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Nabel CS, Ackman JB, Hung YP, Louissaint A, Riely GJ. Single-Cell Sequencing Illuminates Thymic Development: An Updated Framework for Understanding Thymic Epithelial Tumors. Oncologist 2024; 29:473-483. [PMID: 38520743 PMCID: PMC11145005 DOI: 10.1093/oncolo/oyae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024] Open
Abstract
Thymic epithelial tumors (TETs) are rare tumors for which treatment options are limited. The ongoing need for improved systemic therapies reflects a limited understanding of tumor biology as well as the normal thymus. The essential role of the thymus in adaptive immunity is largely effected by its epithelial compartment, which directs thymocyte (T-cell) differentiation and immunologic self-tolerance. With aging, the thymus undergoes involution whereby epithelial tissue is replaced by adipose and other connective tissue, decreasing immature T-cell production. Against this natural drive toward involution, a fraction of thymuses will instead undergo oncologic transformation, leading to the formation of TETs, including thymoma and thymic carcinoma. The rarity of these tumors restricts investigation of the mechanisms of tumorigenesis and development of rational treatment options. To this end, the development of technologies which allow deep molecular profiling of individual tumor cells permits a new window through which to view normal thymic development and contrast the malignant changes that result in oncogenic transformation. In this review, we describe the findings of recent illuminating studies on the diversity of cell types within the epithelial compartment through thymic differentiation and aging. We contextualize these findings around important unanswered questions regarding the spectrum of known somatic tumor alterations, cell of origin, and tumor heterogeneity. The perspectives informed by single-cell molecular profiling offer new approaches to clinical and basic investigation of thymic epithelial tumors, with the potential to accelerate development of improved therapeutic strategies to address ongoing unmet needs in these rare tumors.
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Affiliation(s)
- Christopher S Nabel
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeanne B Ackman
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Yin P Hung
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Abner Louissaint
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Ribeiro C, Ferreirinha P, Landry JJM, Macedo F, Sousa LG, Pinto R, Benes V, Alves NL. Foxo3 regulates cortical and medullary thymic epithelial cell homeostasis with implications in T cell development. Cell Death Dis 2024; 15:352. [PMID: 38773063 PMCID: PMC11109193 DOI: 10.1038/s41419-024-06728-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Within the thymus, thymic epithelial cells (TECs) create dedicated microenvironments for T cell development and selection. Considering that TECs are sensitive to distinct pathophysiological conditions, uncovering the molecular elements that coordinate their thymopoietic role has important fundamental and clinical implications. Particularly, medullary thymic epithelial cells (mTECs) play a crucial role in central tolerance. Our previous studies, along with others, suggest that mTECs depend on molecular factors linked to genome-protecting pathways, but the precise mechanisms underlying their function remain unknown. These observations led us to examine the role of Foxo3, as it is expressed in TECs and involved in DNA damage response. Our findings show that mice with TEC-specific deletion of Foxo3 (Foxo3cKO) displayed a disrupted mTEC compartment, with a more profound impact on the numbers of CCL21+ and thymic tuft mTEClo subsets. At the molecular level, Foxo3 controls distinct functional modules in the transcriptome of cTECs and mTECs under normal conditions, which includes the regulation of ribosomal biogenesis and DNA damage response, respectively. These changes in the TEC compartment resulted in a reduced total thymocyte cellularity and specific changes in regulatory T cell and iNKT cell development in the Foxo3cKO thymus. Lastly, the thymic defects observed in adulthood correlated with mild signs of altered peripheral immunotolerance in aged Foxo3cKO mice. Moreover, the deficiency in Foxo3 moderately aggravated the autoimmune predisposition observed in Aire-deficient mice. Our findings highlight the importance of Foxo3 in preserving the homeostasis of TECs and in supporting their role in T cell development and tolerance.
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Affiliation(s)
- Camila Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Pedro Ferreirinha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fátima Macedo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Departamento de Ciências Médicas, Universidade de Aveiro, Aveiro, Portugal
| | - Laura G Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Rute Pinto
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nuno L Alves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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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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James KD, Cosway EJ, Parnell SM, White AJ, Jenkinson WE, Anderson G. Assembling the thymus medulla: Development and function of epithelial cell heterogeneity. Bioessays 2024; 46:e2300165. [PMID: 38161233 DOI: 10.1002/bies.202300165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
The thymus is a unique primary lymphoid organ that supports the production of self-tolerant T-cells essential for adaptive immunity. Intrathymic microenvironments are microanatomically compartmentalised, forming defined cortical, and medullary regions each differentially supporting critical aspects of thymus-dependent T-cell maturation. Importantly, the specific functional properties of thymic cortical and medullary compartments are defined by highly specialised thymic epithelial cells (TEC). For example, in the medulla heterogenous medullary TEC (mTEC) contribute to the enforcement of central tolerance by supporting deletion of autoreactive T-cell clones, thereby counterbalancing the potential for random T-cell receptor generation to contribute to autoimmune disease. Recent advances have further shed light on the pathways and mechanisms that control heterogeneous mTEC development and how differential mTEC functionality contributes to control self-tolerant T-cell development. Here we discuss recent findings in relation to mTEC development and highlight examples of how mTEC diversity contribute to thymus medulla function.
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Affiliation(s)
- Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Emilie J Cosway
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Sonia M Parnell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Andrea J White
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - William E Jenkinson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
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5
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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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Takakura Y, Machida M, Terada N, Katsumi Y, Kawamura S, Horie K, Miyauchi M, Ishikawa T, Akiyama N, Seki T, Miyao T, Hayama M, Endo R, Ishii H, Maruyama Y, Hagiwara N, Kobayashi TJ, Yamaguchi N, Takano H, Akiyama T, Yamaguchi N. Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity. Nat Commun 2024; 15:953. [PMID: 38296961 PMCID: PMC10831050 DOI: 10.1038/s41467-024-45206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Autophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unclear mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48-dependent induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 show a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48-/- mice develop autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.
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Affiliation(s)
- Yuki Takakura
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Moeka Machida
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Natsumi Terada
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Yuka Katsumi
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Seika Kawamura
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Takao Seki
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Takahisa Miyao
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Rin Endo
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Hiroto Ishii
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan
| | - Naho Hagiwara
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Naoto Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Hiroyuki Takano
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan.
| | - Noritaka Yamaguchi
- Department of Molecular Cardiovascular Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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Tao W, Ye Z, Wei Y, Wang J, Yang W, Yu G, Xiong J, Jia S. Insm1 regulates mTEC development and immune tolerance. Cell Mol Immunol 2023; 20:1472-1486. [PMID: 37990032 PMCID: PMC10687002 DOI: 10.1038/s41423-023-01102-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
The expression of self-antigens in medullary thymic epithelial cells (mTECs) is essential for the establishment of immune tolerance, but the regulatory network that controls the generation and maintenance of the multitude of cell populations expressing self-antigens is poorly understood. Here, we show that Insm1, a zinc finger protein with known functions in neuroendocrine and neuronal cells, is broadly coexpressed with an autoimmune regulator (Aire) in mTECs. Insm1 expression is undetectable in most mimetic cell populations derived from mTECs but persists in neuroendocrine mimetic cells. Mutation of Insm1 in mice downregulated Aire expression, dysregulated the gene expression program of mTECs, and altered mTEC subpopulations and the expression of tissue-restricted antigens. Consistent with these findings, loss of Insm1 resulted in autoimmune responses in multiple peripheral tissues. We found that Insm1 regulates gene expression in mTECs by binding to chromatin. Interestingly, the majority of the Insm1 binding sites are co-occupied by Aire and enriched in superenhancer regions. Together, our data demonstrate the important role of Insm1 in the regulation of the repertoire of self-antigens needed to establish immune tolerance.
