1
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Hughes ES, Tuck LR, He Z, Ballou ER, Wallace EWJ. A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.14.543486. [PMID: 37398450 PMCID: PMC10312749 DOI: 10.1101/2023.06.14.543486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cryptococcus is a fungal pathogen whose virulence relies on proliferation in and dissemination to host sites, and on synthesis of a defensive yet metabolically costly polysaccharide capsule. Regulatory pathways required for Cryptococcus virulence include a GATA-like transcription factor, Gat201, that regulates Cryptococcal virulence in both capsule-dependent and capsule-independent ways. Here we show that Gat201 is part of a negative regulatory pathway that limits fungal survival at alkaline pH. RNA-seq analysis found strong induction of GAT201 expression within minutes of transfer to RPMI media at alkaline pH. Microscopy, growth curves, and colony forming unit assays show that in RPMI at alkaline pH wild-type Cryptococcus neoformans yeast cells produce capsule but do not bud or maintain viability, while gat201Δ cells make buds and maintain viability, yet fail to produce capsule. GAT201 is required for transcriptional upregulation of a specific set of genes, the majority of which are direct Gat201 targets. Evolutionary analysis shows that Gat201 is in a subfamily of GATA-like transcription factors that is conserved within pathogenic fungi but absent in model yeasts. This work identifies the Gat201 pathway as controlling a trade-off between proliferation and production of defensive capsule. The assays established here will allow characterisation of the mechanisms of action of the Gat201 pathway. Together, our findings urge improved understanding of the regulation of proliferation as a driver of fungal pathogenesis.
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Affiliation(s)
- Elizabeth S Hughes
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
| | - Laura R Tuck
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
| | - Zhenzhen He
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
| | | | - Edward W J Wallace
- Institute for Cell Biology, and Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh
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2
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Miccoli A, Pianese V, Bidoli C, Fausto AM, Scapigliati G, Picchietti S. Transcriptome profiling of microdissected cortex and medulla unravels functional regionalization in the European sea bass Dicentrarchus labrax thymus. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109319. [PMID: 38145782 DOI: 10.1016/j.fsi.2023.109319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
The thymus is a sophisticated primary lymphoid organ in jawed vertebrates, but knowledge on teleost thymus remains scarce. In this study, for the first time in the European sea bass, laser capture microdissection was leveraged to collect two thymic regions based on histological features, namely the cortex and the medulla. The two regions were then processed by RNAseq and in-depth functional transcriptome analyses with the aim of revealing differential gene expression patterns and gene sets enrichments, ultimately unraveling unique microenvironments imperative for the development of functional T cells. The sea bass cortex emerged as a hub of T cell commitment, somatic recombination, chromatin remodeling, cell cycle regulation, and presentation of self antigens from autophagy-, proteasome- or proteases-processed proteins. The cortex therefore accommodated extensive thymocyte proliferation and differentiation up to the checkpoint of positive selection. The medulla instead appeared as the center stage in autoimmune regulation by negative selection and deletion of autoreactive T cells, central tolerance mechanisms and extracellular matrix organization. Region-specific canonical markers of T and non-T lineage cells as well as signals for migration to/from, and trafficking within, the thymus were identified, shedding light on the highly coordinated and exquisitely complex bi-directional interactions among thymocytes and stromal components. Markers ascribable to thymic nurse cells and poorly characterized post-aire mTEC populations were found in the cortex and medulla, respectively. An in-depth data mining also exposed previously un-annotated genomic resources with differential signatures. Overall, our findings contribute to a broader understanding of the relationship between regional organization and function in the European sea bass thymus, and provide essential insights into the molecular mechanisms underlying T-cell mediated adaptive immune responses in teleosts.
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Affiliation(s)
- A Miccoli
- National Research Council, Institute for Marine Biological Resources and Biotechnology (IRBIM), 60125, Ancona, Italy
| | - V Pianese
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - C Bidoli
- Dept. of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - A M Fausto
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - G Scapigliati
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - S Picchietti
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy.
