 7:140-158. [PMID: 36695731 PMCID: PMC10563386 DOI: 10.4049/immunohorizons.2200103] [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: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Aire, the defect of which is responsible for the development of autoimmunity, is predominantly expressed in medullary thymic epithelial cells, and it controls a wide variety of genes, including those of tissue-restricted Ags, for establishing thymic tolerance. Aire is also expressed from APCs in the periphery, called extrathymic Aire-expressing cells (eTACs), and their complementing role to thymic tolerance has been suggested. eTACs are composed of two distinct classes of APCs, conventional dendritic cell (cDC)-type and group 3 innate lymphoid cell (ILC3)-like-type expressing retinoic acid receptor-related orphan receptor γt (RORγt). Although the essential role of Aire in the latter in the Th17-mediated immune response against Candida albicans has been reported, the role of Aire in the cDC-type eTACs for this action has not been examined. Furthermore, the significance of Aire in the production of the transcriptome of the cDC-type eTACs remains unknown. We have approached these issues using a high-fidelity Aire-reporter mouse strain. We found that although the cDC-type eTACs dominated ILC3-like-type eTACs in number and they served as efficient APCs for the immune response against an exogenous Ag as well as for the C. albicans-specific Th17 immune response, loss of Aire in cDC-type eTACs showed no clear effect on these functions. Furthermore, loss of Aire showed no major impact on the transcriptome from cDC-type eTACs. These results suggested that Aire in cDC-type eTACs may not have a cell-intrinsic role in the immune response in contrast to the role of Aire in ILC3-like-type eTACs.
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Affiliation(s)
- Ryuichiro Miyazawa
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Jun-ichi Nagao
- Section of Infection Biology, Department of Functional Bioscience, Fukuoka Dental College, Sawara-ku, Fukuoka, Japan
- Oral Medicine Research Center, Fukuoka Dental College, Sawara-ku, Fukuoka, Japan
| | - Ken-ichi Arita-Morioka
- Section of Infection Biology, Department of Functional Bioscience, Fukuoka Dental College, Sawara-ku, Fukuoka, Japan
| | - Minoru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Junko Morimoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Masaki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan; and
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan; and
| | - Yoshihiko Tanaka
- Section of Infection Biology, Department of Functional Bioscience, Fukuoka Dental College, Sawara-ku, Fukuoka, Japan
- Oral Medicine Research Center, Fukuoka Dental College, Sawara-ku, Fukuoka, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
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21
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Abstract
Recent studies shed light on new populations and potential roles of Aire+ and RORγt+ antigen-presenting cells-including unique subsets with surprising properties-in immune homeostasis and host-microbe interactions.
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Affiliation(s)
- James M Gardner
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA.,Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adrian Liston
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT UK
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22
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Travis MA, Romagnani C. How regulatory T cells are primed to aid tolerance of gut bacteria. Nature 2022; 610:638-640. [PMID: 36280729 DOI: 10.1038/d41586-022-03368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Kedmi R, Najar TA, Mesa KR, Grayson A, Kroehling L, Hao Y, Hao S, Pokrovskii M, Xu M, Talbot J, Wang J, Germino J, Lareau CA, Satpathy AT, Anderson MS, Laufer TM, Aifantis I, Bartleson JM, Allen PM, Paidassi H, Gardner JM, Stoeckius M, Littman DR. A RORγt + cell instructs gut microbiota-specific T reg cell differentiation. Nature 2022; 610:737-743. [PMID: 36071167 PMCID: PMC9908423 DOI: 10.1038/s41586-022-05089-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/08/2022] [Indexed: 01/19/2023]
Abstract
The mutualistic relationship of gut-resident microbiota and the host immune system promotes homeostasis that ensures maintenance of the microbial community and of a largely non-aggressive immune cell compartment1,2. The consequences of disturbing this balance include proximal inflammatory conditions, such as Crohn's disease, and systemic illnesses. This equilibrium is achieved in part through the induction of both effector and suppressor arms of the adaptive immune system. Helicobacter species induce T regulatory (Treg) and T follicular helper (TFH) cells under homeostatic conditions, but induce inflammatory T helper 17 (TH17) cells when induced Treg (iTreg) cells are compromised3,4. How Helicobacter and other gut bacteria direct T cells to adopt distinct functions remains poorly understood. Here we investigated the cells and molecular components required for iTreg cell differentiation. We found that antigen presentation by cells expressing RORγt, rather than by classical dendritic cells, was required and sufficient for induction of Treg cells. These RORγt+ cells-probably type 3 innate lymphoid cells and/or Janus cells5-require the antigen-presentation machinery, the chemokine receptor CCR7 and the TGFβ activator αv integrin. In the absence of any of these factors, there was expansion of pathogenic TH17 cells instead of iTreg cells, induced by CCR7-independent antigen-presenting cells. Thus, intestinal commensal microbes and their products target multiple antigen-presenting cells with pre-determined features suited to directing appropriate T cell differentiation programmes, rather than a common antigen-presenting cell that they endow with appropriate functions.
