51
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The Speckled Protein (SP) Family: Immunity's Chromatin Readers. Trends Immunol 2020; 41:572-585. [PMID: 32386862 DOI: 10.1016/j.it.2020.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 01/25/2023]
Abstract
Chromatin 'readers' are central interpreters of the epigenome that facilitate cell-specific transcriptional programs and are therapeutic targets in cancer and inflammation. The Speckled Protein (SP) family of chromatin 'readers' in humans consists of SP100, SP110, SP140, and SP140L. SPs possess functional domains (SAND, PHD, bromodomain) that dock to DNA or post-translationally modified histones and a caspase activation and recruitment domain (CARD) to promote multimerization. Mutations within immune expressed SPs associate with numerous immunological diseases including Crohn's disease, multiple sclerosis, chronic lymphocytic leukemia, veno-occlusive disease with immunodeficiency, as well as Mycobacterium tuberculosis infection, underscoring their importance in immune regulation. In this review, we posit that SPs are central chromatin regulators of gene silencing that establish immune cell identity and function.
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52
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Huoh YS, Wu B, Park S, Yang D, Bansal K, Greenwald E, Wong WP, Mathis D, Hur S. Dual functions of Aire CARD multimerization in the transcriptional regulation of T cell tolerance. Nat Commun 2020; 11:1625. [PMID: 32242017 PMCID: PMC7118133 DOI: 10.1038/s41467-020-15448-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
Aggregate-like biomolecular assemblies are emerging as new conformational states with functionality. Aire, a transcription factor essential for central T cell tolerance, forms large aggregate-like assemblies visualized as nuclear foci. Here we demonstrate that Aire utilizes its caspase activation recruitment domain (CARD) to form filamentous homo-multimers in vitro, and this assembly mediates foci formation and transcriptional activity. However, CARD-mediated multimerization also makes Aire susceptible to interaction with promyelocytic leukemia protein (PML) bodies, sites of many nuclear processes including protein quality control of nuclear aggregates. Several loss-of-function Aire mutants, including those causing autoimmune polyendocrine syndrome type-1, form foci with increased PML body association. Directing Aire to PML bodies impairs the transcriptional activity of Aire, while dispersing PML bodies with a viral antagonist restores this activity. Our study thus reveals a new regulatory role of PML bodies in Aire function, and highlights the interplay between nuclear aggregate-like assemblies and PML-mediated protein quality control.
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Affiliation(s)
- Yu-San Huoh
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
| | - Bin Wu
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
- NTU Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Sehoon Park
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
| | - Darren Yang
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Kushagra Bansal
- Department of Immunology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560 064, India
| | - Emily Greenwald
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
| | - Wesley P Wong
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Diane Mathis
- Department of Immunology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA.
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA.
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53
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Mempel TR, Marangoni F. Guidance factors orchestrating regulatory T cell positioning in tissues during development, homeostasis, and response. Immunol Rev 2020; 289:129-141. [PMID: 30977195 DOI: 10.1111/imr.12761] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/29/2022]
Abstract
Over their lifetime, regulatory T cells (Treg) recalibrate their expression of trafficking receptors multiple times as they progress through development, respond to immune challenges, or adapt to the requirements of functioning in various non-lymphoid tissue environments. These trafficking receptors, which include chemokine receptors and other G-protein coupled receptors, integrins, as well as selectins and their ligands, enable Treg not only to enter appropriate tissues from the bloodstream via post-capillary venules, but also to navigate these tissues to locally execute their immune-regulatory functions, and finally to seek out the right antigen-presenting cells and interact with these, in part in order to receive the signals that sustain their survival, proliferation, and functional activity, in part in order to execute their immuno-regulatory function by altering antigen presenting cell function. Here, we will review our current knowledge of when and in what ways Treg alter their trafficking properties. We will focus on the chemokine system and try to identify specialized, non-redundant roles of individual receptors as well as similarities and differences to the conventional T cell compartment.
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Affiliation(s)
- Thorsten R Mempel
- The Center for Immunology and Inflammatory Diseases at Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Francesco Marangoni
- The Center for Immunology and Inflammatory Diseases at Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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54
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Dhalla F, Baran‐Gale J, Maio S, Chappell L, Holländer GA, Ponting CP. Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells. EMBO J 2020; 39:e101828. [PMID: 31657037 PMCID: PMC6939203 DOI: 10.15252/embj.2019101828] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
To induce central T-cell tolerance, medullary thymic epithelial cells (mTEC) collectively express most protein-coding genes, thereby presenting an extensive library of tissue-restricted antigens (TRAs). To resolve mTEC diversity and whether promiscuous gene expression (PGE) is stochastic or coordinated, we sequenced transcriptomes of 6,894 single mTEC, enriching for 1,795 rare cells expressing either of two TRAs, TSPAN8 or GP2. Transcriptional heterogeneity allowed partitioning of mTEC into 15 reproducible subpopulations representing distinct maturational trajectories, stages and subtypes, including novel mTEC subsets, such as chemokine-expressing and ciliated TEC, which warrant further characterisation. Unexpectedly, 50 modules of genes were robustly defined each showing patterns of co-expression within individual cells, which were mainly not explicable by chromosomal location, biological pathway or tissue specificity. Further, TSPAN8+ and GP2+ mTEC were randomly dispersed within thymic medullary islands. Consequently, these data support observations that PGE exhibits ordered co-expression, although mechanisms underlying this instruction remain biologically indeterminate. Ordered co-expression and random spatial distribution of a diverse range of TRAs likely enhance their presentation and encounter with passing thymocytes, while maintaining mTEC identity.
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Affiliation(s)
- Fatima Dhalla
- Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | | | - Stefano Maio
- Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | | | - Georg A Holländer
- Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Chris P Ponting
- MRC Human Genetics UnitMRC IGMMThe University of EdinburghEdinburghUK
- Wellcome Sanger InstituteHinxtonUK
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55
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Abstract
The generation of a functional T cell repertoire in the thymus is mainly orchestrated by thymic epithelial cells (TECs), which provide developing T cells with cues for their navigation, proliferation, differentiation and survival. The TEC compartment has been segregated historically into two major populations of medullary TECs and cortical TECs, which differ in their anatomical localization, molecular characteristics and functional roles. However, recent studies have shown that TECs are highly heterogeneous and comprise multiple subpopulations with distinct molecular and functional characteristics, including tuft cell-like or corneocyte-like phenotypes. Here, we review the most recent advances in our understanding of TEC heterogeneity from a molecular, functional and developmental perspective. In particular, we highlight the key insights that were recently provided by single-cell genomic technologies and in vivo fate mapping and discuss them in the context of previously published data.