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3
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Fujimori S, Ohigashi I. The role of thymic epithelium in thymus development and age-related thymic involution. THE JOURNAL OF MEDICAL INVESTIGATION 2024; 71:29-39. [PMID: 38735722 DOI: 10.2152/jmi.71.29] [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] [Indexed: 05/14/2024]
Abstract
The establishment of an adaptive immune system is critical for protecting our bodies from neoplastic cancers and invading pathogens such as viruses and bacteria. As a primary lymphoid organ, the thymus generates lymphoid T cells that play a major role in the adaptive immune system. T cell generation in the thymus is controlled by interactions between thymocytes and other thymic cells, primarily thymic epithelial cells. Thus, the normal development and function of thymic epithelial cells are important for the generation of immunocompetent and self-tolerant T cells. On the other hand, the degeneration of the thymic epithelium due to thymic aging causes thymic involution, which is associated with the decline of adaptive immune function. Herein we summarize basic and current knowledge of the development and function of thymic epithelial cells and the mechanism of thymic involution. J. Med. Invest. 71 : 29-39, February, 2024.
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Affiliation(s)
- Sayumi Fujimori
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
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4
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Takahama Y. The thymoproteasome in shaping the CD8 + T-cell repertoire. Curr Opin Immunol 2023; 83:102336. [PMID: 37210932 PMCID: PMC10524569 DOI: 10.1016/j.coi.2023.102336] [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: 12/11/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023]
Abstract
The thymoproteasome is a type of proteasome expressed specifically in thymic cortical epithelial cells. Thymoproteasome affects antigen processing of major histocompatibility complex (MHC)-I-associated peptides and optimizes positive selection of CD8+ T cells. However, it remains unanswered whether and how thymoproteasome-dependent MHC-I-associated self-peptides contribute to positive selection of cortical thymocytes. This short piece discusses the potential mechanisms of thymoproteasome contribution to positive selection of MHC-I-restricted CD8+ T cells.
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Affiliation(s)
- Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda 20892, United States.
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5
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Sato-Fukuba M, Arakaki R, Ushio A, Otsuka K, Nagao R, Matsuzawa S, Tawara H, Tsunematsu T, Ishimaru N. CD4 + T-cell-dependent differentiation of CD23 + follicular B cells contributes to the pulmonary pathology in a primary Sjögren's syndrome mouse model. Front Immunol 2023; 14:1217492. [PMID: 37475871 PMCID: PMC10354287 DOI: 10.3389/fimmu.2023.1217492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/16/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease that affects the function of exocrine glands, such as the lacrimal and the salivary glands. Extraglandular lesions and malignant lymphoma also occur during the progressive stage of pSS. We have, herein, focused on the pulmonary lesions of pSS and have aimed clarifying their pathophysiological mechanism by comparing the glandular with the extraglandular lesions observed in a mouse model of pSS. Results The histopathological analysis of lung tissues obtained from NFS/sld mice that have undergone neonatal thymectomy was performed. Moreover, in vivo and in vitro experiments were conducted along with immunological analyses in order to characterize the unique phenotypes of the pulmonary lesions identified in these pSS model mice. Inflammatory lesions with a bronchus-associated lymphoid tissue-like structure were identified in the lungs of pSS model mice. In addition, relative to salivary gland lesions, pulmonary lesions showed increased CD23+ follicular B (FB) cells. In vitro and pulmonary B cells were more readily driven to CD23+ FB cell phenotype than salivary gland B cells in pSS model mice. Furthermore, the CD23+ FB cell differentiation was found to be enhanced in a CD4+ T-cell-dependent manner under a Th2-type condition in the lungs of herein examined pSS model mice. Discussion A Th2-type response in the pSS lung may promote the progression of autoimmune lesions through an enhanced abnormal differentiation of B cells.
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Affiliation(s)
- Mami Sato-Fukuba
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Department of Oral Medicine, Tokushima University Hospital, Tokushima, Japan
| | - Rieko Arakaki
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Aya Ushio
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kunihiro Otsuka
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Ruka Nagao
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Shigefumi Matsuzawa
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Hiroaki Tawara
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Takaaki Tsunematsu
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
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6
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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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7
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Osei-Amponsa V, Walters KJ. Proteasome substrate receptors and their therapeutic potential. Trends Biochem Sci 2022; 47:950-964. [PMID: 35817651 PMCID: PMC9588529 DOI: 10.1016/j.tibs.2022.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 11/22/2022]
Abstract
The ubiquitin-proteasome system (UPS) is critical for protein quality control and regulating protein lifespans. Following ubiquitination, UPS substrates bind multidomain receptors that, in addition to ubiquitin-binding sites, contain functional domains that bind to deubiquitinating enzymes (DUBs) or the E3 ligase E6AP/UBE3A. We provide an overview of the proteasome, focusing on its receptors and DUBs. We highlight the key role of dynamics and importance of the substrate receptors having domains for both binding and processing ubiquitin chains. The UPS is rich with therapeutic opportunities, with proteasome inhibitors used clinically and ongoing development of small molecule proteolysis targeting chimeras (PROTACs) for the degradation of disease-associated proteins. We discuss the therapeutic potential of proteasome receptors, including hRpn13, for which PROTACs have been developed.