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Affiliation(s)
- Ranit Kedmi
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Tariq A Najar
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Kailin R Mesa
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Allyssa Grayson
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Lina Kroehling
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Maria Pokrovskii
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Calico Life Sciences, LLC, South San Francisco, CA, USA
| | - Mo Xu
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,National Institute for Biological Sciences, Beijing, China
| | - Jhimmy Talbot
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jiaxi Wang
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joe Germino
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Terri M Laufer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, C. Michael Crescenz Veterans Administration Medical Center, Philadelphia, PA, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Juliet M Bartleson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Federation Bio, South San Francisco, CA, USA
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Helena Paidassi
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - James M Gardner
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Marlon Stoeckius
- Technology Innovation Lab, New York Genome Center, New York, NY, USA.,10X Genomics, Stockholm, Sweden
| | - Dan R Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA.
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24
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van Laar GG, van Hamburg JP, Tas SW. Extrathymic AIRE-expressing cells: Friends or foes in autoimmunity and cancer? Clin Exp Rheumatol 2022; 21:103141. [PMID: 35840039 DOI: 10.1016/j.autrev.2022.103141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/10/2022] [Indexed: 11/17/2022]
Abstract
Auto-immune regulator (AIRE) is a transcription factor that is mainly known for its crucial role in the thymus. Here, AIRE ensures central tolerance by promoting the expression of peripheral tissue antigens in thymic epithelial cells, which is essential for the negative selection of autoreactive T cells. Intriguingly, AIRE expressing cells have recently been identified in other tissues outside the thymus as well. However, the exact function of these extrathymic AIRE expressing cells (eTACs) remains largely enigmatic. Human eTACs are mainly found in secondary lymphoid tissues under homeostatic conditions, but are also found in pathologies such as the inflamed tissues of patients with autoimmune diseases and in various cancer tissues. eTACs have been demonstrated to express dendritic cell (DC)-like markers, such as MHCII, CD40 and CD127, but also CCR7, IDO and PD-L1. Interestingly, eTACs lack high expression of co-stimulatory molecules, such as CD80 or CD86. In mice, different types of peripheral AIRE expressing cells have been described, including cells with an innate lymphoid cell-like phenotype and antigen presenting cell (APC) function. These findings suggest that eTACs are APCs with the possibility to modulate or inhibit immune responses, which is confirmed by functional murine studies demonstrating the ability of eTACs to induce tolerance in autoreactive T cells. The potential immunomodulatory function of eTACs makes them promising targets to restore tolerance in autoimmunity or improve immunotherapy in cancer settings. Yet, this requires a better understanding of these cells and the molecular mechanisms involved. In this review we aim to summarize the current knowledge and understanding of eTACs, including their putative roles in health and disease.
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Affiliation(s)
- Gustaaf G van Laar
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam University Medical Centers, University of Amsterdam, Netherlands
| | - Jan Piet van Hamburg
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam University Medical Centers, University of Amsterdam, Netherlands
| | - Sander W Tas
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam University Medical Centers, University of Amsterdam, Netherlands.
