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Li J, Xing H, Liu K, Fan N, Xu K, Zhao H, Jiao D, Wei T, Cheng W, Guo J, Zhang X, Zhu F, Bu Z, Zhao D, Wang W, Wei HJ. Dysfunction of Complementarity Determining Region 1 Encoded by T Cell Receptor Beta Variable Gene Is Potentially Associated with African Swine Fever Virus Infection in Pigs. Microorganisms 2024; 12:1113. [PMID: 38930494 PMCID: PMC11205859 DOI: 10.3390/microorganisms12061113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
The beta T-cell receptor (TRB) expressed by beta T cells is essential for foreign antigen recognition. The TRB locus contains a TRBV family that encodes three complementarity determining regions (CDRs). CDR1 is associated with antigen recognition and interactions with MHC molecules. In contrast to domestic pigs, African suids lack a 284-bp segment spanning exons 1 and 2 of the TRBV27 gene that contains a sequence encoding CDR1. In this study, we used the African swine fever virus (ASFV) as an example to investigate the effect of deleting the TRBV27-encoded CDR1 on the resistance of domestic pigs to exotic pathogens. We first successfully generated TRBV27-edited fibroblasts with disruption of the CDR1 sequence using CRISPR/Cas9 technology and used them as donor cells to generate gene-edited pigs via somatic cell nuclear transfer. The TRBV-edited and wild-type pigs were selected for synchronous ASFV infection. White blood cells were significantly reduced in the genetically modified pigs before ASFV infection. The genetically modified and wild-type pigs were susceptible to ASFV and exhibited typical fevers (>40 °C). However, the TRBV27-edited pigs had a higher viral load than the wild-type pigs. Consistent with this, the gene-edited pigs showed more clinical signs than the wild-type pigs. In addition, both groups of pigs died within 10 days and showed similar severe lesions in organs and tissues. Future studies using lower virulence ASFV isolates are needed to determine the relationship between the TRBV27 gene and ASFV infection in pigs over a relatively long period.
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Affiliation(s)
- Jiayu Li
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Huiyan Xing
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kai Liu
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ninglin Fan
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Kaixiang Xu
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Heng Zhao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Deling Jiao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Taiyun Wei
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Wenjie Cheng
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jianxiong Guo
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Xiong Zhang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Feiyan Zhu
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhigao Bu
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.B.); (D.Z.)
| | - Dongming Zhao
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.B.); (D.Z.)
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Jiang Wei
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (H.X.); (K.L.); (N.F.); (K.X.); (H.Z.); (D.J.); (T.W.); (W.C.); (J.G.); (X.Z.); (F.Z.)
- Xenotransplantation Engineering Research Center in Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
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Shinkai H, Takahagi Y, Matsumoto T, Toki D, Takenouchi T, Kitani H, Sukegawa S, Suzuki K, Uenishi H. A specific promoter-type in ribonuclease L gene is associated with phagocytic activity in pigs. J Vet Med Sci 2021; 83:1407-1415. [PMID: 34321379 PMCID: PMC8498842 DOI: 10.1292/jvms.21-0142] [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] [Indexed: 11/28/2022] Open
Abstract
We have previously generated Large White pigs with high immune competence using a selection strategy based on phagocytic activity (PA), capacity of alternative complement pathway, and
antibody response after vaccination against swine erysipelas. In this study, to identify the genetic changes caused by the immune selection pressure, we compared gene expression and
polymorphisms in the promoter region between pigs subjected to the immune selection (immune-selected pigs) and those that were not (non-selected pigs). After lipid A stimulation, using a
microarray analysis, 37 genes related to immune function and transcription factor activity showed a greater than three-fold difference in expression between macrophages derived from
immune-selected and non-selected pigs. We further performed a polymorphic analysis of the promoter region of the differentially expressed genes, and elucidated the predominant promoter-types
in the immune-selected and non-selected pigs, respectively, in the genes encoding ribonuclease L (RNASEL), sterile α motif and histidine-aspartate domain containing
deoxynucleoside triphosphate triphosphohydrolase 1, signal transducer and activator of transcription 3, and tripartite motif containing 21. Analysis of the association between these promoter
genotypes and the immune phenotypes revealed that the immune-selected promoter-type in RNASEL was associated with increased PA and was inherited recessively. Considering
that RNASEL has been reported to be involved in antimicrobial immune response of mice, it may be possible to enhance the PA of macrophages and improve disease resistance in
pig populations using RNASEL promoter-type as a DNA marker for selection.
