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Sanchez Sanchez G, Emmrich S, Georga M, Papadaki A, Kossida S, Seluanov A, Gorbunova V, Vermijlen D. Invariant γδTCR natural killer-like effector T cells in the naked mole-rat. Nat Commun 2024; 15:4248. [PMID: 38762584 PMCID: PMC11102460 DOI: 10.1038/s41467-024-48652-z] [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: 07/20/2023] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
The naked mole-rat (Heterocephalus glaber) is a long-lived rodent species showing resistance to the development of cancer. Although naked mole-rats have been reported to lack natural killer (NK) cells, γδ T cell-based immunity has been suggested in this species, which could represent an important arm of the immune system for antitumor responses. Here, we investigate the biology of these unconventional T cells in peripheral tissues (blood, spleen) and thymus of the naked mole-rat at different ages by TCR repertoire profiling and single-cell gene expression analysis. Using our own TCR annotation in the naked mole-rat genome, we report that the γδ TCR repertoire is dominated by a public invariant Vγ4-2/Vδ1-4 TCR, containing the complementary-determining-region-3 (CDR3)γ CTYWDSNYAKKLF / CDR3δ CALWELRTGGITAQLVF that are likely generated by short-homology-repeat-driven DNA rearrangements. This invariant TCR is specifically found in γδ T cells expressing genes associated with NK cytotoxicity and is generated in both the thoracic and cervical thymus of the naked mole-rat until adult life. Our results indicate that invariant Vγ4-2/Vδ1-4 NK-like effector T cells in the naked mole-rat can contribute to tumor immunosurveillance by γδ TCR-mediated recognition of a common molecular signal.
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MESH Headings
- Animals
- Mole Rats/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Thymus Gland/immunology
- Thymus Gland/cytology
- Killer Cells, Natural/immunology
- Spleen/immunology
- Complementarity Determining Regions/genetics
- Natural Killer T-Cells/immunology
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Affiliation(s)
- Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Gosselies, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Maria Georga
- IMGT®, the international ImMunoGenetics information system®, Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Ariadni Papadaki
- IMGT®, the international ImMunoGenetics information system®, Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Sofia Kossida
- IMGT®, the international ImMunoGenetics information system®, Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
- Department of Medicine, University of Rochester Medical Center and Medicine, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
- Department of Medicine, University of Rochester Medical Center and Medicine, University of Rochester, Rochester, NY, USA
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Gosselies, Belgium.
- WELBIO Department, WEL Research Institute, Wavre, Belgium.
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Li TT, Xia T, Wu JQ, Hong H, Sun ZL, Wang M, Ding FR, Wang J, Jiang S, Li J, Pan J, Yang G, Feng JN, Dai YP, Zhang XM, Zhou T, Li T. De novo genome assembly depicts the immune genomic characteristics of cattle. Nat Commun 2023; 14:6601. [PMID: 37857610 PMCID: PMC10587341 DOI: 10.1038/s41467-023-42161-1] [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: 02/17/2023] [Accepted: 09/30/2023] [Indexed: 10/21/2023] Open
Abstract
Immunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current reference genome (ARS-UCD1.2), 156 gaps are closed and 467 scaffolds are located in our assembly. Importantly, the immunogenomic regions, including three immunoglobulin (IG) loci, four T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. With the characterization of 258 IG genes and 657 TR genes distributed across seven genomic loci, we present a detailed depiction of immune gene diversity in cattle. Moreover, the MHC gene structures are integrally revealed with properly phased haplotypes. Together, our work describes a more complete cattle genome, and provides a comprehensive view of its complex immune-genome.
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Affiliation(s)
- Ting-Ting Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Tian Xia
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jia-Qi Wu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Hao Hong
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Zhao-Lin Sun
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Ming Wang
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Fang-Rong Ding
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Jing Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Shuai Jiang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jin Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jie Pan
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Guang Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jian-Nan Feng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yun-Ping Dai
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Xue-Min Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Tao Zhou
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China.
| | - Tao Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China.