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Affiliation(s)
- Weihua Tao
- The First Affiliated Hospital of Jinan University, Guangzhou, China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, China
- The Institute of Clinical Medicine, Jinan University, Guangzhou, China
- Key Lab of Guangzhou Basic and Translational Research of Pan-Vascular Diseases, Guangzhou, China
| | - Zhihuan Ye
- The First Affiliated Hospital of Jinan University, Guangzhou, China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, China
- The Institute of Clinical Medicine, Jinan University, Guangzhou, China
| | - Yiqiu Wei
- The First Affiliated Hospital of Jinan University, Guangzhou, China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, China
- The Institute of Clinical Medicine, Jinan University, Guangzhou, China
| | - Jianxue Wang
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weixin Yang
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guoxing Yu
- The First Affiliated Hospital of Jinan University, Guangzhou, China
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, China
- The Institute of Clinical Medicine, Jinan University, Guangzhou, China
| | - Jieyi Xiong
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium.
| | - Shiqi Jia
- The First Affiliated Hospital of Jinan University, Guangzhou, China.
- The Guangdong-Hong Kong-Macao Joint University Laboratory of Metabolic and Molecular Medicine, Jinan University, Guangzhou, China.
- The Institute of Clinical Medicine, Jinan University, Guangzhou, China.
- Key Lab of Guangzhou Basic and Translational Research of Pan-Vascular Diseases, Guangzhou, China.
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8
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Ishikawa T, Horie K, Takakura Y, Ohki H, Maruyama Y, Hayama M, Miyauchi M, Miyao T, Hagiwara N, Kobayashi TJ, Akiyama N, Akiyama T. T-cell receptor repertoire analysis of CD4-positive T cells from blood and an affected organ in an autoimmune mouse model. Genes Cells 2023; 28:929-941. [PMID: 37909727 DOI: 10.1111/gtc.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/15/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
One hallmark of some autoimmune diseases is the variability of symptoms among individuals. Organs affected by the disease differ between patients, posing a challenge in diagnosing the affected organs. Although numerous studies have investigated the correlation between T cell antigen receptor (TCR) repertoires and the development of infectious and immune diseases, the correlation between TCR repertoires and variations in disease symptoms among individuals remains unclear. This study aimed to investigate the correlation of TCRα and β repertoires in blood T cells with the extent of autoimmune signs that varies among individuals. We sequenced TCRα and β of CD4+ CD44high CD62Llow T cells in the blood and stomachs of mice deficient in autoimmune regulator (Aire) (AIRE KO), a mouse model of human autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. Data analysis revealed that the degree of similarity in TCR sequences between the blood and stomach varied among individual AIRE KO mice and reflected the extent of T cell infiltration in the stomach. We identified a set of TCR sequences whose frequencies in blood might correlate with extent of the stomach manifestations. Our results propose a potential of using TCR repertoires not only for diagnosing disease development but also for diagnosing affected organs in autoimmune diseases.
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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
| | - Kenta Horie
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Takakura
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Houko Ohki
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Maki Miyauchi
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Takahisa Miyao
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Naho Hagiwara
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Nobuko Akiyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, 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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Malin J, Martinez-Ruiz GU, Zhao Y, Shissler SC, Cowan JE, Ding Y, Morales-Sanchez A, Ishikawa M, Lavaert M, Das A, Butcher D, Warner AC, Kallarakal M, Chen J, Kedei N, Kelly M, Brinster LR, Allman D, Bhandoola A. Expression of the transcription factor Klf6 by thymic epithelial cells is required for thymus development. SCIENCE ADVANCES 2023; 9:eadg8126. [PMID: 37967174 PMCID: PMC10651122 DOI: 10.1126/sciadv.adg8126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Thymic epithelial cells (TEC) control T cell development and play essential roles in establishing self-tolerance. By using Foxn1-Cre-driven ablation of Klf6 gene in TEC, we identified Klf6 as a critical factor in TEC development. Klf6 deficiency resulted in a hypoplastic thymus-evident from fetal stages into adulthood-in which a dramatic increase in the frequency of apoptotic TEC was observed. Among cortical TEC (cTEC), a previously unreported cTEC population expressing the transcription factor Sox10 was relatively expanded. Within medullary TEC (mTEC), mTEC I and Tuft-like mTEC IV were disproportionately decreased. Klf6 deficiency altered chromatin accessibility and affected TEC chromatin configuration. Consistent with these defects, naïve conventional T cells and invariant natural killer T cells were reduced in the spleen. Late stages of T cell receptor-dependent selection of thymocytes were affected, and mice exhibited autoimmunity. Thus, Klf6 has a prosurvival role and affects the development of specific TEC subsets contributing to thymic function.
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Affiliation(s)
- Justin Malin
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gustavo Ulises Martinez-Ruiz
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Research Division, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Children’s Hospital Federico Gomez, Mexico City, Mexico
| | - Yongge Zhao
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susannah C. Shissler
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E. Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Children’s Hospital Federico Gomez, Mexico City, Mexico
| | - Masaki Ishikawa
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Marieke Lavaert
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew C. Warner
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Melissa Kallarakal
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jingqiu Chen
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- ACROBiosystems, Newark, DE, USA
| | - Noemi Kedei
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kelly
- Single Cell Analysis Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren R. Brinster
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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10
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Horie K, Namiki K, Kinoshita K, Miyauchi M, Ishikawa T, Hayama M, Maruyama Y, Hagiwara N, Miyao T, Murata S, Kobayashi TJ, Akiyama N, Akiyama T. Acute irradiation causes a long-term disturbance in the heterogeneity and gene expression profile of medullary thymic epithelial cells. Front Immunol 2023; 14:1186154. [PMID: 38022666 PMCID: PMC10652284 DOI: 10.3389/fimmu.2023.1186154] [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: 03/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The thymus has the ability to regenerate from acute injury caused by radiation, infection, and stressors. In addition to thymocytes, thymic epithelial cells in the medulla (mTECs), which are crucial for T cell self-tolerance by ectopically expressing and presenting thousands of tissue-specific antigens (TSAs), are damaged by these insults and recover thereafter. However, given recent discoveries on the high heterogeneity of mTECs, it remains to be determined whether the frequency and properties of mTEC subsets are restored during thymic recovery from radiation damage. Here we demonstrate that acute total body irradiation with a sublethal dose induces aftereffects on heterogeneity and gene expression of mTECs. Single-cell RNA-sequencing (scRNA-seq) analysis showed that irradiation reduces the frequency of mTECs expressing AIRE, which is a critical regulator of TSA expression, 15 days after irradiation. In contrast, transit-amplifying mTECs (TA-mTECs), which are progenitors of AIRE-expressing mTECs, and Ccl21a-expressing mTECs, were less affected. Interestingly, a detailed analysis of scRNA-seq data suggested that the proportion of a unique mTEC cluster expressing Ccl25 and a high level of TSAs was severely decreased by irradiation. In sum, we propose that the effects of acute irradiation disrupt the heterogeneity and properties of mTECs over an extended period, which potentially leads to an impairment of thymic T cell selection.