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56
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Marín-Sánchez A, Álvarez-Sierra D, González O, Lucas-Martin A, Sellés-Sánchez A, Rudilla F, Enrich E, Colobran R, Pujol-Borrell R. Regulation of TSHR Expression in the Thyroid and Thymus May Contribute to TSHR Tolerance Failure in Graves' Disease Patients via Two Distinct Mechanisms. Front Immunol 2019; 10:1695. [PMID: 31379878 PMCID: PMC6657650 DOI: 10.3389/fimmu.2019.01695] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
Graves' disease (GD) involves the presence of agonistic auto-antibodies against the thyrotropin receptor (TSHR), which are responsible for the clinical symptoms. While failure of TSHR tolerance is central to GD pathogenesis, the process leading to this failure remains poorly understood. Two mechanisms intimately linked to tolerance have been proposed to explain the association of SNPs located in TSHR intron 1 to GD: (1) differential alternative splicing in the thyroid; and (2) modulation of expression in the thymus. To elucidate the relative contribution to these two mechanisms to GD pathogenesis, we analyzed the level of full-length and ST4 and ST5 isoform expression in the thyroid (n = 49) and thymus (n = 39) glands, and the influence of intron 1-associated SNPs on such expression. The results show that: (1) the level of flTSHR and ST4 expression in the thymus was unexpectedly high (20% that of the thyroid); (2) while flTSHR is the predominant isoform, the levels are similar to ST4 (ratio flTSHR/ST4 = 1.34 in the thyroid and ratio flTSHR/ST4 in the thymus = 1.93); (3) next-generation sequencing confirmed the effect of the TSHR intron 1 polymorphism on TSHR expression in the thymus with a bias of 1.5 ± 0.2 overexpression of the protective allele in the thymus compared to the thyroid; (4) GD-associated intron 1 SNPs did not influence TSHR alternative splicing of ST4 and ST5 in the thyroid and thymus; and (5) three-color confocal imaging showed that TSHR is associated with both thymocytes, macrophages, and dendritic cells in the thymus. Our findings confirm the effect of intron 1 polymorphisms on thymic TSHR expression and we present evidence against an effect on the relative expression of isoforms. The high level of ST4 expression in the thymus and its distribution within the tissue suggest that this would most likely be the isoform that induces central tolerance to TSHR thus omitting most of the hinge and transmembrane portion. The lack of central tolerance to a large portion of TSHR may explain the relatively high frequency of autoimmunity related to TSHR and its clinical consequence, GD.
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Affiliation(s)
- Ana Marín-Sánchez
- Immunology Division, FOCIS Center of Excellence, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Diagnostic Immunology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Daniel Álvarez-Sierra
- Diagnostic Immunology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar González
- Surgery Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ana Lucas-Martin
- Endocrinology Division, Hospital Universitari Germans Trias Pujol, Badalona, Spain
| | | | - Francesc Rudilla
- Immunogenetics and Histocompatibility Laboratory, Blood and Tissue Bank, Transfusional Medicine Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Emma Enrich
- Immunogenetics and Histocompatibility Laboratory, Blood and Tissue Bank, Transfusional Medicine Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Roger Colobran
- Immunology Division, FOCIS Center of Excellence, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Diagnostic Immunology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ricardo Pujol-Borrell
- Immunology Division, FOCIS Center of Excellence, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Diagnostic Immunology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
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57
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Lancaster JN, Thyagarajan HM, Srinivasan J, Li Y, Hu Z, Ehrlich LIR. Live-cell imaging reveals the relative contributions of antigen-presenting cell subsets to thymic central tolerance. Nat Commun 2019; 10:2220. [PMID: 31101805 PMCID: PMC6525199 DOI: 10.1038/s41467-019-09727-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/18/2019] [Indexed: 12/31/2022] Open
Abstract
Both medullary thymic epithelial cells (mTEC) and dendritic cells (DC) present tissue-restricted antigens (TRA) to thymocytes to induce central tolerance, but the relative contributions of these antigen-presenting cell (APC) subsets remain unresolved. Here we developed a two-photon microscopy approach to observe thymocytes interacting with intact APCs presenting TRAs. We find that mTECs and DCs cooperate extensively to induce tolerance, with their relative contributions regulated by the cellular form of the TRA and the class of major histocompatibility complex (MHC) on which antigen is presented. Even when TRA expression is restricted to mTECs, DCs still present self-antigens at least as frequently as mTECs. Notably, the DC subset cDC2 efficiently acquires secreted mTEC-derived TRAs for cross-presentation on MHC-I. By directly imaging interactions between thymocytes and APCs, while monitoring intracellular signaling, this study reveals that distinct DC subsets and AIRE+ mTECs contribute substantially to presentation of diverse self-antigens for establishing central tolerance.
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Affiliation(s)
- J N Lancaster
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E. 24th Street A5000, Austin, TX, 78712, USA
| | - H M Thyagarajan
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E. 24th Street A5000, Austin, TX, 78712, USA
| | - J Srinivasan
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E. 24th Street A5000, Austin, TX, 78712, USA
| | - Y Li
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E. 24th Street A5000, Austin, TX, 78712, USA
| | - Z Hu
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E. 24th Street A5000, Austin, TX, 78712, USA
| | - L I R Ehrlich
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E. 24th Street A5000, Austin, TX, 78712, USA.
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
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58
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Ribeiro C, Alves NL, Ferreirinha P. Medullary thymic epithelial cells: Deciphering the functional diversity beyond promiscuous gene expression. Immunol Lett 2019; 215:24-27. [PMID: 30853502 DOI: 10.1016/j.imlet.2019.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/27/2022]
Abstract
Within the thymus, cortical and medullary thymic epithelial cells (cTECs and mTECs, respectively) provide unique microenvironments for the development of T cells that are responsive to diverse foreign antigens while self-tolerant. Essential for tolerance induction, mTECs play a critical role in negative selection and T regulatory cell differentiation. In this article, we review the current knowledge on the functional diversity within mTECs and discuss how these novel subsets contribute to tolerance induction and are integrated in the complex blueprint of mTEC differentiation.
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Affiliation(s)
- Camila Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Nuno L Alves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Pedro Ferreirinha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.
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59
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Giladi A, Amit I. Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries. Cell 2018; 172:14-21. [PMID: 29328909 DOI: 10.1016/j.cell.2017.11.011] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 02/08/2023]
Abstract
The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. In this Perspective, we consider recent and forthcoming technological and analytical advances in single-cell genomics and the potential impact of those advances on the future of immunology research and immunotherapy.
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Affiliation(s)
- Amir Giladi
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
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60
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Morimoto J, Nishikawa Y, Kakimoto T, Furutani K, Kihara N, Matsumoto M, Tsuneyama K, Kozono Y, Kozono H, Hozumi K, Hosomichi K, Nishijima H, Matsumoto M. Aire Controls in Trans the Production of Medullary Thymic Epithelial Cells Expressing Ly-6C/Ly-6G. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:3244-3257. [PMID: 30389776 DOI: 10.4049/jimmunol.1800950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/27/2018] [Indexed: 11/19/2022]
Abstract
Medullary thymic epithelial cells (mTECs), which express a wide range of tissue-restricted Ags (TRAs), contribute to the establishment of self-tolerance by eliminating autoreactive T cells and/or inducing regulatory T cells. Aire controls a diverse set of TRAs within Aire-expressing cells by employing various transcriptional pathways. As Aire has a profound effect on transcriptomes of mTECs, including TRAs not only at the single-cell but also the population level, we suspected that Aire (Aire+ mTECs) might control the cellular composition of the thymic microenvironment. In this study, we confirmed that this is indeed the case by identifying a novel mTEC subset expressing Ly-6 family protein whose production was defective in Aire-deficient thymi. Reaggregated thymic organ culture experiments demonstrated that Aire did not induce the expression of Ly-6C/Ly-6G molecules from mTECs as Aire-dependent TRAs in a cell-intrinsic manner. Instead, Aire+ mTECs functioned in trans to maintain Ly-6C/Ly-6G+ mTECs. Thus, Aire not only controls TRA expression transcriptionally within the cell but also controls the overall composition of mTECs in a cell-extrinsic manner, thereby regulating the transcriptome from mTECs on a global scale.