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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3
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Lefranc MP, Lefranc G. IMGT®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. Biomolecules 2022; 12:biom12030381. [PMID: 35327572 PMCID: PMC8945572 DOI: 10.3390/biom12030381] [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: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
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Linguiti G, Giannico F, D’Addabbo P, Pala A, Caputi Jambrenghi A, Ciccarese S, Massari S, Antonacci R. The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla. Genes (Basel) 2022; 13:genes13020177. [PMID: 35205222 PMCID: PMC8872565 DOI: 10.3390/genes13020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
The domestic pig (Sus scrofa) is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda, and Cetacea suborders. The pig TRG genomic structure reiterates the peculiarity of the organization of Cetartiodactyla loci in TRGC “cassettes”, each containing the basic V-J-J-C unit. Eighteen genes arranged in four TRGC cassettes, form the pig TRG locus. All the functional TRG genes were expressed, and the TRGV genes preferentially rearrange with the TRGJ genes within their own cassette, which correlates the diversity of the γ-chain repertoire with the number of cassettes. Among them, the TRGC5, located at the 5′ end of the locus, is the only cassette that retains a marked homology with the corresponding TRGC cassettes of all the analyzed species. The preservation of the TRGC5 cassette for such a long evolutionary time presumes a highly specialized function of its genes, which could be essential for the survival of species. Therefore, the maintenance of this cassette in pigs confirms that it is the most evolutionarily ancient within Cetartiodactyla, and it has undergone a process of duplication to give rise to the other TRGC cassettes in the different artiodactyl species in a lineage-specific manner.
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Affiliation(s)
- Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (G.L.); (P.D.); (A.P.); (S.C.)
| | - Francesco Giannico
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Strada Provincial 62 per Casamassima Km 3, 70010 Bari, Italy;
| | - Pietro D’Addabbo
- Department of Biology, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (G.L.); (P.D.); (A.P.); (S.C.)
| | - Angela Pala
- Department of Biology, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (G.L.); (P.D.); (A.P.); (S.C.)
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy;
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (G.L.); (P.D.); (A.P.); (S.C.)
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (G.L.); (P.D.); (A.P.); (S.C.)
- Correspondence:
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5
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Manso T, Folch G, Giudicelli V, Jabado-Michaloud J, Kushwaha A, Nguefack Ngoune V, Georga M, Papadaki A, Debbagh C, Pégorier P, Bertignac M, Hadi-Saljoqi S, Chentli I, Cherouali K, Aouinti S, El Hamwi A, Albani A, Elazami Elhassani M, Viart B, Goret A, Tran A, Sanou G, Rollin M, Duroux P, Kossida S. IMGT® databases, related tools and web resources through three main axes of research and development. Nucleic Acids Res 2021; 50:D1262-D1272. [PMID: 34875068 PMCID: PMC8728119 DOI: 10.1093/nar/gkab1136] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 11/15/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org/, is at the forefront of the immunogenetics and immunoinformatics fields with more than 30 years of experience. IMGT® makes available databases and tools to the scientific community pertaining to the adaptive immune response, based on the IMGT-ONTOLOGY. We focus on the recent features of the IMGT® databases, tools, reference directories and web resources, within the three main axes of IMGT® research and development. Axis I consists in understanding the adaptive immune response, by deciphering the identification and characterization of the immunoglobulin (IG) and T cell receptor (TR) genes in jawed vertebrates. It is the starting point of the two other axes, namely the analysis and exploration of the expressed IG and TR repertoires based on comparison with IMGT reference directories in normal and pathological situations (Axis II) and the analysis of amino acid changes and functions of 2D and 3D structures of antibody and TR engineering (Axis III).