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Affiliation(s)
- Hiroki Shinkai
- Clinical Biochemistry Unit, Division of Pathology and Pathophysiology, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO).,Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | | | - Toshimi Matsumoto
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | - Daisuke Toki
- Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries (JATAFF)
| | - Takato Takenouchi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | - Hiroshi Kitani
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
| | | | - Keiichi Suzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University
| | - Hirohide Uenishi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)
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Giannico F, Massari S, Caputi Jambrenghi A, Soriano A, Pala A, Linguiti G, Ciccarese S, Antonacci R. The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species. BMC Genomics 2020; 21:623. [PMID: 32912163 PMCID: PMC7488459 DOI: 10.1186/s12864-020-07022-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse environmental conditions. Despite the relevance of this species, the genetic research on the goat traits is limited compared to other domestic species. Thanks to the latest goat reference genomic sequence (ARS1), which is considered to be one of the most continuous assemblies in livestock, we deduced the genomic structure of the T cell receptor beta (TRB) and gamma (TRG) loci in this ruminant species. RESULTS Our analyses revealed that although the organization of the goat TRB locus is broadly similar to that of the other artiodactyl species, with three in-tandem D-J-C clusters located at the 3' end, a complex and extensive series of duplications have occurred in the V genes at the 5' end, leading to a marked expansion in the number of the TRBV genes. This phenomenon appears to be a feature of the ruminant lineage since similar gene expansions have also occurred in sheep and cattle. Likewise, the general organization of the goat TRG genes is typical of ruminant species studied so far, with two paralogous TRG loci, TRG1 and TRG2, located in two distinct and distant positions on the same chromosome as result of a split in the ancestral locus. Each TRG locus consists of reiterated V-J-J-C cassettes, with the goat TRG2 containing an additional cassette relative to the corresponding sheep and cattle loci. CONCLUSIONS Taken together, these findings demonstrate that strong evolutionary pressures in the ruminant lineage have selected for the development of enlarged sets of TRB and TRG genes that contribute to a diverse T cell receptor repertoire. However, differences observed among the goat, sheep and cattle TRB and TRG genes indicate that distinct evolutionary histories, with independent expansions and/or contractions, have also affected each ruminant species.
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Affiliation(s)
- Francesco Giannico
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Soriano
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Angela Pala
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Giovanna Linguiti
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | | | - Rachele Antonacci
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy.
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Antonacci R, Massari S, Linguiti G, Caputi Jambrenghi A, Giannico F, Lefranc MP, Ciccarese S. Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals. Genes (Basel) 2020; 11:E624. [PMID: 32517024 PMCID: PMC7349638 DOI: 10.3390/genes11060624] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
T lymphocytes are the principal actors of vertebrates' cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.
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Affiliation(s)
- Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Francesco Giannico
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR9002 CNRS, Université de Montpellier, CEDEX 5, 34396 Montpellier, France;
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
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Radtanakatikanon A, Keller SM, Darzentas N, Moore PF, Folch G, Nguefack Ngoune V, Lefranc MP, Vernau W. Topology and expressed repertoire of the Felis catus T cell receptor loci. BMC Genomics 2020; 21:20. [PMID: 31906850 PMCID: PMC6945721 DOI: 10.1186/s12864-019-6431-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/24/2019] [Indexed: 01/26/2023] Open
Abstract
Background The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack of data on lymphocyte antigen receptor genes and usage. The objectives of this study were to annotate the feline T cell receptor (TR) loci and to characterize the expressed repertoire in lymphoid organs of normal cats using high-throughput sequencing. Results The Felis catus TRG locus contains 30 genes: 12 TRGV, 12 TRGJ and 6 TRGC, the TRB locus contains 48 genes: 33 TRBV, 2 TRBD, 11 TRBJ, 2 TRBC, the TRD locus contains 19 genes: 11 TRDV, 2 TRDD, 5 TRDJ, 1 TRDC, and the TRA locus contains 127 genes: 62 TRAV, 64 TRAJ, 1 TRAC. Functional feline V genes form monophyletic clades with their orthologs, and clustering of multimember subgroups frequently occurs in V genes located at the 5′ end of TR loci. Recombination signal (RS) sequences of the heptamer and nonamer of functional V and J genes are highly conserved. Analysis of the TRG expressed repertoire showed preferential intra-cassette over inter-cassette rearrangements and dominant usage of the TRGV2–1 and TRGJ1–2 genes. The usage of TRBV genes showed minor bias but TRBJ genes of the second J-C-cluster were more commonly rearranged than TRBJ genes of the first cluster. The TRA/TRD V genes almost exclusively rearranged to J genes within their locus. The TRAV/TRAJ gene usage was relatively balanced while the TRD repertoire was dominated by TRDJ3. Conclusions This is the first description of all TR loci in the cat. The genomic organization of feline TR loci was similar to that of previously described jawed vertebrates (gnathostomata) and is compatible with the birth-and-death model of evolution. The large-scale characterization of feline TR genes provides comprehensive baseline data on immune repertoires in healthy cats and will facilitate the development of improved reagents for the diagnosis of lymphoproliferative diseases in cats. In addition, these data might benefit studies using cats as a large animal model for human disease.
