1
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Hu Q, Huang X, Jin Y, Zhang R, Zhao A, Wang Y, Zhou C, Liu W, Liu X, Li C, Fan G, Zhuo M, Wang X, Ling F, Luo W. Long-read assembly of major histocompatibility complex and killer cell immunoglobulin-like receptor genome regions in cynomolgus macaque. Biol Direct 2022; 17:36. [PMID: 36447238 PMCID: PMC9707422 DOI: 10.1186/s13062-022-00350-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) and the killer cell immunoglobulin-like receptors (KIR) are key regulators of immune responses. The cynomolgus macaque, an Old World monkey species, can be applied as an important preclinical model for studying human diseases, including coronavirus disease 2019 (COVID-19). Several MHC-KIR combinations have been associated with either a poor or good prognosis. Therefore, macaques with a well-characterized immunogenetic profile may improve drug evaluation and speed up vaccine development. At present, a complete overview of the MHC and KIR haplotype organizations in cynomolgus macaques is lacking, and characterization by conventional techniques is hampered by the extensive expansion of the macaque MHC-B region that complicates the discrimination between genes and alleles. METHODS We assembled complete MHC and KIR genomic regions of cynomolgus macaque using third-generation long-read sequencing approach. We identified functional Mafa-B loci at the transcriptome level using locus-specific amplification in a cohort of 33 Vietnamese cynomolgus macaques. RESULTS This is the first physical mapping of complete MHC and KIR gene regions in a Vietnamese cynomolgus macaque. Furthermore, we identified four functional Mafa-B loci (B2, B3, B5, and B6) and showed that alleles of the Mafa-I*01, -B*056, -B*034, and -B*001 functional lineages, respectively, are highly frequent in the Vietnamese cynomolgus macaque population. CONCLUSION The insights into the MHC and KIR haplotype organizations and the level of diversity may refine the selection of animals with specific genetic markers for future medical research.
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Affiliation(s)
- Qingxiu Hu
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xiaoqi Huang
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Yabin Jin
- grid.12981.330000 0001 2360 039XThe First People’s Hospital of Foshan, Sun Yat-sen University, Foshan, 528000 China
| | - Rui Zhang
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Aimin Zhao
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Yiping Wang
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Chenyun Zhou
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Weixin Liu
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xunwei Liu
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Chunhua Li
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Guangyi Fan
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Min Zhuo
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xiaoning Wang
- grid.414252.40000 0004 1761 8894National Clinic Center of Geriatric, The Chinese PLA General Hospital, Beijing, 100853 China
| | - Fei Ling
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Wei Luo
- grid.12981.330000 0001 2360 039XThe First People’s Hospital of Foshan, Sun Yat-sen University, Foshan, 528000 China
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Baecklund TM, Donaldson ME, Hueffer K, Kyle CJ. Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations. PLoS One 2021; 16:e0258975. [PMID: 34714859 PMCID: PMC8555846 DOI: 10.1371/journal.pone.0258975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/10/2021] [Indexed: 11/24/2022] Open
Abstract
Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- * E-mail:
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Forensic Science Department, Trent University, Peterborough, ON, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, ON, Canada
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3
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de Groot NG, Heijmans CMC, Bezstarosti S, Bruijnesteijn J, Haasnoot GW, Mulder A, Claas FHJ, Heidt S, Bontrop RE. Two Human Monoclonal HLA-Reactive Antibodies Cross-React with Mamu-B*008, a Rhesus Macaque MHC Allotype Associated with Control of Simian Immunodeficiency Virus Replication. THE JOURNAL OF IMMUNOLOGY 2021; 206:1957-1965. [PMID: 33692147 DOI: 10.4049/jimmunol.2001405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 11/19/2022]
Abstract
MHC class I molecules play an important role in adaptive immune responses against intracellular pathogens. These molecules are highly polymorphic, and many allotypes have been characterized. In a transplantation setting, a mismatch between MHC allotypes may initiate an alloimmune response. Rhesus macaques (Macaca mulatta, Mamu) are valuable as a preclinical model species in transplantation research as well as to evaluate the safety and efficacy of vaccine candidates. In both lines of research, the availability of nonhuman primate MHC-reactive mAbs may enable in vitro monitoring and detection of presence of particular Mamu molecules. In this study, we screened a collection of thoroughly characterized HLA class I-specific human mAbs for cross-reactivity with rhesus macaque MHC class I allotypes. Two mAbs, OK4F9 and OK4F10, recognize an epitope that is defined by isoleucine (I) at amino acid position 142 that is present on the Indian rhesus macaque Mamu-B*008:01 allotype, which is an allotype known to be associated with elite control of SIV replication. The reactive pattern of a third mAb, MUS4H4, is more complex and includes an epitope shared on Mamu-A2*05:01 and -B*001:01-encoded Ags. This is the first description, to our knowledge, of human HLA-reactive mAbs that can recognize Mamu allotypes, and these can be useful tools for in vitro monitoring the presence of the relevant allelic products. Moreover, OK4F9 and OK4F10 can be powerful mAbs for application in SIV-related research.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Suzanne Bezstarosti