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25
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Sun IH, Gillis-Buck E, Mackenzie TC, Gardner JM. Thymic and extrathymic Aire-expressing cells in maternal-fetal tolerance. Immunol Rev 2022; 308:93-104. [PMID: 35535447 DOI: 10.1111/imr.13082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
Healthy pregnancy requires maternal immune tolerance to both fetal and placental tissues which contain a range of self- and non-self-antigens. While many of the components and mechanisms of maternal-fetal tolerance have been investigated in detail and previously and thoroughly reviewed (Erlebacher A. Annu Rev Immunol. 2013;31:387-411), the role of autoimmune regulator (Aire), a critical regulator of central tolerance expressed by medullary thymic epithelial cells (mTECs), has been less explored. Aire is known to facilitate the expression of a range of otherwise tissue-specific antigens (TSAs) in mTECs, and here we highlight recent work showing a role for mTEC-mediated thymic selection in maintaining maternal-fetal tolerance. Recently, however, our group and others have identified additional populations of extrathymic Aire-expressing cells (eTACs) in the secondary lymphoid organs. These hematopoietic antigen-presenting cells possess the ability to induce functional inactivation and/or deletion of cognate T cells, and deletion of maternal eTACs during pregnancy increases T-cell activation in the lymph nodes and lymphocytic infiltration of the uterus, leading to pregnancy complications including intrauterine growth restriction (IUGR) and fetal resorption. In this review, we briefly summarize findings related to essential Aire biology, discuss the known roles of Aire-deficiency related to pregnancy complications and infertility, review the newly discovered role for eTACs in the maintenance of maternal-fetal tolerance-as well as recent work defining eTACs at the single-cell level-and postulate potential mechanisms by which eTACs may regulate this process.
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Affiliation(s)
- Im-Hong Sun
- Department of Surgery, University of California, San Francisco, California, USA.,Diabetes Center, University of California, San Francisco, California, USA
| | - Eva Gillis-Buck
- Department of Surgery, University of California, San Francisco, California, USA
| | - Tippi C Mackenzie
- Department of Surgery, University of California, San Francisco, California, USA.,Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, California, USA
| | - James M Gardner
- Department of Surgery, University of California, San Francisco, California, USA.,Diabetes Center, University of California, San Francisco, California, USA
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26
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27
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Elmentaite R, Domínguez Conde C, Yang L, Teichmann SA. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet 2022; 23:395-410. [PMID: 35217821 DOI: 10.1038/s41576-022-00449-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body. These technology advances are bringing increasing depth and resolution to maps of human organs and tissues, as well as our understanding of individual human cell types. Commonalities as well as tissue-specific features of primary and supportive cell types across human organs are beginning to emerge from these human tissue maps. In this Review, we highlight key biological insights obtained from cross-tissue studies into epithelial, fibroblast, vascular and immune cells based on single-cell gene expression data in humans and contrast it with mechanisms reported in mice.
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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28
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Extrathymic expression of Aire controls the induction of effective T H17 cell-mediated immune response to Candida albicans. Nat Immunol 2022; 23:1098-1108. [PMID: 35761088 DOI: 10.1038/s41590-022-01247-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/18/2022] [Indexed: 01/06/2023]
Abstract
Patients with loss of function in the gene encoding the master regulator of central tolerance AIRE suffer from a devastating disorder called autoimmune polyendocrine syndrome type 1 (APS-1), characterized by a spectrum of autoimmune diseases and severe mucocutaneous candidiasis. Although the key mechanisms underlying the development of autoimmunity in patients with APS-1 are well established, the underlying cause of the increased susceptibility to Candida albicans infection remains less understood. Here, we show that Aire+MHCII+ type 3 innate lymphoid cells (ILC3s) could sense, internalize and present C. albicans and had a critical role in the induction of Candida-specific T helper 17 (TH17) cell clones. Extrathymic Rorc-Cre-mediated deletion of Aire resulted in impaired generation of Candida-specific TH17 cells and subsequent overgrowth of C. albicans in the mucosal tissues. Collectively, our observations identify a previously unrecognized regulatory mechanism for effective defense responses against fungal infections.
