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Chiu H, Weinstein KN, Spath S, Hu A, Varela S, Obata-Ninomiya K, Ziegler SF. SKI Regulates Medullary Thymic Epithelial Cell Differentiation to Control Peripheral T Cell Responses in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:52-62. [PMID: 38767415 PMCID: PMC11182718 DOI: 10.4049/jimmunol.2300262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
The thymus is an important site for the establishment of an appropriate immune response through positive and negative selection of developing T cells. During selection, developing T cells interact with cortical and medullary thymic epithelial cells (TECs), termed cTECs and mTECs, respectively. Using a Foxn1Cre+/-SKIfl/fl mouse model, we found that TEC-specific deletion of SKI reduced the mTEC compartment in the thymus and that tissue-restricted Ag expression in mTECs was altered. This decrease in the medullary area led to a decrease in CD4 thymocyte cellularity; however, mature CD4 cellularity in the spleen remained normal. Interestingly, naive CD4 T cells purified from SKI-deleted mice showed a defect in proliferation in vitro after global TCR stimulation, and these mice were significantly protected from developing experimental autoimmune encephalomyelitis compared with the control mice. Overall, our findings suggest that SKI signaling in the thymus regulates mTEC differentiation and function as well as downstream peripheral T cell responses and provide evidence for targeting SKI in T cell-driven autoimmune diseases such as multiple sclerosis.
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2
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Liu T, Xia S. The Proteostasis of Thymic Stromal Cells in Health and Diseases. Protein J 2024; 43:447-463. [PMID: 38622349 DOI: 10.1007/s10930-024-10197-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2024] [Indexed: 04/17/2024]
Abstract
The thymus is the key immune organ for the development of T cells. Different populations of thymic stromal cells interact with T cells, thereby controlling the dynamic development of T cells through their differentiation and function. Proteostasis represents a balance between protein expression, folding, and modification and protein clearance, and its fluctuation usually depends at least partially on related protein regulatory systems for further survival and effects. However, in terms of the substantial requirement for self-antigens and their processing burden, increasing evidence highlights that protein regulation contributes to the physiological effects of thymic stromal cells. Impaired proteostasis may expedite the progression of thymic involution and dysfunction, accompanied by the development of autoimmune diseases or thymoma. Hence, in this review, we summarize the regulation of proteostasis within different types of thymic stromal cells under physiological and pathological conditions to identify potential targets for thymic regeneration and immunotherapy.
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Affiliation(s)
- Ting Liu
- Department of Immunology, School of Medicine, Jiangsu University, 301, Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Sheng Xia
- Department of Immunology, School of Medicine, Jiangsu University, 301, Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
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3
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Shirafkan F, Hensel L, Rattay K. Immune tolerance and the prevention of autoimmune diseases essentially depend on thymic tissue homeostasis. Front Immunol 2024; 15:1339714. [PMID: 38571951 PMCID: PMC10987875 DOI: 10.3389/fimmu.2024.1339714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
The intricate balance of immune reactions towards invading pathogens and immune tolerance towards self is pivotal in preventing autoimmune diseases, with the thymus playing a central role in establishing and maintaining this equilibrium. The induction of central immune tolerance in the thymus involves the elimination of self-reactive T cells, a mechanism essential for averting autoimmunity. Disruption of the thymic T cell selection mechanisms can lead to the development of autoimmune diseases. In the dynamic microenvironment of the thymus, T cell migration and interactions with thymic stromal cells are critical for the selection processes that ensure self-tolerance. Thymic epithelial cells are particularly significant in this context, presenting self-antigens and inducing the negative selection of autoreactive T cells. Further, the synergistic roles of thymic fibroblasts, B cells, and dendritic cells in antigen presentation, selection and the development of regulatory T cells are pivotal in maintaining immune responses tightly regulated. This review article collates these insights, offering a comprehensive examination of the multifaceted role of thymic tissue homeostasis in the establishment of immune tolerance and its implications in the prevention of autoimmune diseases. Additionally, the developmental pathways of the thymus are explored, highlighting how genetic aberrations can disrupt thymic architecture and function, leading to autoimmune conditions. The impact of infections on immune tolerance is another critical area, with pathogens potentially triggering autoimmunity by altering thymic homeostasis. Overall, this review underscores the integral role of thymic tissue homeostasis in the prevention of autoimmune diseases, discussing insights into potential therapeutic strategies and examining putative avenues for future research on developing thymic-based therapies in treating and preventing autoimmune conditions.
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4
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Lammers S, Barrera V, Brennecke P, Miller C, Yoon J, Balolong J, Anderson MS, Ho Sui S, Steinmetz LM, von Andrian UH, Rattay K. Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development. Front Immunol 2024; 14:1277365. [PMID: 38420512 PMCID: PMC10901246 DOI: 10.3389/fimmu.2023.1277365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 03/02/2024] Open
Abstract
Thymic epithelial cells are indispensable for T cell maturation and selection and the induction of central immune tolerance. The self-peptide repertoire expressed by medullary thymic epithelial cells is in part regulated by the transcriptional regulator Aire (Autoimmune regulator) and the transcription factor Fezf2. Due to the high complexity of mTEC maturation stages (i.e., post-Aire, Krt10+ mTECs, and Dclk1+ Tuft mTECs) and the heterogeneity in their gene expression profiles (i.e., mosaic expression patterns), it has been challenging to identify the additional factors complementing the transcriptional regulation. We aimed to identify the transcriptional regulators involved in the regulation of mTEC development and self-peptide expression in an unbiased and genome-wide manner. We used ATAC footprinting analysis as an indirect approach to identify transcription factors involved in the gene expression regulation in mTECs, which we validated by ChIP sequencing. This study identifies Fezf2 as a regulator of the recently described thymic Tuft cells (i.e., Tuft mTECs). Furthermore, we identify that transcriptional regulators of the ELF, ESE, ERF, and PEA3 subfamily of the ETS transcription factor family and members of the Krüppel-like family of transcription factors play a role in the transcriptional regulation of genes involved in late mTEC development and promiscuous gene expression.
