1
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Waterfield MR, Anderson MS. A balancing act in the control of self-antigen expression. Nat Immunol 2024; 25:1520-1521. [PMID: 39169235 DOI: 10.1038/s41590-024-01940-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Affiliation(s)
- Michael R Waterfield
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
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2
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Huoh YS, Zhang Q, Törner R, Baca SC, Arthanari H, Hur S. Mechanism for controlled assembly of transcriptional condensates by Aire. Nat Immunol 2024; 25:1580-1592. [PMID: 39169234 PMCID: PMC11362013 DOI: 10.1038/s41590-024-01922-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024]
Abstract
Transcriptional condensates play a crucial role in gene expression and regulation, yet their assembly mechanisms remain poorly understood. Here, we report a multi-layered mechanism for condensate assembly by autoimmune regulator (Aire), an essential transcriptional regulator that orchestrates gene expression reprogramming for central T cell tolerance. Aire condensates assemble on enhancers, stimulating local transcriptional activities and connecting disparate inter-chromosomal loci. This functional condensate formation hinges upon the coordination between three Aire domains: polymerization domain caspase activation recruitment domain (CARD), histone-binding domain (first plant homeodomain (PHD1)), and C-terminal tail (CTT). Specifically, CTT binds coactivators CBP/p300, recruiting Aire to CBP/p300-rich enhancers and promoting CARD-mediated condensate assembly. Conversely, PHD1 binds to the ubiquitous histone mark H3K4me0, keeping Aire dispersed throughout the genome until Aire nucleates on enhancers. Our findings showed that the balance between PHD1-mediated suppression and CTT-mediated stimulation of Aire polymerization is crucial to form transcriptionally active condensates at target sites, providing new insights into controlled polymerization of transcriptional regulators.
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Affiliation(s)
- Yu-San Huoh
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Qianxia Zhang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ricarda Törner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sun Hur
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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3
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Peterson P. Novel Insights into the Autoimmunity from the Genetic Approach of the Human Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:3-18. [PMID: 38467969 DOI: 10.1007/978-981-99-9781-7_1] [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
Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a monogenic inborn error of autoimmunity that is caused by damaging germline variants in the AIRE gene and clinically manifests with multiple autoimmune diseases in patients. Studies on the function of the AIRE gene, discovered in 1997, have contributed to fundamental aspects of human immunology as they have been important in understanding the basic mechanism of immune balance between self and non-self. This chapter looks back to the discovery of the AIRE gene, reviews its main properties, and discusses the key findings of its function in the thymus. However, more recent autoantibody profilings in APECED patients have highlighted a gap in our knowledge of the disease pathology and point to the need to revisit the current paradigm of AIRE function. The chapter reviews these new findings in APECED patients, which potentially trigger new thoughts on the mechanism of immune tolerance.
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Affiliation(s)
- Pärt Peterson
- Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia.
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4
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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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5
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Sin JH, Sucharov J, Kashyap S, Wang Y, Proekt I, Liu X, Parent AV, Gupta A, Kastner P, Chan S, Gardner JM, Ntranos V, Miller CN, Anderson MS, Schjerven H, Waterfield MR. Ikaros is a principal regulator of Aire + mTEC homeostasis, thymic mimetic cell diversity, and central tolerance. Sci Immunol 2023; 8:eabq3109. [PMID: 37889983 PMCID: PMC11433069 DOI: 10.1126/sciimmunol.abq3109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.
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Affiliation(s)
- Jun Hyung Sin
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Juliana Sucharov
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Sujit Kashyap
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Yi Wang
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Irina Proekt
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Xian Liu
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Audrey V. Parent
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Gupta
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - James M. Gardner
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Vasilis Ntranos
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Corey N. Miller
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark S. Anderson
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hilde Schjerven
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael R. Waterfield
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
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6
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Aytekin ES, Cagdas D. APECED and the place of AIRE in the puzzle of the immune network associated with autoimmunity. Scand J Immunol 2023; 98:e13299. [PMID: 38441333 DOI: 10.1111/sji.13299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 03/07/2024]
Abstract
In the last 20 years, discoveries about the autoimmune regulator (AIRE) protein and its critical role in immune tolerance have provided fundamental insights into understanding the molecular basis of autoimmunity. This review provides a comprehensive overview of the effect of AIRE on immunological tolerance and the characteristics of autoimmune diseases in Autoimmune Polyendocrinopathy-Candidiasis-Ectodermal Dystrophy (APECED), which is caused by biallelic AIRE mutations. A better understanding of the immunological mechanisms of AIRE deficiency may enlighten immune tolerance mechanisms and new diagnostic and treatment strategies for autoimmune diseases. Considering that not all clinical features of APECED are present in a given follow-up period, the diagnosis is not easy in a patient at the first visit. Longer follow-up and a multidisciplinary approach are essential for diagnosis. It is challenging to prevent endocrine and other organ damage compared with other diseases associated with multiple autoimmunities, such as FOXP3, LRBA, and CTLA4 deficiencies. Unfortunately, no curative therapy like haematopoietic stem cell transplantation or specific immunomodulation is present that is successful in the treatment.
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Affiliation(s)
- Elif Soyak Aytekin
- Pediatric Allergy and Immunology, Department of Pediatrics, SBU Dr. Sami Ulus Children Hospital, Ankara, Turkey
| | - Deniz Cagdas
- Division of Pediatric Immunology, Department of Pediatrics, Ihsan Dogramaci Children`s Hospital, Institute of Child Health, Hacettepe University Medical School, Ankara, Turkey
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7
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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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8
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Michelson DA, Mathis D. Thymic mimetic cells: tolerogenic masqueraders. Trends Immunol 2022; 43:782-791. [PMID: 36008259 PMCID: PMC9509455 DOI: 10.1016/j.it.2022.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Medullary thymic epithelial cells (mTECs) clonally delete or divert autoreactive T cells by ectopically expressing a diverse array of peripheral-tissue antigens (PTAs) within the thymus. Although thymic stromal cells with histological features of extra-thymic cell types, like myocytes or neurons, have been observed by light microscopy since the mid-1800s, most modern work on PTA expression has focused on the transcription factor Aire. Here, we highlight recent work that has refocused attention on such 'misplaced' thymic cells, referred to collectively as thymic mimetic cells. We review the molecular underpinnings of mimetic cells and their roles in establishing T cell tolerance, and we propose that mimetic cells play important roles in autoimmunity. Finally, we suggest future directions for this emerging area.
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Affiliation(s)
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
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9
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Qi Y, Zhang R, Lu Y, Zou X, Yang W. Aire and Fezf2, two regulators in medullary thymic epithelial cells, control autoimmune diseases by regulating TSAs: Partner or complementer? Front Immunol 2022; 13:948259. [PMID: 36110862 PMCID: PMC9468217 DOI: 10.3389/fimmu.2022.948259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The expression of tissue-specific antigens (TSAs) in medullary thymic epithelial cells (mTECs) is believed to be responsible for the elimination of autoreactive T cells, a critical process in the maintenance of central immune tolerance. The transcription factor autoimmune regulator (Aire) and FEZ family zinc finger 2(Fezf2) play an essential role in driving the expression of TSAs in mTECs, while their deficiency in humans and mice causes a range of autoimmune manifestations, such as type 1 diabetes, Sjögren's syndrome and rheumatoid arthritis. However, because of their regulatory mechanisms, the expression profile of TSAs and their relationship with special autoimmune diseases are still in dispute. In this review, we compare the roles of Aire and Fezf2 in regulating TSAs, with an emphasis on their molecular mechanisms in autoimmune diseases, which provides the foundation for devising improved diagnostic and therapeutic approaches for patients.