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29
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Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Wells SB, Gomes T, Howlett SK, Suchanek O, Polanski K, King HW, Mamanova L, Huang N, Szabo PA, Richardson L, Bolt L, Fasouli ES, Mahbubani KT, Prete M, Tuck L, Richoz N, Tuong ZK, Campos L, Mousa HS, Needham EJ, Pritchard S, Li T, Elmentaite R, Park J, Rahmani E, Chen D, Menon DK, Bayraktar OA, James LK, Meyer KB, Yosef N, Clatworthy MR, Sims PA, Farber DL, Saeb-Parsy K, Jones JL, Teichmann SA. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 2022; 376:eabl5197. [PMID: 35549406 PMCID: PMC7612735 DOI: 10.1126/science.abl5197] [Citation(s) in RCA: 273] [Impact Index Per Article: 136.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
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Affiliation(s)
- C Domínguez Conde
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - C Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - LB Jarvis
- Department of Clinical Neurosciences, University of Cambridge
| | - DB Rainbow
- Department of Clinical Neurosciences, University of Cambridge
| | - SB Wells
- Department of Systems Biology, Columbia University Irving Medical Center
| | - T Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - SK Howlett
- Department of Clinical Neurosciences, University of Cambridge
| | - O Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - K Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - HW King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - L Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - PA Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center
| | - L Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - L Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - ES Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - KT Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - M Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - L Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - ZK Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - L Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- West Suffolk Hospital NHS Trust, Bury Saint Edmunds, UK
| | - HS Mousa
- Department of Clinical Neurosciences, University of Cambridge
| | - EJ Needham
- Department of Clinical Neurosciences, University of Cambridge
| | - S Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - T Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - R Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - J Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - E Rahmani
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - D Chen
- Department of Systems Biology, Columbia University Irving Medical Center
| | - DK Menon
- Department of Anaesthesia, University of Cambridge, Cambridge, UK
| | - OA Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - LK James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - KB Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - MR Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - PA Sims
- Department of Systems Biology, Columbia University Irving Medical Center
| | - DL Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center
| | - K Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - JL Jones
- Department of Clinical Neurosciences, University of Cambridge
| | - SA Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
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30
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Nishijima H, Sugita M, Umezawa N, Kimura N, Sasaki H, Kawano H, Nishioka Y, Matsumoto M, Oya T, Tsuneyama K, Morimoto J, Matsumoto M. Development of organ‐specific autoimmunity by dysregulated Aire expression. Immunol Cell Biol 2022; 100:371-377. [PMID: 35313042 PMCID: PMC9541787 DOI: 10.1111/imcb.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/30/2022]
Abstract
Deficiency for AIRE/Aire in both humans and mice results in the development of organ‐specific autoimmune disease. We tested whether augmented and/or dysregulated AIRE/Aire expression might be also prone to the breakdown of self‐tolerance. To define the effect of augmented Aire expression on the development of autoimmunity, antigen‐specific clonal deletion and production of clonotypic regulatory T cells (Tregs) in the thymus were examined using mice expressing two additional copies of Aire in a heterozygous state (3xAire‐knockin mice: 3xAire‐KI). We found that both clonal deletion of autoreactive T cells and production of clonotypic Tregs in the thymus from 3xAire‐KI were impaired in a T‐cell receptor‐transgenic system. Furthermore, 3xAire‐KI females showed higher scores of experimental autoimmune encephalomyelitis induced by myelin oligodendrocyte glycoprotein than wild‐type littermates, suggesting that augmented Aire expression exacerbates organ‐specific autoimmunity under disease‐prone conditions. In humans, we found that one patient with amyopathic dermatomyositis showed CD3–CD19– cells expressing AIRE in the peripheral blood before the treatment but not during the remission phase treated with immunosuppressive drugs. Thus, not only loss of function of AIRE/Aire but also augmented and/or dysregulated expression of AIRE/Aire should be considered for the pathogenesis of organ‐specific autoimmunity. We suggest that further analyses should be pursued to establish a novel link between organ‐specific autoimmune disease and dysregulated AIRE expression in clinical settings.