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Affiliation(s)
- Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kano Namiki
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kyouhei Kinoshita
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Naho Hagiwara
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Takahisa Miyao
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Shigeo Murata
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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11
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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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12
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Michelson DA, Zuo C, Verzi M, Benoist C, Mathis D. Hnf4 activates mimetic-cell enhancers to recapitulate gut and liver development within the thymus. J Exp Med 2023; 220:e20230461. [PMID: 37399024 PMCID: PMC10318407 DOI: 10.1084/jem.20230461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Mimetic cells are medullary thymic epithelial cells (mTECs) that mimic extra-thymic cell types to tolerize T cells to self-antigens. Here, we dissected the biology of entero-hepato mTECs, mimetic cells expressing gut- and liver-associated transcripts. Entero-hepato mTECs conserved their thymic identity yet accessed wide swaths of enterocyte chromatin and transcriptional programs via the transcription factors Hnf4α and Hnf4γ. Deletion of Hnf4α and Hnf4γ in TECs ablated entero-hepato mTECs and downregulated numerous gut- and liver-associated transcripts, with a primary contribution from Hnf4γ. Loss of Hnf4 impaired enhancer activation and CTCF redistribution in mTECs but did not impact Polycomb-mediated repression or promoter-proximal histone marks. By single-cell RNA sequencing, Hnf4 loss produced three distinct effects on mimetic cell state, fate, and accumulation. Serendipitously, a requirement for Hnf4 in microfold mTECs was discovered, which exposed a requirement for Hnf4γ in gut microfold cells and the IgA response. Study of Hnf4 in entero-hepato mTECs thus revealed mechanisms of gene control in the thymus and periphery alike.
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Affiliation(s)
| | - Chong Zuo
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Michael Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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13
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Forsdyke DR. Aggregation-prone peptides from within a non-self-protein homoaggregate are preferred for MHC association: Historical overview. Scand J Immunol 2023; 98:e13306. [PMID: 38441340 DOI: 10.1111/sji.13306] [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: 03/18/2023] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 03/07/2024]
Abstract
New technologies assist re-evaluation of hypotheses on generation of immune cell repertoires and distinctions of self from non-self. Findings include positive correlations between peptide propensities to aggregate and their binding to major histocompatibility complex (MHC) proteins. This recalls the hypothesis that foreign proteins may homoaggregate in host cytosols prior to releasing their peptides (p) to form pMHC complexes. Clues to this included aggregation-related phenomena associated with infections (rouleaux formation, pyrexia, certain brain diseases). By virtue of 'promiscuous' gene expression by thymic presenting cells - perhaps adapted from earlier evolving gonadal mechanisms - developing T cells monitor surface pMHC clusterings. This evaluates intracellular concentrations of the corresponding proteins, and hence, following Burnet's two signal principle, degrees of self-reactivity. After positive selection in the thymic cortex for reactivity with 'near-self', high-level pMHC clustering suffices in the medulla for negatively selection. Following Burnet's principle, in the periphery low-level clustering suffices for T cell stimulation and high-level clustering again provokes negative selection (immunological tolerance). For evolving intracellular pathogens, fine-tuned polymorphisms of their host species have limited to 'near-self' some mimicking adaptations. It is proposed that while entire pathogen proteins may have evolved to minimize their aggregability, the greater aggregability of their peptides remains partially hidden within. Two-step proofreading mechanisms in prospective hosts select proteins containing aggregable peptide for the generation of pMHC clusters at the surface of presenting cells. Through mutations, some proteins of pathogens and cancer cells tend to converge towards the host 'near-self' that its T cells have auditioned to address.
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Affiliation(s)
- Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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14
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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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15
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Klein F, Veiga-Villauriz C, Börsch A, Maio S, Palmer S, Dhalla F, Handel AE, Zuklys S, Calvo-Asensio I, Musette L, Deadman ME, White AJ, Lucas B, Anderson G, Holländer GA. Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells. Nat Commun 2023; 14:4071. [PMID: 37429879 DOI: 10.1038/s41467-023-39722-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 06/21/2023] [Indexed: 07/12/2023] Open
Abstract
The network of thymic stromal cells provides essential niches with unique molecular cues controlling T cell development and selection. Recent single-cell RNA sequencing studies have uncovered previously unappreciated transcriptional heterogeneity among thymic epithelial cells (TEC). However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here, using massively parallel flow cytometry and machine learning, we deconvoluted known TEC phenotypes into novel subpopulations. Using CITEseq, these phenotypes were related to corresponding TEC subtypes defined by the cells' RNA profiles. This approach allowed the phenotypic identification of perinatal cTEC and their physical localisation within the cortical stromal scaffold. In addition, we demonstrate the dynamic change in the frequency of perinatal cTEC in response to developing thymocytes and reveal their exceptional efficiency in positive selection. Collectively, our study identifies markers that allow for an unprecedented dissection of the thymus stromal complexity, as well as physical isolation of TEC populations and assignment of specific functions to individual TEC subtypes.
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Affiliation(s)
- Fabian Klein
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Clara Veiga-Villauriz
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | | | - Stefano Maio
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Sam Palmer
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Fatima Dhalla
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Adam E Handel
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Saulius Zuklys
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children's Hospital Basel, Basel, Switzerland
| | - Irene Calvo-Asensio
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children's Hospital Basel, Basel, Switzerland
| | - Lucas Musette
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children's Hospital Basel, Basel, Switzerland
| | - Mary E Deadman
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Andrea J White
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham, UK
| | - Beth Lucas
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham, UK
| | - Graham Anderson
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham, UK
| | - Georg A Holländer
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK.
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children's Hospital Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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16
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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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17
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Sousa LG, Rodrigues PM, Alves NL. T-cell selection in the thymus: New routes toward the identification of the self-peptide ligandome presented by thymic epithelial cells. Eur J Immunol 2023; 53:e2250202. [PMID: 36642953 DOI: 10.1002/eji.202250202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/30/2022] [Accepted: 01/13/2023] [Indexed: 01/17/2023]
Abstract
Within the thymus, thymic epithelial cells (TECs) provide a dedicated niche for the selection of functional T cells expressing a highly variable and self-tolerant T-cell receptor (TCR) repertoire. In this minireview, we start by summarizing recent studies that have improved our understanding on the composition of cortical TEC and medullary TEC microenvironments. Next, we focus on the molecular processes that control the function of TECs in T-cell selection. In particular, we discuss the role of cortical TECs in positive selection and the pathways employed by these cells to generate and present selecting self-peptides:MHC II complexes. Several studies have underscored the role of the β5t-containing thymoproteasome in the production of unique MHC I-bound peptides critical for CD8 T-cell selection. Contrarily, the identity of the molecular determinants that regulate the generation of MHC II-bound self-peptides capable of positive selecting CD4 T cells is far more uncertain. We highlight recent advances that interconnect the autophagy-lysosomal pathway, the presentation of specific sets of self-peptide:MHC II complexes, and the diversification of CD4 TCR repertoire. Lastly, we discuss how these findings may open up new avenues for deciphering the identity of the MHC I and MHC II ligandome in the thymus.
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Affiliation(s)
- Laura G Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Pedro M Rodrigues
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Nuno L Alves
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular, Porto, Portugal
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18
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Matsumoto M, Yoshida H, Tsuneyama K, Oya T, Matsumoto M. Revisiting Aire and tissue-restricted antigens at single-cell resolution. Front Immunol 2023; 14:1176450. [PMID: 37207224 PMCID: PMC10191227 DOI: 10.3389/fimmu.2023.1176450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
The thymus is a highly specialized organ that plays an indispensable role in the establishment of self-tolerance, a process characterized by the "education" of developing T-cells. To provide competent T-cells tolerant to self-antigens, medullary thymic epithelial cells (mTECs) orchestrate negative selection by ectopically expressing a wide range of genes, including various tissue-restricted antigens (TRAs). Notably, recent advancements in the high-throughput single-cell analysis have revealed remarkable heterogeneity in mTECs, giving us important clues for dissecting the mechanisms underlying TRA expression. We overview how recent single-cell studies have furthered our understanding of mTECs, with a focus on the role of Aire in inducing mTEC heterogeneity to encompass TRAs.