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Affiliation(s)
- Taciana Manso
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Géraldine Folch
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Joumana Jabado-Michaloud
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Anjana Kushwaha
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Viviane Nguefack Ngoune
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Maria Georga
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Ariadni Papadaki
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Chahrazed Debbagh
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Perrine Pégorier
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Morgane Bertignac
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Saida Hadi-Saljoqi
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Imène Chentli
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Karima Cherouali
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Safa Aouinti
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Amar El Hamwi
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Alexandre Albani
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Merouane Elazami Elhassani
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Benjamin Viart
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Agathe Goret
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Anna Tran
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Gaoussou Sanou
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Maël Rollin
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Patrice Duroux
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Sofia Kossida
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
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Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immunol 2021; 12:753960. [PMID: 34733285 PMCID: PMC8559430 DOI: 10.3389/fimmu.2021.753960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.
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Affiliation(s)
- Eva-Stina Edholm
- Faculty of Biosciences, Fisheries & Economics, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier Cedex, France
| | - Pierre Boudinot
- Université Paris Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadan
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.,Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
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7
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Zhou H, Ma L, Liu L, Yao X. TR Locus Annotation and Characteristics of Rhinolophus ferrumequinum. Front Immunol 2021; 12:741408. [PMID: 34659234 PMCID: PMC8514952 DOI: 10.3389/fimmu.2021.741408] [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: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
T-cell antigen receptors (TRs) in vertebrates can be divided into αβ or γδ, encoded by TRA/D, TRG, or TRB loci. TRs play a central role in mammal cellular immunity, which occurs by rearrangement of V, D, J, and C genes in the loci. The bat is the only mammal with flying ability and is considered the main host of zoonotic viruses, an important public health concern. However, at present, little is known about the composition of bat TR genes. Based on the whole genome sequence of the greater horseshoe bat (Rhinolophus ferrumequinum) and referring to the TR/IG annotation rules formulated by the international ImMunoGeneTics information system (IMGT), we present a complete annotation of TRA/D, TRG, and TRB loci of R. ferrumequinum. A total of 128 V segments, three D segments, 85 J segments, and 6 C segments were annotated and compared with other known mammalian data. The characteristics of the TR locus and germline genes of R. ferrumequinum are analyzed.
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Affiliation(s)
- Hao Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Longyu Liu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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8
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The T Cell Receptor (TRB) Locus in Tursiops truncatus: From Sequence to Structure of the Alpha/Beta Heterodimer in the Human/Dolphin Comparison. Genes (Basel) 2021; 12:genes12040571. [PMID: 33919966 PMCID: PMC8070946 DOI: 10.3390/genes12040571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/27/2021] [Accepted: 04/12/2021] [Indexed: 01/25/2023] Open
Abstract
The bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and, similarly to other cetaceans, represents the most successful mammalian colonization of the aquatic environment. Here we report a genomic, evolutionary, and expression study of T. truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3' end, its uniqueness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rearranged T cell receptor α (TRA) and TRB cDNA from the peripheral blood of one of the two specimens, and the human/dolphin amino acids multi-sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the complementarity-determining region according to IMGT numbering (CDR-IMGT) of the dolphin variable V-alpha and beta domains were identified. According to comparative modelization, the atom pair contact sites analysis between the human MH1 grove (G) domains and the T cell receptor (TR) V domains confirms conservation of the structure of the dolphin TR/pMH.
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Massari S, Linguiti G, Giannico F, D’Addabbo P, Ciccarese S, Antonacci R. The Genomic Organisation of the TRA/TRD Locus Validates the Peculiar Characteristics of Dromedary δ-Chain Expression. Genes (Basel) 2021; 12:genes12040544. [PMID: 33918850 PMCID: PMC8069558 DOI: 10.3390/genes12040544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) account for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage of the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR α (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site.
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MESH Headings
- Animals
- Camelus/genetics
- Computational Biology/methods
- Genetic Loci
- Genome
- Phylogeny
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
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Affiliation(s)
- Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy
- Correspondence:
| | - Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
| | - Francesco Giannico
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Bari, Italy;
| | - Pietro D’Addabbo
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
| | - Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
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