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Affiliation(s)
- Sören Lammers
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Victor Barrera
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Philip Brennecke
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
| | - Corey Miller
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Joon Yoon
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Jared Balolong
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Shannan Ho Sui
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lars M. Steinmetz
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ulrich H. von Andrian
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Kristin Rattay
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- Pharmacological Institute, Biochemical Pharmacological Center, University of Marburg, Marburg, Germany
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5
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Borelli A, Zamit C, Irla M. Medullary Thymic Epithelial Cell Antigen-presentation Assays. Bio Protoc 2023; 13:e4865. [PMID: 37969750 PMCID: PMC10632154 DOI: 10.21769/bioprotoc.4865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 11/17/2023] Open
Abstract
Medullary thymic epithelial cells (mTEC) are bona fide antigen-presenting cells that play a crucial role in the induction of T-cell tolerance. By their unique ability to express a broad range of tissue-restricted self-antigens, mTEC control the clonal deletion (also known as negative selection) of potentially hazardous autoreactive T cells and the generation of Foxp3+ regulatory T cells. Here, we describe a protocol to assess major histocompatibility complex (MHC) class II antigen-presentation capacity of mTEC to CD4+ T cells. We detail the different steps of thymus enzymatic digestion, immunostaining, cell sorting of mTEC and CD4+ T cells, peptide-loading of mTEC, and the co-culture between these two cell types. Finally, we describe the flow cytometry protocol and the subsequent analysis to assess the activation of CD4+ T cells. This rapid co-culture assay enables the evaluation of the ability of mTEC to present antigens to CD4+ T cells in an antigen-specific context. Key features • This protocol builds upon the method used by Lopes et al. (2018 and 2022) and Charaix et al. (2022). • This protocol requires transgenic mice, such as OTIIxRag2-/- mice and the cognate peptide OVA323-339, to assess mTEC antigen presentation to CD4+ T cells. • This requires specific equipment such as a Miltenyi Biotec AutoMACS® Pro Separator, a BD FACSAriaTM III cell sorter, and a BD® LSR II flow cytometer.
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Affiliation(s)
- Alexia Borelli
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Cloé Zamit
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Magali Irla
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
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6
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Yayon N, Kedlian VR, Boehme L, Suo C, Wachter B, Beuschel RT, Amsalem O, Polanski K, Koplev S, Tuck E, Dann E, Van Hulle J, Perera S, Putteman T, Predeus AV, Dabrowska M, Richardson L, Tudor C, Kreins AY, Engelbert J, Stephenson E, Kleshchevnikov V, De Rita F, Crossland D, Bosticardo M, Pala F, Prigmore E, Chipampe NJ, Prete M, Fei L, To K, Barker RA, He X, Van Nieuwerburgh F, Bayraktar O, Patel M, Davies GE, Haniffa MA, Uhlmann V, Notarangelo LD, Germain RN, Radtke AJ, Marioni JC, Taghon T, Teichmann SA. A spatial human thymus cell atlas mapped to a continuous tissue axis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.562925. [PMID: 37986877 PMCID: PMC10659407 DOI: 10.1101/2023.10.25.562925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassall's Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.
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Affiliation(s)
- Nadav Yayon
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | | | - Lena Boehme
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | - Chenqu Suo
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Brianna Wachter
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Rebecca T Beuschel
- National Institute of Allergy and Infectious Diseases, NIH, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Bethesda, MD, United States
| | - Oren Amsalem
- Beth Israel Deaconess Medical Center, Harvard Medical School, Division of Endocrinology, Diabetes and Metabolism, Boston, MA, United States
| | | | - Simon Koplev
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Emma Dann
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Jolien Van Hulle
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | - Shani Perera
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Tom Putteman
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
| | | | - Monika Dabrowska
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Laura Richardson
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Catherine Tudor
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Alexandra Y Kreins
- Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Immunology and Gene Therapy, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, Infection, Immunity and Inflammation Research & Teaching Department, London, United Kingdom
| | - Justin Engelbert
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Emily Stephenson
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | | | - Fabrizio De Rita
- Freeman Hospital, Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Newcastle upon Tyne, United Kingdom
| | - David Crossland
- Freeman Hospital, Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Newcastle upon Tyne, United Kingdom
| | - Marita Bosticardo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Francesca Pala
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Elena Prigmore
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | | | - Martin Prete
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Lijiang Fei
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Ken To
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Roger A Barker
- University of Cambridge, John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Xiaoling He
- University of Cambridge, John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Filip Van Nieuwerburgh
- Ghent University, Laboratory of Pharmaceutical Biotechnology, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Omer Bayraktar
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Minal Patel
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
| | - Graham E Davies
- Great Ormond Street Hospital for Children NHS Foundation Trust, Department of Immunology and Gene Therapy, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, Infection, Immunity and Inflammation Research & Teaching Department, London, United Kingdom
| | - Muzlifah A Haniffa
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, United Kingdom
| | - Virginie Uhlmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, Bethesda, MD, United States
| | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, NIH, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Bethesda, MD, United States
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, NIH, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Bethesda, MD, United States
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- University of Cambridge, Cancer Research UK, Cambridge, United Kingdom
| | - Tom Taghon
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cellular Genetics, Cambridge, United Kingdom
- University of Cambridge, Cavendish Laboratory, Cambridge, United Kingdom
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7
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Givony T, Leshkowitz D, Del Castillo D, Nevo S, Kadouri N, Dassa B, Gruper Y, Khalaila R, Ben-Nun O, Gome T, Dobeš J, Ben-Dor S, Kedmi M, Keren-Shaul H, Heffner-Krausz R, Porat Z, Golani O, Addadi Y, Brenner O, Lo DD, Goldfarb Y, Abramson J. Thymic mimetic cells function beyond self-tolerance. Nature 2023; 622:164-172. [PMID: 37674082 DOI: 10.1038/s41586-023-06512-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Development of immunocompetent T cells in the thymus is required for effective defence against all types of pathogens, including viruses, bacteria and fungi. To this end, T cells undergo a very strict educational program in the thymus, during which both non-functional and self-reactive T cell clones are eliminated by means of positive and negative selection1.Thymic epithelial cells (TECs) have an indispensable role in these processes, and previous studies have shown the notable heterogeneity of these cells2-7. Here, using multiomic analysis, we provide further insights into the functional and developmental diversity of TECs in mice, and reveal a detailed atlas of the TEC compartment according to cell transcriptional states and chromatin landscapes. Our analysis highlights unconventional TEC subsets that are similar to functionally well-defined parenchymal populations, including endocrine cells, microfold cells and myocytes. By focusing on the endocrine and microfold TEC populations, we show that endocrine TECs require Insm1 for their development and are crucial to maintaining thymus cellularity in a ghrelin-dependent manner; by contrast, microfold TECs require Spib for their development and are essential for the generation of thymic IgA+ plasma cells. Collectively, our study reveals that medullary TECs have the potential to differentiate into various types of molecularly distinct and functionally defined cells, which not only contribute to the induction of central tolerance, but also regulate the homeostasis of other thymus-resident populations.