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Affiliation(s)
- Minoru Matsumoto
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- *Correspondence: Minoru Matsumoto,
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
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19
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Morales-Sanchez A, Shissler SC, Cowan JE, Bhandoola A. Revelations in Thymic Epithelial Cell Biology and Heterogeneity from Single-Cell RNA Sequencing and Lineage Tracing Methodologies. Methods Mol Biol 2023; 2580:25-49. [PMID: 36374449 PMCID: PMC10802793 DOI: 10.1007/978-1-0716-2740-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Thymic epithelial cells (TECs) make up the thymic microenvironments that support the generation of a functionally competent and self-tolerant T-cell repertoire. Cortical (c)TECs, present in the cortex, are essential for early thymocyte development including selection of thymocytes expressing functional TCRs (positive selection). Medullary (m)TECs, located in the medulla, play a key role in late thymocyte development, including depletion of self-reactive T cells (negative selection) and selection of regulatory T cells. In recent years, transcriptomic analysis by single-cell (sc)RNA sequencing (Seq) has revealed TEC heterogeneity previously masked by population-level RNA-Seq or phenotypic studies. We summarize the discoveries made possible by scRNA-Seq, including the identification of novel mTEC subsets, advances in understanding mTEC promiscuous gene expression, and TEC alterations from embryonic to adult stages. Whereas pseudotime analyses of scRNA-Seq data can suggest relationships between TEC subsets, experimental methods such as lineage tracing and reaggregate thymic organ culture (RTOC) are required to test these hypotheses. Lineage tracing - namely, of β5t or Aire expressing cells - has exposed progenitor and parent-daughter cellular relationships within TEC.
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Affiliation(s)
- Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico.
| | - Susannah C Shissler
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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20
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Ohigashi I, Matsuda-Lennikov M, Takahama Y. Large-Scale Isolation of Mouse Thymic Epithelial Cells. Methods Mol Biol 2023; 2580:189-197. [PMID: 36374458 PMCID: PMC10280300 DOI: 10.1007/978-1-0716-2740-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The thymus is compartmentalized into the cortex and the medulla. Cortical and medullary thymic epithelial cells (TECs) characterize T cell-producing and T cell-selecting functions of cortical and medullary microenvironments in the thymus. Enzymatic digestion of the thymus and flow cytometric isolation of TECs and their subpopulations are useful for molecular and cellular characterization of TECs. However, the cellularity of cTECs and mTECs isolated from mouse thymus is limited. In this chapter, we describe the method for isolation of a large number of TECs using enlarged mouse thymus, which enables biochemical and proteomic analysis of TEC subpopulations.
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Affiliation(s)
- Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Mami Matsuda-Lennikov
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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21
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Yasumizu Y, Ohkura N, Murata H, Kinoshita M, Funaki S, Nojima S, Kido K, Kohara M, Motooka D, Okuzaki D, Suganami S, Takeuchi E, Nakamura Y, Takeshima Y, Arai M, Tada S, Okumura M, Morii E, Shintani Y, Sakaguchi S, Okuno T, Mochizuki H. Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma. Nat Commun 2022; 13:4230. [PMID: 35869073 PMCID: PMC9305039 DOI: 10.1038/s41467-022-31951-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractMyasthenia gravis (MG) is a neurological disease caused by autoantibodies against neuromuscular-associated proteins. While MG frequently develops in thymoma patients, the etiologic factors for MG are not well understood. Here, by constructing a comprehensive atlas of thymoma using bulk and single-cell RNA-sequencing, we identify ectopic expression of neuromuscular molecules in MG-type thymoma. These molecules are found within a distinct subpopulation of medullary thymic epithelial cells (mTECs), which we name neuromuscular mTECs (nmTECs). MG-thymoma also exhibits microenvironments dedicated to autoantibody production, including ectopic germinal center formation, T follicular helper cell accumulation, and type 2 conventional dendritic cell migration. Cell–cell interaction analysis also predicts the interaction between nmTECs and T/B cells via CXCL12-CXCR4. The enrichment of nmTECs presenting neuromuscular molecules within MG-thymoma is further confirmed immunohistochemically and by cellular composition estimation from the MG-thymoma transcriptome. Altogether, this study suggests that nmTECs have a significant function in MG pathogenesis via ectopic expression of neuromuscular molecules.
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22
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Michelson DA, Mathis D. Thymic mimetic cells: tolerogenic masqueraders. Trends Immunol 2022; 43:782-791. [PMID: 36008259 PMCID: PMC9509455 DOI: 10.1016/j.it.2022.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Medullary thymic epithelial cells (mTECs) clonally delete or divert autoreactive T cells by ectopically expressing a diverse array of peripheral-tissue antigens (PTAs) within the thymus. Although thymic stromal cells with histological features of extra-thymic cell types, like myocytes or neurons, have been observed by light microscopy since the mid-1800s, most modern work on PTA expression has focused on the transcription factor Aire. Here, we highlight recent work that has refocused attention on such 'misplaced' thymic cells, referred to collectively as thymic mimetic cells. We review the molecular underpinnings of mimetic cells and their roles in establishing T cell tolerance, and we propose that mimetic cells play important roles in autoimmunity. Finally, we suggest future directions for this emerging area.
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Affiliation(s)
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
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23
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Provin N, Giraud M. Differentiation of Pluripotent Stem Cells Into Thymic Epithelial Cells and Generation of Thymic Organoids: Applications for Therapeutic Strategies Against APECED. Front Immunol 2022; 13:930963. [PMID: 35844523 PMCID: PMC9277542 DOI: 10.3389/fimmu.2022.930963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 01/01/2023] Open
Abstract
The thymus is a primary lymphoid organ essential for the induction of central immune tolerance. Maturing T cells undergo several steps of expansion and selection mediated by thymic epithelial cells (TECs). In APECED and other congenital pathologies, a deficiency in genes that regulate TEC development or their ability to select non auto-reactive thymocytes results in a defective immune balance, and consequently in a general autoimmune syndrome. Restoration of thymic function is thus crucial for the emergence of curative treatments. The last decade has seen remarkable progress in both gene editing and pluripotent stem cell differentiation, with the emergence of CRISPR-based gene correction, the trivialization of reprogramming of somatic cells to induced pluripotent stem cells (iPSc) and their subsequent differentiation into multiple cellular fates. The combination of these two approaches has paved the way to the generation of genetically corrected thymic organoids and their use to control thymic genetic pathologies affecting self-tolerance. Here we review the recent advances in differentiation of iPSc into TECs and the ability of the latter to support a proper and efficient maturation of thymocytes into functional and non-autoreactive T cells. A special focus is given on thymus organogenesis and pathway modulation during iPSc differentiation, on the impact of the 2/3D structure on the generated TECs, and on perspectives for therapeutic strategies in APECED based on patient-derived iPSc corrected for AIRE gene mutations.
