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Liang C, Sun L, Zhu Y, Wu J, Zhao A, Huang T, Yan F, He K. Local chicken breeds exhibit abundant TCR-V segments but similar repertoire diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 157:105196. [PMID: 38762097 DOI: 10.1016/j.dci.2024.105196] [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: 11/28/2023] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
The thymus-derived lymphocytes of jawed vertebrates have four T-cell receptor (TCR) chains that play a significant role in immunity. As chickens have commercial value, their immune systems require a great deal of attention. Local chicken breeds are an essential part of poultry genetic resources in China. Here, we used high-throughput sequencing to analyze the TCRα and TCRβ repertoires and their relative expression levels in the native chicken breeds Baier Buff, Longyou Partridge, Xiaoshan, and Xianju. We found that TCR Vα and TCR Vβ were expressed and included 17, 19, 17, and six segments of the Vα2, Vα3, Vβ1, and Vβ2 subgroups, respectively. V-J pairing was biased; Jα11 was utilized by nearly all Vα segments and was the most commonly used. Breed-specific V segments and V-J pairings were detected as well. The results of the principal coordinate analysis (PCoA) as well as the V-J pairing and CDR3 diversity analyses suggested that the four local chicken breeds did not significantly differ in terms of TCR diversity. Hence, they expressed not significant differentiation, and they are rich genetic resources for the development and utilization of immune-related poultry breeding.
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Affiliation(s)
- Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Lin Sun
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Jianqing Wu
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Tao Huang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Feifei Yan
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, 311300, China.
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Liang C, Sun L, Zhu Y, Zhao A, Liu H, He K. Macroevolution of avian T cell receptor C segments using genomic data. Immunogenetics 2023; 75:531-541. [PMID: 37804321 DOI: 10.1007/s00251-023-01322-8] [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: 08/07/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
All jawed vertebrates have four T cell receptor (TCR) chains expressed by thymus-derived lymphocytes that play a significant role in animal immune defense. However, avian TCR studies have been limited to a few species, although their co-functional major histocompatibility complexes (MHCs) have been studied for decades, showing various copy numbers and polymorphisms. Here, using public genome data, we characterized the copy numbers, the phylogenic relationship and selection of T cell receptor complex (TCR-C) segments, and the genomic organization of TCR loci across birds. Various numbers of C segments were found in the TCRα/TCRδ, TCRβ, and TCRγ loci, and phylogenetic analysis reflected both ancient gene duplication events (two Cβ segments and Cδ segments divergent into CδI and CδII) and contemporary evolution (lineage-specific and species-specific characteristics). Most passerines lack CδII segments and a second TRD locus, except Meliphagidae and Maluridae. A relatively stable structure was verified in four TCR loci of birds, except for the arrangement of V segment groups. In this study, we explored the phylogenetic relationships of TCR-C segments across avians for the first time. We inferred gene duplication and loss events during the evolution process. The finding of diverse TCR germline repertoires provides a better understanding of the immune systems of birds.
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Affiliation(s)
- Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Lin Sun
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China.
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Morrissey KA, Stammnitz MR, Murchison E, Miller RD. Comparative genomics of the T cell receptor μ locus in marsupials and monotremes. Immunogenetics 2023; 75:507-515. [PMID: 37747540 PMCID: PMC7615758 DOI: 10.1007/s00251-023-01320-w] [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: 07/12/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023]
Abstract
T cells are a primary component of the vertebrate adaptive immune system. There are three mammalian T cell lineages based on their T cell receptors (TCR). The αβ T cells and γδ T cells are ancient and found broadly in vertebrates. The more recently discovered γμ T cells are uniquely mammalian and only found in marsupials and monotremes. In this study, we compare the TCRμ locus (TRM) across the genomes of two marsupials, the gray short-tailed opossum and Tasmanian devil, and one monotreme, the platypus. These analyses revealed lineage-specific duplications, common to all non-eutherian mammals described. There is conserved synteny in the TRM loci of both marsupials but not in the monotreme. Our results are consistent with an ancestral cluster organization which was present in the last common mammalian ancestor which underwent lineage-specific duplications and divergence among the non-eutherian mammals.
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Affiliation(s)
- K A Morrissey
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, Albuquerque, NM, USA
| | - M R Stammnitz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - E Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, Albuquerque, NM, USA.