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Affiliation(s)
- Araya Radtanakatikanon
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Stefan M Keller
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Nikos Darzentas
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Peter F Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Géraldine Folch
- IMGT® the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Viviane Nguefack Ngoune
- IMGT® the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Marie-Paule Lefranc
- IMGT® the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
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Ciccarese S, Burger PA, Ciani E, Castelli V, Linguiti G, Plasil M, Massari S, Horin P, Antonacci R. The Camel Adaptive Immune Receptors Repertoire as a Singular Example of Structural and Functional Genomics. Front Genet 2019; 10:997. [PMID: 31681428 PMCID: PMC6812646 DOI: 10.3389/fgene.2019.00997] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 09/18/2019] [Indexed: 01/08/2023] Open
Abstract
The adaptive immune receptors repertoire is highly plastic, with its ability to produce antigen-binding molecules and select those with high affinity for their antigen. Species have developed diverse genetic and structural strategies to create their respective repertoires required for their survival in the different environments. Camelids, until now, considered as a case of evolutionary innovation because of their only heavy-chain antibodies, represent a new mammalian model particularly useful for understanding the role of diversity in the immune system function. Here, we review the structural and functional characteristics and the current status of the genomic organization of camel immunoglobulins (IG) or antibodies, α/ß and γ/δ T cell receptors (TR), and major histocompatibility complex (MHC). In camelid humoral response, in addition to the conventional antibodies, there are IG with “only-heavy-chain” (no light chain, and two identical heavy gamma chains lacking CH1 and with a VH domain designated as VHH). The unique features of these VHH offer advantages in biotechnology and for clinical applications. The TRG and TRD rearranged variable domains of Camelus dromedarius (Arabian camel) display somatic hypermutation (SHM), increasing the intrinsic structural stability in the γ/δ heterodimer and influencing the affinity maturation to a given antigen similar to immunoglobulin genes. The SHM increases the dromedary γ/δ repertoire diversity. In Camelus genus, the general structural organization of the TRB locus is similar to that of the other artiodactyl species, with a pool of TRBV genes positioned at the 5’ end of three in tandem D-J-C clusters, followed by a single TRBV gene with an inverted transcriptional orientation located at the 3’ end. At the difference of TRG and TRD, the diversity of the TRB variable domains is not shaped by SHM and depends from the classical combinatorial and junctional diversity. The MHC locus is located on chromosome 20 in Camelus dromedarius. Cytogenetic and comparative whole genome analyses revealed the order of the three major regions “Centromere-ClassII-ClassIII-ClassI”. Unexpectedly low extent of polymorphisms and haplotypes was observed in all Old World camels despite different geographic origins.
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Affiliation(s)
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro," Bari, Italy
| | - Vito Castelli
- Department of Biology, University of Bari "Aldo Moro," Bari, Italy
| | | | - Martin Plasil
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, RG Animal Immunogenomics, Brno, Czechia
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Petr Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, RG Animal Immunogenomics, Brno, Czechia
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Cizkova J, Sinkorova Z, Strnadova K, Cervinkova M, Horak V, Sinkora J, Stepanova K, Sinkora M. The role of αβ T-cells in spontaneous regression of melanoma tumors in swine. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:60-68. [PMID: 30308209 DOI: 10.1016/j.dci.2018.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
Using a porcine model, we describe Melanoma-Associated CD4+CD8hi T-lymphocytes (MATL) in peripheral blood that increase during melanoma regression. These MATL possess the CD4+CD8hi phenotype and they have their direct counterparts in Tumor Infiltrating Lymphocytes (TIL) isolated from melanoma loci. Both MATL and CD4+CD8hi TIL have a similar expression of selected markers indicating that they represent effector/memory αβ T-cell subset. Moreover, although TIL also contain CD4-CD8+ T-cells, only CD4+CD8hi TIL expand during melanoma regression. Importantly, TIL isolated from different pigs and different melanoma loci among the same pig have similar composition of CD4/CD8 subsets, indicating that the composition of the MATL and TIL compartment is identical. Analysis of sorted cells from regressing pigs revealed a unique MATL subpopulation with mono-specific T-cell receptor that was further analyzed by sequencing. These results indicate that pigs regressing melanomas possess a characteristic population of recirculating T-cells playing a role in tumor control and regression.
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Affiliation(s)
- Jana Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic; Laboratory of Tumor Biology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic; Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czech Republic
| | - Zuzana Sinkorova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic.
| | - Kristyna Strnadova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic; Laboratory of Tumor Biology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic; Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czech Republic
| | - Monika Cervinkova
- Laboratory of Tumor Biology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic; Surgical Department, 1st Medical Faculty of Charles University and Hospital Na Bulovce, Prague, Czech Republic
| | - Vratislav Horak
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic; Laboratory of Tumor Biology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Jiri Sinkora
- Life Sciences, Becton Dickinson Czechia, s.r.o., Prague, Czech Republic
| | - Katerina Stepanova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
| | - Marek Sinkora
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic.
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8
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Yang G, Artiaga BL, Lomelino CL, Jayaprakash AD, Sachidanandam R, Mckenna R, Driver JP. Next Generation Sequencing of the Pig αβ TCR Repertoire Identifies the Porcine Invariant NKT Cell Receptor. THE JOURNAL OF IMMUNOLOGY 2019; 202:1981-1991. [PMID: 30777925 DOI: 10.4049/jimmunol.1801171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/22/2019] [Indexed: 12/16/2022]
Abstract
Swine represent the only livestock with an established invariant NKT (iNKT) cell-CD1d system. In this study, we exploited the fact that pig iNKT cells can be purified using a mouse CD1d tetramer reagent to establish their TCR repertoire by next generation sequencing. CD1d tetramer-positive pig cells predominantly expressed an invariant Vα-Jα rearrangement, without nontemplate nucleotide diversity, homologous to the Vα24-Jα18 and Vα14-Jα18 rearrangements of human and murine iNKT cells. The coexpressed β-chain used a Vβ segment homologous to the semivariant Vβ11 and Vβ8.2 segments of human and murine iNKT cell receptors. Molecular modeling found that contacts within CD1d and CDR1α that underlie fine specificity differences between mouse and human iNKT cells are conserved between pigs and humans, indicating that the response of porcine and human iNKT cells to CD1d-restricted Ags may be similar. Accordingly, pigs, which are an important species for diverse fields of biomedical research, may be useful for developing human-based iNKT cell therapies for cancer, infectious diseases, and other disorders. Our study also sequenced the expressed TCR repertoire of conventional porcine αβ T cells, which identified 48 Vα, 50 Jα, 18 Vβ, and 18 Jβ sequences, most of which correspond to human gene segments. These findings provide information on the αβ TCR usage of pigs, which is understudied and deserves further attention.