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Affiliation(s)
| | | | | | - Xueyang Zou
- Department of Immunology, College of Basic Medical Sciences, School of Public Health, Jilin University, Changchun, China
| | - Wei Yang
- Department of Immunology, College of Basic Medical Sciences, School of Public Health, Jilin University, Changchun, China
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10
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Kaiser C, Bradu A, Gamble N, Caldwell JA, Koh AS. AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression. Immunol Rev 2022; 305:59-76. [PMID: 34545959 PMCID: PMC9250823 DOI: 10.1111/imr.13026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022]
Abstract
The emergence of antigen receptor diversity in clonotypic lymphocytes drove the evolution of a novel gene, Aire, that enabled the adaptive immune system to discriminate foreign invaders from self-constituents. AIRE functions in the epithelial cells of the thymus to express genes highly restricted to alternative cell lineages. This somatic plasticity facilitates the selection of a balanced repertoire of T cells that protects the host from harmful self-reactive clones, yet maintains a wide range of affinities for virtually any foreign antigen. Here, we review the latest understanding of AIRE's molecular actions with a focus on its interplay with chromatin. We argue that AIRE is a multi-valent chromatin effector that acts late in the transcription cycle to modulate the activity of previously poised non-coding regulatory elements of tissue-specific genes. We postulate a role for chromatin instability-caused in part by ATP-dependent chromatin remodeling-that variably sets the scope of the accessible landscape on which AIRE can act. We highlight AIRE's intrinsic repressive function and its relevance in providing feedback control. We synthesize these recent advances into a putative model for the mechanistic modes by which AIRE triggers ectopic transcription for immune repertoire selection.
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Affiliation(s)
- Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Noah Gamble
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jason A. Caldwell
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Andrew S. Koh
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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11
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Bacchetta R, Weinberg K. Thymic origins of autoimmunity-lessons from inborn errors of immunity. Semin Immunopathol 2021; 43:65-83. [PMID: 33532929 PMCID: PMC7925499 DOI: 10.1007/s00281-020-00835-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
During their intrathymic development, nascent T cells are empowered to protect against pathogens and to be operative for a life-long acceptance of self. While autoreactive effector T (Teff) cell progenitors are eliminated by clonal deletion, the intrathymic mechanisms by which thymic regulatory T cell (tTreg) progenitors maintain specificity for self-antigens but escape deletion to exert their regulatory functions are less well understood. Both tTreg and Teff development and selection result from finely coordinated interactions between their clonotypic T cell receptors (TCR) and peptide/MHC complexes expressed by antigen-presenting cells, such as thymic epithelial cells and thymic dendritic cells. tTreg function is dependent on expression of the FOXP3 transcription factor, and induction of FOXP3 gene expression by tTreg occurs during their thymic development, particularly within the thymic medulla. While initial expression of FOXP3 is downstream of TCR activation, constitutive expression is fixed by interactions with various transcription factors that are regulated by other extracellular signals like TCR and cytokines, leading to epigenetic modification of the FOXP3 gene. Most of the understanding of the molecular events underlying tTreg generation is based on studies of murine models, whereas gaining similar insight in the human system has been very challenging. In this review, we will elucidate how inborn errors of immunity illuminate the critical non-redundant roles of certain molecules during tTreg development, shedding light on how their abnormal development and function cause well-defined diseases that manifest with autoimmunity alone or are associated with states of immune deficiency and autoinflammation.
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Affiliation(s)
- Rosa Bacchetta
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Lokey Stem Cell Research Building 265 Campus Drive, West Stanford, CA, 94305, USA.
- Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Kenneth Weinberg
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Lokey Stem Cell Research Building 265 Campus Drive, West Stanford, CA, 94305, USA
- Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, CA, USA
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12
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Kondo K, Ohigashi I, Takahama Y. Thymus machinery for T-cell selection. Int Immunol 2020; 31:119-125. [PMID: 30476234 DOI: 10.1093/intimm/dxy081] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/20/2018] [Indexed: 01/01/2023] Open
Abstract
An immunocompetent and self-tolerant pool of naive T cells is formed in the thymus through the process of repertoire selection. T cells that are potentially capable of responding to foreign antigens are positively selected in the thymic cortex and are further selected in the thymic medulla to help prevent self-reactivity. The affinity between T-cell antigen receptors expressed by newly generated T cells and self-peptide-major histocompatibility complexes displayed in the thymic microenvironments plays a key role in determining the fate of developing T cells during thymic selection. Recent advances in our knowledge of the biology of thymic epithelial cells have revealed unique machinery that contributes to positive and negative selection in the thymus. In this article, we summarize recent findings on thymic T-cell selection, focusing on the machinery unique to thymic epithelial cells.
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Affiliation(s)
- Kenta Kondo
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Kuramoto, Tokushima, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Kuramoto, Tokushima, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Kuramoto, Tokushima, Japan
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13
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Karagianni P, Tzioufas AG. Epigenetic perspectives on systemic autoimmune disease. J Autoimmun 2019; 104:102315. [PMID: 31421964 DOI: 10.1016/j.jaut.2019.102315] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/28/2019] [Indexed: 12/12/2022]
Abstract
Autoimmune diseases are characterized by increased reactivity of the immune system towards self-antigens, causing tissue damage. Although their etiology remains largely unknown, genetic, microbial, environmental and psychological factors are recognized as contributing elements. Epigenetic changes, including covalent modifications of the DNA and histones, are critical signaling mediators between the genome and the environment, and thus potent regulators of cellular functions. The most extensively studied epigenetic modifications are Cytosine DNA methylation and histone acetylation and methylation on various residues. These are thought to affect chromatin structure and binding of specific effectors that regulate transcription, replication, and other processes. Recent studies have uncovered significant epigenetic alterations in cells or tissues derived from autoimmune disease patients compared to samples from healthy individuals and have linked them with disease phenotypes. Epigenetic changes in specific genes correlate with upregulated or downregulated transcription. For instance, in many systems, reduced DNA methylation and increased histone acetylation of interferon-inducible genes correlate with their increased expression in autoimmune disease patients. Also, reduced DNA methylation of retroelements has been proposed as an activating mechanism and has been linked with increased immune reactivity, while epigenetic differences on the X chromosome could indicate incomplete dosage compensation and explain to some extent the increased susceptibility of females over males towards the development of most autoimmune diseases. Besides changes in epigenetic modifications, differences in the levels of many enzymes catalyzing the addition or removal of these marks as well as proteins that recognize them and function as effector molecules have also been detected in autoimmune patients. Although the existing knowledge cannot fully explain whether epigenetic alterations cause or follow the increased immune activation, their characterization is very useful for understanding the pathogenetic mechanisms and complements genetic and clinical studies. Furthermore, specific epigenetic marks have the potential to serve as biomarkers for disease status, prognosis, and response to treatment. Finally, epigenetic factors are currently being examined as candidate therapeutic targets.
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Affiliation(s)
- Panagiota Karagianni
- Department of Pathophysiology, School of Medicine, University of Athens, Mikras Asias Str 75, 115 27, Athens, Greece
| | - Athanasios G Tzioufas
- Department of Pathophysiology, School of Medicine, University of Athens, Mikras Asias Str 75, 115 27, Athens, Greece.
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14
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Constantine GM, Lionakis MS. Lessons from primary immunodeficiencies: Autoimmune regulator and autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. Immunol Rev 2019; 287:103-120. [PMID: 30565240 PMCID: PMC6309421 DOI: 10.1111/imr.12714] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/19/2018] [Indexed: 12/12/2022]
Abstract
The discovery of the autoimmune regulator (AIRE) protein and the delineation of its critical contributions in the establishment of central immune tolerance has significantly expanded our understanding of the immunological mechanisms that protect from the development of autoimmune disease. The parallel identification and characterization of patient cohorts with the monogenic disorder autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), which is typically caused by biallelic AIRE mutations, has underscored the critical contribution of AIRE in fungal immune surveillance at mucosal surfaces and in prevention of multiorgan autoimmunity in humans. In this review, we synthesize the current clinical, genetic, molecular and immunological knowledge derived from basic studies in Aire-deficient animals and from APECED patient cohorts. We also outline major advances and research endeavors that show promise for informing improved diagnostic and therapeutic approaches for patients with APECED.