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Affiliation(s)
- Junko Morimoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
| | - Yumiko Nishikawa
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
| | - Takumi Kakimoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
- Student Lab, Tokushima University Faculty of Medicine, Tokushima 770-8503, Japan
| | - Kohei Furutani
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
- Student Lab, Tokushima University Faculty of Medicine, Tokushima 770-8503, Japan
| | - Naoki Kihara
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
- Student Lab, Tokushima University Faculty of Medicine, Tokushima 770-8503, Japan
| | - Minoru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
- Department of Molecular and Environmental Pathology, Institute of Biomedical Sciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan
| | - Koichi Tsuneyama
- Department of Molecular and Environmental Pathology, Institute of Biomedical Sciences, The University of Tokushima Graduate School, Tokushima 770-8503, Japan
| | - Yuko Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba 278-0022, Japan
| | - Haruo Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba 278-0022, Japan
| | - Katsuto Hozumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-0934, Japan; and
| | - Hitoshi Nishijima
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan;
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo 100-0004, Japan
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61
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62
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Banerjee S, Chapman SJ. Influence of correlated antigen presentation on T-cell negative selection in the thymus. J R Soc Interface 2018; 15:rsif.2018.0311. [PMID: 30404905 PMCID: PMC6283997 DOI: 10.1098/rsif.2018.0311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/08/2018] [Indexed: 11/12/2022] Open
Abstract
The thymus is the primary organ for the generation of naive T cells, a key component of the immune system. Tolerance of T cells to self is achieved primarily in the thymic medulla, where immature T cells (thymocytes) sample self-peptides presented by medullary thymic epithelial cells (mTECs). A sufficiently strong interaction activates the thymocytes leading to negative selection. A key question of current interest is whether there is any structure in the manner in which mTECs present peptides: can any mTEC present any peptide at any time, or are there particular patterns of correlated peptide presentation? We investigate this question using a mathematical model of negative selection. We find that correlated patterns of peptide presentation may be advantageous in negatively selecting low-degeneracy thymocytes (that is, those thymocytes which respond to relatively few peptides). We also quantify the probability that an auto-reactive thymocyte exits the thymus before it encounters a cognate antigen. The results suggest that heterogeneity of gene co-expression in mTECs has an effect on the probability of escape of autoreactive thymocytes.
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63
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Sykes M. IXA Honorary Member Lecture, 2017: The long and winding road to tolerance. Xenotransplantation 2018; 25:e12419. [PMID: 29913040 DOI: 10.1111/xen.12419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/03/2018] [Indexed: 12/18/2022]
Abstract
The last 15 years or so have seen exciting progress in xenotransplantation, with porcine organ grafts surviving months or even years in non-human primates. These advances reflect the application of new scientific knowledge, improved immunosuppressive agents, and genetic engineering. The field has recently enjoyed a renaissance of interest and hope, largely due to the exponential increase in our capacity to genetically engineer porcine source animals. However, immune responses to xenografts are very powerful and widespread clinical application of xenotransplantation will depend on the ability to suppress these immune responses while preserving the capacity to protect both the recipient and the graft from infectious microorganisms. Our work over the last three decades has aimed to engineer the immune system of the recipient in a manner that achieves specific tolerance to the xenogeneic donor while preserving otherwise normal immune function. Important proofs of principle have been obtained, first in rodents, and later in human immune systems in "humanized mice" and finally in non-human primates, demonstrating the capacity and potential synergy of mixed xenogeneic chimerism and xenogeneic thymic transplantation in tolerizing multiple arms of the immune system. Considering the fact that clinical tolerance has recently been achieved for allografts and the even greater importance of avoiding excessive immunosuppression for xenografts, it is my belief that it is both possible and imperative that we likewise achieve xenograft tolerance. I expect this to be accomplished through the availability of targeted approaches to recipient immune conditioning, understanding of immunological mechanisms of tolerance, advanced knowledge of physiological incompatibilities, and the availability of inbred miniature swine with optimized use of genetic engineering.
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Affiliation(s)
- Megan Sykes
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA.,Department of Microbiology & Immunology, Columbia University, New York, NY, USA.,Department of Surgery, Columbia University, New York, NY, USA
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64
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Handel AE, Shikama-Dorn N, Zhanybekova S, Maio S, Graedel AN, Zuklys S, Ponting CP, Holländer GA. Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development. Front Immunol 2018; 9:2120. [PMID: 30283453 PMCID: PMC6156148 DOI: 10.3389/fimmu.2018.02120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/28/2018] [Indexed: 01/11/2023] Open
Abstract
Thymic epithelial cells (TEC) effect crucial roles in thymopoiesis including the control of negative thymocyte selection. This process depends on their capacity to express promiscuously genes encoding tissue-restricted antigens. This competence is accomplished in medullary TEC (mTEC) in part by the presence of the transcriptional facilitator AutoImmune REgulator, AIRE. AIRE-regulated gene transcription is marked by repressive chromatin modifications, including H3K27me3. When during TEC development these chromatin marks are established, however, remains unclear. Here we use a comprehensive ChIP-seq dataset of multiple chromatin modifications in different TEC subtypes to demonstrate that the chromatin landscape is established early in TEC differentiation. Much of the chromatin architecture found in mature mTEC was found to be present already over earlier stages of mTEC lineage differentiation as well as in non-TEC tissues. This was reflected by the fact that a machine learning approach accurately classified genes as AIRE-induced or AIRE-independent both in immature and mature mTEC. Moreover, analysis of TEC specific enhancer elements identified candidate transcription factors likely to be important in mTEC development and function. Our findings indicate that the mature mTEC chromatin landscape is laid down early in mTEC differentiation, and that AIRE is not required for large-scale re-patterning of chromatin in mTEC.
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Affiliation(s)
- Adam E. Handel
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
| | | | | | - Stefano Maio
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
| | - Annina N. Graedel
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
| | - Saulius Zuklys
- Department of Biomedicine, Universität Basel, BaselSwitzerland
| | - Chris P. Ponting
- MRC Human Genetics Unit, University of Edinburgh, EdinburghUnited Kingdom
| | - Georg A. Holländer
- Department of Paediatrics, University of Oxford, OxfordUnited Kingdom
- Department of Biomedicine, Universität Basel, BaselSwitzerland
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Pohar J, Simon Q, Fillatreau S. Antigen-Specificity in the Thymic Development and Peripheral Activity of CD4 +FOXP3 + T Regulatory Cells. Front Immunol 2018; 9:1701. [PMID: 30083162 PMCID: PMC6064734 DOI: 10.3389/fimmu.2018.01701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/10/2018] [Indexed: 01/12/2023] Open
Abstract
CD4+Foxp3+ T regulatory cells (Treg) are essential for the life of the organism, in particular because they protect the host against its own autoaggressive CD4+Foxp3- T lymphocytes (Tconv). Treg distinctively suppress autoaggressive immunity while permitting efficient defense against infectious diseases. This split effect indicates that Treg activity is controlled in an antigen-specific manner. This specificity is achieved first by the formation of the Treg repertoire during their development, and second by their activation in the periphery. This review presents novel information on the antigen-specificity of Treg development in the thymus, and Treg function in the periphery. These aspects have so far remained imprecisely understood due to the lack of knowledge of the actual antigens recognized by Treg during the different steps of their life, so that most previous studies have been performed using artificial antigens. However, recent studies identified some antigens mediating the positive selection of autoreactive Treg in the thymus, and the function of Treg in the periphery in autoimmune and allergic disorders. These investigations emphasized the remarkable specificity of Treg development and function. Indeed, the development of autoreactive Treg in the thymus was found to be mediated by single autoantigens, so that the absence of one antigen led to a dramatic loss of Treg reacting toward that antigen. The specificity of Treg development is important because the constitution of the Treg repertoire, and especially the presence of holes in this repertoire, was found to crucially influence human immunopathology. Indeed, it was found that the development of human immunopathology was permitted by the lack of Treg against the antigens driving the autoimmune or allergic T cell responses rather than by the impairment of Treg activation or function. The specificity of Treg suppression in the periphery is therefore intimately associated with the mechanisms shaping the formation of the Treg repertoire during their development. This novel information refines significantly our understanding of the antigen-specificity of Treg protective function, which is required to envision how these cells distinctively regulate unwanted immune responses as well as for the development of appropriate approaches to optimally harness them therapeutically in autoimmune, malignant, and infectious diseases.