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Affiliation(s)
- Guan Yang
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - Bianca L Artiaga
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610
| | | | - Ravi Sachidanandam
- Girihlet Inc., Oakland, CA 94609; and.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Robert Mckenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610
| | - John P Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611;
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9
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Massari S, Bellini M, Ciccarese S, Antonacci R. Overview of the Germline and Expressed Repertoires of the TRB Genes in Sus scrofa. Front Immunol 2018; 9:2526. [PMID: 30455691 PMCID: PMC6230588 DOI: 10.3389/fimmu.2018.02526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022] Open
Abstract
The α/β T cell receptor (TR) is a complex heterodimer that recognizes antigenic peptides and binds to major histocompatibility complex (MH) molecules. Both α and β chains are encoded by different genes localized on two distinct chromosomal loci: TRA and TRB. The present study employed the recent release of the swine genome assembly to define the genomic organization of the TRB locus. According to the sequencing data, the pig TRB locus spans approximately 400 kb of genomic DNA and consists of 38 TRBV genes belonging to 24 subgroups located upstream of three in tandem TRBD-J-C clusters, which are followed by a TRBV gene in an inverted transcriptional orientation. Comparative analysis confirms that the general organization of the TRB locus is similar among mammalian species, but the number of germline TRBV genes varies greatly even between species belonging to the same order, determining the diversity and specificity of the immune response. However, sequence analysis of the TRB locus also suggests the presence of blocks of conserved homology in the genomic region across mammals. Furthermore, by analysing a public cDNA collection, we identified the usage pattern of the TRBV, TRBD, and TRBJ genes in the adult pig TRB repertoire, and we noted that the expressed TRBV repertoire seems to be broader and more diverse than the germline repertoire, in line with the presence of a high level of TRBV gene polymorphisms. Because the nucleotide differences seems to be principally concentrated in the CDR2 region, it is reasonable to presume that most T cell β-chain diversity can be related to polymorphisms in pig MH molecules. Domestic pigs represent a valuable animal model as they are even more anatomically, genetically and physiologically similar to humans than are mice. Therefore, present knowledge on the genomic organization of the pig TRB locus allows the collection of increased information on the basic aspects of the porcine immune system and contributes to filling the gaps left by rodent models.
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Affiliation(s)
- Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
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10
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Wang X, Wang P, Wang R, Wang C, Bai J, Ke C, Yu D, Li K, Ma Y, Han H, Zhao Y, Zhou X, Ren L. Analysis of TCRβ and TCRγ genes in Chinese alligator provides insights into the evolution of TCR genes in jawed vertebrates. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 85:31-43. [PMID: 29574022 DOI: 10.1016/j.dci.2018.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
All jawed vertebrates have four T cell receptor (TCR) chains that are expressed by thymus-derived lymphocytes and play a major role in animal immune defence. However, few studies have investigated the TCR chains of crocodilians compared with those of birds and mammals, despite their key evolutionary position linking amphibians, reptiles, birds and mammals. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization, evolution and expression of TRB and TRG loci in Alligator sinensis. According to the sequencing data, the Alligator sinensis TRB locus spans approximately 500 Kb of genomic DNA containing two D-J-C clusters and 43 V gene segments and is organized as Vβ(39)-pJβ1-pCβ1-pDβ1-Dβ2- Jβ2(12)-Cβ2-Vβ(4), whereas the TRG locus spans 115 Kb of DNA genomic sequence consisting of 18 V gene segments, nine J gene segments and one C gene segment and is organized in a classical translocon pattern as Vγ(18)-Jγ(9)-Cγ. Moreover, syntenic analysis of TRB and TRG chain loci suggested a high degree of conserved synteny in the genomic regions across mammals, birds and Alligator sinensis. By analysing the cloned TRB/TRG cDNA, we identified the usage pattern of V families in the expressed TRB and TRG. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed TRB and TRG sequences. Phylogenetic analysis revealed that TRB and TRG loci possess distinct evolutionary patterns. Most Alligator sinensis V subgroups have closely related orthologues in chicken and duck, and a small number of Alligator sinensis V subgroups have orthologues in mammals, which supports the hypothesis that crocodiles are the closest relatives of birds and mammals. Collectively, these data provide insights into TCR gene evolution in vertebrates and improve our understanding of the Alligator sinensis immune system.
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Affiliation(s)
- Xifeng Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Peng Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Renping Wang
- Administration Bureau of Chinese Alligator National Nature Reserve Protection, Anhui, People's Republic of China
| | - Chaolin Wang
- Administration Bureau of Chinese Alligator National Nature Reserve Protection, Anhui, People's Republic of China
| | - Jianhui Bai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Cuncun Ke
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Di Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Kongpan Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yonghe Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100193, People's Republic of China; College of Plant Protection, China Agricultural University, Beijing, People's Republic of China.
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China.
