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Huang S, Huang X, Li S, Zhu M, Zhuo M. MHC class I allele diversity in cynomolgus macaques of Vietnamese origin. PeerJ 2019; 7:e7941. [PMID: 31720104 PMCID: PMC6836755 DOI: 10.7717/peerj.7941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/23/2019] [Indexed: 11/20/2022] Open
Abstract
Cynomolgus macaques (Macaca fascicularis, Mafa) have been used as important experimental animal models for carrying out biomedical researches. The results of biomedical experiments strongly depend on the immunogenetic background of animals, especially on the diversity of major histocompatibility complex (MHC) alleles. However, there is much less information available on the polymorphism of MHC class I genes in cynomolgus macaques, than is currently available for humans. In this study, we have identified 40 Mafa-A and 60 Mafa-B exons 2 and 3 sequences from 30 unrelated cynomolgus macaques of Vietnamese origin. Among these alleles, 28 are novel. As for the remaining 72 known alleles, 15 alleles are shared with other cynomolgus macaque populations and 32 are identical to alleles previously reported in other macaque species. A potential recombination event was observed between Mafa-A1*091:02 and Mafa-A1*057:01. In addition, the Mafa-A1 genes were found to be more diverse than human HLA-A and the functional residues for peptide binding sites (PBS) or TCR binding sites (TBS) in Mafa-A1 have greater variability than that for non-PBS or non-TBS regions. Overall, this study provides important information on the diversity of Mafa-A and Mafa-B alleles from Vietnamese origin, which may help researchers to choose the most appropriate animals for their studies.
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Affiliation(s)
- Shuting Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Xia Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Mingjun Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Min Zhuo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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Hilton HG, McMurtrey CP, Han AS, Djaoud Z, Guethlein LA, Blokhuis JH, Pugh JL, Goyos A, Horowitz A, Buchli R, Jackson KW, Bardet W, Bushnell DA, Robinson PJ, Mendoza JL, Birnbaum ME, Nielsen M, Garcia KC, Hildebrand WH, Parham P. The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep 2018; 19:1394-1405. [PMID: 28514659 PMCID: PMC5510751 DOI: 10.1016/j.celrep.2017.04.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023] Open
Abstract
HLA-B∗46:01 was formed by an intergenic mini-conversion, between HLA-B∗15:01 and HLA-C∗01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B∗46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B∗46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B∗46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B∗46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B∗46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia. The interlocus recombinant HLA-B∗46:01 is found at high frequency in Southeast Asia HLA-B∗46:01 has a low-diversity peptidome that is distinct from both its parents A subset of HLA-B∗46:01 peptides provides ligands for the NK cell receptor KIR2DL3 The unique features of HLA-B∗46:01 correlate with protection against leprosy
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Curtis P McMurtrey
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alex S Han
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zakia Djaoud
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jeroen H Blokhuis
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jason L Pugh
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ana Goyos
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amir Horowitz
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, OK 73104, USA
| | - Ken W Jackson
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wilfred Bardet
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David A Bushnell
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip J Robinson
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Juan L Mendoza
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael E Birnbaum
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - K Christopher Garcia
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William H Hildebrand
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Adamek M, Klages C, Bauer M, Kudlek E, Drechsler A, Leuser B, Scherer S, Opelz G, Tran TH. Seven novel HLA alleles reflect different mechanisms involved in the evolution of HLA diversity: description of the new alleles and review of the literature. Hum Immunol 2014; 76:30-5. [PMID: 25500251 DOI: 10.1016/j.humimm.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/22/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Abstract
The human leukocyte antigen (HLA) loci are among the most polymorphic genes in the human genome. The diversity of these genes is thought to be generated by different mechanisms including point mutation, gene conversion and crossing-over. During routine HLA typing, we discovered seven novel HLA alleles which were probably generated by different evolutionary mechanisms. HLA-B*41:21, HLA-DQB1*02:10 and HLA-DQA1*01:12 likely emerged from the common alleles of their groups by point mutations, all of which caused non-synonymous amino acid substitutions. In contrast, a deletion of one nucleotide leading to a frame shift with subsequent generation of a stop codon is responsible for the appearance of a null allele, HLA-A*01:123N. Whereas HLA-B*35:231 and HLA-B*53:31 were probably products of intralocus gene conversion between HLA-B alleles, HLA-C*07:294 presumably evolved by interlocus gene conversion between an HLA-C and an HLA-B allele. Our analysis of these novel alleles illustrates the different mechanisms which may have contributed to the evolution of HLA polymorphism.
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Affiliation(s)
- Martina Adamek
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Cornelia Klages
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Manuela Bauer
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Evelina Kudlek
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Alina Drechsler
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Birte Leuser
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Sabine Scherer
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Gerhard Opelz
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Thuong Hien Tran
- Department of Transplantation Immunology, Institute of Immunology, University of Heidelberg, Heidelberg, Germany.