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Geert W Haasnoot
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
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4
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Baecklund TM, Morrison J, Donaldson ME, Hueffer K, Kyle CJ. The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes). PLoS One 2021; 16:e0249176. [PMID: 33831031 PMCID: PMC8031376 DOI: 10.1371/journal.pone.0249176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022] Open
Abstract
Populations are exposed to different types and strains of pathogens across heterogeneous landscapes, where local interactions between host and pathogen may present reciprocal selective forces leading to correlated patterns of spatial genetic structure. Understanding these coevolutionary patterns provides insight into mechanisms of disease spread and maintenance. Arctic rabies (AR) is a lethal disease with viral variants that occupy distinct geographic distributions across North America and Europe. Red fox (Vulpes vulpes) are a highly susceptible AR host, whose range overlaps both geographically distinct AR strains and regions where AR is absent. It is unclear if genetic structure exists among red fox populations relative to the presence/absence of AR or the spatial distribution of AR variants. Acquiring these data may enhance our understanding of the role of red fox in AR maintenance/spread and inform disease control strategies. Using a genotyping-by-sequencing assay targeting 116 genomic regions of immunogenetic relevance, we screened for sequence variation among red fox populations from Alaska and an outgroup from Ontario, including areas with different AR variants, and regions where the disease was absent. Presumed neutral SNP data from the assay found negligible levels of neutral genetic structure among Alaskan populations. The immunogenetically-associated data identified 30 outlier SNPs supporting weak to moderate genetic structure between regions with and without AR in Alaska. The outliers included SNPs with the potential to cause missense mutations within several toll-like receptor genes that have been associated with AR outcome. In contrast, there was a lack of genetic structure between regions with different AR variants. Combined, we interpret these data to suggest red fox populations respond differently to the presence of AR, but not AR variants. This research increases our understanding of AR dynamics in the Arctic, where host/disease patterns are undergoing flux in a rapidly changing Arctic landscape, including the continued northward expansion of red fox into regions previously predominated by the arctic fox (Vulpes lagopus).
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- * E-mail:
| | - Jaycee Morrison
- Forensic Science Undergraduate Program, Trent University, Peterborough, Ontario, Canada
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, Ontario, Canada
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5
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Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
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Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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6
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Limited MHC class II gene polymorphism in the West African chimpanzee is distributed maximally by haplotype diversity. Immunogenetics 2018; 71:13-23. [PMID: 30159708 DOI: 10.1007/s00251-018-1080-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/22/2018] [Indexed: 10/28/2022]
Abstract
Chimpanzees have been used for some time as an animal model in research on immune-related diseases in humans. The major histocompatibility complex (MHC) region of the chimpanzee has also been the subject of studies in which the attention was mainly on the class I genes. Although full-length sequence information is available on the DRB region genes, such detailed information is lacking for the other class II genes and, if present, is based mainly on exon 2 sequences. In the present study, full-length sequencing was performed on DQ, DP, and DRA genes in a cohort of 67 pedigreed animals, thereby allowing a thorough analysis of the MHC class II repertoire. The results demonstrate that the number of MHC class II lineages and alleles is relatively low, whereas haplotype diversity (combination of genes/alleles on a chromosome) seems to have been maximised by crossing-over processes.
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7
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Fuselli S, Baptista RP, Panziera A, Magi A, Guglielmi S, Tonin R, Benazzo A, Bauzer LG, Mazzoni CJ, Bertorelle G. A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra). Heredity (Edinb) 2018; 121:293-303. [PMID: 29572469 PMCID: PMC6133961 DOI: 10.1038/s41437-018-0070-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/24/2018] [Accepted: 02/25/2018] [Indexed: 12/13/2022] Open
Abstract
The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.