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11
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Wang C, Li S, Jia H, Chen G, Fang Y, Zeng S, He X, Yao W, Jin Q, Cheng W, Feng Y, Yin H, Jing Z. Monoclonal and oligoclonal TCR AV and BV gene usage in CD4 + T cells from pigs immunised with C-strain CSFV vaccine. Sci Rep 2018; 8:1655. [PMID: 29374266 PMCID: PMC5786037 DOI: 10.1038/s41598-018-19974-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/05/2018] [Indexed: 11/23/2022] Open
Abstract
The classical swine fever virus C-strain vaccine (C-strain vaccine) plays a vital role in preventing and controlling the spread of classical swine fever (CSF). However, the protective mechanisms of C-strain vaccine and cellular immunity conferred by T cell receptors (TCRs) are less well defined. We aimed to analyse the association between the complementarity determining region 3 (CDR3) spectratype of αβTCR in CD4+ T cells and C-strain vaccine; and to find conserved CDR3 amino acid motifs in specific TCR α- and β-chains. We found that the CDR3 spectratype showed dynamic changes correlating with C-strain vaccine immunisation and that TCR AV5S/8–3S/8–4S/14/38 and BV4S/6S/7S/15S/30 gene families showed clonal expansion in immunised pigs. The sequences of CDR3 from these clonally expanded T cells indicated a high frequency of the ‘KLX’ motif in the TCR α chain and the ‘GGX’ motif in β chain, and Jα39, Jα43, Jβ2.5 and Jβ2.3 genes were also found in high frequency. To the best of our knowledge, this is the first report describing the dynamic changes of αβTCRs and conserved CDR3 amino acid motifs in CD4+ T cells from C-strain vaccine-immunised pigs, which will provide a basis for the development of high-efficiency epitope vaccines.
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Affiliation(s)
- Chunyan Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Shoujie Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Huaijie Jia
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Guohua Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Yongxiang Fang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Shuang Zeng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Xiaobing He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Wenjuan Yao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Qiwang Jin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Wenyu Cheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Yuan Feng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, P.R. China
| | - Zhizhong Jing
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, P.R. China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, 225009, P.R. China.
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12
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Antonacci R, Bellini M, Pala A, Mineccia M, Hassanane MS, Ciccarese S, Massari S. The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 76:105-119. [PMID: 28577760 DOI: 10.1016/j.dci.2017.05.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
The αβ T cells are important components of the adaptive immune system and can recognize a vast array of peptides presented by MHC molecules. The ability of these T cells to recognize the complex depends on the diversity of the αβ TR, which is generated by a recombination of specific Variable, Diversity and Joining genes for the β chain, and Variable and Joining genes for the α chain. In this study, we analysed the genomic structure and the gene content of the TRB locus in Camelus dromedarius, which is a species belonging to the Tylopoda suborder. The most noteworthy result is the presence of three in tandem TRBD-J-C clusters in the dromedary TRB locus, which is similar to clusters found in sheep, cattle and pigs and suggests a common duplication event occurred prior to the Tylopoda/Ruminantia/Suina divergence. Conversely, a significant contraction of the dromedary TRBV genes, which was previously found in the TRG and TRD loci, was observed with respect to the other artiodactyl species.
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Affiliation(s)
| | | | - Angela Pala
- Department of Biology, University "Aldo Moro" of Bari, Bari, Italy.
| | - Micaela Mineccia
- Department of Biology, University "Aldo Moro" of Bari, Bari, Italy.
| | | | | | - Serafina Massari
- Department of Biological and Environmental Science e Technologies, University of Salento, Lecce, Italy.
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13
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Eguchi-Ogawa T, Matsubara T, Toki D, Okumura N, Ando A, Kitagawa H, Uenishi H. Distribution of the CD4 Alleles in Sus scrofa Demonstrates the Genetic Profiles of Western Breeds and Miniature Pigs. Anim Biotechnol 2017; 29:227-233. [PMID: 29035142 DOI: 10.1080/10495398.2017.1367691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Widely used antipig CD4 monoclonal antibodies (mAbs) fail to recognize CD4 alleles characteristic of miniature pig lines such as the National Institutes of Health (NIH) miniature pigs and microminipigs. We surveyed polymorphisms in the coding sequence of the porcine CD4 gene among Western and Oriental pig breeds and Japanese wild boars and investigated their distribution. Of the 13 alleles that we identified among the 47 animals, 2 in group I and 3 in group II were found exclusively in Western breed pigs. Group IV alleles, which included mAb-nonbinding alleles, were found frequently in Oriental breed pigs, suggesting that the mAb-nonbinding allele arose from the gene pool of Oriental pigs. Group IV alleles were also found in Duroc and Large White pigs, suggesting genetic inflow from Oriental pig breeds into Western breeds. Comparison of the CD4 sequences of species in Cetartiodactyla suggested that the group IV alleles in Sus scrofa occurred before the divergence of this species from the other artiodactyls. The different antibody specificities of the various CD4 alleles may facilitate the discrimination of T-cell populations in transplantation studies using miniature pigs. The significance of the preservation of CD4 polymorphisms to immune function in pigs warrants further investigation.