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Affiliation(s)
- Tal Givony
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Del Castillo
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Shir Nevo
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kadouri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Gruper
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osher Ben-Nun
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Gome
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jan Dobeš
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shifra Ben-Dor
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | | | - Ziv Porat
- Flow Cytometry Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - David D Lo
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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8
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Chiu H, Linsley PS, Ziegler SF. Investigating Thymic Epithelial Cell Diversity Using Systems Biology. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:888-894. [PMID: 36947816 PMCID: PMC10037528 DOI: 10.4049/jimmunol.2200610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/12/2022] [Indexed: 03/24/2023]
Abstract
The thymus is an intricate organ consisting of a diverse population of thymic epithelial cells (TECs). Cortical and medullary TECs and their subpopulations have distinct roles in coordinating the development and selection of functionally competent and self-tolerant T cells. Recent advances made in technologies such as single-cell RNA sequencing have made it possible to investigate and resolve the heterogeneity in TECs. These findings have provided further understanding of the molecular mechanisms regulating TEC function and expression of tissue-restricted Ags. In this brief review, we focus on the newly characterized subsets of TECs and their diversity in relation to their functions in supporting T cell development. We also discuss recent discoveries in expression of self-antigens in the context of TEC development as well as the cellular and molecular changes occurring during embryonic development to thymic involution.
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9
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Matsumoto M, Yoshida H, Tsuneyama K, Oya T, Matsumoto M. Revisiting Aire and tissue-restricted antigens at single-cell resolution. Front Immunol 2023; 14:1176450. [PMID: 37207224 PMCID: PMC10191227 DOI: 10.3389/fimmu.2023.1176450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
The thymus is a highly specialized organ that plays an indispensable role in the establishment of self-tolerance, a process characterized by the "education" of developing T-cells. To provide competent T-cells tolerant to self-antigens, medullary thymic epithelial cells (mTECs) orchestrate negative selection by ectopically expressing a wide range of genes, including various tissue-restricted antigens (TRAs). Notably, recent advancements in the high-throughput single-cell analysis have revealed remarkable heterogeneity in mTECs, giving us important clues for dissecting the mechanisms underlying TRA expression. We overview how recent single-cell studies have furthered our understanding of mTECs, with a focus on the role of Aire in inducing mTEC heterogeneity to encompass TRAs.
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Affiliation(s)
- Minoru Matsumoto
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- *Correspondence: Minoru Matsumoto,
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
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10
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Gao H, Cao M, Deng K, Yang Y, Song J, Ni M, Xie C, Fan W, Ou C, Huang D, Lin L, Liu L, Li Y, Sun H, Cheng X, Wu J, Xia C, Deng X, Mou L, Chen P. The Lineage Differentiation and Dynamic Heterogeneity of Thymic Epithelial Cells During Thymus Organogenesis. Front Immunol 2022; 13:805451. [PMID: 35273595 PMCID: PMC8901506 DOI: 10.3389/fimmu.2022.805451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/24/2022] [Indexed: 12/19/2022] Open
Abstract
Although much progress has been made recently in revealing the heterogeneity of the thymic stromal components, the molecular programs of cell lineage divergency and temporal dynamics of thymic epithelial cell (TEC) development are largely elusive. Here, we constructed a single-cell transcriptional landscape of non-hematopoietic cells from mouse thymus spanning embryonic to adult stages, producing transcriptomes of 30,959 TECs. We resolved the transcriptional heterogeneity of developing TECs and highlighted the molecular nature of early TEC lineage determination and cortico-medullary thymic epithelial cell lineage divergency. We further characterized the differentiation dynamics of TECs by clarification of molecularly distinct cell states in the thymus developing trajectory. We also identified a population of Bpifa1+ Plet1+ mTECs that was preserved during thymus organogenesis and highly expressed tissue-resident adult stem cell markers. Finally, we highlighted the expression of Aire-dependent tissue-restricted antigens mainly in Aire+ Csn2+ mTECs and Spink5+ Dmkn+ mTECs in postnatal thymus. Overall, our data provided a comprehensive characterization of cell lineage differentiation, maturation, and temporal dynamics of thymic epithelial cells during thymus organogenesis.