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24
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Wang C, Daley SR. How Thymocyte Deletion in the Cortex May Curtail Antigen-Specific T-Regulatory Cell Development in the Medulla. Front Immunol 2022; 13:892498. [PMID: 35693793 PMCID: PMC9176388 DOI: 10.3389/fimmu.2022.892498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cell responses to self-antigens are pivotal for immunological self-tolerance. Activation of Foxp3– T-conventional (T-conv) cells can precipitate autoimmune disease, whereas activation of Foxp3+ T-regulatory (T-reg) cells is essential to prevent autoimmune disease. This distinction indicates the importance of the thymus in controlling the differentiation of self-reactive CD4+ T cells. Thymocytes and thymic antigen-presenting cells (APC) depend on each other for normal maturation and differentiation. In this Hypothesis and Theory article, we propose this mutual dependence dictates which self-antigens induce T-reg cell development in the thymic medulla. We postulate self-reactive CD4+ CD8– thymocytes deliver signals that stabilize and amplify the presentation of their cognate self-antigen by APC in the thymic medulla, thereby seeding a niche for the development of T-reg cells specific for the same self-antigen. By limiting the number of antigen-specific CD4+ thymocytes in the medulla, thymocyte deletion in the cortex may impede the formation of medullary T-reg niches containing certain self-antigens. Susceptibility to autoimmune disease may arise from cortical deletion creating a “hole” in the self-antigen repertoire recognized by T-reg cells.
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Affiliation(s)
- Chenglong Wang
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Stephen R Daley
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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25
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Zhang Q, Zhang J, Lei T, Liang Z, Dong X, Sun L, Zhao Y. Sirt6-mediated epigenetic modification of DNA accessibility is essential for Pou2f3-induced thymic tuft cell development. Commun Biol 2022; 5:544. [PMID: 35668088 PMCID: PMC9170729 DOI: 10.1038/s42003-022-03484-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThymic epithelial cells (TECs) are essential for the production of self-tolerant T cells. The newly identified thymic tuft cells are regulated by Pou2f3 and represent important elements for host type 2 immunity. However, epigenetic involvement in thymic tuft cell development remains unclear. We performed single-cell ATAC-seq of medullary TEC (mTEC) and established single-cell chromatin accessibility profiling of mTECs. The results showed that mTEC III cells can be further divided into three groups (Late Aire 1, 2, and 3) and that thymic tuft cells may be derived from Late Aire 2 cells. Pou2f3 is expressed in both Late Aire 2 cells and thymic tuft cells, while Pou2f3-regulated genes are specifically expressed in thymic tuft cells with simultaneous opening of chromatin accessibility, indicating the involvement of epigenetic modification in this process. Using the epigenetic regulator Sirt6-defect mouse model, we found that Sirt6 deletion increased Late Aire 2 cells and decreased thymic tuft cells and Late Aire 3 cells without affecting Pou2f3 expression. However, Sirt6 deletion reduced the chromatin accessibility of Pou2f3-regulated genes in thymic tuft cells, which may be caused by Sirt6–mediated regulation of Hdac9 expression. These data indicate that epigenetic regulation is indispensable for Pou2f3-mediated thymic tuft cell development.
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26
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Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells. Cell 2022; 185:2542-2558.e18. [DOI: 10.1016/j.cell.2022.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/21/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022]
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27
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MIyao T, Miyauchi M, Kelly ST, Terooatea TW, Ishikawa T, Oh E, Hirai S, Horie K, Takakura Y, Ohki H, Hayama M, Maruyama Y, Seki T, Ishii H, Yabukami H, Yoshida M, Inoue A, Sakaue-Sawano A, Miyawaki A, Muratani M, Minoda A, Akiyama N, Akiyama T. Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator. eLife 2022; 11:73998. [PMID: 35578835 PMCID: PMC9113748 DOI: 10.7554/elife.73998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/21/2022] [Indexed: 12/03/2022] Open
Abstract
Medullary thymic epithelial cells (mTECs) are critical for self-tolerance induction in T cells via promiscuous expression of tissue-specific antigens (TSAs), which are controlled by the transcriptional regulator, AIRE. Whereas AIRE-expressing (Aire+) mTECs undergo constant turnover in the adult thymus, mechanisms underlying differentiation of postnatal mTECs remain to be discovered. Integrative analysis of single-cell assays for transposase-accessible chromatin (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) suggested the presence of proliferating mTECs with a specific chromatin structure, which express high levels of Aire and co-stimulatory molecules, CD80 (Aire+CD80hi). Proliferating Aire+CD80hi mTECs detected using Fucci technology express a minimal number of Aire-dependent TSAs and are converted into quiescent Aire+CD80hi mTECs expressing high levels of TSAs after a transit amplification. These data provide evidence for the existence of transit-amplifying Aire+mTEC precursors during the Aire+mTEC differentiation process of the postnatal thymus.
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Affiliation(s)
- Takahisa MIyao
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - S Thomas Kelly
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tommy W Terooatea
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Eugene Oh
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sotaro Hirai
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Takakura
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Houko Ohki
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Takao Seki
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroto Ishii
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Haruka Yabukami
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Asako Sakaue-Sawano
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Saitama, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Saitama, Japan
| | - Masafumi Muratani
- Transborder Medical Research Center, and Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Aki Minoda
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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28
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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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29
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Padonou F, Gonzalez V, Provin N, Yayilkan S, Jmari N, Maslovskaja J, Kisand K, Peterson P, Irla M, Giraud M. Aire-dependent transcripts escape Raver2-induced splice-event inclusion in the thymic epithelium. EMBO Rep 2022; 23:e53576. [PMID: 35037357 PMCID: PMC8892270 DOI: 10.15252/embr.202153576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022] Open
Abstract
Aire allows medullary thymic epithelial cells (mTECs) to express and present a large number of self-antigens for central tolerance. Although mTECs express a high diversity of self-antigen splice isoforms, the extent and regulation of alternative splicing events (ASEs) in their transcripts, notably in those induced by Aire, is unknown. In contrast to Aire-neutral genes, we find that transcripts of Aire-sensitive genes show only a low number of ASEs in mTECs, with about a quarter present in peripheral tissues excluded from the thymus. We identify Raver2, as a splicing-related factor overexpressed in mTECs and dependent on H3K36me3 marks, that promotes ASEs in transcripts of Aire-neutral genes, leaving Aire-sensitive ones unaffected. H3K36me3 profiling reveals its depletion at Aire-sensitive genes and supports a mechanism that is preceding Aire expression leading to transcripts of Aire-sensitive genes with low ASEs that escape Raver2-induced alternative splicing. The lack of ASEs in Aire-induced transcripts would result in an incomplete Aire-dependent negative selection of autoreactive T cells, thus highlighting the need of complementary tolerance mechanisms to prevent activation of these cells in the periphery.
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Affiliation(s)
- Francine Padonou
- Nantes UniversitéINSERMCenter for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,Institut CochinINSERMCNRSParis UniversitéParisFrance
| | | | - Nathan Provin
- Nantes UniversitéINSERMCenter for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance
| | - Sümeyye Yayilkan
- Nantes UniversitéINSERMCenter for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance
| | - Nada Jmari
- Institut CochinINSERMCNRSParis UniversitéParisFrance
| | | | - Kai Kisand
- Molecular Pathology Research GroupUniversity of TartuTartuEstonia
| | - Pärt Peterson
- Molecular Pathology Research GroupUniversity of TartuTartuEstonia
| | - Magali Irla
- Aix‐Marseille UniversitéCNRSINSERMCIML, Centre d'Immunologie de Marseille‐LuminyMarseilleFrance
| | - Matthieu Giraud
- Nantes UniversitéINSERMCenter for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,Institut CochinINSERMCNRSParis UniversitéParisFrance
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30
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Lopes N, Boucherit N, Santamaria JC, Provin N, Charaix J, Ferrier P, Giraud M, Irla M. Thymocytes trigger self-antigen-controlling pathways in immature medullary thymic epithelial stages. eLife 2022; 11:69982. [PMID: 35188458 PMCID: PMC8860447 DOI: 10.7554/elife.69982] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/14/2022] [Indexed: 12/20/2022] Open
Abstract
Interactions of developing T cells with Aire+ medullary thymic epithelial cells expressing high levels of MHCII molecules (mTEChi) are critical for the induction of central tolerance in the thymus. In turn, thymocytes regulate the cellularity of Aire+ mTEChi. However, it remains unknown whether thymocytes control the precursors of Aire+ mTEChi that are contained in mTEClo cells or other mTEClo subsets that have recently been delineated by single-cell transcriptomic analyses. Here, using three distinct transgenic mouse models, in which antigen presentation between mTECs and CD4+ thymocytes is perturbed, we show by high-throughput RNA-seq that self-reactive CD4+ thymocytes induce key transcriptional regulators in mTEClo and control the composition of mTEClo subsets, including Aire+ mTEChi precursors, post-Aire and tuft-like mTECs. Furthermore, these interactions upregulate the expression of tissue-restricted self-antigens, cytokines, chemokines, and adhesion molecules important for T-cell development. This gene activation program induced in mTEClo is combined with a global increase of the active H3K4me3 histone mark. Finally, we demonstrate that these self-reactive interactions between CD4+ thymocytes and mTECs critically prevent multiorgan autoimmunity. Our genome-wide study thus reveals that self-reactive CD4+ thymocytes control multiple unsuspected facets from immature stages of mTECs, which determines their heterogeneity.