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Affiliation(s)
- Tomoko Eguchi-Ogawa
- a Animal Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences , Tsukuba , Ibaraki , Japan.,b Office of Evaluation, National Agriculture and Food Research Organization , Tsukuba , Ibaraki , Japan
| | - Tatsuya Matsubara
- c United Graduate School of Veterinary Sciences, Gifu University , Gifu , Japan
| | - Daisuke Toki
- d Animal Research DIvision , Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries , Tsukuba , Ibaraki , Japan.,e Daisuke Toki, National Livestock Breeding Center , Nishigo , Fukushima , Japan
| | - Naohiko Okumura
- d Animal Research DIvision , Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries , Tsukuba , Ibaraki , Japan
| | - Asako Ando
- f Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine , Isehara , Kanagawa , Japan
| | - Hitoshi Kitagawa
- c United Graduate School of Veterinary Sciences, Gifu University , Gifu , Japan
| | - Hirohide Uenishi
- a Animal Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences , Tsukuba , Ibaraki , Japan.,g Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization , Tsukuba , Ibaraki , Japan
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14
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Wang CY, Fang YX, Chen GH, Jia HJ, Zeng S, He XB, Feng Y, Li SJ, Jin QW, Cheng WY, Jing ZZ. Analysis of the CDR3 length repertoire and the diversity of T cell receptor α and β chains in swine CD4+ and CD8+ T lymphocytes. Mol Med Rep 2017; 16:75-86. [PMID: 28534993 PMCID: PMC5482108 DOI: 10.3892/mmr.2017.6601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 02/20/2017] [Indexed: 11/13/2022] Open
Abstract
The T cell receptor (TCR) is a complex heterodimer that recognizes fragments of antigens as peptides and binds to major histocompatibility complex molecules. The TCR α and β chains possess three hypervariable regions termed complementarity determining regions (CDR1, 2 and 3). CDR3 is responsible for recognizing processed antigen peptides. Immunoscope spectratyping is a simple technique for analyzing CDR3 polymorphisms and sequence length diversity, in order to investigate T cell function and the pattern of TCR utilization. The present study employed this technique to analyze CDR3 polymorphisms and the sequence length diversity of TCR α and β chains in porcine CD4+ and CD8+ T cells. Polymerase chain reaction products of 19 TCR α variable regions (AV) and 20 TCR β variable regions (BV) gene families obtained from the CD4+ and CD8+ T cells revealed a clear band following separation by 1.5% agarose gel electrophoresis, and each family exhibited >8 bands following separation by 6% sequencing gel electrophoresis. CDR3 spectratyping of all identified TCR AV and BV gene families in the sorted CD4+ and CD8+ T cells by GeneScan, demonstrated a standard Gaussian distribution with >8 peaks. CDR3 in CD4+ and CD8+ T cells demonstrated different expression patterns. The majority of CDR3 recombined in frame and the results revealed that there were 10 and 14 amino acid discrepancies between the longest and shortest CDR3 lengths in specific TCR AV and TCR BV gene families, respectively. The results demonstrated that CDR3 polymorphism and length diversity demonstrated different expression and utilization patterns in CD4+ and CD8+ T cells. These results may facilitate future research investigating the porcine TCR CDR3 gene repertoire as well as the functional complexity and specificity of the TCR molecule.
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Affiliation(s)
- Chun-Yan Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Yong-Xiang Fang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Guo-Hua Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Huai-Jie Jia
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Shuang Zeng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Xiao-Bing He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Yuan Feng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Shou-Jie Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Qi-Wang Jin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Wen-Yu Cheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
| | - Zhi-Zhong Jing
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Public Health of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, P.R. China
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15
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Suzuki S, Iwamoto M, Hashimoto M, Suzuki M, Nakai M, Fuchimoto D, Sembon S, Eguchi-Ogawa T, Uenishi H, Onishi A. Generation and characterization of RAG2 knockout pigs as animal model for severe combined immunodeficiency. Vet Immunol Immunopathol 2016; 178:37-49. [PMID: 27496741 DOI: 10.1016/j.vetimm.2016.06.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 12/17/2022]
Abstract
Pigs with severe combined immunodeficiency (SCID) are versatile animal models for human medical research because of their biological similarities to humans, suitable body size, and longevity for practical research. SCID pigs with defined mutation(s) can be an invaluable tool for research on porcine immunity. In this study, we produced RAG2-knockout pigs via somatic cell nuclear transfer and analyzed their phenotype. The V(D)J recombination processes were confirmed as being inactivated. They consistently lacked mature T and B cells but had substantial numbers of cells considered to be T- or B-cell progenitors as well as NK cells. They also lacked thymic medulla and lymphoid aggregations in the spleen, mesenteric lymph nodes, and ileal Peyer's patches. We showed more severe immunological defects in the RAG2 and IL2RG double-knockout pig through this study. Thus, SCID pigs could be promising animal models not only for translational medical research but also for immunological studies of pigs themselves.
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Affiliation(s)
- Shunichi Suzuki
- Transgenic Pig Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan.