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Zimmerman LM. Adaptive Immunity in Reptiles: Conventional Components but Unconventional Strategies. Integr Comp Biol 2022; 62:1572-1583. [PMID: 35482599 DOI: 10.1093/icb/icac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 01/05/2023] Open
Abstract
Recent studies have established that the innate immune system of reptiles is broad and robust, but the question remains: What role does the reptilian adaptive immune system play? Conventionally, adaptive immunity is described as involving T and B lymphocytes that display variable receptors, is highly specific, improves over the course of the response, and produces a memory response. While reptiles do have B and T lymphocytes that utilize variable receptors, their adaptive response is relatively non-specific, generates a prolonged antibody response, and does not produce a typical memory response. This alternative adaptive strategy may allow reptiles to produce a broad adaptive response that complements a strong innate system. Further studies into reptile adaptive immunity cannot only clarify outstanding questions on the reptilian immune system but can shed light on a number of important immunological concepts, including the evolution of the immune system and adaptive immune responses that take place outside of germinal centers.
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Morrissey KA, Sampson JM, Rivera M, Bu L, Hansen VL, Gemmell NJ, Gardner MG, Bertozzi T, Miller RD. Comparison of Reptilian Genomes Reveals Deletions Associated with the Natural Loss of γδ T Cells in Squamates. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1960-1967. [PMID: 35346964 DOI: 10.4049/jimmunol.2101158] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 01/06/2023]
Abstract
T lymphocytes or T cells are key components of the vertebrate response to pathogens and cancer. There are two T cell classes based on their TCRs, αβ T cells and γδ T cells, and each plays a critical role in immune responses. The squamate reptiles may be unique among the vertebrate lineages by lacking an entire class of T cells, the γδ T cells. In this study, we investigated the basis of the loss of the γδ T cells in squamates. The genome and transcriptome of a sleepy lizard, the skink Tiliqua rugosa, were compared with those of tuatara, Sphenodon punctatus, the last living member of the Rhynchocephalian reptiles. We demonstrate that the lack of TCRγ and TCRδ transcripts in the skink are due to large deletions in the T. rugosa genome. We also show that tuataras are on a growing list of species, including sharks, frogs, birds, alligators, and platypus, that can use an atypical TCRδ that appears to be a chimera of a TCR chain with an Ab-like Ag-binding domain. Tuatara represents the nearest living relative to squamates that retain γδ T cells. The loss of γδTCR in the skink is due to genomic deletions that appear to be conserved in other squamates. The genes encoding the αβTCR chains in the skink do not appear to have increased in complexity to compensate for the loss of γδ T cells.
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Affiliation(s)
- Kimberly A Morrissey
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM
| | - Jordan M Sampson
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM
| | - Megan Rivera
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM
| | - Lijing Bu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM
| | - Victoria L Hansen
- Department of Orthopedics and Rehabilitation, Center for Musculoskeletal Research, University of Rochester, Rochester, NY
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael G Gardner
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia; and
| | - Terry Bertozzi
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia; and .,The University of Adelaide, Adelaide, South Australia, Australia
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM;
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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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Ott JA, Ohta Y, Flajnik MF, Criscitiello MF. Lost structural and functional inter-relationships between Ig and TCR loci in mammals revealed in sharks. Immunogenetics 2021; 73:17-33. [PMID: 33449123 PMCID: PMC7909615 DOI: 10.1007/s00251-020-01183-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Immunoglobulins and T cell receptors (TCR) have obvious structural similarities as well as similar immunogenetic diversification and selection mechanisms. Nevertheless, the two receptor systems and the loci that encode them are distinct in humans and classical murine models, and the gene segments comprising each repertoire are mutually exclusive. Additionally, while both B and T cells employ recombination-activating genes (RAG) for primary diversification, immunoglobulins are afforded a supplementary set of activation-induced cytidine deaminase (AID)-mediated diversification tools. As the oldest-emerging vertebrates sharing the same adaptive B and T cell receptor systems as humans, extant cartilaginous fishes allow a potential view of the ancestral immune system. In this review, we discuss breakthroughs we have made in studies of nurse shark (Ginglymostoma cirratum) T cell receptors demonstrating substantial integration of loci and diversification mechanisms in primordial B and T cell repertoires. We survey these findings in this shark model where they were first described, while noting corroborating examples in other vertebrate groups. We also consider other examples where the gnathostome common ancestry of the B and T cell receptor systems have allowed dovetailing of genomic elements and AID-based diversification approaches for the TCR. The cartilaginous fish seem to have retained this T/B cell plasticity to a greater extent than more derived vertebrate groups, but representatives in all vertebrate taxa except bony fish and placental mammals show such plasticity.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
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