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Affiliation(s)
- Hanchao Gao
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Mengtao Cao
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Kai Deng
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Yang Yang
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Jinqi Song
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Ming Ni
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Chuntao Xie
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Wenna Fan
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Chunpei Ou
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Dinggen Huang
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Lizhong Lin
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Lixia Liu
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Yangyang Li
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Huimin Sun
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Xinyu Cheng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Jinmei Wu
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Cuilan Xia
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Xuefeng Deng
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, Shenzhen University Health Science Center, Shenzhen University School of Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Pengfei Chen
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China.,Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
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11
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Nishijima H, Matsumoto M, Morimoto J, Hosomichi K, Akiyama N, Akiyama T, Oya T, Tsuneyama K, Yoshida H, Matsumoto M. Aire Controls Heterogeneity of Medullary Thymic Epithelial Cells for the Expression of Self-Antigens. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:303-320. [PMID: 34930780 DOI: 10.4049/jimmunol.2100692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
The deficiency of Aire, a transcriptional regulator whose defect results in the development of autoimmunity, is associated with reduced expression of tissue-restricted self-Ags (TRAs) in medullary thymic epithelial cells (mTECs). Although the mechanisms underlying Aire-dependent expression of TRAs need to be explored, the physical identification of the target(s) of Aire has been hampered by the low and promiscuous expression of TRAs. We have tackled this issue by engineering mice with augmented Aire expression. Integration of the transcriptomic data from Aire-augmented and Aire-deficient mTECs revealed that a large proportion of so-called Aire-dependent genes, including those of TRAs, may not be direct transcriptional targets downstream of Aire. Rather, Aire induces TRA expression indirectly through controlling the heterogeneity of mTECs, as revealed by single-cell analyses. In contrast, Ccl25 emerged as a canonical target of Aire, and we verified this both in vitro and in vivo. Our approach has illuminated the Aire's primary targets while distinguishing them from the secondary targets.
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Affiliation(s)
- Hitoshi Nishijima
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Minoru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Junko Morimoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Nobuko Akiyama
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; and
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan;
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12
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Wakitani S, Kawabata R, Yasuda M. Insufficiency of CD205-positive cortical thymic epithelial cells in immature Japanese Black cattle with severe thymic abnormalities and poor prognosis. Vet Immunol Immunopathol 2022; 245:110379. [PMID: 35038635 DOI: 10.1016/j.vetimm.2021.110379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 11/19/2022]
Abstract
To investigate the involvement of thymic function in the development of diseases with poor prognosis in calves, this study conducted a survey for the assessment of thymus cell composition in immature Japanese Black cattle with poor prognosis. Histopathological evaluation of 47 cattle showed signs of acute thymic involution in most cases. Less than half of the cases had a cortex predominant over the medulla in the thymic parenchyma, and a quarter of the cases indicated severe histological condition with an unclear boundary between the cortex and medulla. Correlation analysis revealed a close relationship between the corresponding stages of acute involution, cortical occupancy, and the expression of CD4, CD8B, and CD205. When cases were grouped by cortical occupancy, the expression of CD4 and CD8B expression was lower in the severe group with less than 25 % cortical occupancy, and the expression of CD205 was lower in the group with an unclear cortical-medullary boundary. Meanwhile, there was no difference in the expressions of IL7, CD80, FEZF2, and FOXN1 according to cortical occupancy. Immunohistochemistry has shown that cytokeratin-positive thymic epithelial cells are more densely populated in the severe thymus. UEA-I-binding medullary thymic epithelial cells were also present, but CD205-positive cortical thymic epithelial cells were rare in severe thymus. Moreover, there were significantly fewer Ki-67-positive cells in cattle with severe thymus. Therefore, these results indicate that thymic histological abnormalities frequently occur in immature cattle with a poor prognosis, and the presence of CD205-positive cortical thymic epithelial cells is associated with the severity of the abnormalities.
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Affiliation(s)
- Shoichi Wakitani
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
| | - Risako Kawabata
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Masahiro Yasuda
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
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13
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Dong M, Chang J, Lebel MÈ, Gervais N, Fournier M, Mallet Gauthier È, Suh WK, Melichar HJ. The ICOS-ICOSL pathway tunes thymic selection. Immunol Cell Biol 2021; 100:205-217. [PMID: 34962663 PMCID: PMC9304562 DOI: 10.1111/imcb.12520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/11/2021] [Accepted: 12/27/2021] [Indexed: 11/30/2022]
Abstract
Negative selection of developing T cells plays a significant role in T cell tolerance to self-antigen. This process relies on thymic antigen presenting cells which express both self-antigens as well as co-signaling molecules. Inducible T cell costimulator (ICOS) belongs to the CD28 family of co-signaling molecules and binds to ICOS ligand (ICOSL). The ICOS signaling pathway plays important roles in shaping the immune response to infections, but its role in central tolerance is less well understood. Here we show that ICOSL is expressed by subsets of thymic dendritic cells and medullary thymic epithelial cells as well as thymic B cells. ICOS expression is upregulated as T cells mature in the thymus and correlates with T cell receptor signal strength during thymic selection. We also provide evidence of a role for ICOS signaling in mediating negative selection. Our findings suggest that ICOS may fine-tune T cell receptor signals during thymic selection contributing to the generation of a tolerant T cell population.
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Affiliation(s)
- Mengqi Dong
- Département de microbiologie, Université de Montréal, infectiologie et immunologie, Montréal, Québec, H3T 1J4, Canada.,Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, H1T 2M4, Canada
| | - Jinsam Chang
- Institut de recherches cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Programme de biologie moléculaire, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
| | - Marie-Ève Lebel
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, H1T 2M4, Canada
| | - Noémie Gervais
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, H1T 2M4, Canada
| | - Marilaine Fournier
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, H1T 2M4, Canada
| | - Ève Mallet Gauthier
- Département de microbiologie, Université de Montréal, infectiologie et immunologie, Montréal, Québec, H3T 1J4, Canada.,Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, H1T 2M4, Canada
| | - Woong-Kyung Suh
- Département de microbiologie, Université de Montréal, infectiologie et immunologie, Montréal, Québec, H3T 1J4, Canada.,Institut de recherches cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Programme de biologie moléculaire, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, Québec, H1T 2M4, Canada.,Département de médecine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
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14
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Barthlott T, Handel AE, Teh HY, Wirasinha RC, Hafen K, Žuklys S, Roch B, Orkin SH, de Villartay JP, Daley SR, Holländer GA. Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2. Nat Commun 2021; 12:3933. [PMID: 34168132 PMCID: PMC8225857 DOI: 10.1038/s41467-021-24158-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Thymic T cell development and T cell receptor repertoire selection are dependent on essential molecular cues provided by thymic epithelial cells (TEC). TEC development and function are regulated by their epigenetic landscape, in which the repressive H3K27me3 epigenetic marks are catalyzed by polycomb repressive complex 2 (PRC2). Here we show that a TEC-targeted deficiency of PRC2 function results in a hypoplastic thymus with reduced ability to express antigens and select a normal repertoire of T cells. The absence of PRC2 activity reveals a transcriptomically distinct medullary TEC lineage that incompletely off-sets the shortage of canonically-derived medullary TEC whereas cortical TEC numbers remain unchanged. This alternative TEC development is associated with the generation of reduced TCR diversity. Hence, normal PRC2 activity and placement of H3K27me3 marks are required for TEC lineage differentiation and function and, in their absence, the thymus is unable to compensate for the loss of a normal TEC scaffold.