| | | | | | - Misae Suzuki
- Transgenic Pig Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
| | - Michiko Nakai
- Transgenic Pig Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
| | - Daiichiro Fuchimoto
- Transgenic Pig Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
| | - Shoichiro Sembon
- Transgenic Pig Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
| | - Tomoko Eguchi-Ogawa
- Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
| | - Hirohide Uenishi
- Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan; Animal Immune and Cell Biology Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
| | - Akira Onishi
- Transgenic Pig Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan; Laboratory of Animal Reproduction, Department of Animal Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
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16
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Drbalova J, Musilova P, Kubickova S, Sebestova H, Vahala J, Rubes J. Impact of karyotype organization on interlocus recombination between T cell receptor genes in Equidae. Cytogenet Genome Res 2015; 144:306-14. [PMID: 25765057 DOI: 10.1159/000377712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 11/19/2022] Open
Abstract
The T cell receptor (TCR) genes (TRA, TRB, TRD and TRG) reside in 3 different chromosomal regions. During the maturation of T lymphocytes, the TCR genes are rearranged by site-specific recombination, a process that also predisposes T cells to aberrant rearrangements. Illegitimate recombination between the TCR genes occurs at a low level in healthy individuals, but this frequency may correlate with the risk of lymphoma. The aim of this work was to investigate interlocus recombination in equids. Illegitimate rearrangements were studied in peripheral blood lymphocytes by FISH with painting and BAC probes and by sequencing of PCR products, and the frequencies of recombination were assessed in horses and 4 other equids. The presence of several trans-rearrangement products between the TRA and TRG genes was verified by PCR in all investigated equids. Frequencies of trans-rearrangements in horses are higher than in humans, and colocalization of the TCR genes on the same chromosome increases the incidence of trans-rearrangements between them. The orientation of the TCR genes does not impact interlocus recombination itself but does affect the viability of cells carrying its products and consequently the number of trans-rearrangements observed in lymphocytes.
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Affiliation(s)
- Jitka Drbalova
- Central European Institute of Technology, Veterinary Research Institute, Brno, Czech Republic
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Musilova P, Drbalova J, Kubickova S, Cernohorska H, Stepanova H, Rubes J. Illegitimate recombination between T cell receptor genes in humans and pigs (Sus scrofa domestica). Chromosome Res 2014; 22:483-93. [PMID: 25038896 DOI: 10.1007/s10577-014-9434-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/16/2014] [Accepted: 07/08/2014] [Indexed: 02/07/2023]
Abstract
T cell receptor (TCR) genes (TRA/TRD, TRB and TRG) reside in three regions on human chromosomes (14q11.2, 7q34 and 7p14, respectively) and pig chromosomes (7q15.3-q21, 18q11.3-q12 and 9q21-22, respectively). During the maturation of T cells, TCR genes are rearranged by site-specific recombination. Occasionally, interlocus recombination of different TCR genes takes place, resulting in chromosome rearrangements. It has been suggested that the absolute number of these "innocent" trans-rearrangements correlates with the risk of lymphoma. The aims of this work were to assess the frequencies of rearrangements with breakpoints in TCR genes in domestic pig lymphocytes and to compare these with the frequencies of corresponding rearrangements in human lymphocytes by using fluorescence in situ hybridization with chromosome painting probes. We show that frequencies of trans-rearrangements involving TRA/TRD locus in pigs are significantly higher than the frequency of translocations with breakpoints in TRB and TRG genes in pigs and the frequencies of corresponding trans-rearrangements involving TRA/TRD locus in humans. Complex structure of the pig TRA/TRD locus with high number of potential V(D)J rearrangements compared to the human locus may account for the observed differences. Furthermore, we demonstrated that trans-rearrangements involving pig TRA/TRD locus occur at lower frequencies in γδ T cells than in αβ T lymphocytes. The decrease of the frequencies in γδ T cells is probably caused by the absence of TRA recombination during maturation of this T cell lineage. High numbers of innocent trans-rearrangements in pigs may indicate a higher risk of T-cell lymphoma than in humans.
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Affiliation(s)
- Petra Musilova
- Department of Genetics and Reproduction, Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic,
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Abstract
In veterinary animal species, vaccines are the primary tool for disease prevention, a key tool for treatment of infection, and essential for helping maintain animal welfare and productivity. Traditional vaccine development by trial-and-error has achieved many successes. However, effective vaccines that provide solid cross-protective immunity with excellent safety are still needed for many diseases. The path to development of vaccines against difficult pathogens requires recognition of uniquely evolved immunological interactions of individual animal hosts and their specific pathogens. Here, general principles that currently guide veterinary immunology and vaccinology research are reviewed, with an emphasis on examples from swine. Advances in genomics and proteomics now provide the community with powerful tools for elucidation of regulatory and effector mechanisms of protective immunity that provide new opportunities for successful translation of immunological discoveries into safe and effective vaccines.
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Dawson HD, Loveland JE, Pascal G, Gilbert JGR, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RPY, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed’Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK. Structural and functional annotation of the porcine immunome. BMC Genomics 2013; 14:332. [PMID: 23676093 PMCID: PMC3658956 DOI: 10.1186/1471-2164-14-332] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/03/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. RESULTS The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome. CONCLUSIONS This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig's adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response.
