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Grammer C, Komorowska JA, Swann JB. Vhl safeguards thymic epithelial cell identity and thymopoietic capacity by constraining Hif1a activity during development. iScience 2024; 27:110258. [PMID: 39040069 PMCID: PMC11261450 DOI: 10.1016/j.isci.2024.110258] [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: 07/12/2022] [Revised: 03/15/2024] [Accepted: 06/10/2024] [Indexed: 07/24/2024] Open
Abstract
The thymus is a physiologically hypoxic organ and fulfills its role of generating T cells under low-oxygen conditions. We have therefore investigated how thymic epithelial cells (TECs) cope with physiological hypoxia by focusing on the role of the Hif1a-Vhl axis. In most cell types, the oxygen-labile transcriptional regulator Hif1a is a central player in co-ordinating responses to low oxygen: under normoxic conditions Hif1a is rapidly degraded in a Vhl-guided manner; however, under hypoxic conditions Hif1a is stabilized and can execute its transcriptional functions. Unexpectedly, we find that, although TECs reside in a hypoxic microenvironment, they express little Hif1a protein and do not require Hif1a for their development or function. Instead, we find that Vhl function in TECs is vital to constrain Hif1a activity, as loss of Vhl results in dramatic defects in TEC differentiation and thymopoiesis, which can be rescued by Hif1a co-depletion.
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Affiliation(s)
- Christiane Grammer
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Julia A. Komorowska
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Albert Ludwig University, Faculty of Biology, Freiburg, Germany
| | - Jeremy B. Swann
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
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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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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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Moses A, Bhalla P, Thompson A, Lai L, Coskun FS, Seroogy CM, de la Morena MT, Wysocki CA, van Oers NSC. Comprehensive phenotypic analysis of diverse FOXN1 variants. J Allergy Clin Immunol 2023; 152:1273-1291.e15. [PMID: 37419334 PMCID: PMC11071152 DOI: 10.1016/j.jaci.2023.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/05/2023] [Accepted: 06/08/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Thymus hypoplasia due to stromal cell problems has been linked to mutations in several transcription factors, including Forkhead box N1 (FOXN1). FOXN1 supports T-cell development by regulating the formation and expansion of thymic epithelial cells (TECs). While autosomal recessive FOXN1 mutations result in a nude and severe combined immunodeficiency phenotype, the impact of single-allelic or compound heterozygous FOXN1 mutations is less well-defined. OBJECTIVE With more than 400 FOXN1 mutations reported, their impact on protein function and thymopoiesis remains unclear for most variants. We developed a systematic approach to delineate the functional impact of diverse FOXN1 variants. METHODS Selected FOXN1 variants were tested with transcriptional reporter assays and imaging studies. Thymopoiesis was assessed in mouse lines genocopying several human FOXN1 variants. Reaggregate thymus organ cultures were used to compare the thymopoietic potential of the FOXN1 variants. RESULTS FOXN1 variants were categorized into benign, loss- or gain-of-function, and/or dominant-negatives. Dominant negative activities mapped to frameshift variants impacting the transactivation domain. A nuclear localization signal was mapped within the DNA binding domain. Thymopoiesis analyses with mouse models and reaggregate thymus organ cultures revealed distinct consequences of particular Foxn1 variants on T-cell development. CONCLUSIONS The potential effect of a FOXN1 variant on T-cell output from the thymus may relate to its effects on transcriptional activity, nuclear localization, and/or dominant negative functions. A combination of functional assays and thymopoiesis comparisons enabled a categorization of diverse FOXN1 variants and their potential impact on T-cell output from the thymus.
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Affiliation(s)
- Angela Moses
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Pratibha Bhalla
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Austin Thompson
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Laijun Lai
- Department of Allied Health Sciences, University of Connecticut, Storrs, Conn
| | - Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Christine M Seroogy
- the Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Maria Teresa de la Morena
- the Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Wash
| | - Christian A Wysocki
- Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex; Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Nicolai S C van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex; Departments of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex; Microbiology, University of Texas Southwestern Medical Center, Dallas, Tex.
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Boehm T, Morimoto R, Trancoso I, Aleksandrova N. Genetic conflicts and the origin of self/nonself-discrimination in the vertebrate immune system. Trends Immunol 2023; 44:372-383. [PMID: 36941153 DOI: 10.1016/j.it.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/22/2023]
Abstract
Genetic conflicts shape the genomes of prokaryotic and eukaryotic organisms. Here, we argue that some of the key evolutionary novelties of adaptive immune systems of vertebrates are descendants of prokaryotic toxin-antitoxin (TA) systems. Cytidine deaminases and RAG recombinase have evolved from genotoxic enzymes to programmable editors of host genomes, supporting the astounding discriminatory capability of variable lymphocyte receptors of jawless vertebrates, as well as immunoglobulins and T cell receptors of jawed vertebrates. The evolutionarily recent lymphoid lineage is uniquely sensitive to mutations of the DNA maintenance methylase, which is an orphaned distant relative of prokaryotic restriction-modification systems. We discuss how the emergence of adaptive immunity gave rise to higher order genetic conflicts between genetic parasites and their vertebrate host.