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Affiliation(s)
- Thomas Barthlott
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Adam E Handel
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Hong Ying Teh
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Katrin Hafen
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Saulius Žuklys
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Benoit Roch
- Genome Dynamics in the Immune System Laboratory, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Jean-Pierre de Villartay
- Genome Dynamics in the Immune System Laboratory, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Georg A Holländer
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland.
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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15
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Tao H, Li L, Liao NS, Schluns KS, Luckhart S, Sleasman JW, Zhong XP. Thymic Epithelial Cell-Derived IL-15 and IL-15 Receptor α Chain Foster Local Environment for Type 1 Innate Like T Cell Development. Front Immunol 2021; 12:623280. [PMID: 33732245 PMCID: PMC7957058 DOI: 10.3389/fimmu.2021.623280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
Expression of tissue-restricted antigens (TRAs) in thymic epithelial cells (TECs) ensures negative selection of highly self-reactive T cells to establish central tolerance. Whether some of these TRAs could exert their canonical biological functions to shape thymic environment to regulate T cell development is unclear. Analyses of publicly available databases have revealed expression of transcripts at various levels of many cytokines and cytokine receptors such as IL-15, IL-15Rα, IL-13, and IL-23a in both human and mouse TECs. Ablation of either IL-15 or IL-15Rα in TECs selectively impairs type 1 innate like T cell, such as iNKT1 and γδT1 cell, development in the thymus, indicating that TECs not only serve as an important source of IL-15 but also trans-present IL-15 to ensure type 1 innate like T cell development. Because type 1 innate like T cells are proinflammatory, our data suggest the possibility that TEC may intrinsically control thymic inflammatory innate like T cells to influence thymic environment.
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Affiliation(s)
- Huishan Tao
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States
| | - Lei Li
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States
| | - Nan-Shih Liao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kimberly S Schluns
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shirley Luckhart
- Department of Entomology, Plant Pathology and Nematology, Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - John W Sleasman
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States
| | - Xiao-Ping Zhong
- Department of Pediatrics-Allergy and Immunology, Duke University Medical Center, Durham, NC, United States.,Department of Immunology, Duke University Medical Center, Durham, NC, United States.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
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16
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Perniola R, Fierabracci A, Falorni A. Autoimmune Addison's Disease as Part of the Autoimmune Polyglandular Syndrome Type 1: Historical Overview and Current Evidence. Front Immunol 2021; 12:606860. [PMID: 33717087 PMCID: PMC7953157 DOI: 10.3389/fimmu.2021.606860] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
The autoimmune polyglandular syndrome type 1 (APS1) is caused by pathogenic variants of the autoimmune regulator (AIRE) gene, located in the chromosomal region 21q22.3. The related protein, AIRE, enhances thymic self-representation and immune self-tolerance by localization to chromatin and anchorage to multimolecular complexes involved in the initiation and post-initiation events of tissue-specific antigen-encoding gene transcription. Once synthesized, the self-antigens are presented to, and cause deletion of, the self-reactive thymocyte clones. The clinical diagnosis of APS1 is based on the classic triad idiopathic hypoparathyroidism (HPT)—chronic mucocutaneous candidiasis—autoimmune Addison's disease (AAD), though new criteria based on early non-endocrine manifestations have been proposed. HPT is in most cases the first endocrine component of the syndrome; however, APS1-associated AAD has received the most accurate biochemical, clinical, and immunological characterization. Here is a comprehensive review of the studies on APS1-associated AAD from initial case reports to the most recent scientific findings.
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Affiliation(s)
- Roberto Perniola
- Department of Pediatrics-Neonatal Intensive Care, V. Fazzi Hospital, ASL LE, Lecce, Italy
| | - Alessandra Fierabracci
- Infectivology and Clinical Trials Research Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alberto Falorni
- Section of Internal Medicine and Endocrinological and Metabolic Sciences, Department of Medicine, University of Perugia, Perugia, Italy
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17
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Ishikawa T, Akiyama N, Akiyama T. In Pursuit of Adult Progenitors of Thymic Epithelial Cells. Front Immunol 2021; 12:621824. [PMID: 33717123 PMCID: PMC7946825 DOI: 10.3389/fimmu.2021.621824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/08/2021] [Indexed: 12/25/2022] Open
Abstract
Peripheral T cells capable of discriminating between self and non-self antigens are major components of a robust adaptive immune system. The development of self-tolerant T cells is orchestrated by thymic epithelial cells (TECs), which are localized in the thymic cortex (cortical TECs, cTECs) and medulla (medullary TECs, mTECs). cTECs and mTECs are essential for differentiation, proliferation, and positive and negative selection of thymocytes. Recent advances in single-cell RNA-sequencing technology have revealed a previously unknown degree of TEC heterogeneity, but we still lack a clear picture of the identity of TEC progenitors in the adult thymus. In this review, we describe both earlier and recent findings that shed light on features of these elusive adult progenitors in the context of tissue homeostasis, as well as recovery from stress-induced thymic atrophy.