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Affiliation(s)
- Jelka Pohar
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Paris, France
| | - Quentin Simon
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Paris, France
| | - Simon Fillatreau
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Paris, France.,Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,AP-HP, Hôpital Necker Enfants Malades, Paris, France
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66
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Thyagarajan HM, Lancaster JN, Lira SA, Ehrlich LIR. CCR8 is expressed by post-positive selection CD4-lineage thymocytes but is dispensable for central tolerance induction. PLoS One 2018; 13:e0200765. [PMID: 30024927 PMCID: PMC6053179 DOI: 10.1371/journal.pone.0200765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/02/2018] [Indexed: 12/19/2022] Open
Abstract
Following positive selection, thymocytes migrate into the medulla where they encounter diverse self-antigens that induce central tolerance. Thymocytes expressing T cell receptors (TCRs) with high affinity for self-antigens displayed by medullary antigen presenting cells (APCs) undergo either negative selection or diversion to the regulatory T cell (Treg) lineage, thus ensuring maturation of non-autoreactive T cells. Because many self-antigens are expressed by only a small percentage of medullary thymic epithelial cells, thymocytes must enter the medulla and efficiently scan APCs therein to encounter the full array of self-antigens that induce central tolerance. Chemokine receptors play a critical role in promoting medullary entry and rapid motility of post-positive selection thymocytes. We found that the chemokine receptor CCR8 is expressed by post-positive selection CD4+ single positive (SP) thymocytes in mice, while the corresponding chemokine ligands are expressed by medullary APCs, and thus hypothesized that CCR8 would promote thymocyte medullary entry and/or rapid motility to induce negative selection. However, despite a subtle decline in thymocyte medullary accumulation and the presence of autoantibodies in aged CCR8-deficient mice, CCR8 was not required for thymocyte differentiation, rapid motility, or negative selection.
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Affiliation(s)
- Hiran M. Thyagarajan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jessica N. Lancaster
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Sergio A. Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Lauren I. R. Ehrlich
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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67
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Cheng M, Anderson MS. Thymic tolerance as a key brake on autoimmunity. Nat Immunol 2018; 19:659-664. [PMID: 29925986 PMCID: PMC6370479 DOI: 10.1038/s41590-018-0128-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022]
Abstract
Although the thymus has long been recognized as a key organ for T cell selection, the intricate details linking these selection events to human autoimmunity have been challenging to decipher. Over the last two decades, there has been rapid progress in understanding the role of thymic tolerance mechanisms in autoimmunity through genetics. Here we review some of the recent progress in understanding key thymic tolerance processes that are critical for preventing autoimmune disease.
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Affiliation(s)
- Mickie Cheng
- Diabetes Center, 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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68
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Bornstein C, Nevo S, Giladi A, Kadouri N, Pouzolles M, Gerbe F, David E, Machado A, Chuprin A, Tóth B, Goldberg O, Itzkovitz S, Taylor N, Jay P, Zimmermann VS, Abramson J, Amit I. Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells. Nature 2018; 559:622-626. [PMID: 30022162 DOI: 10.1038/s41586-018-0346-1] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 06/06/2018] [Indexed: 12/18/2022]
Abstract
T cell development and selection are coordinated in the thymus by a specialized niche of diverse stromal populations1-3. Although much progress has been made over the years in identifying the functions of the different cell types of the thymic stromal compartment, there is no comprehensive characterization of their diversity and heterogeneity. Here we combined massively parallel single-cell RNA-sequencing4,5, spatial mapping, chromatin profiling and gene targeting to characterize de novo the entire stromal compartment of the mouse thymus. We identified dozens of cell states, with thymic epithelial cells (TECs) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient in Pou2f3, a master regulator of tuft cells, have complete and specific depletion of mTEC IV cells, which results in increased levels of thymus-resident type-2 innate lymphoid cells. Overall, our study provides a comprehensive characterization of the thymic stroma and identifies a new tuft-like TEC population, which is critical for shaping the immune niche in the thymus.
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Affiliation(s)
- Chamutal Bornstein
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Nevo
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kadouri
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Marie Pouzolles
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - François Gerbe
- IGF, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alice Machado
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Anna Chuprin
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Beáta Tóth
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Goldberg
- Department of Pediatrics, Schneider Children's Medical Center, Petach Tikva, Israel
| | - Shalev Itzkovitz
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Philippe Jay
- IGF, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Valérie S Zimmermann
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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69
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Kernfeld EM, Genga RMJ, Neherin K, Magaletta ME, Xu P, Maehr R. A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation. Immunity 2018; 48:1258-1270.e6. [PMID: 29884461 DOI: 10.1016/j.immuni.2018.04.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
Thymus development is critical to the adaptive immune system, yet a comprehensive transcriptional framework capturing thymus organogenesis at single-cell resolution is still needed. We applied single-cell RNA sequencing (RNA-seq) to capture 8 days of thymus development, perturbations of T cell receptor rearrangement, and in vitro organ cultures, producing profiles of 24,279 cells. We resolved transcriptional heterogeneity of developing lymphocytes, and genetic perturbation confirmed T cell identity of conventional and non-conventional lymphocytes. We characterized maturation dynamics of thymic epithelial cells in vivo, classified cell maturation state in a thymic organ culture, and revealed the intrinsic capacity of thymic epithelium to preserve transcriptional regularity despite exposure to exogenous retinoic acid. Finally, by integrating the cell atlas with human genome-wide association study (GWAS) data and autoimmune-disease-related genes, we implicated embryonic thymus-resident cells as possible participants in autoimmune disease etiologies. This resource provides a single-cell transcriptional framework for biological discovery and molecular analysis of thymus organogenesis.
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Affiliation(s)
- Eric M Kernfeld
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kashfia Neherin
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Margaret E Magaletta
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ping Xu
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - René Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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70
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O’Sullivan BJ, Yekollu S, Ruscher R, Mehdi AM, Maradana MR, Chidgey AP, Thomas R. Autoimmune-Mediated Thymic Atrophy Is Accelerated but Reversible in RelB-Deficient Mice. Front Immunol 2018; 9:1092. [PMID: 29872433 PMCID: PMC5972300 DOI: 10.3389/fimmu.2018.01092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/01/2018] [Indexed: 01/28/2023] Open
Abstract
Polymorphisms impacting thymic function may decrease peripheral tolerance and hasten autoimmune disease. The NF-κB transcription factor subunit, RelB, is essential for the development and differentiation of medullary thymic epithelial cells (mTECs): RelB-deficient mice have reduced thymic cellularity and markedly fewer mTECs, lacking AIRE. The precise mechanism of this mTEC reduction in the absence of RelB is unclear. To address this, we studied mTECs and dendritic cells (DCs), which critically regulate negative selection, and thymic regulatory T-cells (tTreg) in RelB-/- mice, which have spontaneous multiorgan autoimmune disease. RelB-/- thymi were organized, with medullary structures containing AIRE- mTECs, DCs, and CD4+ thymocytes, but fewer tTreg. Granulocytes infiltrated the RelB-/- thymic cortex, capsule, and medulla, producing inflammatory thymic medullary atrophy, which could be treated by granulocyte depletion or RelB+ DC immunotherapy, with concomitant recovery of mTEC and tTreg numbers. These data indicate that central tolerance defects may be accelerated by autoimmune thymic inflammation where impaired RelB signaling impairs the medullary niche, and may be reversible by therapies enhancing peripheral Treg or suppressing inflammation.