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Affiliation(s)
- Gregory M Constantine
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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15
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Lovewell TRJ, McDonagh AJG, Messenger AG, Azzouz M, Tazi-Ahnini R. Meta-Analysis of Autoimmune Regulator-Regulated Genes in Human and Murine Models: A Novel Human Model Provides Insights on the Role of Autoimmune Regulator in Regulating STAT1 and STAT1-Regulated Genes. Front Immunol 2018; 9:1380. [PMID: 30002654 PMCID: PMC6031710 DOI: 10.3389/fimmu.2018.01380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/04/2018] [Indexed: 12/14/2022] Open
Abstract
Autoimmune regulator (AIRE) regulates promiscuous expression of tissue-restricted antigens in medullary epithelial cells (mTEC) of the thymus. To understand the diverse effects of AIRE, it is crucial to elucidate the molecular mechanisms underlying the process of AIRE-regulated gene expression. In this study, we generated a recombinant AIRE expression variant of the TEC 1A3 human cell line, TEC 1A3 AIREhi, to determine genes targeted by AIRE, and using microarray analysis, we identified 482 genes showing significant differential expression (P < 0.05; false discovery rate <5%), with 353 upregulated and 129 downregulated by AIRE expression. Microarray data were validated by quantitative PCR, confirming the differential expression of 12 known AIRE-regulated genes. Comparison of AIRE-dependent differential expression in our cell line model with murine datasets identified 447 conserved genes with a number of transcription regulatory interactions, forming several key nodes, including STAT1, which had over 30 interactions with other AIRE-regulated genes. As STAT1 mutations cause dominant chronic mucocutaneous candidiasis and decreased STAT1 levels in monocytes of autoimmune polyglandular syndrome 1 (APS-1) patients, it was important to further characterize AIRE–STAT1 interactions. TEC 1A3AIREhi were treated with the STAT1 phosphorylation inhibitors fludarabine and LLL3 showed that phosphorylated STAT1 (p-STAT1) was not responsible for any of the observed differential expression. Moreover, treatment of TEC 1A3 AIREhi with STAT1 shRNA did not induce any significant variation in the expression of unphosphorylated STAT1 (U-STAT1) downstream genes, suggesting that these genes were directly regulated by AIRE but not via U-STAT1. The novel model system we have developed provides potential opportunities for further analysis of the pathogenesis of (APS-1) and the wider roles of the AIRE gene.
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Affiliation(s)
- Thomas R J Lovewell
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Andrew J G McDonagh
- Department of Dermatology, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Andrew G Messenger
- Department of Dermatology, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Mimoun Azzouz
- Department of Neuroscience, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Rachid Tazi-Ahnini
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, United Kingdom
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16
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Abstract
The immune system is remarkably responsive to a myriad of invading microorganisms and provides continuous surveillance against tissue damage and developing tumor cells. To achieve these diverse functions, multiple soluble and cellular components must react in an orchestrated cascade of events to control the specificity, magnitude and persistence of the immune response. Numerous catabolic and anabolic processes are involved in this process, and prominent roles for l-arginine and l-glutamine catabolism have been described, as these amino acids serve as precursors of nitric oxide, creatine, agmatine, tricarboxylic acid cycle intermediates, nucleotides and other amino acids, as well as for ornithine, which is used to synthesize putrescine and the polyamines spermidine and spermine. Polyamines have several purported roles and high levels of polyamines are manifest in tumor cells as well in autoreactive B- and T-cells in autoimmune diseases. In the tumor microenvironment, l-arginine catabolism by both tumor cells and suppressive myeloid cells is known to dampen cytotoxic T-cell functions suggesting there might be links between polyamines and T-cell suppression. Here, we review studies suggesting roles of polyamines in normal immune cell function and highlight their connections to autoimmunity and anti-tumor immune cell function.
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Affiliation(s)
- Rebecca S Hesterberg
- University of South Florida Cancer Biology Graduate Program, University of South Florida, 4202 East Fowler Ave, Tampa, FL 33620, USA.
- Department Immunology, PharmD, Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, 23033 SRB, Tampa, FL 33612, USA.
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| | - Pearlie K Epling-Burnette
- Department Immunology, PharmD, Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, 23033 SRB, Tampa, FL 33612, USA.
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17
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Abstract
About two decades ago, cloning of the autoimmune regulator (AIRE) gene materialized one of the most important actors on the scene of self-tolerance. Thymic transcription of genes encoding tissue-specific antigens (ts-ags) is activated by AIRE protein and embodies the essence of thymic self-representation. Pathogenic AIRE variants cause the autoimmune polyglandular syndrome type 1, which is a rare and complex disease that is gaining attention in research on autoimmunity. The animal models of disease, although not identically reproducing the human picture, supply fundamental information on mechanisms and extent of AIRE action: thanks to its multidomain structure, AIRE localizes to chromatin enclosing the target genes, binds to histones, and offers an anchorage to multimolecular complexes involved in initiation and post-initiation events of gene transcription. In addition, AIRE enhances mRNA diversity by favoring alternative mRNA splicing. Once synthesized, ts-ags are presented to, and cause deletion of the self-reactive thymocyte clones. However, AIRE function is not restricted to the activation of gene transcription. AIRE would control presentation and transfer of self-antigens for thymic cellular interplay: such mechanism is aimed at increasing the likelihood of engagement of the thymocytes that carry the corresponding T-cell receptors. Another fundamental role of AIRE in promoting self-tolerance is related to the development of thymocyte anergy, as thymic self-representation shapes at the same time the repertoire of regulatory T cells. Finally, AIRE seems to replicate its action in the secondary lymphoid organs, albeit the cell lineage detaining such property has not been fully characterized. Delineation of AIRE functions adds interesting data to the knowledge of the mechanisms of self-tolerance and introduces exciting perspectives of therapeutic interventions against the related diseases.
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Affiliation(s)
- Roberto Perniola
- Department of Pediatrics, Neonatal Intensive Care, Vito Fazzi Regional Hospital, Lecce, Italy
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18
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Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR. Rapid chromatin repression by Aire provides precise control of immune tolerance. Nat Immunol 2018; 19:162-172. [PMID: 29335648 PMCID: PMC6049828 DOI: 10.1038/s41590-017-0032-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/07/2017] [Indexed: 01/23/2023]
Abstract
Aire mediates the expression of tissue-specific antigens in thymic epithelial cells to promote tolerance against self-reactive T lymphocytes. However, the mechanism that allows expression of tissue-specific genes at levels that prevent harm is unknown. Here we show that Brg1 generates accessibility at tissue-specific loci to impose central tolerance. We found that Aire has an intrinsic repressive function that restricts chromatin accessibility and opposes Brg1 across the genome. Aire exerted this repressive influence within minutes after recruitment to chromatin and restrained the amplitude of active transcription. Disease-causing mutations that impair Aire-induced activation also impair the protein's repressive function, which indicates dual roles for Aire. Together, Brg1 and Aire fine-tune the expression of tissue-specific genes at levels that prevent toxicity yet promote immune tolerance.
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Affiliation(s)
- Andrew S Koh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Erik L Miller
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - David M Moskowitz
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerburg Biohub, San Francisco, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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19
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Takaba H, Takayanagi H. The Mechanisms of T Cell Selection in the Thymus. Trends Immunol 2017; 38:805-816. [PMID: 28830733 DOI: 10.1016/j.it.2017.07.010] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022]
Abstract
T cells undergo positive and negative selection in the thymic cortex and medulla, respectively. A promiscuous expression of a wide array of self-antigens in the thymus is essential for the negative selection of self-reactive T cells and the establishment of central tolerance. Aire was originally thought to be the exclusive factor regulating the expression of tissue-restricted antigens, but Fezf2 recently emerged as a critical transcription factor in this regulatory activity. Fezf2 is selectively expressed in thymic medullary epithelial cells, regulates a large number of tissue-restricted antigens and suppresses the onset of autoimmune responses. Here, we discuss novel findings on the transcriptional mechanisms of tissue restricted-antigen expression in the medullary thymic epithelial cells and its effects on T cell selection.
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Affiliation(s)
- Hiroyuki Takaba
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Tokyo, Japan.