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Affiliation(s)
- S Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.
| | - R P Baptista
- Center for Tropical & Emerging Global Diseases, University of Georgia, 107 Paul D. Coverdell Center, 500 D. W. Brooks Drive, Athens, GA, 30602-7394, USA
| | - A Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, San Michele all'Adige, I-38010, Italy
| | - A Magi
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, Florence, 3-50134, Italy
| | - S Guglielmi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - R Tonin
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, Bolzano, Italy
| | - A Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - L G Bauzer
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - C J Mazzoni
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - G Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
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8
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Zhang P, Huang K, Zhang B, Dunn DW, Chen D, Li F, Qi X, Guo S, Li B. High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations. BMC Evol Biol 2018. [PMID: 29534675 PMCID: PMC5851093 DOI: 10.1186/s12862-018-1148-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Maintaining variation in immune genes, such as those of the major histocompatibility complex (MHC), is important for individuals in small, isolated populations to resist pathogens and parasites. The golden snub-nosed monkey (Rhinopithecus roxellana), an endangered primate endemic to China, has experienced a rapid reduction in numbers and severe population fragmentation over recent years. For this study, we measured the DRB diversity among 122 monkeys from three populations in the Qinling Mountains, and estimated the relative importance of different agents of selection in maintaining variation of DRB genes. Results We identified a total of 19 DRB sequences, in which five alleles were novel. We found high DRB variation in R. roxellana and three branches of evidence suggesting that balancing selection has contributed to maintaining MHC polymorphism over the long term in this species: i) different patterns of both genetic diversity and population differentiation were detected at MHC and neutral markers; ii) an excess of non-synonymous substitutions compared to synonymous substitutions at antigen binding sites, and maximum-likelihood-based random-site models, showed significant positive selection; and iii) phylogenetic analyses revealed a pattern of trans-species evolution for DRB genes. Conclusions High levels of DRB diversity in these R. roxellana populations may reflect strong selection pressure in this species. Patterns of genetic diversity and population differentiation, positive selection, as well as trans-species evolution, suggest that pathogen-mediated balancing selection has contributed to maintaining MHC polymorphism in R. roxellana over the long term. This study furthers our understanding of the role pathogen-mediated balancing selection has in maintaining variation in MHC genes in small and fragmented populations of free-ranging vertebrates. Electronic supplementary material The online version of this article (10.1186/s12862-018-1148-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bingyi Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Dan Chen
- Middle School Affiliated to Northwest University, Xi'an, China
| | - Fan Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaoguang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China. .,Xi'an Branch of Chinese Academy of Science, Xi'an, China.
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9
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Ramesh A, Darko S, Hua A, Overman G, Ransier A, Francica JR, Trama A, Tomaras GD, Haynes BF, Douek DC, Kepler TB. Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies. Front Immunol 2017; 8:1407. [PMID: 29163486 PMCID: PMC5663730 DOI: 10.3389/fimmu.2017.01407] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
The rhesus macaque is a critically important animal model in biomedical research, most recently playing a key role in the development of vaccines against human immunodeficiency virus-1. Nevertheless, the immunoglobulin (Ig) loci of macaques are as yet incompletely determined and our understanding of differences between human and macaque humoral immunity remains deficient. We completed a high-coverage, high-quality whole genome sequencing and assembly project with a single rhesus macaque of Indian origin, and partial genome assemblies using genomic molecular targeting of the Ig loci in nine other rhesus macaques of Indian origin. These data indicate that the macaque Ig loci are substantially more diverse than those in humans, including greater sequence diversity and copy-number variation between individuals. It appears likely that such copy-number variation even occurs between allelic loci within individuals. Different Ig gene families in the macaque show distinct relationships to the corresponding human gene families and appear to evolve under different mechanisms. These results raise intriguing questions about the evolution of antigen receptors in primates but also have important practical implications for the design and interpretation of biomedical studies.
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Affiliation(s)
- Akshaya Ramesh
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, United States
| | - Sam Darko
- NIH Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Axin Hua
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
| | - Glenn Overman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
| | - Amy Ransier
- NIH Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Joseph R Francica
- NIH Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Ashley Trama
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
| | - Daniel C Douek
- NIH Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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10
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Sterck EHM, Bontrop RE, de Groot N, de Vos-Rouweler AJM, Doxiadis GGM. No postcopulatory selection against MHC-homozygous offspring: Evidence from a pedigreed captive rhesus macaque colony. Mol Ecol 2017; 26:3785-3793. [PMID: 28437562 DOI: 10.1111/mec.14153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The heterozygosity status of polymorphic elements of the immune system, such as the major histocompatibility complex (MHC), is known to increase the potential to cope with a wider variety of pathogens. Pre- and postcopulatory processes may regulate MHC heterozygosity. In a population where mating occurs among individuals that share identical MHC haplotypes, postcopulatory selection may disfavour homozygous offspring or ones with two MHC haplotypes identical to its mother. We tested these ideas by determining the incidence of MHC-heterozygous and MHC-homozygous individuals in a pedigreed, partially consanguineous captive rhesus monkey colony. Bayesian statistics showed that when parents share MHC haplotypes, the distribution of MHC-heterozygous and MHC-homozygous individuals significantly fitted the expected Mendelian distribution, both for the complete MHC haplotypes, and for MHC class I or II genes separately. Altogether, we found in this captive colony no evidence for postcopulatory selection against MHC-homozygous individuals. However, the distribution of paternally and maternally inherited MHC haplotypes tended to differ significantly from expected. Individuals with two MHC haplotypes identical to their mother were underrepresented and offspring with MHC haplotypes identical to their father tended to be overrepresented. This suggests that postcopulatory processes affect MHC haplotype combination in offspring, but do not prevent low MHC heterozygosity.