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Affiliation(s)
- Brendan J. O’Sullivan
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Suman Yekollu
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Roland Ruscher
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Ahmed M. Mehdi
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Muralidhara Rao Maradana
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Ann P. Chidgey
- Stem Cells and Immune Regeneration Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Ranjeny Thomas
- Diamantina Institute, Translational Research Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD, Australia
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71
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Apert C, Romagnoli P, van Meerwijk JPM. IL-2 and IL-15 dependent thymic development of Foxp3-expressing regulatory T lymphocytes. Protein Cell 2018; 9:322-332. [PMID: 28540653 PMCID: PMC5876181 DOI: 10.1007/s13238-017-0425-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/04/2017] [Indexed: 12/15/2022] Open
Abstract
Immunosuppressive regulatory T lymphocytes (Treg) expressing the transcription factor Foxp3 play a vital role in the maintenance of tolerance of the immune-system to self and innocuous non-self. Most Treg that are critical for the maintenance of tolerance to self, develop as an independent T-cell lineage from common T cell precursors in the thymus. In this organ, their differentiation requires signals from the T cell receptor for antigen, from co-stimulatory molecules, as well as from cytokine-receptors. Here we focus on the cytokines implicated in thymic development of Treg, with a particular emphasis on the roles of interleukin-2 (IL-2) and IL-15. The more recently appreciated involvement of TGF-β in thymic Treg development is also briefly discussed. Finally, we discuss how cytokine-dependence of Treg development allows for temporal, quantitative, and potentially qualitative modulation of this process.
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Affiliation(s)
- Cécile Apert
- CPTP, Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France
| | - Paola Romagnoli
- CPTP, Université de Toulouse, CNRS, Inserm, UPS, Toulouse, France.
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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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73
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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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74
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Enteric α-defensins on the verge of intestinal immune tolerance and inflammation. Semin Cell Dev Biol 2018; 88:138-146. [PMID: 29355606 DOI: 10.1016/j.semcdb.2018.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 12/18/2022]
Abstract
The gut is the biggest immune organ in the body that encloses commensal microbiota which aids in food digestion. Paneth cells, positioned at the frontline of host-microbiota interphase, can modulate the composition of microbiota. Paneth cells achieve this via the delivery of microbicidal substances, among which enteric α-defensins play the primary role. If microbiota is dysregulated, it can impact the function of the local mucosal immune system. Importantly, this system is also exposed to an enormous number of antigens which are derived from the gut-resident microbiota and processed food, and may potentially trigger undesirable local inflammatory responses. To understand the intricate regulations and liaisons between Paneth cells, microbiota and the immune system in this intestinal-specific setting, one must consider their mode of interaction in a wider context of regulatory processes which impose immune tolerance not only to self, but also to microbiota and food-derived antigens. These include, but are not limited to, tolerogenic mechanisms of central tolerance in the thymus and peripheral tolerance in the secondary lymphoid organs, and the intestine itself. Defects in these processes can compromise homeostasis in the intestinal mucosal immunity. In this review, which is focused on tolerance to intestinal antigens and its relevance for the pathogenesis of gut immune diseases, we provide an outline of such multilayered immune control mechanisms and highlight functional links that underpin their cooperative nature.
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Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G, Lönnberg T. Single-cell RNA-sequencing resolves self-antigen expression during mTEC development. Sci Rep 2018; 8:685. [PMID: 29330484 PMCID: PMC5766627 DOI: 10.1038/s41598-017-19100-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/14/2017] [Indexed: 01/03/2023] Open
Abstract
The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization. Furthermore, expression patterns of TRA genes have been suggested to change over the course of mTEC development. Herein we have used single-cell RNA-sequencing to resolve patterns of TRA expression during mTEC development. Our data indicated that mTEC development consists of three distinct stages, correlating with previously described jTEC, mTEChi and mTEClo phenotypes. For each subpopulation, we have identified marker genes useful in future studies. Aire-induced TRAs were switched on during jTEC-mTEC transition and were expressed in genomic clusters, while otherwise the subsets expressed largely overlapping sets of TRAs. Moreover, population-level analysis of TRA expression frequencies suggested that such differences might not be necessary to achieve efficient thymocyte selection.
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Affiliation(s)
- Ricardo J Miragaia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Xiuwei Zhang
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- University of California, Berkeley, USA
| | - Tomás Gomes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Valentine Svensson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Tomislav Ilicic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Johan Henriksson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Gozde Kar
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Tapio Lönnberg
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
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76
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Passos GA, Speck‐Hernandez CA, Assis AF, Mendes‐da‐Cruz DA. Update on Aire and thymic negative selection. Immunology 2018; 153:10-20. [PMID: 28871661 PMCID: PMC5721245 DOI: 10.1111/imm.12831] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 08/31/2017] [Indexed: 12/17/2022] Open
Abstract
Twenty years ago, the autoimmune regulator (Aire) gene was associated with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy, and was cloned and sequenced. Its importance goes beyond its abstract link with human autoimmune disease. Aire identification opened new perspectives to better understand the molecular basis of central tolerance and self-non-self distinction, the main properties of the immune system. Since 1997, a growing number of immunologists and molecular geneticists have made important discoveries about the function of Aire, which is essentially a pleiotropic gene. Aire is one of the functional markers in medullary thymic epithelial cells (mTECs), controlling their differentiation and expression of peripheral tissue antigens (PTAs), mTEC-thymocyte adhesion and the expression of microRNAs, among other functions. With Aire, the immunological tolerance became even more apparent from the molecular genetics point of view. Currently, mTECs represent the most unusual cells because they express almost the entire functional genome but still maintain their identity. Due to the enormous diversity of PTAs, this uncommon gene expression pattern was termed promiscuous gene expression, the interpretation of which is essentially immunological - i.e. it is related to self-representation in the thymus. Therefore, this knowledge is strongly linked to the negative selection of autoreactive thymocytes. In this update, we focus on the most relevant results of Aire as a transcriptional and post-transcriptional controller of PTAs in mTECs, its mechanism of action, and its influence on the negative selection of autoreactive thymocytes as the bases of the induction of central tolerance and prevention of autoimmune diseases.
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Affiliation(s)
- Geraldo A. Passos
- Molecular Immunogenetics GroupDepartment of GeneticsRibeirão Preto Medical SchoolUniversity of São PauloRibeirão PretoSPBrazil
- Discipline of Genetics and Molecular BiologyDepartment of Morphology, Physiology and Basic PathologySchool of Dentistry of Ribeirão PretoUniversity of São PauloRibeirão PretoSPBrazil
| | - Cesar A. Speck‐Hernandez
- Graduate Programme in Basic and Applied ImmunologyRibeirão Preto Medical SchoolUniversity of São PauloRibeirão PretoSPBrazil
| | - Amanda F. Assis
- Molecular Immunogenetics GroupDepartment of GeneticsRibeirão Preto Medical SchoolUniversity of São PauloRibeirão PretoSPBrazil
| | - Daniella A. Mendes‐da‐Cruz
- Laboratory on Thymus ResearchOswaldo Cruz InstituteOswaldo Cruz FoundationRio de JaneiroRJBrazil
- National Institute of Science and Technology on NeuroimmunomodulationRio de JaneiroRJBrazil
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77
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Mouri Y, Ueda Y, Yamano T, Matsumoto M, Tsuneyama K, Kinashi T, Matsumoto M. Mode of Tolerance Induction and Requirement for Aire Are Governed by the Cell Types That Express Self-Antigen and Those That Present Antigen. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:3959-3971. [PMID: 29101311 DOI: 10.4049/jimmunol.1700892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022]
Abstract
Aire controls the fate of autoreactive thymocytes (i.e., clonal deletion or development into regulatory T cells [Tregs]) through transcriptional control of the expression of tissue-restricted self-antigens (TRAs) from medullary thymic epithelial cells (mTECs) and bone marrow (BM)-derived cells. Although TRAs expressed by mTECs and BM-derived cells are suggested to complement each other to generate a full spectrum of TRAs, little is known about the relative contribution of TRAs from each component for establishment of self-tolerance. Furthermore, the precise role of Aire in specific types of Aire-expressing APCs remains elusive. We have approached these issues by generating two different types of transgenic mouse (Tg) model, which express a prefixed model self-antigen driven by the insulin promoter or the Aire promoter. In the insulin-promoter Tg model, mTECs alone were insufficient for clonal deletion, and BM-derived APCs were required for this action by utilizing Ag transferred from mTECs. In contrast, mTECs alone were able to induce Tregs, although at a much lower efficiency in the absence of BM-derived APCs. Importantly, lack of Aire in mTECs, but not in BM-derived APCs, impaired both clonal deletion and production of Tregs. In the Aire-promoter Tg model, both mTECs and BM-derived APCs could independently induce clonal deletion without Aire, and production of Tregs was impaired by the lack of Aire in mTECs, but not in BM-derived APCs. These results suggest that the fate of autoreactive thymocytes together with the requirement for Aire depend on the cell types that express self-antigens and the types of APCs involved in tolerance induction.