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Affiliation(s)
- Hitoshi Nishijima
- Division of Molecular Immunology Institute for Enzyme Research Tokushima University Tokushima Japan
| | - Mizuki Sugita
- Division of Molecular Immunology Institute for Enzyme Research Tokushima University Tokushima Japan
| | - Natsuka Umezawa
- Department of Rheumatology Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University Tokyo Japan
| | - Naoki Kimura
- Department of Rheumatology Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University Tokyo Japan
| | - Hirokazu Sasaki
- Department of Rheumatology Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University Tokyo Japan
| | - Hiroshi Kawano
- Department of Respiratory Medicine and Rheumatology Tokushima University Graduate School of Biomedical Sciences Tokushima Japan
| | - Yasuhiko Nishioka
- Department of Respiratory Medicine and Rheumatology Tokushima University Graduate School of Biomedical Sciences Tokushima Japan
| | - Minoru Matsumoto
- Division of Molecular Immunology Institute for Enzyme Research Tokushima University Tokushima Japan
- Department of Molecular Pathology Tokushima University Graduate School of Biomedical Sciences Tokushima Japan
- Department of Pathology and Laboratory Medicine Tokushima University Graduate School of Biomedical Sciences Tokushima Japan
| | - Takeshi Oya
- Department of Molecular Pathology Tokushima University Graduate School of Biomedical Sciences Tokushima Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine Tokushima University Graduate School of Biomedical Sciences Tokushima Japan
| | - Junko Morimoto
- Division of Molecular Immunology Institute for Enzyme Research Tokushima University Tokushima Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology Institute for Enzyme Research Tokushima University Tokushima Japan
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31
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Shevyrev D, Tereshchenko V, Kozlov V, Sennikov S. Phylogeny, Structure, Functions, and Role of AIRE in the Formation of T-Cell Subsets. Cells 2022; 11:194. [PMID: 35053310 PMCID: PMC8773594 DOI: 10.3390/cells11020194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
It is well known that the most important feature of adaptive immunity is the specificity that provides highly precise recognition of the self, altered-self, and non-self. Due to the high specificity of antigen recognition, the adaptive immune system participates in the maintenance of genetic homeostasis, supports multicellularity, and protects an organism from different pathogens at a qualitatively different level than innate immunity. This seemingly simple property is based on millions of years of evolution that led to the formation of diversification mechanisms of antigen-recognizing receptors and later to the emergence of a system of presentation of the self and non-self antigens. The latter could have a crucial significance because the presentation of nearly complete diversity of auto-antigens in the thymus allows for the "calibration" of the forming repertoires of T-cells for the recognition of self, altered-self, and non-self antigens that are presented on the periphery. The central role in this process belongs to promiscuous gene expression by the thymic epithelial cells that express nearly the whole spectrum of proteins encoded in the genome, meanwhile maintaining their cellular identity. This complex mechanism requires strict control that is executed by several transcription factors. One of the most important of them is AIRE. This noncanonical transcription factor not only regulates the processes of differentiation and expression of peripheral tissue-specific antigens in the thymic medullar epithelial cells but also controls intercellular interactions in the thymus. Besides, it participates in an increase in the diversity and transfer of presented antigens and thus influences the formation of repertoires of maturing thymocytes. Due to these complex effects, AIRE is also called a transcriptional regulator. In this review, we briefly described the history of AIRE discovery, its structure, functions, and role in the formation of antigen-recognizing receptor repertoires, along with other transcription factors. We focused on the phylogenetic prerequisites for the development of modern adaptive immunity and emphasized the importance of the antigen presentation system.
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Affiliation(s)
- Daniil Shevyrev
- Research Institute for Fundamental and Clinical Immunology (RIFCI), 630099 Novosibirsk, Russia; (V.T.); (V.K.); (S.S.)