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Affiliation(s)
- Vasty Osei-Amponsa
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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8
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Blanco DB, Chapman NM, Raynor JL, Xu C, Su W, Kc A, Li W, Lim SA, Schattgen S, Shi H, Risch I, Sun Y, Dhungana Y, Kim Y, Wei J, Rankin S, Neale G, Thomas PG, Yang K, Chi H. PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis. Nat Cell Biol 2022; 24:1642-1654. [PMID: 36302969 PMCID: PMC10080469 DOI: 10.1038/s41556-022-01011-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/12/2022] [Indexed: 01/18/2023]
Abstract
Phosphatase and tensin homologue (PTEN) is frequently mutated in human cancer, but its roles in lymphopoiesis and tissue homeostasis remain poorly defined. Here we show that PTEN orchestrates a two-step developmental process linking antigen receptor and IL-23-Stat3 signalling to type-17 innate-like T cell generation. Loss of PTEN leads to pronounced accumulation of mature IL-17-producing innate-like T cells in the thymus. IL-23 is essential for their accumulation, and ablation of IL-23 or IL-17 signalling rectifies the reduced survival of female PTEN-haploinsufficient mice that model human patients with PTEN mutations. Single-cell transcriptome and network analyses revealed the dynamic regulation of PTEN, mTOR and metabolic activities that accompanied type-17 cell programming. Furthermore, deletion of mTORC1 or mTORC2 blocks PTEN loss-driven type-17 cell accumulation, and this is further shaped by the Foxo1 and Stat3 pathways. Collectively, our study establishes developmental and metabolic signalling networks underpinning type-17 cell fate decisions and their functional effects at coordinating PTEN-dependent tissue homeostasis.
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Affiliation(s)
- Daniel Bastardo Blanco
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nicole M Chapman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jana L Raynor
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chengxian Xu
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wei Su
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anil Kc
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wei Li
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seon Ah Lim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefan Schattgen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Isabel Risch
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Sun
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yogesh Dhungana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yunjung Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun Wei
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sherri Rankin
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kai Yang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Matsuda-Lennikov M, Ohigashi I, Takahama Y. Tissue-specific proteasomes in generation of MHC class I peptides and CD8 + T cells. Curr Opin Immunol 2022; 77:102217. [PMID: 35689940 PMCID: PMC9339533 DOI: 10.1016/j.coi.2022.102217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/21/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Thymoproteasomes and immunoproteasomes are two types of tissue-specific proteasomes, which contribute to the production of major histocompatibility complex (MHC) class I (MHC-I)-associated peptides that are important for the development and function of CD8+ cytotoxic T cells. Thymoproteasomes are specifically expressed by cortical thymic epithelial cells and are important for MHC-I-dependent positive selection of developing thymocytes, whereas immunoproteasomes are abundant in many other cells, including hematopoietic cells and medullary thymic epithelial cells. Here we summarize the role of these two tissue-specific proteasomes, focusing on their functions in the development of CD8+ T cells in the thymus.
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Affiliation(s)
- Mami Matsuda-Lennikov
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda 20892, USA
| | - Izumi Ohigashi
- Institute for Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda 20892, USA.