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Affiliation(s)
- Harry D Dawson
- USDA-ARS, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, MD 20705, USA
| | - Jane E Loveland
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Géraldine Pascal
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France
| | - James GR Gilbert
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Hirohide Uenishi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Katherine M Mann
- USDA ARS BA Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA
| | - Yongming Sang
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Jie Zhang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Denise Carvalho-Silva
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK,Current affiliation: EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambs CB10 1SD, UK
| | - Toby Hunt
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Matthew Hardy
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Zhiliang Hu
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Shu-Hong Zhao
- Laboratory of Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Anna Anselmo
- Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy
| | - Hiroki Shinkai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Celine Chen
- USDA-ARS, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, MD 20705, USA
| | - Bouabid Badaoui
- Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy
| | - Daniel Berman
- USDA ARS BA Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA
| | - Clara Amid
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK,Current affiliation: EMBL Outstation-Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambs CB10 1SD, UK
| | - Mike Kay
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - David Lloyd
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Catherine Snow
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Takeya Morozumi
- Institute of Japan Association for Technology in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Ryan Pei-Yen Cheng
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Megan Bystrom
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Ronan Kapetanovic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - John C Schwartz
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA
| | - Ranjit Kataria
- National Bureau of Animal Genetic Resources, P.B. 129, GT Road By-Pass, Karnal 132001, (Haryana), India
| | - Matthew Astley
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Eric Fritz
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Charles Steward
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Mark Thomas
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Laurens Wilming
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Daisuke Toki
- Institute of Japan Association for Technology in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Bertrand Bed’Hom
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France
| | - Dario Beraldi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Ting-Hua Huang
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Tahar Ait-Ali
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Frank Blecha
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Sara Botti
- Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy
| | - Tom C Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Elisabetta Giuffra
- Parco Tecnologico Padano, Integrative Biology Unit, via A. Einstein, 26900, Lodi, Italy,INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Joan K Lunney
- USDA ARS BA Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jennifer L Harrow
- Informatics Department, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, UK
| | - Claire Rogel-Gaillard
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France
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Groenen MAM, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LAF, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RPMA, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JGR, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012; 491:393-8. [PMID: 23151582 PMCID: PMC3566564 DOI: 10.1038/nature11622] [Citation(s) in RCA: 966] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/27/2012] [Indexed: 01/03/2023]
Abstract
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.
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Inman CF, Laycock GM, Mitchard L, Harley R, Warwick J, Burt R, van Diemen PM, Stevens M, Bailey M. Neonatal colonisation expands a specific intestinal antigen-presenting cell subset prior to CD4 T-cell expansion, without altering T-cell repertoire. PLoS One 2012; 7:e33707. [PMID: 22442714 PMCID: PMC3307746 DOI: 10.1371/journal.pone.0033707] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/15/2012] [Indexed: 11/18/2022] Open
Abstract
Interactions between the early-life colonising intestinal microbiota and the developing immune system are critical in determining the nature of immune responses in later life. Studies in neonatal animals in which this interaction can be examined are central to understanding the mechanisms by which the microbiota impacts on immune development and to developing therapies based on manipulation of the microbiome. The inbred piglet model represents a system that is comparable to human neonates and allows for control of the impact of maternal factors. Here we show that colonisation with a defined microbiota produces expansion of mucosal plasma cells and of T-lymphocytes without altering the repertoire of alpha beta T-cells in the intestine. Importantly, this is preceded by microbially-induced expansion of a signal regulatory protein α-positive (SIRPα+) antigen-presenting cell subset, whilst SIRPα−CD11R1+ antigen-presenting cells (APCs) are unaffected by colonisation. The central role of intestinal APCs in the induction and maintenance of mucosal immunity implicates SIRPα+ antigen-presenting cells as orchestrators of early-life mucosal immune development.
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Affiliation(s)
- Charlotte F Inman
- School of Clinical Veterinary Science, University of Bristol, Langford, Bristol, United Kingdom.
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Di Tommaso S, Antonacci R, Ciccarese S, Massari S. Extensive analysis of D-J-C arrangements allows the identification of different mechanisms enhancing the diversity in sheep T cell receptor beta-chain repertoire. BMC Genomics 2010; 11:3. [PMID: 20047680 PMCID: PMC2806336 DOI: 10.1186/1471-2164-11-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 01/04/2010] [Indexed: 11/10/2022] Open
Abstract
Background In most species of mammals, the TRB locus has the common feature of a library of TRBV genes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a single TRBD gene, 6-7 TRBJ genes and one TRBC gene. An enhancer located at the 3'end of the last TRBC and a well-defined promoter situated at the 5'end of the TRBD gene and/or a undefined promoter situated at the 5'end of the TRBD2 are sufficient to generate the full recombinase accessibility at the locus. In ruminant species, the 3'end of the TRB locus is characterized by the presence of three D-J-C clusters, each constituted by a single TRBD, 5-7 TRBJ and one TRBC genes with the center cluster showing a structure combined with the clusters upstream and downstream, suggesting that a unequal crossover occurred in the duplication. An enhancer downstream the last TRBC, and a promoter at the 5'-end of each TRBD gene are also present. Results In this paper we focused our attention on the analysis of a large number of sheep TR β-chain transcripts derived from four different lymphoid tissues of three diverse sheep breed animals to certify the use and frequency of the three gene clusters in the β-chain repertoire. As the sheep TRB locus genomic organization is known, the exact interpretation of the V-D-J rearrangements was fully determined. Our results clearly demonstrate that sheep β-chain constitutes a level of variability that is substantially larger than that described in other mammalian species. This is due not only to the increase of the number of D and J genes available to the somatic recombination, but also to the presence of the trans-rearrangement process. Moreover, the functional complexity of β-chain repertoire is resolved by other mechanisms such as alternative cis- and trans-splicing and recombinational diversification that seems to affect the variety of the constant region. Conclusion All together our data demonstrate that a disparate set of molecular mechanisms operate to perform a diversified repertoire in the sheep β-chain and this could confer some special biological properties to the corresponding αβ T cells in the ruminant lineage.
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Affiliation(s)
- Silvia Di Tommaso
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita' del Salento, Lecce, Italy.
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