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Affiliation(s)
- Noella Lopes
- Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Nicolas Boucherit
- Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Jérémy C Santamaria
- Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Nathan Provin
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Jonathan Charaix
- Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Pierre Ferrier
- Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Matthieu Giraud
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Magali Irla
- Aix-Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
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31
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Vobořil M, Březina J, Brabec T, Dobeš J, Ballek O, Dobešová M, Manning J, Blumberg RS, Filipp D. A model of preferential pairing between epithelial and dendritic cells in thymic antigen transfer. eLife 2022; 11:71578. [PMID: 35099391 PMCID: PMC8803313 DOI: 10.7554/elife.71578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/22/2021] [Indexed: 12/22/2022] Open
Abstract
Medullary thymic epithelial cells (mTECs), which produce and present self-antigens, are essential for the establishment of central tolerance. Since mTEC numbers are limited, their function is complemented by thymic dendritic cells (DCs), which transfer mTEC-produced self-antigens via cooperative antigen transfer (CAT). While CAT is required for effective T cell selection, many aspects remain enigmatic. Given the recently described heterogeneity of mTECs and DCs, it is unclear whether the antigen acquisition from a particular TEC subset is mediated by preferential pairing with a specific subset of DCs. Using several relevant Cre-based mouse models that control for the expression of fluorescent proteins, we have found that, in regards to CAT, each subset of thymic DCs preferentially targets a distinct mTEC subset(s). Importantly, XCR1+-activated DC subset represented the most potent subset in CAT. Interestingly, thymic DCs can also acquire antigens from more than one mTEC, and of these, monocyte-derived dendritic cells (moDCs) were determined to be the most efficient. moDCs also represented the most potent DC subset in the acquisition of antigen from other DCs. These findings suggest a preferential pairing model for the distribution of mTEC-derived antigens among distinct populations of thymic DCs.
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Affiliation(s)
- Matouš Vobořil
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Březina
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Charles University, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Brabec
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Dobeš
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Charles University, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Ballek
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Dobešová
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jasper Manning
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Richard S Blumberg
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dominik Filipp
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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32
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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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33
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Kaiser C, Bradu A, Gamble N, Caldwell JA, Koh AS. AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression. Immunol Rev 2022; 305:59-76. [PMID: 34545959 PMCID: PMC9250823 DOI: 10.1111/imr.13026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022]
Abstract
The emergence of antigen receptor diversity in clonotypic lymphocytes drove the evolution of a novel gene, Aire, that enabled the adaptive immune system to discriminate foreign invaders from self-constituents. AIRE functions in the epithelial cells of the thymus to express genes highly restricted to alternative cell lineages. This somatic plasticity facilitates the selection of a balanced repertoire of T cells that protects the host from harmful self-reactive clones, yet maintains a wide range of affinities for virtually any foreign antigen. Here, we review the latest understanding of AIRE's molecular actions with a focus on its interplay with chromatin. We argue that AIRE is a multi-valent chromatin effector that acts late in the transcription cycle to modulate the activity of previously poised non-coding regulatory elements of tissue-specific genes. We postulate a role for chromatin instability-caused in part by ATP-dependent chromatin remodeling-that variably sets the scope of the accessible landscape on which AIRE can act. We highlight AIRE's intrinsic repressive function and its relevance in providing feedback control. We synthesize these recent advances into a putative model for the mechanistic modes by which AIRE triggers ectopic transcription for immune repertoire selection.
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Affiliation(s)
- Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Noah Gamble
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jason A. Caldwell
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Andrew S. Koh
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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34
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Wang J, Lareau CA, Bautista J, Gupta A, Sandor K, Germino J, Yin Y, Arvedson M, Reeder GC, Cramer NT, Xie F, Ntranos V, Satpathy AT, Anderson MS, Gardner JM. Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. Sci Immunol 2021; 6:eabl5053. [PMID: 34767455 PMCID: PMC8855935 DOI: 10.1126/sciimmunol.abl5053] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The autoimmune regulator (Aire), a well-defined transcriptional regulator in the thymus, is also found in extrathymic Aire-expressing cells (eTACs) in the secondary lymphoid organs. eTACs are hematopoietic antigen-presenting cells and inducers of immune tolerance, but their precise identity has remained unclear. Here, we use single-cell multiomics, transgenic murine models, and functional approaches to define eTACs at the transcriptional, genomic, and proteomic level. We find that eTACs consist of two similar cell types: CCR7+ Aire-expressing migratory dendritic cells (AmDCs) and an Airehi population coexpressing Aire and retinoic acid receptor–related orphan receptor γt (RORγt) that we term Janus cells (JCs). Both JCs and AmDCs have the highest transcriptional and genomic homology to CCR7+ migratory dendritic cells. eTACs, particularly JCs, have highly accessible chromatin and broad gene expression, including a range of tissue-specific antigens, as well as remarkable homology to medullary thymic epithelium and RANK-dependent Aire expression. Transgenic self-antigen expression by eTACs is sufficient to induce negative selection and prevent autoimmune diabetes. This transcriptional, genomic, and functional symmetry between eTACs (both JCs and AmDCs) and medullary thymic epithelium—the other principal Aire-expressing population and a key regulator of central tolerance—identifies a core program that may influence self-representation and tolerance across the spectrum of immune development.