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20
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Roberts NA, Adams BD, McCarthy NI, Tooze RM, Parnell SM, Anderson G, Kaech SM, Horsley V. Prdm1 Regulates Thymic Epithelial Function To Prevent Autoimmunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:1250-1260. [PMID: 28701508 PMCID: PMC5544928 DOI: 10.4049/jimmunol.1600941] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/10/2017] [Indexed: 01/10/2023]
Abstract
Autoimmunity is largely prevented by medullary thymic epithelial cells (TECs) through their expression and presentation of tissue-specific Ags to developing thymocytes, resulting in deletion of self-reactive T cells and supporting regulatory T cell development. The transcription factor Prdm1 has been implicated in autoimmune diseases in humans through genome-wide association studies and in mice using cell type-specific deletion of Prdm1 in T and dendritic cells. In this article, we demonstrate that Prdm1 functions in TECs to prevent autoimmunity in mice. Prdm1 is expressed by a subset of mouse TECs, and conditional deletion of Prdm1 in either Keratin 14- or Foxn1-expressing cells in mice resulted in multisymptom autoimmune pathology. Notably, the development of Foxp3+ regulatory T cells occurs normally in the absence of Blimp1. Importantly, nude mice developed anti-nuclear Abs when transplanted with Prdm1 null TECs, but not wild-type TECs, indicating that Prdm1 functions in TECs to regulate autoantibody production. We show that Prdm1 acts independently of Aire, a crucial transcription factor implicated in medullary TEC function. Collectively, our data highlight a previously unrecognized role for Prdm1 in regulating thymic epithelial function.
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Affiliation(s)
- Natalie A Roberts
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Brian D Adams
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Investigative Medicine Program, Yale University School of Medicine, New Haven, CT 06520
| | - Nicholas I McCarthy
- School of Immunity and Infection, Medical Research Council Centre for Immune Regulation, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Reuben M Tooze
- Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sonia M Parnell
- School of Immunity and Infection, Medical Research Council Centre for Immune Regulation, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Graham Anderson
- School of Immunity and Infection, Medical Research Council Centre for Immune Regulation, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Susan M Kaech
- Department of Immunobiology, Yale University, New Haven, CT 06520; and
| | - Valerie Horsley
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520;
- Department of Dermatology, Yale University, New Haven, CT 06520
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21
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Kondo K, Takada K, Takahama Y. Antigen processing and presentation in the thymus: implications for T cell repertoire selection. Curr Opin Immunol 2017; 46:53-57. [PMID: 28477557 DOI: 10.1016/j.coi.2017.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/29/2017] [Indexed: 01/25/2023]
Abstract
The processing and presentation of major histocompatibility complex (MHC)-associated antigens depend on the intracellular digestion of self- and nonself-proteins, the loading of digested peptides onto MHC molecules, and the traffic of peptide-MHC complexes to plasma membrane surface for display to interacting T cells. Recent studies have revealed unique machineries for antigen processing and presentation in thymic antigen-presenting cells that display self-antigens to developing thymocytes for the formation of functionally competent yet self-tolerant T cell repertoire. Here, we briefly summarize those machineries, focusing on the biology of cortical and medullary thymic epithelial cells.
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Affiliation(s)
- Kenta Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kensuke Takada
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, 3-18-15 Kuramoto, Tokushima 770-8503, Japan; Laboratory of Molecular Medicine, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, N18W9 Kita-ku, Sapporo 060-0818, Japan
| | - Yousuke Takahama
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, 3-18-15 Kuramoto, Tokushima 770-8503, Japan.
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22
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Takahama Y, Ohigashi I, Baik S, Anderson G. Generation of diversity in thymic epithelial cells. Nat Rev Immunol 2017; 17:295-305. [PMID: 28317923 DOI: 10.1038/nri.2017.12] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the thymus, diverse populations of thymic epithelial cells (TECs), including cortical and medullary TECs and their subpopulations, have distinct roles in coordinating the development and repertoire selection of functionally competent and self-tolerant T cells. Here, we review the expanding diversity in TEC subpopulations in relation to their functions in T cell development and selection as well as their origins and development.
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Affiliation(s)
- Yousuke Takahama
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Song Baik
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Graham Anderson
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
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23
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Fujikado N, Mann AO, Bansal K, Romito KR, Ferre EMN, Rosenzweig SD, Lionakis MS, Benoist C, Mathis D. Aire Inhibits the Generation of a Perinatal Population of Interleukin-17A-Producing γδ T Cells to Promote Immunologic Tolerance. Immunity 2016; 45:999-1012. [PMID: 27851927 PMCID: PMC5133707 DOI: 10.1016/j.immuni.2016.10.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 08/02/2016] [Accepted: 08/22/2016] [Indexed: 01/13/2023]
Abstract
Aire's primary mechanism of action is to regulate transcription of a battery of genes in medullary thymic epithelial cells (mTECs) and, consequently, negative selection of effector T cells and positive selection of regulatory T cells. We found that Aire-deficient mice had expanded thymic and peripheral populations of perinatally generated IL-17A+Vγ6+Vδ1+ T cells, considered to be "early responders" to tissue stress and drivers of inflammatory reactions. Aire-dependent control of Il7 expression in mTECs regulated the size of thymic IL-17A+Vγ6+Vδ1+ compartments. In mice lacking Aire and γδ T cells, certain tissues typically targeted in the "Aire-less" disease, notably the retina, were only minimally infiltrated. IL-17A+Vγ6+Vδ1+ cells were present in the retina of wild-type mice and expanded very early in Aire-deficient mice. A putatively parallel population of IL-17A+Vγ9+Vδ2+ T cells was increased in humans lacking Aire. Thus, Aire exerts multi-faceted autoimmune control that extends to a population of innate-like T cells.
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Affiliation(s)
- Noriyuki Fujikado
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander O Mann
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kushagra Bansal
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly R Romito
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, MD 20892, USA
| | - Elise M N Ferre
- Fungal Pathogenesis Unit, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Fungal Pathogenesis Unit, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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24
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Abstract
More than 15 years ago, mutations in the autoimmune regulator (AIRE) gene were identified as the cause of autoimmune polyglandular syndrome type 1 (APS1). It is now clear that this transcription factor has a crucial role in promoting self-tolerance in the thymus by regulating the expression of a wide array of self-antigens that have the commonality of being tissue-restricted in their expression pattern in the periphery. In this Review, we highlight many of the recent advances in our understanding of the complex biology that is related to AIRE, with a particular focus on advances in genetics, molecular interactions and the effect of AIRE on thymic selection of regulatory T cells. Furthermore, we highlight new areas of biology that are potentially affected by this key regulator of immune tolerance.
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Affiliation(s)
- Maureen A. Su
- Department of Pediatrics, School of Medicine, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Microbiology/Immunology, School of Medicine, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143
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25
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Takaba H, Morishita Y, Tomofuji Y, Danks L, Nitta T, Komatsu N, Kodama T, Takayanagi H. Fezf2 Orchestrates a Thymic Program of Self-Antigen Expression for Immune Tolerance. Cell 2015; 163:975-87. [PMID: 26544942 DOI: 10.1016/j.cell.2015.10.013] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/19/2015] [Accepted: 09/21/2015] [Indexed: 01/02/2023]
Abstract
Self-tolerance to immune reactions is established via promiscuous expression of tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs), leading to the elimination of T cells that respond to self-antigens. The transcriptional regulator Aire has been thought to be sufficient for the induction of TRAs, despite some indications that other factors may promote TRA expression in the thymus. Here, we show that the transcription factor Fezf2 directly regulates various TRA genes in mTECs independently of Aire. Mice lacking Fezf2 in mTECs displayed severe autoimmune symptoms, including the production of autoantibodies and inflammatory cell infiltration targeted to peripheral organs. These responses differed from those detected in Aire-deficient mice. Furthermore, Fezf2 expression and Aire expression are regulated by distinct signaling pathways and promote the expression of different classes of proteins. Thus, two independent factors, Fezf2 and Aire, permit the expression of TRAs in the thymus to ensure immune tolerance.
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Affiliation(s)
- Hiroyuki Takaba
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Takayanagi Osteonetwork Project, Exploratory Research for Advanced Technology Program, Japan Science and Technology Agency (JST), Tokyo 113-0033, Japan
| | - Yasuyuki Morishita
- Department of Molecular Pathology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshihiko Tomofuji
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Lynett Danks
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Takayanagi Osteonetwork Project, Exploratory Research for Advanced Technology Program, Japan Science and Technology Agency (JST), Tokyo 113-0033, Japan
| | - Takeshi Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Noriko Komatsu
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tatsuhiko Kodama
- Research Center for Advanced Science and Technology, Department of Systems Biology and Medicine, The University of Tokyo, Tokyo 153-8904, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Takayanagi Osteonetwork Project, Exploratory Research for Advanced Technology Program, Japan Science and Technology Agency (JST), Tokyo 113-0033, Japan.