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Affiliation(s)
- E H M Sterck
- Department of Animal Ecology, Utrecht University, Utrecht, The Netherlands.,Department of Animal Science, Ethology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - R E Bontrop
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Department of Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - N de Groot
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - A J M de Vos-Rouweler
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - G G M Doxiadis
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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11
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Song X, Zhang P, Huang K, Chen D, Guo S, Qi X, He G, Pan R, Li B. The influence of positive selection and trans-species evolution on DPB diversity in the golden snub-nosed monkeys (Rhinopithecus roxellana). Primates 2016; 57:489-99. [PMID: 27209173 DOI: 10.1007/s10329-016-0544-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
Genetic variation plays a significant role in the adaptive potential of the endangered species. The variation at major histocompatibility complex (MHC) genes can offer valuable information on selective pressure related to natural selection and environmental adaptation, particularly the ability of a host to continuously resist evolving parasites. Thus, the genetic polymorphism on exon 2 of the MHC DPB1 gene in the golden snub-nosed monkeys (Rhinopithecus roxellana) was specifically analyzed. The results show that the 6 Rhro-DPB1 alleles identified from 87 individuals exhibit positive selection and trans-species polymorphism. The results also imply that although the populations of the species have experienced dramatic reduction and severe habitat fragmentation in recent Chinese history, balancing selection still maintains relatively consistent, with moderate DPB1 polymorphism. Thus, the study provides valuable information and evidence in developing effective strategies and tactics for genetic health and population size expansion of the species. It also offers strong genetic background for further studies on other primate species, particularly those in Rhinopithecus-a further endeavor that would result in fully understanding the MHC genetic information of the Asian colobines.
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Affiliation(s)
- Xiaoyue Song
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Dan Chen
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiaoguang Qi
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Gang He
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China.,The School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Australia
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China. .,Xi'an Branch of Chinese Academy of Sciences, Xi'an, China.
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12
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Patterns of Immune Regulation in Rhesus Macaque and Human Families. Transplant Direct 2015; 1:e20. [PMID: 27500222 PMCID: PMC4946471 DOI: 10.1097/txd.0000000000000530] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/03/2015] [Indexed: 12/29/2022] Open
Abstract
Supplemental digital content is available in the text. Naturally acquired immune regulation amongst family members can result in mutual regulation between living related renal transplant donor and recipients. Pretransplant bidirectional regulation predisposed to superior renal allograft outcome in a CAMPATH-1H protocol. We tested whether Rhesus macaques, a large animal model of choice for preclinical transplant studies, share these immunoregulatory properties.
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13
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Smith GR, Bauer L, Crane MM, Johnson ZP. Immunogenetic characterization of a captive colony of sooty mangabeys (Cercocebus atys) used for SIV research. J Med Primatol 2015; 44:76-88. [PMID: 25645218 DOI: 10.1111/jmp.12161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND African non-human primates are SIV natural hosts and do not develop disease following infection. Understanding disease avoidance mechanisms in these species is important for HIV vaccine development. The largest captive population of sooty mangabeys, a SIV natural host species, resides at the Yerkes National Primate Research Center. METHODS Thirteen primer sets that amplify polymorphic microsatellite loci within the MHC region were used to genotype 144 animals. Immunogenetic Management Software (IMS) was used to identify MHC haplotypes and organize data. RESULTS Seventy-three haplotypes were identified. Limited haplotype diversity was observed in this population with 88.2% of included animals carrying one of 18 haplotypes. Differences in haplotype frequency were observed between SIV (+) and SIV (-) populations. CONCLUSIONS We have developed a novel tool for others to use in the analysis of the role of the MHC in a natural host non-human primate model species used for SIV research.