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Affiliation(s)
- Tatsuya Ishikawa
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Nobuko Akiyama
- Laboratory for Immunogenetics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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18
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Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nat Commun 2021; 12:1096. [PMID: 33597545 PMCID: PMC7889611 DOI: 10.1038/s41467-021-21346-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/22/2021] [Indexed: 01/02/2023] Open
Abstract
The thymus' key function in the immune system is to provide the necessary environment for the development of diverse and self-tolerant T lymphocytes. While recent evidence suggests that the thymic stroma is comprised of more functionally distinct subpopulations than previously appreciated, the extent of this cellular heterogeneity in the human thymus is not well understood. Here we use single-cell RNA sequencing to comprehensively profile the human thymic stroma across multiple stages of life. Mesenchyme, pericytes and endothelial cells are identified as potential key regulators of thymic epithelial cell differentiation and thymocyte migration. In-depth analyses of epithelial cells reveal the presence of ionocytes as a medullary population, while the expression of tissue-specific antigens is mapped to different subsets of epithelial cells. This work thus provides important insight on how the diversity of thymic cells is established, and how this heterogeneity contributes to the induction of immune tolerance in humans.
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Affiliation(s)
- Jhoanne L Bautista
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan T Cramer
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Corey N Miller
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Chavez
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David I Berrios
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren E Byrnes
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joe Germino
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vasilis Ntranos
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Julie B Sneddon
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, San Francisco, CA, USA
| | - Trevor D Burt
- Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Division of Neonatology and the Children's Health & Discovery Initiative, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - James M Gardner
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Chun J Ye
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Audrey V Parent
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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19
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Besnard M, Padonou F, Provin N, Giraud M, Guillonneau C. AIRE deficiency, from preclinical models to human APECED disease. Dis Model Mech 2021; 14:dmm046359. [PMID: 33729987 PMCID: PMC7875492 DOI: 10.1242/dmm.046359] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) is a rare life-threatening autoimmune disease that attacks multiple organs and has its onset in childhood. It is an inherited condition caused by a variety of mutations in the autoimmune regulator (AIRE) gene that encodes a protein whose function has been uncovered by the generation and study of Aire-KO mice. These provided invaluable insights into the link between AIRE expression in medullary thymic epithelial cells (mTECs), and the broad spectrum of self-antigens that these cells express and present to the developing thymocytes. However, these murine models poorly recapitulate all phenotypic aspects of human APECED. Unlike Aire-KO mice, the recently generated Aire-KO rat model presents visual features, organ lymphocytic infiltrations and production of autoantibodies that resemble those observed in APECED patients, making the rat model a main research asset. In addition, ex vivo models of AIRE-dependent self-antigen expression in primary mTECs have been successfully set up. Thymus organoids based on pluripotent stem cell-derived TECs from APECED patients are also emerging, and constitute a promising tool to engineer AIRE-corrected mTECs and restore the generation of regulatory T cells. Eventually, these new models will undoubtedly lead to main advances in the identification and assessment of specific and efficient new therapeutic strategies aiming to restore immunological tolerance in APECED patients.
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Affiliation(s)
- Marine Besnard
- Université de Nantes, Inserm, CNRS, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Francine Padonou
- Université de Nantes, Inserm, CNRS, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Nathan Provin
- Université de Nantes, Inserm, CNRS, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Matthieu Giraud
- Université de Nantes, Inserm, CNRS, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carole Guillonneau
- Université de Nantes, Inserm, CNRS, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
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20
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Campinoti S, Gjinovci A, Ragazzini R, Zanieri L, Ariza-McNaughton L, Catucci M, Boeing S, Park JE, Hutchinson JC, Muñoz-Ruiz M, Manti PG, Vozza G, Villa CE, Phylactopoulos DE, Maurer C, Testa G, Stauss HJ, Teichmann SA, Sebire NJ, Hayday AC, Bonnet D, Bonfanti P. Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds. Nat Commun 2020; 11:6372. [PMID: 33311516 PMCID: PMC7732825 DOI: 10.1038/s41467-020-20082-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/04/2020] [Indexed: 12/22/2022] Open
Abstract
The thymus is a primary lymphoid organ, essential for T cell maturation and selection. There has been long-standing interest in processes underpinning thymus generation and the potential to manipulate it clinically, because alterations of thymus development or function can result in severe immunodeficiency and autoimmunity. Here, we identify epithelial-mesenchymal hybrid cells, capable of long-term expansion in vitro, and able to reconstitute an anatomic phenocopy of the native thymus, when combined with thymic interstitial cells and a natural decellularised extracellular matrix (ECM) obtained by whole thymus perfusion. This anatomical human thymus reconstruction is functional, as judged by its capacity to support mature T cell development in vivo after transplantation into humanised immunodeficient mice. These findings establish a basis for dissecting the cellular and molecular crosstalk between stroma, ECM and thymocytes, and offer practical prospects for treating congenital and acquired immunological diseases.
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Affiliation(s)
- Sara Campinoti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Asllan Gjinovci
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Luca Zanieri
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Linda Ariza-McNaughton
- Haematopoietic Stem Cell laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Marco Catucci
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, DIBIT 20132, Milan, Italy
| | - Stefan Boeing
- Bioinformatics Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - John C Hutchinson
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 1EH, UK
| | - Miguel Muñoz-Ruiz
- Immunosurveillance laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Pierluigi G Manti
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Gianluca Vozza
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Carlo E Villa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Demetra-Ellie Phylactopoulos
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Constance Maurer
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Hans J Stauss
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Neil J Sebire
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 1EH, UK
| | - Adrian C Hayday
- Immunosurveillance laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Dominique Bonnet
- Haematopoietic Stem Cell laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK.
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK.