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26
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Abstract
The autoimmune regulator (Aire) was initially identified as the gene causing multiorgan system autoimmunity in humans, and deletion of this gene in mice also resulted in organ-specific autoimmunity. Aire regulates the expression of tissue-specific antigens (TSAs) in medullary thymic epithelial cells (mTECs), which play a critical role in the negative selection of autoreactive T cells and the generation of regulatory T cells. More recently, the role of Aire in the development of mTECs has helped elucidate its ability to present the spectrum of TSAs needed to prevent autoimmunity. Molecular characterization of the functional domains of Aire has revealed multiple binding partners that assist Aire's function in altering gene transcription and chromatin remodeling. These recent advances have further highlighted the importance of Aire in central tolerance.
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Affiliation(s)
- Alice Chan
- Diabetes Center, University of California, San Francisco, San Francisco, California
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, California
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27
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28
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Passos GA, Mendes-da-Cruz DA, Oliveira EH. The Thymic Orchestration Involving Aire, miRNAs, and Cell-Cell Interactions during the Induction of Central Tolerance. Front Immunol 2015; 6:352. [PMID: 26236310 PMCID: PMC4500981 DOI: 10.3389/fimmu.2015.00352] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/29/2015] [Indexed: 01/23/2023] Open
Abstract
Developing thymocytes interact sequentially with two distinct structures within the thymus: the cortex and medulla. Surviving single-positive and double-positive thymocytes from the cortex migrate into the medulla, where they interact with medullary thymic epithelial cells (mTECs). These cells ectopically express a vast set of peripheral tissue antigens (PTAs), a property termed promiscuous gene expression that is associated with the presentation of PTAs by mTECs to thymocytes. Thymocyte clones that have a high affinity for PTAs are eliminated by apoptosis in a process termed negative selection, which is essential for tolerance induction. The Aire gene is an important factor that controls the expression of a large set of PTAs. In addition to PTAs, Aire also controls the expression of miRNAs in mTECs. These miRNAs are important in the organization of the thymic architecture and act as posttranscriptional controllers of PTAs. Herein, we discuss recent discoveries and highlight open questions regarding the migration and interaction of developing thymocytes with thymic stroma, the ectopic expression of PTAs by mTECs, the association between Aire and miRNAs and its effects on central tolerance.
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Affiliation(s)
- Geraldo Aleixo Passos
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto, São Paulo , Brazil ; Disciplines of Genetics and Molecular Biology, Department of Morphology, Physiology and Basic Pathology, School of Dentistry of Ribeirão Preto, University of São Paulo , Ribeirão Preto, São Paulo , Brazil
| | - Daniella Arêas Mendes-da-Cruz
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation , Rio de Janeiro, Rio de Janeiro , Brazil
| | - Ernna Hérida Oliveira
- Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto, São Paulo , Brazil
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29
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Oftedal BE, Hellesen A, Erichsen MM, Bratland E, Vardi A, Perheentupa J, Kemp EH, Fiskerstrand T, Viken MK, Weetman AP, Fleishman SJ, Banka S, Newman WG, Sewell WAC, Sozaeva LS, Zayats T, Haugarvoll K, Orlova EM, Haavik J, Johansson S, Knappskog PM, Løvås K, Wolff ASB, Abramson J, Husebye ES. Dominant Mutations in the Autoimmune Regulator AIRE Are Associated with Common Organ-Specific Autoimmune Diseases. Immunity 2015; 42:1185-96. [PMID: 26084028 DOI: 10.1016/j.immuni.2015.04.021] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/06/2015] [Accepted: 04/06/2015] [Indexed: 01/13/2023]
Abstract
The autoimmune regulator (AIRE) gene is crucial for establishing central immunological tolerance and preventing autoimmunity. Mutations in AIRE cause a rare autosomal-recessive disease, autoimmune polyendocrine syndrome type 1 (APS-1), distinguished by multi-organ autoimmunity. We have identified multiple cases and families with mono-allelic mutations in the first plant homeodomain (PHD1) zinc finger of AIRE that followed dominant inheritance, typically characterized by later onset, milder phenotypes, and reduced penetrance compared to classical APS-1. These missense PHD1 mutations suppressed gene expression driven by wild-type AIRE in a dominant-negative manner, unlike CARD or truncated AIRE mutants that lacked such dominant capacity. Exome array analysis revealed that the PHD1 dominant mutants were found with relatively high frequency (>0.0008) in mixed populations. Our results provide insight into the molecular action of AIRE and demonstrate that disease-causing mutations in the AIRE locus are more common than previously appreciated and cause more variable autoimmune phenotypes.
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Affiliation(s)
- Bergithe E Oftedal
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Alexander Hellesen
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Martina M Erichsen
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Eirik Bratland
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Ayelet Vardi
- Department of Immunology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jaakko Perheentupa
- Hospital for Children and Adolescents, University of Helsinki, 00100 Helsinki, Finland
| | - E Helen Kemp
- Department of Human Metabolism, The Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Torunn Fiskerstrand
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marte K Viken
- Department of Immunology, Oslo University Hospital and University of Oslo, 0316 Oslo, Norway
| | - Anthony P Weetman
- Department of Human Metabolism, The Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Sarel J Fleishman
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - William G Newman
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK
| | - W A C Sewell
- Path Links Immunology, Scunthorpe General Hospital, Scunthorpe DN15 7BH, UK
| | - Leila S Sozaeva
- Endocrinological Research Center, Institute of Pediatric Endocrinology, Moscow 117036, Russian Federation
| | - Tetyana Zayats
- K.G. Jebsen Centre for Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | | | - Elizaveta M Orlova
- Endocrinological Research Center, Institute of Pediatric Endocrinology, Moscow 117036, Russian Federation
| | - Jan Haavik
- K.G. Jebsen Centre for Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Stefan Johansson
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Per M Knappskog
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Kristian Løvås
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Anette S B Wolff
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Jakub Abramson
- Department of Immunology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Eystein S Husebye
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway.
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30
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Yang S, Fujikado N, Kolodin D, Benoist C, Mathis D. Immune tolerance. Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance. Science 2015; 348:589-94. [PMID: 25791085 PMCID: PMC4710357 DOI: 10.1126/science.aaa7017] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/04/2015] [Indexed: 12/26/2022]
Abstract
Aire is an important regulator of immunological tolerance, operating in a minute subset of thymic stromal cells to induce transcripts encoding peptides that guide T cell selection. Expression of Aire during a perinatal age window is necessary and sufficient to prevent the multiorgan autoimmunity characteristic of Aire-deficient mice. We report that Aire promotes the perinatal generation of a distinct compartment of Foxp3(+)CD4(+) regulatory T (Treg) cells, which stably persists in adult mice. This population has a role in maintaining self-tolerance, a transcriptome and an activation profile distinguishable from those of Tregs produced in adults. Underlying the distinct Treg populations are age-dependent, Aire-independent differences in the processing and presentation of thymic stromal-cell peptides, resulting in different T cell receptor repertoires. Our findings expand the notion of a developmentally layered immune system.
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Affiliation(s)
- Siyoung Yang
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Noriyuki Fujikado
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Dmitriy Kolodin
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston MA 02115, USA.
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston MA 02115, USA.
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31
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Sansom SN, Shikama-Dorn N, Zhanybekova S, Nusspaumer G, Macaulay IC, Deadman ME, Heger A, Ponting CP, Holländer GA. Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome Res 2014; 24:1918-31. [PMID: 25224068 PMCID: PMC4248310 DOI: 10.1101/gr.171645.113] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 09/12/2014] [Indexed: 12/18/2022]
Abstract
Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
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Affiliation(s)
- Stephen N Sansom
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom;
| | - Noriko Shikama-Dorn
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Saule Zhanybekova
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Gretel Nusspaumer
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mary E Deadman
- Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Andreas Heger
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Chris P Ponting
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Georg A Holländer
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland; Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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32
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Abstract
A critical function of the thymus is to help enforce tolerance to self. The importance of central tolerance in preventing autoimmunity has been enlightened by a deeper understanding of the interactions of developing T cells with a diverse population of thymic antigen presenting cell populations. Furthermore, there has been rapid progress in our understanding of how autoreactive T cell specificities are diverted into the T regulatory lineage. Here we review and highlight the recent progress in how tolerance is imposed on the developing thymocyte repertoire.