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10
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Fujimori S, Ohigashi I, Abe H, Matsushita Y, Katagiri T, Taketo MM, Takahama Y, Takada S. Fine-tuning of β-catenin in mouse thymic epithelial cells is required for postnatal T-cell development. eLife 2022; 11:69088. [PMID: 35042581 PMCID: PMC8769649 DOI: 10.7554/elife.69088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 01/05/2022] [Indexed: 11/26/2022] Open
Abstract
In the thymus, the thymic epithelium provides a microenvironment essential for the development of functionally competent and self-tolerant T cells. Previous findings showed that modulation of Wnt/β-catenin signaling in mouse thymic epithelial cells (TECs) disrupts embryonic thymus organogenesis. However, the role of β-catenin in TECs for postnatal T-cell development remains to be elucidated. Here, we analyzed gain-of-function (GOF) and loss-of-function (LOF) of β-catenin highly specific in mouse TECs. We found that GOF of β-catenin in TECs results in severe thymic dysplasia and T-cell deficiency beginning from the embryonic period. By contrast, LOF of β-catenin in TECs reduces the number of cortical TECs and thymocytes modestly and only postnatally. These results indicate that fine-tuning of β-catenin expression within a permissive range is required for TECs to generate an optimal microenvironment to support postnatal T-cell development.
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Affiliation(s)
- Sayumi Fujimori
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University
- National Institute for Basic Biology, National Institutes of Natural Sciences
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University
| | - Hayato Abe
- Student Laboratory, School of Medicine, Tokushima University
| | - Yosuke Matsushita
- Division of Genome Medicine, Institute of Advanced Medical Sciences, Tokushima University
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute of Advanced Medical Sciences, Tokushima University
| | - Makoto M Taketo
- Institute for Advancement of Clinical and Translational Science, Kyoto University Hospital
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health
| | - Shinji Takada
- National Institute for Basic Biology, National Institutes of Natural Sciences
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences
- Department of Basic Biology in the School of Life Science, The Graduate University for Advanced Studies (SOKENDAI)
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11
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Shevyrev D, Tereshchenko V, Kozlov V, Sennikov S. Phylogeny, Structure, Functions, and Role of AIRE in the Formation of T-Cell Subsets. Cells 2022; 11:194. [PMID: 35053310 PMCID: PMC8773594 DOI: 10.3390/cells11020194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
It is well known that the most important feature of adaptive immunity is the specificity that provides highly precise recognition of the self, altered-self, and non-self. Due to the high specificity of antigen recognition, the adaptive immune system participates in the maintenance of genetic homeostasis, supports multicellularity, and protects an organism from different pathogens at a qualitatively different level than innate immunity. This seemingly simple property is based on millions of years of evolution that led to the formation of diversification mechanisms of antigen-recognizing receptors and later to the emergence of a system of presentation of the self and non-self antigens. The latter could have a crucial significance because the presentation of nearly complete diversity of auto-antigens in the thymus allows for the "calibration" of the forming repertoires of T-cells for the recognition of self, altered-self, and non-self antigens that are presented on the periphery. The central role in this process belongs to promiscuous gene expression by the thymic epithelial cells that express nearly the whole spectrum of proteins encoded in the genome, meanwhile maintaining their cellular identity. This complex mechanism requires strict control that is executed by several transcription factors. One of the most important of them is AIRE. This noncanonical transcription factor not only regulates the processes of differentiation and expression of peripheral tissue-specific antigens in the thymic medullar epithelial cells but also controls intercellular interactions in the thymus. Besides, it participates in an increase in the diversity and transfer of presented antigens and thus influences the formation of repertoires of maturing thymocytes. Due to these complex effects, AIRE is also called a transcriptional regulator. In this review, we briefly described the history of AIRE discovery, its structure, functions, and role in the formation of antigen-recognizing receptor repertoires, along with other transcription factors. We focused on the phylogenetic prerequisites for the development of modern adaptive immunity and emphasized the importance of the antigen presentation system.
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Affiliation(s)
- Daniil Shevyrev
- Research Institute for Fundamental and Clinical Immunology (RIFCI), 630099 Novosibirsk, Russia; (V.T.); (V.K.); (S.S.)