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Affiliation(s)
- Yasuhiro Mouri
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
| | - Yoshihiro Ueda
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Osaka 570-8506, Japan
| | - Tomoyoshi Yamano
- Institute for Immunology, Ludwig-Maximilians-University Munich, Munich 80336, Germany
| | - Minoru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan
- Department of Pathology and Laboratory Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan; and
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan; and
| | - Tatsuo Kinashi
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Osaka 570-8506, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima 770-8503, Japan;
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo 100-0004, Japan
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78
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Michel C, Miller CN, Küchler R, Brors B, Anderson MS, Kyewski B, Pinto S. Revisiting the Road Map of Medullary Thymic Epithelial Cell Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:3488-3503. [PMID: 28993517 DOI: 10.4049/jimmunol.1700203] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022]
Abstract
The basic two-step terminal differentiation model of the medullary thymic epithelial cell (mTEC) lineage from immature MHC class II (MHCII)lo to mature MHCIIhi mTECs has recently been extended to include a third stage, namely the post-Aire MHCIIlo subset as identified by lineage-tracing models. However, a suitable surface marker distinguishing the phenotypically overlapping pre- from the post-Aire MHCIIlo stage has been lacking. In this study, we introduce the lectin Tetragonolobus purpureas agglutinin (TPA) as a novel cell surface marker that allows for such delineation. Based on our data, we derived the following sequence of mTEC differentiation: TPAloMHCIIlo → TPAloMHCIIhi → TPAhiMHCIIhi → TPAhiMHCIIlo Surprisingly, in the steady-state postnatal thymus TPAloMHCIIlo pre-Aire rather than terminally differentiated post-Aire TPAhiMHCIIlo mTECs were marked for apoptosis at an exceptionally high rate of ∼70%. Hence, only the minor cycling fraction of the MHCIIlo subset (<20%) potentially qualified as mTEC precursors. FoxN1 expression inversely correlated with the fraction of slow cycling and apoptotic cells within the four TPA subsets. TPA also further subdivided human mTECs, although with different subset distribution. Our revised road map emphazises close parallels of terminal mTEC development with that of skin, undergoing an alternative route of cell death, namely cornification rather than apoptosis. The high rate of apoptosis in pre-Aire MHCIIlo mTECs points to a "quality control" step during early mTEC differentiation.
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Affiliation(s)
- Chloé Michel
- Division of Developmental Immunology, German Cancer Research Center, Heidelberg 69120, Germany
| | - Corey N Miller
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143
| | - Rita Küchler
- Division of Developmental Immunology, German Cancer Research Center, Heidelberg 69120, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg 69120, Germany
- National Center for Tumor Diseases, Heidelberg 69120, Germany; and
- German Cancer Consortium, Heidelberg 69120, Germany
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143
| | - Bruno Kyewski
- Division of Developmental Immunology, German Cancer Research Center, Heidelberg 69120, Germany;
| | - Sheena Pinto
- Division of Developmental Immunology, German Cancer Research Center, Heidelberg 69120, Germany;
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79
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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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80
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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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81
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Ki S, Thyagarajan HM, Hu Z, Lancaster JN, Ehrlich LIR. EBI2 contributes to the induction of thymic central tolerance in mice by promoting rapid motility of medullary thymocytes. Eur J Immunol 2017; 47:1906-1917. [PMID: 28741728 DOI: 10.1002/eji.201747020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/14/2017] [Accepted: 07/21/2017] [Indexed: 11/08/2022]
Abstract
Maturing thymocytes enter the thymic medulla, where they encounter numerous self-antigens presented by antigen presenting cells (APCs). Those thymocytes that are strongly self-reactive undergo either negative selection or diversion into the regulatory T-cell lineage. Although the majority of the proteome is expressed in the medulla, many self-antigens are expressed by only a minor fraction of medullary APCs; thus, thymocytes must efficiently enter the medulla and scan APCs to ensure central tolerance. Chemokine receptors promote lymphocyte migration, organization within tissues, and interactions with APCs in lymphoid organs. The chemokine receptor EBI2 governs localization of T cells, B cells, and dendritic cells (DCs) during immune responses in secondary lymphoid organs. However, the role of EBI2 in thymocyte development has not been elucidated. Here, we demonstrate that EBI2 is expressed by murine CD4+ single positive (CD4SP) thymocytes and thymic DCs. EBI2 deficiency alters the TCR repertoire, but does not grossly impact thymocyte cellularity or subset distribution. EBI2 deficiency also impairs negative selection of OT-II TCR transgenic thymocytes responding to an endogenous self-antigen. Two-photon imaging revealed that EBI2 deficiency results in reduced migration and impaired medullary accumulation of CD4SP thymocytes. These data identify a role for EBI2 in promoting efficient thymic central tolerance.
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Affiliation(s)
- Sanghee Ki
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Hiran M Thyagarajan
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Zicheng Hu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jessica N Lancaster
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Lauren I R Ehrlich
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
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82
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Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol 2017; 18:35-45. [DOI: 10.1038/nri.2017.76] [Citation(s) in RCA: 692] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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83
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Thymic epithelial cells require p53 to support their long-term function in thymopoiesis in mice. Blood 2017; 130:478-488. [PMID: 28559356 DOI: 10.1182/blood-2016-12-758961] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/24/2017] [Indexed: 01/22/2023] Open
Abstract
Thymic epithelial cells (TECs) provide crucial microenvironments for T-cell development and tolerance induction. As the regular function of the thymus declines with age, it is of fundamental and clinical relevance to decipher new determinants that control TEC homeostasis in vivo. Beyond its recognized tumor suppressive function, p53 controls several immunoregulatory pathways. To study the cell-autonomous role of p53 in thymic epithelium functioning, we developed and analyzed mice with conditional inactivation of Trp53 in TECs (p53cKO). We report that loss of p53 primarily disrupts the integrity of medullary TEC (mTEC) niche, a defect that spreads to the adult cortical TEC compartment. Mechanistically, we found that p53 controls specific and broad programs of mTEC differentiation. Apart from restraining the expression and responsiveness of the receptor activator of NF-κB (RANK), which is central for mTEC differentiation, deficiency of p53 in TECs altered multiple functional modules of the mTEC transcriptome, including tissue-restricted antigen expression. As a result, p53cKO mice presented premature defects in mTEC-dependent regulatory T-cell differentiation and thymocyte maturation, which progressed to a failure in regular and regenerative thymopoiesis and peripheral T-cell homeostasis in the adulthood. Lastly, peripheral signs of altered immunological tolerance unfold in mutant mice and in immunodeficient mice that received p53cKO-derived thymocytes. Our findings position p53 as a novel molecular determinant of thymic epithelium function throughout life.