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Affiliation(s)
- Maria L Mouchess
- Diabetes Center, University of California-San Francisco, Box 0540, San Francisco, CA, 94143, USA
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33
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Waterfield M, Khan IS, Cortez JT, Fan U, Metzger T, Greer A, Fasano K, Martinez-Llordella M, Pollack JL, Erle DJ, Su M, Anderson MS. The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotolerance. Nat Immunol 2014; 15:258-65. [PMID: 24464130 PMCID: PMC4172453 DOI: 10.1038/ni.2820] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/18/2013] [Indexed: 12/13/2022]
Abstract
The maintenance of immunological tolerance requires the deletion of self-reactive T cells in the thymus. The expression of genes encoding tissue-specific antigens (TSAs) by thymic epithelial cells is critical for this process and depends on activity of the transcriptional regulator Aire; however, the molecular mechanisms Aire uses to target loci encoding TSAs are unknown. Here we identified two Aire-interacting proteins known to be involved in gene repression, ATF7ip and MBD1, that were required for Aire's targeting of loci encoding TSAs. Moreover, Mbd1(-/-) mice developed pathological autoimmunity and had a defect in Aire-dependent thymic expression of genes encoding TSAs, which underscores the importance of Aire's interaction with the ATF7ip-MBD1 protein complex in maintaining central tolerance.
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Affiliation(s)
- Michael Waterfield
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
- Department of Pediatrics, University of California San Francisco, 533 Parnassus Avenue, San Francisco, CA 94143
| | - Imran S. Khan
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
| | - Jessica T. Cortez
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
| | - Una Fan
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
| | - Todd Metzger
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
| | - Alexandra Greer
- Department of Microbiology & Immunology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
| | - Kayla Fasano
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
| | - Marc Martinez-Llordella
- Department Liver Sciences, Division of Transplantation Immunology & Mucosal Biology, King’s College London, Institute of Liver Studies, 3rd Floor Cheyne Wing, Denmark Hill, SE5 9RS
| | - Joshua L. Pollack
- Department of Medicine, University of California San Francisco, 15504 Street, San Francisco, CA 94158
| | - David J. Erle
- Department of Medicine, University of California San Francisco, 15504 Street, San Francisco, CA 94158
| | - Maureen Su
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Mark S. Anderson
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143
- Department of Medicine, University of California San Francisco, 15504 Street, San Francisco, CA 94158
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34
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Perniola R, Musco G. The biophysical and biochemical properties of the autoimmune regulator (AIRE) protein. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:326-37. [PMID: 24275490 DOI: 10.1016/j.bbadis.2013.11.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 01/20/2023]
Abstract
AIRE (for autoimmune regulator) is a multidomain protein that performs a fundamental function in the thymus and possibly in the secondary lymphoid organs: the regulation, especially in the sense of activation, of the process of gene transcription in cell lines deputed to the presentation of self-antigens to the maturing T lymphocytes. The apoptosis of the elements bearing T-cell receptors with critical affinity for the exhibited self-antigens prevents the escape of autoreactive clones and represents a simple and efficient mechanism of deletional self-tolerance. However, AIRE action relies on an articulated complex of biophysical and biochemical properties, in most cases attributable to single subspecialized domains. Here a thorough review of the matter is presented, with a privileged look at the pathogenic changes of AIRE that interfere with such properties and lead to the impairment in its chief function.
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Affiliation(s)
- Roberto Perniola
- Department of Pediatrics - Neonatal Intensive Care, V. Fazzi Regional Hospital, Piazza F. Muratore, I-73100, Lecce, Italy.
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute at San Raffaele Scientific Institute, Via Olgettina 58, I-20132, Milan, Italy.
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35
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Radic M, Muller S. Epigenetics of autoantigens: new opportunities for therapy of autoimmune diseases. GENETICS & EPIGENETICS 2013; 5:63-70. [PMID: 25512708 PMCID: PMC4222337 DOI: 10.4137/geg.s12144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The field of epigenetics requires that traditional divisions between scientific disciplines give way to cross-fertilization of concepts and ideas from different areas of investigation. Such is the case with research in autoimmunity. Recent discoveries of stimuli that induce autoimmunity reveal that epigenetic marks of autoantigens are recognized by autoreactive B and T cell receptors. Thus, insights into the initiation of autoimmunity, its prevention and therapy will arise from understanding the biochemistry, cell biology and microbiology of autoantigen epigenetics. Here, we highlight potential benefits from the inhibition of a histone modifying enzyme and the administration of a phosphorylated, spliceosome-derived peptide, in the treatment of autoimmunity.
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Affiliation(s)
- Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sylviane Muller
- Immunopathology and therapeutic chemistry/Laboratory of excellence MEDALIS, Institut de Biologie Moléculaire et Cellulaire, CNRS, Strasbourg, France
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36
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Matsumoto M, Nishikawa Y, Nishijima H, Morimoto J, Matsumoto M, Mouri Y. Which model better fits the role of aire in the establishment of self-tolerance: the transcription model or the maturation model? Front Immunol 2013; 4:210. [PMID: 23885257 PMCID: PMC3717480 DOI: 10.3389/fimmu.2013.00210] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/09/2013] [Indexed: 11/13/2022] Open
Abstract
The discovery of Aire-dependent transcriptional control of many tissue-restricted self-antigen (TRA) genes in thymic epithelial cells in the medulla (medullary thymic epithelial cells, mTECs) has raised the intriguing question of how the single Aire gene can influence the transcription of such a large number of TRA genes within mTECs. From a mechanistic viewpoint, there are two possible models to explain the function of Aire in this action. In the first model, TRAs are considered to be the direct target genes of Aire’s transcriptional activity. In this scenario, the lack of Aire protein within cells would result in the defective TRA gene expression, while the maturation program of mTECs would be unaffected in principle. The second model hypothesizes that Aire is necessary for the maturation program of mTECs. In this case, we assume that the mTEC compartment does not mature normally in the absence of Aire. If acquisition of the properties of TRA gene expression depends on the maturation status of mTECs, a defect of such an Aire-dependent maturation program in Aire-deficient mTECs can also result in impaired TRA gene expression. In this brief review, we will focus on these two contrasting models for the roles of Aire in controlling the expression of TRAs within mTECs.
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Affiliation(s)
- Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, University of Tokushima , Tokushima , Japan
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37
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Macedo C, Evangelista AF, Marques MM, Octacílio-Silva S, Donadi EA, Sakamoto-Hojo ET, Passos GA. Autoimmune regulator (Aire) controls the expression of microRNAs in medullary thymic epithelial cells. Immunobiology 2013; 218:554-60. [PMID: 22883565 DOI: 10.1016/j.imbio.2012.06.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 06/25/2012] [Accepted: 06/26/2012] [Indexed: 01/12/2023]
Abstract
The autoimmune regulator (Aire) is a transcription factor that controls the ectopic expression of a large set of peripheral tissue antigen (PTA) genes in medullary thymic epithelial cells (mTECs). Recent evidence has demonstrated that Aire releases stalled RNA polymerase II (RNA Pol II) from blockage at the promoter region of its target genes. Given that, in addition to messenger RNAs (mRNA), RNA Pol II also transcribes microRNAs (miRNAs), we raised the hypothesis that Aire might play a role as an upstream controller of miRNA transcription. To test this, we initially analyzed the expression profiles of 662 miRNAs in control and Aire-silenced (siRNA) murine mTEC 3.10 cells using microarrays. The bioinformatics programs SAM and Cluster-TreeView were then used to identify the differentially expressed miRNAs and their profiles, respectively. Thirty Aire-dependent miRNAs were identified in the Aire-silenced mTECs, of which 18 were up- and 12 were down-regulated. The down-regulated miR-376 family was the focus of this study because its members (miR-376a, miR-376b and miR-376c) are located in the genome within the Gm2922 open-reading frame (ORF) gene segment on the chromosome 12F1. The T-boxes (TTATTA) and G-boxes (GATTGG), which represent putative RNA Pol II promoter motifs, were located in a portion spanning 10 kb upstream of the ATG codon of Gm2922. Moreover, we found that Gm2922 encodes an mRNA, which was also down-regulated in Aire-silenced mTECs. These results represent the first evidence that Aire can play a role as a controller of transcription of miRNAs located within genomic regions encompassing ORF and/or mRNA genes.