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Orysiuk D, Lawrence J, Prashar T, Spangelo L, Pilon R, Fournier J, Rud E, Sandstrom P, Plummer FA, Luo M. Evidence of recombination producing allelic diversity in MHC class I Mafa-B and -A alleles in cynomolgus macaques. ACTA ACUST UNITED AC 2012; 79:351-8. [PMID: 22489944 DOI: 10.1111/j.1399-0039.2012.01867.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MHC class I-A and -B genes of cynomolgus macaques are highly polymorphic. These genes encode proteins presenting peptides to CD8+ T cells to initiate adaptive immune response. Recombination events are one way the diversity of these alleles can be increased. Such events have been well characterized in humans, but have not been as well characterized in macaques. In order to identify and examine recombinations that create new alleles, it is important to analyze intron sequences. Intron sequences have been shown to be important to understand the evolutionary mechanisms involved in the generation of major histocompatibility complex (MHC) alleles and loci. Thus far, there have been relatively few intron sequences reported for MHC class I alleles in macaques, and this has hampered the understanding of MHC organization and evolution in macaques. In this study, we present evidence of a gene conversion event generating the Mafa-B*099 allele lineage by the combination of Mafa-B*054 and Mafa-B*095 allele lineages. A potential recombination between the Mafa-A3*13 and Mafa-A4:14 lineages was also observed, but it is less clear due to lack of intron 2 sequence. This report stresses the role that recombination can play in MHC class I diversity in cynomologus macaques, and the importance of introns in identifying and analyzing such events.
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Affiliation(s)
- D Orysiuk
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Smith DM, Martens GW, Ho CS, Asbury JM. DNA sequence based typing of swine leukocyte antigens in Yucatan Miniature Pigs. Xenotransplantation 2005; 12:481-8. [PMID: 16202072 DOI: 10.1111/j.1399-3089.2005.00252.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND We have established a breeding program to develop additional lines of swine leukocyte antigens (SLA) homozygous miniature pigs derived from the Yucatan Miniature Pig. Yucatan pigs have been used extensively in biomedical research since the 1970s and are known for their docile nature and small size. The breed has no consanguinity with the Hormel or Pittman-Moore breeds used to produce the NIH Miniature Pigs, the only other SLA homozygous miniature pigs in the USA. METHODS SLA typing was initially done by restriction fragment length polymorphism. Then a cDNA library was constructed using spleen cells from these pigs, from which we cloned and sequenced nearly all alleles for the SLA-1, 3, 2, 6, DRB1, DQA and DQB1 loci. RESULTS Four SLA homozygous lines were established with haplotypes that we have designated 'w, x, y and z'. An SLA class I/II crossover haplotype, designated 'q', with the SLA class I alleles of 'w' and the SLA class II alleles of 'z' was discovered and used to establish a fifth line. The cDNA sequences were used to develop locus specific primers for each locus and an reverse transcription-polymerase chain reaction sequence based typing (SBT) method. We have used this method to perform SBT on SLA homozygous Yucatan pigs with these haplotypes and on the NIH pig 'a, c and d' haplotypes. CONCLUSIONS These pig lines represent a new resource for transplantation research and the methods we describe can be used to SLA type any herd of pigs.
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Affiliation(s)
- Douglas M Smith
- Department of Pathology, Baylor University Medical Center, Dallas, TX 75246, USA.
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Cardenas PP, Suarez CF, Martinez P, Patarroyo ME, Patarroyo MA. MHC class I genes in the owl monkey: mosaic organisation, convergence and loci diversity. Immunogenetics 2005; 56:818-32. [PMID: 15654599 DOI: 10.1007/s00251-004-0751-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 11/09/2004] [Accepted: 11/09/2004] [Indexed: 10/25/2022]
Abstract
The MHC class I molecule plays an important role in immune response, pathogen recognition and response against vaccines and self- versus non-self-recognition. Studying MHC class I characteristics thus became a priority when dealing with Aotus to ensure its use as an animal model for biomedical research. Isolation, cloning and sequencing of exons 1-8 from 27 MHC class I alleles obtained from 13 individuals classified as belonging to three owl monkey species (A. nancymaae, A. nigriceps and A. vociferans) were carried out to establish similarities between Aotus MHC class I genes and those expressed by other New and Old World primates. Six Aotus MHC class I sequence groups (Ao-g1, Ao-g2, Ao-g3, Ao-g4, Ao-g5 and Ao-g6) weakly related to non-classical Catarrhini MHC were identified. An allelic lineage was also identified in one A. nancymaae and two A. vociferans monkeys, exhibiting a high degree of conservation, negative selection along the molecule and premature termination of the open reading frame at exon 5 (Ao-g5). These sequences' high conservation suggests that they more likely correspond to a soluble form of Aotus MHC class I molecules than to a new group of processed pseudogenes. Another group, named Ao-g6, exhibited a strong relationship with Catarrhini's classical MHC-B-C loci. Sequence evolution and variability analysis indicated that Aotus MHC class I molecules experience inter-locus gene conversion phenomena, contributing towards their high variability.
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Affiliation(s)
- Paula P Cardenas
- Molecular Biology Department, Fundacion Instituto de Inmunologia de Colombia, Bogota, Colombia
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