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84
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Dal Molin A, Baruzzo G, Di Camillo B. Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods. Front Genet 2017; 8:62. [PMID: 28588607 PMCID: PMC5440469 DOI: 10.3389/fgene.2017.00062] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 05/08/2017] [Indexed: 01/17/2023] Open
Abstract
The sequencing of the transcriptomes of single-cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types and for the study of stochastic gene expression. In recent years, various tools for analyzing single-cell RNA-sequencing data have been proposed, many of them with the purpose of performing differentially expression analysis. In this work, we compare four different tools for single-cell RNA-sequencing differential expression, together with two popular methods originally developed for the analysis of bulk RNA-sequencing data, but largely applied to single-cell data. We discuss results obtained on two real and one synthetic dataset, along with considerations about the perspectives of single-cell differential expression analysis. In particular, we explore the methods performance in four different scenarios, mimicking different unimodal or bimodal distributions of the data, as characteristic of single-cell transcriptomics. We observed marked differences between the selected methods in terms of precision and recall, the number of detected differentially expressed genes and the overall performance. Globally, the results obtained in our study suggest that is difficult to identify a best performing tool and that efforts are needed to improve the methodologies for single-cell RNA-sequencing data analysis and gain better accuracy of results.
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Affiliation(s)
| | - Giacomo Baruzzo
- Department of Information Engineering, University of PadovaPadova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of PadovaPadova, Italy
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85
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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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86
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Abstract
Intrathymic T cell development is a complex process that depends upon continuous guidance from thymus stromal cell microenvironments. The thymic epithelium within the thymic stroma comprises highly specialized cells with a high degree of anatomic, phenotypic, and functional heterogeneity. These properties are collectively required to bias thymocyte development toward production of self-tolerant and functionally competent T cells. The importance of thymic epithelial cells (TECs) is evidenced by clear links between their dysfunction and multiple diseases where autoimmunity and immunodeficiency are major components. Consequently, TECs are an attractive target for cell therapies to restore effective immune system function. The pathways and molecular regulators that control TEC development are becoming clearer, as are their influences on particular stages of T cell development. Here, we review both historical and the most recent advances in our understanding of the cellular and molecular mechanisms controlling TEC development, function, dysfunction, and regeneration.
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Affiliation(s)
- Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Graham Anderson
- MRC Centre for Immune Regulation, Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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87
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Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Power analysis of single-cell RNA-sequencing experiments. Nat Methods 2017; 14:381-387. [PMID: 28263961 PMCID: PMC5376499 DOI: 10.1038/nmeth.4220] [Citation(s) in RCA: 370] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, we assessed the protocol sensitivity and accuracy of many published data sets, on the basis of spike-in standards and uniform data processing. For our workflow, we developed a flexible tool for counting the number of unique molecular identifiers (https://github.com/vals/umis/). We compared 15 protocols computationally and 4 protocols experimentally for batch-matched cell populations, in addition to investigating the effects of spike-in molecular degradation. Our analysis provides an integrated framework for comparing scRNA-seq protocols.
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Affiliation(s)
- Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ricardo J Miragaia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Charlotte Labalette
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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88
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Li H, Courtois ET, Sengupta D, Tan Y, Chen KH, Goh JJL, Kong SL, Chua C, Hon LK, Tan WS, Wong M, Choi PJ, Wee LJK, Hillmer AM, Tan IB, Robson P, Prabhakar S. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet 2017; 49:708-718. [PMID: 28319088 DOI: 10.1038/ng.3818] [Citation(s) in RCA: 694] [Impact Index Per Article: 99.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/24/2017] [Indexed: 12/23/2022]
Abstract
Intratumoral heterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs). Additionally, epithelial-mesenchymal transition (EMT)-related genes were found to be upregulated only in the CAF subpopulation of tumor samples. Notably, colorectal tumors previously assigned to a single subtype on the basis of bulk transcriptomics could be divided into subgroups with divergent survival probability by using single-cell signatures, thus underscoring the prognostic value of our approach. Overall, our results demonstrate that unbiased single-cell RNA-seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor.
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Affiliation(s)
- Huipeng Li
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Elise T Courtois
- Computational and Systems Biology, Genome Institute of Singapore, Singapore.,Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Debarka Sengupta
- Computational and Systems Biology, Genome Institute of Singapore, Singapore.,Department of Computer Science and Engineering and Center for Computational Biology, Indraprastha Institute of Information Technology, Delhi, India
| | - Yuliana Tan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore.,Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore
| | - Kok Hao Chen
- Synthetic Biology, Genome Institute of Singapore, Singapore
| | | | - Say Li Kong
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Clarinda Chua
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Lim Kiat Hon
- Department of Pathology, Singapore General Hospital, Singapore
| | - Wah Siew Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Mark Wong
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | | | - Lawrence J K Wee
- Data Analytics Department, Institute for Infocomm Research, Singapore
| | - Axel M Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Iain Beehuat Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,Department of Medical Oncology, National Cancer Centre Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Paul Robson
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore.,The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut, Farmington, Connecticut, USA.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
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89
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Bansal K, Yoshida H, Benoist C, Mathis D. The transcriptional regulator Aire binds to and activates super-enhancers. Nat Immunol 2017; 18:263-273. [PMID: 28135252 PMCID: PMC5310976 DOI: 10.1038/ni.3675] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/21/2016] [Indexed: 12/15/2022]
Abstract
Aire is a transcription factor that controls T cell tolerance by inducing the expression of a large repertoire of genes specifically in thymic stromal cells. It interacts with scores of protein partners of diverse functional classes. We found that Aire and some of its partners, notably those implicated in the DNA-damage response, preferentially localized to and activated long chromatin stretches that were overloaded with transcriptional regulators, known as super-enhancers. We also identified topoisomerase 1 as a cardinal Aire partner that colocalized on super-enhancers and was required for the interaction of Aire with all of its other associates. We propose a model that entails looping of super-enhancers to efficiently deliver Aire-containing complexes to local and distal transcriptional start sites.
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Affiliation(s)
- Kushagra Bansal
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - Hideyuki Yoshida
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA 02115
| | - 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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90
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Pearson H, Daouda T, Granados DP, Durette C, Bonneil E, Courcelles M, Rodenbrock A, Laverdure JP, Côté C, Mader S, Lemieux S, Thibault P, Perreault C. MHC class I-associated peptides derive from selective regions of the human genome. J Clin Invest 2016; 126:4690-4701. [PMID: 27841757 DOI: 10.1172/jci88590] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/30/2016] [Indexed: 12/24/2022] Open
Abstract
MHC class I-associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology.
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91
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Liu J, Cao X. Cellular and molecular regulation of innate inflammatory responses. Cell Mol Immunol 2016; 13:711-721. [PMID: 27818489 PMCID: PMC5101451 DOI: 10.1038/cmi.2016.58] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 10/16/2016] [Indexed: 02/07/2023] Open
Abstract
Innate sensing of pathogens by pattern-recognition receptors (PRRs) plays essential roles in the innate discrimination between self and non-self components, leading to the generation of innate immune defense and inflammatory responses. The initiation, activation and resolution of innate inflammatory response are mediated by a complex network of interactions among the numerous cellular and molecular components of immune and non-immune system. While a controlled and beneficial innate inflammatory response is critical for the elimination of pathogens and maintenance of tissue homeostasis, dysregulated or sustained inflammation leads to pathological conditions such as chronic infection, inflammatory autoimmune diseases. In this review, we discuss some of the recent advances in our understanding of the cellular and molecular mechanisms for the establishment and regulation of innate immunity and inflammatory responses.