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Affiliation(s)
- Claudia Macedo
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo (USP), 14040-900 Ribeirão Preto, SP, Brazil
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38
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Zumer K, Saksela K, Peterlin BM. The mechanism of tissue-restricted antigen gene expression by AIRE. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 190:2479-82. [PMID: 23456700 DOI: 10.4049/jimmunol.1203210] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The autoimmune regulator is a critical transcription factor for generating central tolerance in the thymus. Recent studies have revealed how the autoimmune regulator targets many otherwise tissue-restricted Ag genes to enable negative selection of autoreactive T cells.
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Affiliation(s)
- Kristina Zumer
- Department of Virology, Haartman Institute, Helsinki University Central Hospital, University of Helsinki, FIN-00014 Helsinki, Finland
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39
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Yang S, Bansal K, Lopes J, Benoist C, Mathis D. Aire's plant homeodomain(PHD)-2 is critical for induction of immunological tolerance. Proc Natl Acad Sci U S A 2013; 110:1833-8. [PMID: 23319629 PMCID: PMC3562810 DOI: 10.1073/pnas.1222023110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aire impacts immunological tolerance by regulating the expression of a large set of genes in thymic medullary epithelial cells, thereby controlling the repertoire of self-antigens encountered by differentiating thymocytes. Both humans and mice lacking Aire develop multiorgan autoimmunity. Currently, there are few molecular details on how Aire performs this crucial function. The more amino-terminal of its two plant homeodomains (PHDs), PHD1, helps Aire target poorly transcribed loci by "reading" the methylation status of a particular lysine residue of histone-3, a process that does not depend on the more carboxyl-terminal PHD-2. This study addresses the role of PHD2 in Aire function by comparing the behavior of wild-type and PHD2-deleted Aire in both transfected cells and transgenic mice. PHD2 was required for Aire to interact with sets of protein partners involved in chromatin structure/binding or transcription but not with those implicated in pre-mRNA processing; it also was not required for Aire's nuclear translocation or regional distribution. PHD2 strongly influenced the ability of Aire to regulate the medullary epithelial cell transcriptome and so was crucial for effective central tolerance induction. Thus, Aire's two PHDs seem to play distinct roles in the scenario by which it assures immunological tolerance.
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Affiliation(s)
| | | | | | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
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40
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Gaetani M, Matafora V, Saare M, Spiliotopoulos D, Mollica L, Quilici G, Chignola F, Mannella V, Zucchelli C, Peterson P, Bachi A, Musco G. AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome. Nucleic Acids Res 2012; 40:11756-68. [PMID: 23074189 PMCID: PMC3526288 DOI: 10.1093/nar/gks933] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 09/11/2012] [Accepted: 09/14/2012] [Indexed: 12/21/2022] Open
Abstract
Mutations in autoimmune regulator (AIRE) gene cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of peripheral-tissue antigens to mediate deletional tolerance, thereby preventing self-reactivity. AIRE contains two plant homeodomains (PHDs) which are sites of pathological mutations. AIRE-PHD fingers are important for AIRE transcriptional activity and presumably play a crucial role in the formation of multimeric protein complexes at chromatin level which ultimately control immunological tolerance. As a step forward the understanding of AIRE-PHD fingers in normal and pathological conditions, we investigated their structure and used a proteomic SILAC approach to assess the impact of patient mutations targeting AIRE-PHD fingers. Importantly, both AIRE-PHD fingers are structurally independent and mutually non-interacting domains. In contrast to D297A and V301M on AIRE-PHD1, the C446G mutation on AIRE-PHD2 destroys the structural fold, thus causing aberrant AIRE localization and reduction of AIRE target genes activation. Moreover, mutations targeting AIRE-PHD1 affect the formation of a multimeric protein complex at chromatin level. Overall our results reveal the importance of AIRE-PHD domains in the interaction with chromatin-associated nuclear partners and gene regulation confirming the role of PHD fingers as versatile protein interaction hubs for multiple binding events.
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Affiliation(s)
- Massimiliano Gaetani
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Vittoria Matafora
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Mario Saare
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Dimitrios Spiliotopoulos
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Luca Mollica
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Giacomo Quilici
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Francesca Chignola
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Valeria Mannella
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Chiara Zucchelli
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Pärt Peterson
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Angela Bachi
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Center of Translational Genomics and Bioinformatics, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular Mass Spectrometry Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milano, Italy and Department of Molecular Pathology, University of Tartu, 50411 Tartu, Estonia
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41
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Spiliotopoulos D, Spitaleri A, Musco G. Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study. PLoS One 2012; 7:e46902. [PMID: 23077531 PMCID: PMC3471955 DOI: 10.1371/journal.pone.0046902] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/06/2012] [Indexed: 01/13/2023] Open
Abstract
PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0). As a case study we focused on the first PHD finger of autoimmune regulator protein (AIRE-PHD1) in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a "flapping" movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.
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Affiliation(s)
- Dimitrios Spiliotopoulos
- Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular NMR Laboratory, Center for Translational Genomics and Bioinformatics, Milano, Italy
| | - Andrea Spitaleri
- Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular NMR Laboratory, Center for Translational Genomics and Bioinformatics, Milano, Italy
| | - Giovanna Musco
- Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular NMR Laboratory, Center for Translational Genomics and Bioinformatics, Milano, Italy
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Greer JM, McCombe PA. The role of epigenetic mechanisms and processes in autoimmune disorders. Biologics 2012; 6:307-27. [PMID: 23055689 PMCID: PMC3459549 DOI: 10.2147/btt.s24067] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Indexed: 12/18/2022]
Abstract
The lack of complete concordance of autoimmune disease in identical twins suggests that nongenetic factors play a major role in determining disease susceptibility. In this review, we consider how epigenetic mechanisms could affect the immune system and effector mechanisms in autoimmunity and/or the target organ of autoimmunity and thus affect the development of autoimmune diseases. We also consider the types of stimuli that lead to epigenetic modifications and how these relate to the epidemiology of autoimmune diseases and the biological pathways operative in different autoimmune diseases. Increasing our knowledge of these epigenetic mechanisms and processes will increase the prospects for controlling or preventing autoimmune diseases in the future through the use of drugs that target the epigenetic pathways.
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Affiliation(s)
- Judith M Greer
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Pamela A McCombe
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, Queensland, Australia
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Žumer K, Low AK, Jiang H, Saksela K, Peterlin BM. Unmodified histone H3K4 and DNA-dependent protein kinase recruit autoimmune regulator to target genes. Mol Cell Biol 2012; 32:1354-62. [PMID: 22310661 PMCID: PMC3318594 DOI: 10.1128/mcb.06359-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/26/2012] [Indexed: 11/20/2022] Open
Abstract
Autoimmune regulator (AIRE) directs the expression of otherwise tissue-restricted antigens (TRAs) in medullary thymic epithelial cells, allowing their presentation to developing T cells, which leads to central tolerance. We addressed the conundrum of how AIRE is recruited to these otherwise silent genes in cells. Our studies confirmed that interactions between AIRE and the unmodified histone H3K4 (H3K4me0) are important for targeting AIRE to the mouse insulin promoter in chromatin. By replacing its H3K4me0-binding module with one that binds to the methylated H3K4me3, we redirected the mutant AIRE.ING protein to an actively transcribed gene. Nevertheless, the mutant AIRE D297A protein, which could not bind to H3K4me0, still activated the human insulin promoter on an episomal plasmid target. This targeting was due to DNA-dependent protein kinase (DNA-PK). Thus, in cells that lacked the catalytic subunit of DNA-PK (DNA-PKcs), the assembly and activity of AIRE on DNA, whether in chromatin or on episomal plasmids, was abrogated. However, by the heterologous tethering of AIRE to DNA, we could restore its activity on a plasmid target in DNA-PKcs-negative cells. Importantly, mutations in the putative DNA-binding residues in its SAND domain had no effect on the transcriptional effects of AIRE. Thus, AIRE is recruited to TRA genes in chromatin via cooperative interactions with H3K4me0 and DNA-PK.