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Affiliation(s)
- Thomas Boehm
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Ryo Morimoto
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Inês Trancoso
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Bhalla P, Du Q, Kumar A, Xing C, Moses A, Dozmorov I, Wysocki CA, Cleaver OB, Pirolli TJ, Markert ML, de la Morena MT, Baldini A, van Oers NS. Mesenchymal cell replacement corrects thymic hypoplasia in murine models of 22q11.2 deletion syndrome. J Clin Invest 2022; 132:e160101. [PMID: 36136514 PMCID: PMC9663160 DOI: 10.1172/jci160101] [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: 03/15/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
22q11.2 deletion syndrome (22q11.2DS) is the most common human chromosomal microdeletion, causing developmentally linked congenital malformations, thymic hypoplasia, hypoparathyroidism, and/or cardiac defects. Thymic hypoplasia leads to T cell lymphopenia, which most often results in mild SCID. Despite decades of research, the molecular underpinnings leading to thymic hypoplasia in 22q11.2DS remain unknown. Comparison of embryonic thymuses from mouse models of 22q11.2DS (Tbx1neo2/neo2) revealed proportions of mesenchymal, epithelial, and hematopoietic cell types similar to those of control thymuses. Yet, the small thymuses were growth restricted in fetal organ cultures. Replacement of Tbx1neo2/neo2 thymic mesenchymal cells with normal ones restored tissue growth. Comparative single-cell RNA-Seq of embryonic thymuses uncovered 17 distinct cell subsets, with transcriptome differences predominant in the 5 mesenchymal subsets from the Tbx1neo2/neo2 cell line. The transcripts affected included those for extracellular matrix proteins, consistent with the increased collagen deposition we observed in the small thymuses. Attenuating collagen cross-links with minoxidil restored thymic tissue expansion for hypoplastic lobes. In colony-forming assays, the Tbx1neo2/neo2-derived mesenchymal cells had reduced expansion potential, in contrast to the normal growth of thymic epithelial cells. These findings suggest that mesenchymal cells were causal to the small embryonic thymuses in the 22q11.2DS mouse models, which was correctable by substitution with normal mesenchyme.
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Affiliation(s)
| | | | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development
- Departments of Bioinformatics and
- Population and Data Sciences, Departments of
| | | | | | | | | | - Timothy J. Pirolli
- Division of Pediatric Cardiothoracic Surgery, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mary Louise Markert
- Departments of Pediatrics and Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Maria Teresa de la Morena
- Division of Immunology, Department of Pediatrics, University of Washington, and Seattle Children’s Hospital, Seattle, Washington, USA
| | - Antonio Baldini
- Department Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Nicolai S.C. van Oers
- Department of Immunology
- Pediatrics
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Bhalla P, Su DM, van Oers NSC. Thymus Functionality Needs More Than a Few TECs. Front Immunol 2022; 13:864777. [PMID: 35757725 PMCID: PMC9229346 DOI: 10.3389/fimmu.2022.864777] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/03/2022] [Indexed: 12/18/2022] Open
Abstract
The thymus, a primary lymphoid organ, produces the T cells of the immune system. Originating from the 3rd pharyngeal pouch during embryogenesis, this organ functions throughout life. Yet, thymopoiesis can be transiently or permanently damaged contingent on the types of systemic stresses encountered. The thymus also undergoes a functional decline during aging, resulting in a progressive reduction in naïve T cell output. This atrophy is evidenced by a deteriorating thymic microenvironment, including, but not limited, epithelial-to-mesenchymal transitions, fibrosis and adipogenesis. An exploration of cellular changes in the thymus at various stages of life, including mouse models of in-born errors of immunity and with single cell RNA sequencing, is revealing an expanding number of distinct cell types influencing thymus functions. The thymus microenvironment, established through interactions between immature and mature thymocytes with thymus epithelial cells (TEC), is well known. Less well appreciated are the contributions of neural crest cell-derived mesenchymal cells, endothelial cells, diverse hematopoietic cell populations, adipocytes, and fibroblasts in the thymic microenvironment. In the current review, we will explore the contributions of the many stromal cell types participating in the formation, expansion, and contraction of the thymus under normal and pathophysiological processes. Such information will better inform approaches for restoring thymus functionality, including thymus organoid technologies, beneficial when an individuals’ own tissue is congenitally, clinically, or accidentally rendered non-functional.