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Affiliation(s)
- Jiaxi Wang
- Diabetes Center, University of California San Francisco
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Alexander Gupta
- Diabetes Center, University of California San Francisco
- Department of Surgery, University of California San Francisco
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joe Germino
- Diabetes Center, University of California San Francisco
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Matt Arvedson
- Diabetes Center, University of California San Francisco
| | | | | | - Fang Xie
- Diabetes Center, University of California San Francisco
- Department of Surgery, University of California San Francisco
| | - Vasilis Ntranos
- Diabetes Center, University of California San Francisco
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Mark S. Anderson
- Diabetes Center, University of California San Francisco
- Department of Medicine, University of California San Francisco
| | - James M. Gardner
- Diabetes Center, University of California San Francisco
- Department of Surgery, University of California San Francisco
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35
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Jansen K, Shikama-Dorn N, Attar M, Maio S, Lopopolo M, Buck D, Holländer GA, Sansom SN. RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus. Genome Res 2021; 31:2022-2034. [PMID: 34649931 PMCID: PMC8559713 DOI: 10.1101/gr.275245.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022]
Abstract
Thymic epithelial cells (TEC) control the selection of a T cell repertoire reactive to pathogens but tolerant of self. This process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire, but the extent to which TEC recapitulate peripheral isoforms, and the mechanisms by which they do so, remain largely unknown. We performed the first assembly-based transcriptomic census of transcript structures and splicing factor (SF) expression in mouse medullary TEC (mTEC) and 21 peripheral tissues. Mature mTEC expressed 60.1% of all protein-coding transcripts, more than was detected in any of the peripheral tissues. However, for genes with tissue-restricted expression, mTEC produced fewer isoforms than did the relevant peripheral tissues. Analysis of exon inclusion revealed an absence of brain-specific microexons in mTEC. We did not find unusual numbers of novel transcripts in TEC, and we show that Aire, the facilitator of promiscuous gene expression, promotes the generation of long “classical” transcripts (with 5′ and 3′ UTRs) but has only a limited impact on alternative splicing in mTEC. Comprehensive assessment of SF expression in mTEC identified a small set of nonpromiscuously expressed SF genes, among which we confirmed RBFOX to be present with AIRE in mTEC nuclei. Using a conditional loss-of-function approach, we show that Rbfox2 promotes mTEC development and regulates the alternative splicing of promiscuously expressed genes. These data indicate that TEC recommission a small number of peripheral SFs, including members of the RBFOX family, to generate a broad but selective representation of the peripheral splice isoform repertoire.
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Affiliation(s)
- Kathrin Jansen
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom.,Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Noriko Shikama-Dorn
- The University Children's Hospital of Basel and the Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Moustafa Attar
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Stefano Maio
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Maria Lopopolo
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - David Buck
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Georg A Holländer
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,The University Children's Hospital of Basel and the Department of Biomedicine, University of Basel, 4056 Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Stephen N Sansom
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom
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36
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Duah M, Li L, Shen J, Lan Q, Pan B, Xu K. Thymus Degeneration and Regeneration. Front Immunol 2021; 12:706244. [PMID: 34539637 PMCID: PMC8442952 DOI: 10.3389/fimmu.2021.706244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023] Open
Abstract
The immune system’s ability to resist the invasion of foreign pathogens and the tolerance to self-antigens are primarily centered on the efficient functions of the various subsets of T lymphocytes. As the primary organ of thymopoiesis, the thymus performs a crucial role in generating a self-tolerant but diverse repertoire of T cell receptors and peripheral T cell pool, with the capacity to recognize a wide variety of antigens and for the surveillance of malignancies. However, cells in the thymus are fragile and sensitive to changes in the external environment and acute insults such as infections, chemo- and radiation-therapy, resulting in thymic injury and degeneration. Though the thymus has the capacity to self-regenerate, it is often insufficient to reconstitute an intact thymic function. Thymic dysfunction leads to an increased risk of opportunistic infections, tumor relapse, autoimmunity, and adverse clinical outcome. Thus, exploiting the mechanism of thymic regeneration would provide new therapeutic options for these settings. This review summarizes the thymus’s development, factors causing thymic injury, and the strategies for improving thymus regeneration.
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Affiliation(s)
- Maxwell Duah
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Lingling Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Jingyi Shen
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Qiu Lan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Bin Pan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, China.,Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China
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37
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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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38
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Pinheiro RGR, Alves NL. The Early Postnatal Life: A Dynamic Period in Thymic Epithelial Cell Differentiation. Front Immunol 2021; 12:668528. [PMID: 34220815 PMCID: PMC8250140 DOI: 10.3389/fimmu.2021.668528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/04/2021] [Indexed: 11/20/2022] Open
Abstract
The microenvironments formed by cortical (c) and medullary (m) thymic epithelial cells (TECs) play a non-redundant role in the generation of functionally diverse and self-tolerant T cells. The role of TECs during the first weeks of the murine postnatal life is particularly challenging due to the significant augment in T cell production. Here, we critically review recent studies centered on the timely coordination between the expansion and maturation of TECs during this period and their specialized role in T cell development and selection. We further discuss how aging impacts on the pool of TEC progenitors and maintenance of functionally thymic epithelial microenvironments, and the implications of these chances in the capacity of the thymus to sustain regular thymopoiesis throughout life.
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Affiliation(s)
- Ruben G R Pinheiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Doctoral Program in Cell and Molecular Biology, Instituto de Ciências Biomédicas, Universidade do Porto, Porto, Portugal
| | - Nuno L Alves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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39
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Srinivasan J, Lancaster JN, Singarapu N, Hale LP, Ehrlich LIR, Richie ER. Age-Related Changes in Thymic Central Tolerance. Front Immunol 2021; 12:676236. [PMID: 33968086 PMCID: PMC8100025 DOI: 10.3389/fimmu.2021.676236] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 01/03/2023] Open
Abstract
Thymic epithelial cells (TECs) and hematopoietic antigen presenting cells (HAPCs) in the thymus microenvironment provide essential signals to self-reactive thymocytes that induce either negative selection or generation of regulatory T cells (Treg), both of which are required to establish and maintain central tolerance throughout life. HAPCs and TECs are comprised of multiple subsets that play distinct and overlapping roles in central tolerance. Changes that occur in the composition and function of TEC and HAPC subsets across the lifespan have potential consequences for central tolerance. In keeping with this possibility, there are age-associated changes in the cellular composition and function of T cells and Treg. This review summarizes changes in T cell and Treg function during the perinatal to adult transition and in the course of normal aging, and relates these changes to age-associated alterations in thymic HAPC and TEC subsets.
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Affiliation(s)
- Jayashree Srinivasan
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | | | - Nandini Singarapu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, TX, United States
| | - Laura P Hale
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Lauren I R Ehrlich
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, TX, United States
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40
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Laan M, Salumets A, Klein A, Reintamm K, Bichele R, Peterson H, Peterson P. Post-Aire Medullary Thymic Epithelial Cells and Hassall's Corpuscles as Inducers of Tonic Pro-Inflammatory Microenvironment. Front Immunol 2021; 12:635569. [PMID: 33868260 PMCID: PMC8050345 DOI: 10.3389/fimmu.2021.635569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
While there is convincing evidence on the role of Aire-positive medullary thymic epithelial cells (mTEC) in the induction of central tolerance, the nature and function of post-Aire mTECs and Hassall's corpuscles have remained enigmatic. Here we summarize the existing data on these late stages of mTEC differentiation with special focus on their potential to contribute to central tolerance induction by triggering the unique pro-inflammatory microenvironment in the thymus. In order to complement the existing evidence that has been obtained from mouse models, we performed proteomic analysis on microdissected samples from human thymic medullary areas at different differentiation stages. The analysis confirms that at the post-Aire stages, the mTECs lose their nuclei but maintain machinery required for translation and exocytosis and also upregulate proteins specific to keratinocyte differentiation and cornification. In addition, at the late stages of differentiation, the human mTECs display a distinct pro-inflammatory signature, including upregulation of the potent endogenous TLR4 agonist S100A8/S100A9. Collectively, the study suggests a novel mechanism by which the post-Aire mTECs and Hassall's corpuscles contribute to the thymic microenvironment with potential cues on the induction of central tolerance.