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Affiliation(s)
- Kristina Žumer
- Department of Virology, Haartman Institute, University of Helsinki, Helsinki, Finland
- Department of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, USA
| | - Audrey K. Low
- Department of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, USA
| | - Huimin Jiang
- Department of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, USA
- Complete Genomics Inc., Mountain View, California, USA
| | - Kalle Saksela
- Department of Virology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - B. Matija Peterlin
- Department of Virology, Haartman Institute, University of Helsinki, Helsinki, Finland
- Department of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, USA
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Giraud M, Yoshida H, Abramson J, Rahl PB, Young RA, Mathis D, Benoist C. Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells. Proc Natl Acad Sci U S A 2012; 109:535-40. [PMID: 22203960 PMCID: PMC3258631 DOI: 10.1073/pnas.1119351109] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aire is a transcriptional regulator that induces expression of peripheral tissue antigens (PTA) in thymic medullary epithelial cells (MECs), driving immunological self-tolerance in differentiating T cells. To elucidate its mechanistic pathways, we examined its transcriptional impact in MECs in vivo by microarray analysis with mRNA-spanning probes. This analysis revealed initiation of Aire-activated genes to be comparable in Aire-deficient and wild-type MECs, but with a block to elongation after 50-100 bp in the absence of Aire, suggesting activation by release of stalled polymerases by Aire. In contrast, patterns of activation by transcription factors such as Klf4 were consistent with regulation of initiation. Mapping of Aire and RNA polymerase-II (Pol-II) by ChIP and high-throughput sequencing (ChIP-seq) revealed that Aire bound all Pol-II-rich transcriptional start sites (TSS), irrespective of its eventual effect. However, the genes it preferentially activated were characterized by a relative surfeit of stalled polymerases at the TSS, which resolved once Aire was introduced into cells. Thus, transcript mapping and ChIP-seq data indicate that Aire activates ectopic transcription not through specific recognition of PTA gene promoters but by releasing stalled polymerases.
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Affiliation(s)
- Matthieu Giraud
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | - Hideyuki Yoshida
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | - Jakub Abramson
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | | | - Richard A. Young
- Whitehead Institute for Biomedical Research and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and
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Abstract
Monogenic autoimmune syndromes provide a rare yet powerful glimpse into the fundamental mechanisms of immunologic tolerance. Such syndromes reveal not only the contribution of an individual breakpoint in tolerance but also patterns in the pathogenesis of autoimmunity. Disturbances in innate immunity, a system built for ubiquitous sensing of danger signals, tend to generate systemic autoimmunity. For example, defects in the clearance of self-antigens and chronic stimulation of type 1 interferons lead to the systemic autoimmunity seen in C1q deficiency, SPENCDI, and AGS. In contrast, disturbances of adaptive immunity, which is built for antigen specificity, tend to produce organ-specific autoimmunity. Thus, the loss of lymphocyte homeostasis, whether through defects in apoptosis, suppression, or negative selection, leads to organ-specific autoimmunity in ALPS, IPEX, and APS1. We discuss the unique mechanisms of disease in these prominent syndromes as well as how they contribute to the spectrum of organ-specific or systemic autoimmunity. The continued study of rare variants in autoimmune disease will inform future investigations and treatments directed at rare and common autoimmune diseases alike.
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Affiliation(s)
- Mickie H. Cheng
- Diabetes Center; Department of Medicine, Division of Endocrinology and Metabolism, University of California at San Francisco, San Francisco, California 94143;
| | - Mark S. Anderson
- Diabetes Center; Department of Medicine, Division of Endocrinology and Metabolism, University of California at San Francisco, San Francisco, California 94143;
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Lovewell T, Tazi-Ahnini R. Models to explore the molecular function and regulation of AIRE. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2011. [DOI: 10.1016/j.ejmhg.2011.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Danso-Abeam D, Humblet-Baron S, Dooley J, Liston A. Models of aire-dependent gene regulation for thymic negative selection. Front Immunol 2011; 2:14. [PMID: 22566805 PMCID: PMC3342030 DOI: 10.3389/fimmu.2011.00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 04/21/2011] [Indexed: 11/13/2022] Open
Abstract
Mutations in the autoimmune regulator (AIRE) gene lead to autoimmune polyendocrinopathy syndrome type 1 (APS1), characterized by the development of multi-organ autoimmune damage. The mechanism by which defects in AIRE result in autoimmunity has been the subject of intense scrutiny. At the cellular level, the working model explains most of the clinical and immunological characteristics of APS1, with AIRE driving the expression of tissue-restricted antigens (TRAs) in the epithelial cells of the thymic medulla. This TRA expression results in effective negative selection of TRA-reactive thymocytes, preventing autoimmune disease. At the molecular level, the mechanism by which AIRE initiates TRA expression in the thymic medulla remains unclear. Multiple different models for the molecular mechanism have been proposed, ranging from classical transcriptional activity, to random induction of gene expression, to epigenetic tag recognition effect, to altered cell biology. In this review, we evaluate each of these models and discuss their relative strengths and weaknesses.
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Abstract
The negative selection of self-reactive thymocytes depends on the expression of tissue-specific antigens by medullary thymic epithelial cells. The autoimmune regulator (Aire) protein plays an important role in turning on these antigens, and the absence of even one Aire-induced tissue-specific antigen in the thymus can lead to autoimmunity in the antigen-expressing target organ. Recently, Aire protein has been detected in peripheral lymphoid organs, suggesting that peripheral Aire plays a complementary role here. In these peripheral sites, Aire was found to regulate the expression of a group of tissue-specific antigens that is distinct from those expressed in the thymus. Furthermore, transgenic antigen expression in extrathymic Aire-expressing cells (eTACs) can mediate deletional tolerance, but the immunological relevance of Aire-dependent, endogenous tissue-specific antigens remains to be determined.
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Affiliation(s)
- Todd C Metzger
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
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49
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Abstract
In the thymus, developing T cells that react against self-antigens with high affinity are deleted in the process of negative selection. An essential component of this process is the display of self-antigens, including those whose expression are usually restricted to specific tissues, to developing T cells within the thymus. The Autoimmune Regulator (Aire) gene plays a crucial role in the expression of tissue specific self-antigens within the thymus, and disruption of Aire function results in spontaneous autoimmunity in both humans and mice. Recent advances have been made in our understanding of how Aire influences the expression of thousands of tissue-specific antigens in the thymus. Additional roles of Aire, including roles in chemokine and cytokine expression, have also been revealed. Factors important in the differentiation of Aire-expressing medullary thymic epithelial cells have been defined. Finally, the identity of antigen presenting cells in negative selection, including the role of medullary thymic epithelial cells in displaying tissue specific antigens to T cells, has also been clarified.
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Affiliation(s)
- Mark S. Anderson
- Diabetes Center and Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Maureen A. Su
- Inflammatory Diseases Institute and Department of Pediatrics, University of North Carolina, Chapel Hill, Chapel Hill, NC
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Matsumoto M. Contrasting models for the roles of Aire in the differentiation program of epithelial cells in the thymic medulla. Eur J Immunol 2011; 41:12-7. [PMID: 21182071 DOI: 10.1002/eji.201041024] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The current prevailing view regarding the role of Aire in self-tolerance is that it is involved in the transcriptional control of many tissue-restricted self-antigen genes in thymic epithelial cells in the medulla (mTECs); however, accumulating evidence also suggests that Aire has other roles, e.g. in mTEC differentiation, and furthermore that Aire can either promote or inhibit the mTEC differentiation program, i.e. Aire does not play a neutral role in mTEC differentiation. This review discusses when and how Aire plays an important role in controlling the organization of mTECs required for the expression of self-antigen genes.
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Affiliation(s)
- Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, University of Tokushima, Tokushima, Japan.
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