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Affiliation(s)
- Pratibha Bhalla
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Dong-Ming Su
- Department of Microbiology, Immunology & Genetics, The University of North Texas Health Sciences Center, Fort Worth, TX, United States
| | - Nicolai S C van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Zapata AG. Lympho-Hematopoietic Microenvironments and Fish Immune System. BIOLOGY 2022; 11:747. [PMID: 35625475 PMCID: PMC9138301 DOI: 10.3390/biology11050747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/20/2022]
Abstract
In the last 50 years information on the fish immune system has increased importantly, particularly that on species of marked commercial interest (i.e., salmonids, cods, catfish, sea breams), that occupy a key position in the vertebrate phylogenetical tree (i.e., Agnatha, Chondrichtyes, lungfish) or represent consolidated experimental models, such as zebrafish or medaka. However, most obtained information was based on genetic sequence analysis with little or no information on the cellular basis of the immune responses. Although jawed fish contain a thymus and lympho-hematopoietic organs equivalents to mammalian bone marrow, few studies have accounted for the presumptive relationships between the organization of these cell microenvironments and the known immune capabilities of the fish immune system. In the current review, we analyze this topic providing information on: (1) The origins of T and B lymphopoiesis in Agnatha and jawed fish; (2) the remarkable organization of the thymus of teleost fish; (3) the occurrence of numerous, apparently unrelated organs housing lympho-hematopoietic progenitors and, presumably, B lymphopoiesis; (4) the existence of fish immunological memory in the absence of germinal centers.
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Affiliation(s)
- Agustín G. Zapata
- Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; ; Tel.: +34-913-944-979
- Health Research Institute, Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
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Hirano KI, Hosokawa H, Yahata T, Ando K, Tanaka M, Imai J, Yazawa M, Ohtsuka M, Negishi N, Habu S, Sato T, Hozumi K. Dll1 Can Function as a Ligand of Notch1 and Notch2 in the Thymic Epithelium. Front Immunol 2022; 13:852427. [PMID: 35371023 PMCID: PMC8968733 DOI: 10.3389/fimmu.2022.852427] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
T-cell development in the thymus is dependent on Notch signaling induced by the interaction of Notch1, present on immigrant cells, with a Notch ligand, delta-like (Dll) 4, on the thymic epithelial cells. Phylogenetic analysis characterizing the properties of the Dll4 molecule suggests that Dll4 emerged from the common ancestor of lobe- and ray-finned fishes and diverged into bony fishes and terrestrial organisms, including mammals. The thymus evolved in cartilaginous fishes before Dll4, suggesting that T-cell development in cartilaginous fishes is dependent on Dll1 instead of Dll4. In this study, we compared the function of both Dll molecules in the thymic epithelium using Foxn1-cre and Dll4-floxed mice with conditional transgenic alleles in which the Dll1 or Dll4 gene is transcribed after the cre-mediated excision of the stop codon. The expression of Dll1 in the thymic epithelium completely restored the defect in the Dll4-deficient condition, suggesting that Dll1 can trigger Notch signaling that is indispensable for T-cell development in the thymus. Moreover, using bone marrow chimeras with Notch1- or Notch2-deficient hematopoietic cells, we showed that Dll1 is able to activate Notch signaling, which is sufficient to induce T-cell development, with both the receptors, in contrast to Dll4, which works only with Notch1, in the thymic environment. These results strongly support the hypothesis that Dll1 regulates T-cell development via Notch1 and/or Notch2 in the thymus of cartilaginous fishes and that Dll4 has replaced Dll1 in inducing thymic Notch signaling via Notch1 during evolution.
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Affiliation(s)
- Ken-ichi Hirano
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
| | - Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
- Institute of Medical Sciences, Tokai University, Isehara, Japan
| | - Takashi Yahata
- Institute of Medical Sciences, Tokai University, Isehara, Japan
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Kiyoshi Ando
- Institute of Medical Sciences, Tokai University, Isehara, Japan
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Masayuki Tanaka
- Support Center of Medical Research and Education, Tokai University School of Medicine, Isehara, Japan
| | - Jin Imai
- Divison of Gastroenterology and Hepatology, Tokai University School of Medicine, Isehara, Japan
| | - Masaki Yazawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
| | - Masato Ohtsuka
- Institute of Medical Sciences, Tokai University, Isehara, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Naoko Negishi
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Sonoko Habu
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Takehito Sato
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
| | - Katsuto Hozumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Japan
- *Correspondence: Katsuto Hozumi,
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