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32
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Akagbosu B, Tayyebi Z, Shibu G, Paucar Iza YA, Deep D, Parisotto YF, Fisher L, Pasolli HA, Thevin V, Elmentaite R, Knott M, Hemmers S, Jahn L, Friedrich C, Verter J, Wang ZM, van den Brink M, Gasteiger G, Grünewald TGP, Marie JC, Leslie C, Rudensky AY, Brown CC. Novel antigen-presenting cell imparts T reg-dependent tolerance to gut microbiota. Nature 2022; 610:752-760. [PMID: 36070798 PMCID: PMC9605865 DOI: 10.1038/s41586-022-05309-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/01/2022] [Indexed: 01/21/2023]
Abstract
Establishing and maintaining tolerance to self-antigens or innocuous foreign antigens is vital for the preservation of organismal health. Within the thymus, medullary thymic epithelial cells (mTECs) expressing autoimmune regulator (AIRE) have a critical role in self-tolerance through deletion of autoreactive T cells and promotion of thymic regulatory T (Treg) cell development1-4. Within weeks of birth, a separate wave of Treg cell differentiation occurs in the periphery upon exposure to antigens derived from the diet and commensal microbiota5-8, yet the cell types responsible for the generation of peripheral Treg (pTreg) cells have not been identified. Here we describe the identification of a class of RORγt+ antigen-presenting cells called Thetis cells, with transcriptional features of both mTECs and dendritic cells, comprising four major sub-groups (TC I-TC IV). We uncover a developmental wave of Thetis cells within intestinal lymph nodes during a critical window in early life, coinciding with the wave of pTreg cell differentiation. Whereas TC I and TC III expressed the signature mTEC nuclear factor AIRE, TC IV lacked AIRE expression and was enriched for molecules required for pTreg generation, including the TGF-β-activating integrin αvβ8. Loss of either major histocompatibility complex class II (MHCII) or ITGB8 by Thetis cells led to a profound impairment in intestinal pTreg differentiation, with ensuing colitis. By contrast, MHCII expression by RORγt+ group 3 innate lymphoid cells (ILC3) and classical dendritic cells was neither sufficient nor required for pTreg generation, further implicating TC IV as the tolerogenic RORγt+ antigen-presenting cell with an essential function in early life. Our studies reveal parallel pathways for the establishment of tolerance to self and foreign antigens in the thymus and periphery, respectively, marked by the involvement of shared cellular and transcriptional programmes.
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Affiliation(s)
- Blossom Akagbosu
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Zakieh Tayyebi
- grid.51462.340000 0001 2171 9952Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XTri-Institutional Program in Computational Biology and Medicine, Weill Cornell Graduate School, New York, NY USA
| | - Gayathri Shibu
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA
| | - Yoselin A. Paucar Iza
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA
| | - Deeksha Deep
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XTri-Institutional MD-PhD Program, Weill Cornell Medicine, The Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Yollanda Franco Parisotto
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Logan Fisher
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA
| | - H. Amalia Pasolli
- grid.134907.80000 0001 2166 1519Electron Microscopy Resource Center, The Rockefeller University, New York, NY USA
| | - Valentin Thevin
- grid.462282.80000 0004 0384 0005Tumor Escape Resistance Immunity Department, CRCL, INSERM U1052, CNRS 5286, Centre Léon Bérard, Université de Lyon, Lyon, France ,Equipe Labellisée Ligue Nationale contre le Cancer, Lyon, France
| | - Rasa Elmentaite
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton UK
| | - Maximilian Knott
- grid.5252.00000 0004 1936 973XInstitute of PathologyFaculty of Medicine, LMU Munich, Munich, Germany
| | - Saskia Hemmers
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.26009.3d0000 0004 1936 7961Present Address: Department of Immunology, Duke University, Durham, NC USA
| | - Lorenz Jahn
- grid.51462.340000 0001 2171 9952Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christin Friedrich
- grid.8379.50000 0001 1958 8658Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jacob Verter
- grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Zhong-Min Wang
- grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Marcel van den Brink
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Georg Gasteiger
- grid.8379.50000 0001 1958 8658Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Thomas G. P. Grünewald
- grid.510964.fHopp—Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Julien C. Marie
- grid.462282.80000 0004 0384 0005Tumor Escape Resistance Immunity Department, CRCL, INSERM U1052, CNRS 5286, Centre Léon Bérard, Université de Lyon, Lyon, France ,Equipe Labellisée Ligue Nationale contre le Cancer, Lyon, France
| | - Christina Leslie
- grid.51462.340000 0001 2171 9952Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Alexander Y. Rudensky
- grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Chrysothemis C. Brown
- grid.51462.340000 0001 2171 9952Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA ,grid.5386.8000000041936877XImmunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY USA ,grid.51462.340000 0001 2171 9952Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.51462.340000 0001 2171 9952Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY USA
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