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Affiliation(s)
- Martti Laan
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ahto Salumets
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Annabel Klein
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kerli Reintamm
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Rudolf Bichele
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hedi Peterson
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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41
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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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42
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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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43
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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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44
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Thymic origins of autoimmunity-lessons from inborn errors of immunity. Semin Immunopathol 2021; 43:65-83. [PMID: 33532929 PMCID: PMC7925499 DOI: 10.1007/s00281-020-00835-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
During their intrathymic development, nascent T cells are empowered to protect against pathogens and to be operative for a life-long acceptance of self. While autoreactive effector T (Teff) cell progenitors are eliminated by clonal deletion, the intrathymic mechanisms by which thymic regulatory T cell (tTreg) progenitors maintain specificity for self-antigens but escape deletion to exert their regulatory functions are less well understood. Both tTreg and Teff development and selection result from finely coordinated interactions between their clonotypic T cell receptors (TCR) and peptide/MHC complexes expressed by antigen-presenting cells, such as thymic epithelial cells and thymic dendritic cells. tTreg function is dependent on expression of the FOXP3 transcription factor, and induction of FOXP3 gene expression by tTreg occurs during their thymic development, particularly within the thymic medulla. While initial expression of FOXP3 is downstream of TCR activation, constitutive expression is fixed by interactions with various transcription factors that are regulated by other extracellular signals like TCR and cytokines, leading to epigenetic modification of the FOXP3 gene. Most of the understanding of the molecular events underlying tTreg generation is based on studies of murine models, whereas gaining similar insight in the human system has been very challenging. In this review, we will elucidate how inborn errors of immunity illuminate the critical non-redundant roles of certain molecules during tTreg development, shedding light on how their abnormal development and function cause well-defined diseases that manifest with autoimmunity alone or are associated with states of immune deficiency and autoinflammation.
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45
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Irla M. RANK Signaling in the Differentiation and Regeneration of Thymic Epithelial Cells. Front Immunol 2021; 11:623265. [PMID: 33552088 PMCID: PMC7862717 DOI: 10.3389/fimmu.2020.623265] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/07/2020] [Indexed: 11/24/2022] Open
Abstract
Thymic epithelial cells (TECs) provide essential clues for the proliferation, survival, migration, and differentiation of thymocytes. Recent advances in mouse and human have revealed that TECs constitute a highly heterogeneous cell population with distinct functional properties. Importantly, TECs are sensitive to thymic damages engendered by myeloablative conditioning regimen used for bone marrow transplantation. These detrimental effects on TECs delay de novo T-cell production, which can increase the risk of morbidity and mortality in many patients. Alike that TECs guide the development of thymocytes, reciprocally thymocytes control the differentiation and organization of TECs. These bidirectional interactions are referred to as thymic crosstalk. The tumor necrosis factor receptor superfamily (TNFRSF) member, receptor activator of nuclear factor kappa-B (RANK) and its cognate ligand RANKL have emerged as key players of the crosstalk between TECs and thymocytes. RANKL, mainly provided by positively selected CD4+ thymocytes and a subset of group 3 innate lymphoid cells, controls mTEC proliferation/differentiation and TEC regeneration. In this review, I discuss recent advances that have unraveled the high heterogeneity of TECs and the implication of the RANK-RANKL signaling axis in TEC differentiation and regeneration. Targeting this cell-signaling pathway opens novel therapeutic perspectives to recover TEC function and T-cell production.
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Affiliation(s)
- Magali Irla
- Aix Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
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46
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Deng Y, Chen H, Zeng Y, Wang K, Zhang H, Hu H. Leaving no one behind: tracing every human thymocyte by single-cell RNA-sequencing. Semin Immunopathol 2021; 43:29-43. [PMID: 33449155 DOI: 10.1007/s00281-020-00834-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/22/2020] [Indexed: 02/05/2023]
Abstract
The thymus is the primary organ for T-cell development, providing an essential microenvironment consisting of the appropriate cytokine milieu and specialized stromal cells. Thymus-seeding progenitors from circulation immigrate into the thymus and undergo the stepwise T-cell specification, commitment, and selection processes. The transcriptional factors, epigenetic regulators, and signaling pathways involved in the T-cell development have been intensively studied using mouse models. Despite our growing knowledge of T-cell development, major questions remain unanswered regarding the ontogeny and early events of T-cell development at the fetal stage, especially in humans. The recently developed single-cell RNA-sequencing technique provides an ideal tool to investigate the heterogeneity of T-cell precursors and the molecular mechanisms underlying the divergent fates of certain T-cell precursors at the single-cell level. In this review, we aim to summarize the current progress of the study on human thymus organogenesis and thymocyte and thymic epithelial cell development, which is to shed new lights on developing novel strategies for in vitro T-cell regeneration and thymus rejuvenation.
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Affiliation(s)
- Yujun Deng
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Chen
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China.,State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Keyue Wang
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Huiyuan Zhang
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
| | - Hongbo Hu
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
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47
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Cosway EJ, James KD, Lucas B, Anderson G, White AJ. The thymus medulla and its control of αβT cell development. Semin Immunopathol 2020; 43:15-27. [PMID: 33306154 PMCID: PMC7925449 DOI: 10.1007/s00281-020-00830-z] [Citation(s) in RCA: 5] [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: 07/21/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023]
Abstract
αβT cells are an essential component of effective immune responses. The heterogeneity that lies within them includes subsets that express diverse self-MHC-restricted αβT cell receptors, which can be further subdivided into CD4+ helper, CD8+ cytotoxic, and Foxp3+ regulatory T cells. In addition, αβT cells also include invariant natural killer T cells that are very limited in αβT cell receptor repertoire diversity and recognise non-polymorphic CD1d molecules that present lipid antigens. Importantly, all αβT cell sublineages are dependent upon the thymus as a shared site of their development. Ongoing research has examined how the thymus balances the intrathymic production of multiple αβT cell subsets to ensure correct formation and functioning of the peripheral immune system. Experiments in both wild-type and genetically modified mice have been essential in revealing complex cellular and molecular mechanisms that regulate thymus function. In particular, studies have demonstrated the diverse and critical role that the thymus medulla plays in shaping the peripheral T cell pool. In this review, we summarise current knowledge on functional properties of the thymus medulla that enable the thymus to support the production of diverse αβT cell types.
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Affiliation(s)
- Emilie J Cosway
- Institute of Immunology and Immunotherapy, Floor 4 Institute for Biomedical Research, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kieran D James
- Institute of Immunology and Immunotherapy, Floor 4 Institute for Biomedical Research, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
| | - Beth Lucas
- Institute of Immunology and Immunotherapy, Floor 4 Institute for Biomedical Research, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, Floor 4 Institute for Biomedical Research, Medical School, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Andrea J White
- Institute of Immunology and Immunotherapy, Floor 4 Institute for Biomedical Research, Medical School, University of Birmingham, Birmingham, B15 2TT, UK
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48
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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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The contribution of thymic tolerance to central nervous system autoimmunity. Semin Immunopathol 2020; 43:135-157. [PMID: 33108502 PMCID: PMC7925481 DOI: 10.1007/s00281-020-00822-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022]
Abstract
Autoimmune diseases of the central nervous system (CNS) are associated with high levels of morbidity and economic cost. Research efforts have previously focused on the contribution of the peripheral adaptive and innate immune systems to CNS autoimmunity. However, a failure of thymic negative selection is a necessary step in CNS-reactive T cells escaping into the periphery. Even with defective thymic or peripheral tolerance, the development of CNS inflammation is rare. The reasons underlying this are currently poorly understood. In this review, we examine evidence implicating thymic selection in the pathogenesis of CNS autoimmunity. Animal models suggest that thymic negative selection is an important factor in determining susceptibility to and severity of CNS inflammation. There are indirect clinical data that suggest thymic function is also important in human CNS autoimmune diseases. Specifically, the association between thymoma and paraneoplastic encephalitis and changes in T cell receptor excision circles in multiple sclerosis implicate thymic tolerance in these diseases. We identify potential associations between CNS autoimmunity susceptibility factors and thymic tolerance. The therapeutic manipulation of thymopoiesis has the potential to open up new treatment modalities, but a better understanding of thymic tolerance in CNS autoimmunity is required before this can be realised.
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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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