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21
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Wells KL, Miller CN, Gschwind AR, Wei W, Phipps JD, Anderson MS, Steinmetz LM. Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells. eLife 2020; 9:60188. [PMID: 33226342 PMCID: PMC7771965 DOI: 10.7554/elife.60188] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/21/2020] [Indexed: 12/14/2022] Open
Abstract
Medullary thymic epithelial cells (mTECs) play a critical role in central immune tolerance by mediating negative selection of autoreactive T cells through the collective expression of the peripheral self-antigen compartment, including tissue-specific antigens (TSAs). Recent work has shown that gene-expression patterns within the mTEC compartment are heterogenous and include multiple differentiated cell states. To further define mTEC development and medullary epithelial lineage relationships, we combined lineage tracing and recovery from transient in vivo mTEC ablation with single-cell RNA-sequencing in Mus musculus. The combination of bioinformatic and experimental approaches revealed a non-stem transit-amplifying population of cycling mTECs that preceded Aire expression. We propose a branching model of mTEC development wherein a heterogeneous pool of transit-amplifying cells gives rise to Aire- and Ccl21a-expressing mTEC subsets. We further use experimental techniques to show that within the Aire-expressing developmental branch, TSA expression peaked as Aire expression decreased, implying Aire expression must be established before TSA expression can occur. Collectively, these data provide a roadmap of mTEC development and demonstrate the power of combinatorial approaches leveraging both in vivo models and high-dimensional datasets. Specialized cells in the immune system known as T cells protect the body from infection by destroying disease-causing microbes, such as bacteria or viruses. T cells use proteins on their surface called receptors to stick to infectious microbes and remove them from the body. Some newly developed T-cells, however, contain receptors that recognize and bind to cells that belong in the body. If these faulty T cells are released, they can attack healthy tissues and cause an autoimmune disease. After a new T cell is developed, it gets carried to a gland in the chest known as the thymus. Cells in the thymus called mTECs screen T cells for receptors that may bind to the body’s tissues. mTECs do this by presenting T cells with proteins that are commonly found on the surface of healthy cells in the body. If a T cell recognizes any of these ‘tissue specific proteins’, it is destroyed or given a new role in the body. Some faulty T cells, however, still manage to evade detection. One way to uncover why this might happen is to investigate how mTECs develop. Previous work showed that mTECs transition through various stages before reaching their final form. However, the order in which these events occur remained unclear. To gain a better understanding of these developmental steps, Wells, Miller et al. extracted mTECs from the thymus of mice and analyzed the genetic make-up of individual cells. This uncovered a missing link in mTEC development: a new type of cell that is the immediate predecessor of the final mTEC. These ‘predecessor’ cells were actively growing, highlighting that mTECs can be constantly generated in the body. By probing the genes that generate tissue-specific proteins in mTECs, Wells, Miller et al. revealed that these proteins were only produced for short periods and in the late stages of mTEC development. These findings contribute to our understanding of how mTECs develop to screen T cells. Mapping these developmental stages will make it easier to identify when faulty T cells are able to evade mTECs. This will lead to earlier detection of autoimmune diseases which could result in better treatments.
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Affiliation(s)
- Kristen L Wells
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Corey N Miller
- Diabetes Center, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Andreas R Gschwind
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, United States
| | - Jonah D Phipps
- Diabetes Center, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Lars M Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, United States.,Stanford Genome Technology Center, Stanford University, Palo Alto, United States.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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22
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García-Ceca J, Montero-Herradón S, Zapata AG. Intrathymic Selection and Defects in the Thymic Epithelial Cell Development. Cells 2020; 9:cells9102226. [PMID: 33023072 PMCID: PMC7601110 DOI: 10.3390/cells9102226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Intimate interactions between thymic epithelial cells (TECs) and thymocytes (T) have been repeatedly reported as essential for performing intrathymic T-cell education. Nevertheless, it has been described that animals exhibiting defects in these interactions were capable of a proper positive and negative T-cell selection. In the current review, we first examined distinct types of TECs and their possible role in the immune surveillance. However, EphB-deficient thymi that exhibit profound thymic epithelial (TE) alterations do not exhibit important immunological defects. Eph and their ligands, the ephrins, are implicated in cell attachment/detachment and govern, therefore, TEC–T interactions. On this basis, we hypothesized that a few normal TE areas could be enough for a proper phenotypical and functional maturation of T lymphocytes. Then, we evaluated in vivo how many TECs would be necessary for supporting a normal T-cell differentiation, concluding that a significantly low number of TEC are still capable of supporting normal T lymphocyte maturation, whereas with fewer numbers, T-cell maturation is not possible.
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Affiliation(s)
- Javier García-Ceca
- Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (J.G.-C.); (S.M.-H.)
- Health Research Institute, Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Sara Montero-Herradón
- Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (J.G.-C.); (S.M.-H.)
- Health Research Institute, Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Agustín G. Zapata
- Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (J.G.-C.); (S.M.-H.)
- Health Research Institute, Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Correspondence: ; Tel.: +34-91-394-4979
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23
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O'Donovan B, Mandel-Brehm C, Vazquez SE, Liu J, Parent AV, Anderson MS, Kassimatis T, Zekeridou A, Hauser SL, Pittock SJ, Chow E, Wilson MR, DeRisi JL. High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display. Brain Commun 2020; 2:fcaa059. [PMID: 32954318 PMCID: PMC7425417 DOI: 10.1093/braincomms/fcaa059] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/08/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Paraneoplastic neurological disorders are immune-mediated diseases understood to manifest as part of a misdirected anti-tumor immune response. Paraneoplastic neurological disorder-associated autoantibodies can assist with diagnosis and enhance our understanding of tumor-associated immune processes. We designed a comprehensive library of 49-amino-acid overlapping peptides spanning the entire human proteome, including all splicing isoforms and computationally predicted coding regions. Using this library, we optimized a phage immunoprecipitation and sequencing protocol with multiple rounds of enrichment to create high-resolution epitope profiles in serum and cerebrospinal fluid (CSF) samples from patients suffering from two common paraneoplastic neurological disorders, the anti-Yo (n = 36 patients) and anti-Hu (n = 44 patients) syndromes. All (100%) anti-Yo patient samples yielded enrichment of peptides from the canonical anti-Yo (CDR2 and CDR2L) antigens, while 38% of anti-Hu patients enriched peptides deriving from the nELAVL (neuronal embryonic lethal abnormal vision like) family of proteins, the anti-Hu autoantigenic target. Among the anti-Hu patient samples that were positive for nELAVL, we noted a restricted region of immunoreactivity. To achieve single amino acid resolution, we designed a novel deep mutational scanning phage library encoding all possible single-point mutants targeting the reactive nELAVL region. This analysis revealed a distinct preference for the degenerate motif, RLDxLL, shared by ELAVL2, 3 and 4. Lastly, phage immunoprecipitation sequencing identified several known autoantigens in these same patient samples, including peptides deriving from the cancer-associated antigens ZIC and SOX families of transcription factors. Overall, this optimized phage immunoprecipitation sequencing library and protocol yielded the high-resolution epitope mapping of the autoantigens targeted in anti-Yo and anti-Hu encephalitis patients to date. The results presented here further demonstrate the utility and high-resolution capability of phage immunoprecipitation sequencing for both basic science and clinical applications and for better understanding the antigenic targets and triggers of paraneoplastic neurological disorders.