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Affiliation(s)
- Juan Liu
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Xuetao Cao
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
- National Key Laboratory of Medical Molecular Biology, Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
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92
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Danan-Gotthold M, Guyon C, Giraud M, Levanon EY, Abramson J. Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells. Genome Biol 2016; 17:219. [PMID: 27776542 PMCID: PMC5078920 DOI: 10.1186/s13059-016-1079-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/05/2016] [Indexed: 01/28/2023] Open
Abstract
Background In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. This educational program is, to a large extent, mediated by medullary thymic epithelial cells that have a unique capacity to express, and subsequently present, a large fraction of body antigens. While the scope of promiscuously expressed genes by medullary thymic epithelial cells is well-established, relatively little is known about the expression of variants that are generated by co-transcriptional and post-transcriptional processes. Results Our study reveals that in comparison to other cell types, medullary thymic epithelial cells display significantly higher levels of alternative splicing, as well as A-to-I and C-to-U RNA editing, which thereby further expand the diversity of their self-antigen repertoire. Interestingly, Aire, the key mediator of promiscuous gene expression in these cells, plays a limited role in the regulation of these transcriptional processes. Conclusions Our results highlight RNA processing as another layer by which the immune system assures a comprehensive self-representation in the thymus which is required for the establishment of self-tolerance and prevention of autoimmunity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1079-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Clotilde Guyon
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Matthieu Giraud
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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93
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Ke R, Mignardi M, Hauling T, Nilsson M. Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences. Hum Mutat 2016; 37:1363-1367. [PMID: 27406789 PMCID: PMC5111608 DOI: 10.1002/humu.23051] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/08/2016] [Accepted: 07/07/2016] [Indexed: 01/02/2023]
Abstract
In this review, we discuss the emergence of the fourth‐generation sequencing technologies that preserve the spatial coordinates of RNA and DNA sequences with up to subcellular resolution, thus enabling back mapping of sequencing reads to the original histological context. This information is used, for example, in two current large‐scale projects that aim to unravel the function of the brain. Also in cancer research, fourth‐generation sequencing has the potential to revolutionize the field. Cancer Research UK has named “Mapping the molecular and cellular tumor microenvironment in order to define new targets for therapy and prognosis” one of the grand challenges in tumor biology. We discuss the advantages of sequencing nucleic acids directly in fixed cells over traditional next‐generation sequencing (NGS) methods, the limitations and challenges that these new methods have to face to become broadly applicable, and the impact that the information generated by the combination of in situ sequencing and NGS methods will have in research and diagnostics.
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Affiliation(s)
- Rongqin Ke
- School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian, 362021, China
| | - Marco Mignardi
- Department of Information Technology, Centre for Image Analysis, Science for Life Laboratory, Uppsala University, Uppsala, SE-75105, Sweden.,Department of Bioengineering, Stanford University, Stanford, California, 75105
| | - Thomas Hauling
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
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94
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Abramson J, Husebye ES. Autoimmune regulator and self-tolerance - molecular and clinical aspects. Immunol Rev 2016; 271:127-40. [PMID: 27088911 DOI: 10.1111/imr.12419] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The establishment of central tolerance in the thymus is critical for avoiding deleterious autoimmune diseases. Autoimmune regulator (AIRE), the causative gene in autoimmune polyendocrine syndrome type-1 (APS-1), is crucial for the establishment of self-tolerance in the thymus by promoting promiscuous expression of a wide array of tissue-restricted self-antigens. This step is critical for elimination of high-affinity self-reactive T cells from the immunological repertoire, and for the induction of a specific subset of Foxp3(+) T-regulatory (Treg ) cells. In this review, we discuss the most recent advances in our understanding of how AIRE operates on molecular and cellular levels, as well as of how its loss of function results in breakdown of self-tolerance mechanisms characterized by a broad and heterogeneous repertoire of autoimmune phenotypes.
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Affiliation(s)
- Jakub Abramson
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Eystein S Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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95
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Perry JSA, Hsieh CS. Development of T-cell tolerance utilizes both cell-autonomous and cooperative presentation of self-antigen. Immunol Rev 2016; 271:141-55. [PMID: 27088912 PMCID: PMC4837647 DOI: 10.1111/imr.12403] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of T-cell self-tolerance in the thymus is important for establishing immune homeostasis and preventing autoimmunity. Here, we review the components of T-cell tolerance, which includes T-cell receptor (TCR) self-reactivity, costimulation, cytokines, and antigen presentation by a variety of antigen-presenting cells (APCs) subsets. We discuss the current evidence on the process of regulatory T (Treg) cell and negative selection and the importance of TCR signaling. We then examine recent evidence showing unique roles for bone marrow (BM)-derived APCs and medullary thymic epithelial cells (mTECs) on the conventional and Treg TCR repertoire, as well as emerging data on the role of B cells in tolerance. Finally, we review the accumulating data that suggest that cooperative antigen presentation is a prominent component of T -ell tolerance. With the development of tools to interrogate the function of individual APC subsets in the medulla, we have gained greater understanding of the complex cellular and molecular events that determine T-cell tolerance.
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Affiliation(s)
- Justin S A Perry
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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96
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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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97
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Mathis D, Benoist C. Promiscuity Promotes Tolerance. THE JOURNAL OF IMMUNOLOGY 2016; 196:2913-4. [PMID: 26994302 DOI: 10.4049/jimmunol.1600225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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98
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Alves NL, Ribeiro AR. Thymus medulla under construction: Time and space oddities. Eur J Immunol 2016; 46:829-33. [PMID: 26947141 DOI: 10.1002/eji.201646329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 02/14/2016] [Accepted: 03/01/2016] [Indexed: 12/31/2022]
Abstract
The development of effective T-cell-based immunotherapies to treat infection, cancer, and autoimmunity should incorporate the ground rules that control differentiation of T cells in the thymus. Within the thymus, thymic epithelial cells (TECs) provide microenvironments supportive of the generation and selection of T cells that are responsive to pathogen-derived antigens, and yet tolerant to self-determinants. Defects in TEC differentiation cause syndromes that range from immunodeficiency to autoimmunity, which makes the study of TECs of fundamental and clinical importance to comprehend how immunity and tolerance are balanced. Critical to tolerance induction are medullary thymic epithelial cells (mTECs), which purge autoreactive T cells, or redirect them to a regulatory T-cell lineage. In this issue of the European Journal of Immunology, studies by Baik et al. and Mayer et al. [Eur. J. Immunol. 2016. 46: XXXX-XXXX and 46: XXXX-XXXX]) document novel spatial-temporal singularities in the lineage specification and maintenance of mTECs. While Baik et al. define a developmental checkpoint during mTEC specification in the embryo, Mayer et al. reveal that the generation and maintenance of the adult mTEC compartment is temporally controlled in vivo. The two reports described new developmentally related, but temporally distinct principles that underlie the homeostasis of the thymic medulla across life.
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Affiliation(s)
- Nuno L Alves
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porot, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
| | - Ana R Ribeiro
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porot, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
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99
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Abstract
The excitement surrounding checkpoint inhibitors in the treatment of patients with cancer exemplifies a triumph of the long-term value of investing in basic science and fundamental questions of T-cell signaling. The pharmaceutical future actively embraces ways of making more patients’ cancers responsive to these inhibitors. Such a process will be aided by elucidation of signaling and regulation. With thousands of articles spread across almost 30 years, this commentary can touch only on portions of the canonical picture of T-cell signaling and provide a few parables from work on mammalian (or mechanistic) target of rapamycin (mTOR) pathways as they link to early and later phases of lymphocyte activation. The piece will turn a critical eye to some issues with models about these pathways in T cells. Many of the best insights lie in the future despite all that is uncovered already, but a contention is that further therapeutic successes will be fostered by dealing with disparities among findings and attention to the temporal, spatial, and stochastic aspects of T-cell responses. Finally, thoughts on some (though not all) items urgently needed for future progress will be mooted.
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Affiliation(s)
- Mark Boothby
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
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100
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Evolutionary conserved gene co-expression drives generation of self-antigen diversity in medullary thymic epithelial cells. J Autoimmun 2016; 67:65-75. [DOI: 10.1016/j.jaut.2015.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/23/2015] [Accepted: 10/05/2015] [Indexed: 01/01/2023]
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