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12
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Ohigashi I, Matsuda-Lennikov M, Takahama Y. Peptides for T cell selection in the thymus. Peptides 2021; 146:170671. [PMID: 34624431 DOI: 10.1016/j.peptides.2021.170671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/15/2022]
Abstract
Major histocompatibility complex (MHC)-associated peptides generated and displayed by antigen-presenting cells in the thymus are essential for the generation of functional and self-tolerant T cells that protect our body from various pathogens. The peptides displayed by cortical thymic epithelial cells (cTECs) are generated by unique enzymatic machineries including the thymoproteasomes, and are involved in the positive selection of self-protective T cells. On the other hand, the peptides displayed by medullary thymic epithelial cells (mTECs) and thymic dendritic cells (DCs) are involved in further selection to establish self-tolerance in T cells. Although the biochemical nature of the peptide repertoire displayed in the thymus remains unclear, many studies have suggested a thymus-specific mechanism for the generation of MHC-associated peptides in the thymus. In this review, we summarize basic knowledge and recent advances in MHC-associated thymic peptides, focusing on the generation and function of thymoproteasome-dependent peptides specifically displayed by cTECs.
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Affiliation(s)
- Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, 770-8503, Japan.
| | - Mami Matsuda-Lennikov
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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13
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Ohigashi I, Takahama Y. Specific impact of β5t on proteasome subunit composition in cortical thymic epithelial cells. Cell Rep 2021; 36:109657. [PMID: 34496235 PMCID: PMC8442848 DOI: 10.1016/j.celrep.2021.109657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/28/2021] [Accepted: 08/12/2021] [Indexed: 01/16/2023] Open
Abstract
β5t is a cortical thymic epithelial cell (cTEC)-specific component of the thymoproteasome, which is essential for the optimal production of functionally competent CD8+ T cells. Our recent analysis showed a specific impact of β5t on proteasome subunit composition in cTECs, supporting the possibility that the thymoproteasome optimizes CD8+ T cell development through the production of MHC-I-associated unique self-peptides in cTECs. However, a recent article reports that β5t regulates the expression of hundreds of cTEC genes and affects both CD4+ and CD8+ thymocytes by causing oxidative stress in thymocytes. The authors further analyze our published data and describe that they confirm their conclusions. Here, we examine the issues that they raise and conclude that, rather than regulating hundreds of genes in cTECs, β5t has a highly specific impact in cTECs on proteasome subunit composition. This Matters Arising Response article addresses the Apavaloaei et al. (2021) Matters Arising paper, published concurrently in Cell Reports.
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Affiliation(s)
- Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Ohigashi I, Takahama Y. Thymoproteasome optimizes positive selection of CD8 + T cells without contribution of negative selection. Adv Immunol 2021; 149:1-23. [PMID: 33993918 DOI: 10.1016/bs.ai.2021.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Functionally competent and self-tolerant T cell repertoire is shaped through positive and negative selection in the cortical and medullary microenvironments of the thymus. The thymoproteasome specifically expressed in the cortical thymic epithelium is essential for the optimal generation of CD8+ T cells. Although how the thymoproteasome governs the generation of CD8+ T cells is not fully understood, accumulating evidence suggests that the thymoproteasome optimizes CD8+ T cell production through the processing of self-peptides associated with MHC class I molecules expressed by cortical thymic epithelial cells. In this review, we describe recent advances in the mechanism of thymoproteasome-dependent generation of CD8+ T cells, focusing on the process of cortical positive selection independent of apoptosis-mediated negative selection.
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Affiliation(s)
- Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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Frantzeskakis M, Takahama Y, Ohigashi I. The Role of Proteasomes in the Thymus. Front Immunol 2021; 12:646209. [PMID: 33815406 PMCID: PMC8017227 DOI: 10.3389/fimmu.2021.646209] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/05/2021] [Indexed: 12/26/2022] Open
Abstract
The thymus provides a microenvironment that supports the generation and selection of T cells. Cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells (mTECs) are essential components of the thymic microenvironment and present MHC-associated self-antigens to developing thymocytes for the generation of immunocompetent and self-tolerant T cells. Proteasomes are multicomponent protease complexes that degrade ubiquitinated proteins and produce peptides that are destined to be associated with MHC class I molecules. cTECs specifically express thymoproteasomes that are essential for optimal positive selection of CD8+ T cells, whereas mTECs, which contribute to the establishment of self-tolerance in T cells, express immunoproteasomes. Immunoproteasomes are also detectable in dendritic cells and developing thymocytes, additionally contributing to T cell development in the thymus. In this review, we summarize the functions of proteasomes expressed in the thymus, focusing on recent findings pertaining to the functions of the thymoproteasomes and the immunoproteasomes.
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Affiliation(s)
- Melina Frantzeskakis
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, Bethesda, MD, United States
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, Bethesda, MD, United States
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
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