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Affiliation(s)
- Brian O'Donovan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94158, USA
| | - Audrey V Parent
- Department of Medicine, Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark S Anderson
- Department of Medicine, Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Travis Kassimatis
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anastasia Zekeridou
- Department of Neurology, Mayo Clinic, Rochester, MN 55902, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sean J Pittock
- Department of Neurology, Mayo Clinic, Rochester, MN 55902, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Eric Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,Chan Zuckerberg Biohub, University of California, San Francisco, San Francisco, CA 94158, USA
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24
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Alawam AS, Anderson G, Lucas B. Generation and Regeneration of Thymic Epithelial Cells. Front Immunol 2020; 11:858. [PMID: 32457758 PMCID: PMC7221188 DOI: 10.3389/fimmu.2020.00858] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/15/2020] [Indexed: 01/04/2023] Open
Abstract
The thymus is unique in its ability to support the maturation of phenotypically and functionally distinct T cell sub-lineages. Through its combined production of MHC-restricted conventional CD4+ and CD8+, and Foxp3+ regulatory T cells, as well as non-conventional CD1d-restricted iNKT cells and invariant γδT cells, the thymus represents an important orchestrator of immune system development and control. It is now clear that thymus function is largely determined by the availability of stromal microenvironments. These specialized areas emerge during thymus organogenesis and are maintained throughout life. They are formed from both epithelial and mesenchymal components, and collectively they support a stepwise program of thymocyte development. Of these stromal cells, cortical, and medullary thymic epithelial cells represent functional components of thymic microenvironments in both the cortex and medulla. Importantly, a key feature of thymus function is that levels of T cell production are not constant throughout life. Here, multiple physiological factors including aging, stress and pregnancy can have either short- or long-term detrimental impact on rates of thymus function. Here, we summarize our current understanding of the development and function of thymic epithelial cells, and relate this to strategies to protect and/or restore thymic epithelial cell function for therapeutic benefit.
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Affiliation(s)
- Abdullah S Alawam
- Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Graham Anderson
- Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Beth Lucas
- Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
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25
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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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26
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Single-Cell Expression Variability Implies Cell Function. Cells 2019; 9:cells9010014. [PMID: 31861624 PMCID: PMC7017299 DOI: 10.3390/cells9010014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022] Open
Abstract
As single-cell RNA sequencing (scRNA-seq) data becomes widely available, cell-to-cell variability in gene expression, or single-cell expression variability (scEV), has been increasingly appreciated. However, it remains unclear whether this variability is functionally important and, if so, what are its implications for multi-cellular organisms. Here, we analyzed multiple scRNA-seq data sets from lymphoblastoid cell lines (LCLs), lung airway epithelial cells (LAECs), and dermal fibroblasts (DFs) and, for each cell type, selected a group of homogenous cells with highly similar expression profiles. We estimated the scEV levels for genes after correcting the mean-variance dependency in that data and identified 465, 466, and 364 highly variable genes (HVGs) in LCLs, LAECs, and DFs, respectively. Functions of these HVGs were found to be enriched with those biological processes precisely relevant to the corresponding cell type’s function, from which the scRNA-seq data used to identify HVGs were generated—e.g., cytokine signaling pathways were enriched in HVGs identified in LCLs, collagen formation in LAECs, and keratinization in DFs. We repeated the same analysis with scRNA-seq data from induced pluripotent stem cells (iPSCs) and identified only 79 HVGs with no statistically significant enriched functions; the overall scEV in iPSCs was of negligible magnitude. Our results support the “variation is function” hypothesis, arguing that scEV is required for cell type-specific, higher-level system function. Thus, quantifying and characterizing scEV are of importance for our understating of normal and pathological cellular processes.
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27
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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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28
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Yue S, Zheng X, Zheng Y. Cell-type-specific role of lamin-B1 in thymus development and its inflammation-driven reduction in thymus aging. Aging Cell 2019; 18:e12952. [PMID: 30968547 PMCID: PMC6612680 DOI: 10.1111/acel.12952] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 02/21/2019] [Accepted: 03/01/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular architectural proteins often participate in organ development and maintenance. Although functional decay of some of these proteins during aging is known, the cell-type-specific developmental role and the cause and consequence of their subsequent decay remain to be established especially in mammals. By studying lamins, the nuclear structural proteins, we demonstrate that lamin-B1 functions specifically in the thymic epithelial cells (TECs) for proper thymus organogenesis. An up-regulation of proinflammatory cytokines in the intra-thymic myeloid immune cells during aging accompanies a gradual reduction of lamin-B1 in adult TECs. We show that these cytokines can cause senescence and lamin-B1 reduction of the young adult TECs. Lamin-B1 supports the expression of TEC genes that can help maintain the adult TEC subtypes we identified by single-cell RNA-sequencing, thymic architecture, and function. Thus, structural proteins involved in organ building and maintenance can undergo inflammation-driven decay which can in turn contribute to age-associated organ degeneration.
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Affiliation(s)
- Sibiao Yue
- Department of EmbryologyCarnegie Institution for ScienceBaltimoreMaryland
- Department of BiologyJohns Hopkins UniversityBaltimoreMaryland
| | - Xiaobin Zheng
- Department of BiologyJohns Hopkins UniversityBaltimoreMaryland
| | - Yixian Zheng
- Department of EmbryologyCarnegie Institution for ScienceBaltimoreMaryland
- Department of BiologyJohns Hopkins UniversityBaltimoreMaryland
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29
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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: 110] [Impact Index Per Article: 18.3] [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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