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Affiliation(s)
- Geary R Smith
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
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14
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de Groot N, Doxiadis GGM, Otting N, de Vos-Rouweler AJM, Bontrop RE. Differential recombination dynamics within the MHC of macaque species. Immunogenetics 2014; 66:535-44. [PMID: 24934118 PMCID: PMC4156779 DOI: 10.1007/s00251-014-0783-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/21/2014] [Indexed: 10/27/2022]
Abstract
A panel of 15 carefully selected microsatellites (short tandem repeats, STRs) has allowed us to study segregation and haplotype stability in various macaque species. The STRs span the major histocompatibility complex (MHC) region and map in more detail from the centromeric part of the Mhc-A to the DR region. Two large panels of Indian rhesus and Indonesian/Indochinese cynomolgus macaques have been subjected to pedigree analysis, allowing the definition of 161 and 36 different haplotypes and the physical mapping of 10 and 5 recombination sites, respectively. Although most recombination sites within the studied section of the Indian rhesus monkey MHC are situated between the Mhc-A and Mhc-B regions, the resulting recombination rate for this genomic segment is low and similar to that in humans. In contrast, in Indonesian/Indochinese macaques, two recombination sites, which appear to be absent in rhesus macaques, map between the class III and II regions. As a result, the mean recombination frequency of the core MHC, Mhc-A to class II, is higher in Indonesian/Indochinese cynomolgus than in Indian rhesus macaques, but as such is comparable to that in humans. The present communication demonstrates that the dynamics of recombination 'hot/cold spots' in the MHC, as well as their frequencies, may differ substantially between highly related macaque species.
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Affiliation(s)
- Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
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15
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Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns. PLoS Genet 2014; 10:e1004417. [PMID: 24901252 PMCID: PMC4046983 DOI: 10.1371/journal.pgen.1004417] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 04/14/2014] [Indexed: 11/19/2022] Open
Abstract
Many genes important in immunity are found as multigene families. The butyrophilin genes are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen presentation. In humans, a fixed number of butyrophilin genes are found in and around the major histocompatibility complex (MHC), and show striking association with particular autoimmune diseases. In chickens, BG genes encode homologues with somewhat different domain organisation. Only a few BG genes have been characterised, one involved in actin-myosin interaction in the intestinal brush border, and another implicated in resistance to viral diseases. We characterise all BG genes in B12 chickens, finding a multigene family organised as tandem repeats in the BG region outside the MHC, a single gene in the MHC (the BF-BL region), and another single gene on a different chromosome. There is a precise cell and tissue expression for each gene, but overall there are two kinds, those expressed by haemopoietic cells and those expressed in tissues (presumably non-haemopoietic cells), correlating with two different kinds of promoters and 5′ untranslated regions (5′UTR). However, the multigene family in the BG region contains many hybrid genes, suggesting recombination and/or deletion as major evolutionary forces. We identify BG genes in the chicken whole genome shotgun sequence, as well as by comparison to other haplotypes by fibre fluorescence in situ hybridisation, confirming dynamic expansion and contraction within the BG region. Thus, the BG genes in chickens are undergoing much more rapid evolution compared to their homologues in mammals, for reasons yet to be understood. Many immune genes are multigene families, presumably in response to pathogen variation. Some multigene families undergo expansion and contraction, leading to copy number variation (CNV), presumably due to more intense selection. Recently, the butyrophilin family in humans and other mammals has come under scrutiny, due to genetic associations with autoimmune diseases as well as roles in immune co-regulation and antigen presentation. Butyrophilin genes exhibit allelic polymorphism, but gene number appears stable within a species. We found that the BG homologues in chickens are very different, with great changes between haplotypes. We characterised one haplotype in detail, showing that there are two single BG genes, one on chromosome 2 and the other in the major histocompatibility complex (BF-BL region) on chromosome 16, and a family of BG genes in a tandem array in the BG region nearby. These genes have specific expression in cells and tissues, but overall are expressed in either haemopoietic cells or tissues. The two singletons have relatively stable evolutionary histories, but the BG region undergoes dynamic expansion and contraction, with the production of hybrid genes. Thus, chicken BG genes appear to evolve much more quickly than their closest homologs in mammals, presumably due to increased pressure from pathogens.
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16
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Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques. Immunogenetics 2013; 65:569-84. [PMID: 23715823 PMCID: PMC3710572 DOI: 10.1007/s00251-013-0707-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/23/2013] [Indexed: 12/11/2022]
Abstract
The Mamu-A, Mamu-B, and Mamu-DRB genes of the rhesus macaque show several levels of complexity such as allelic heterogeneity (polymorphism), copy number variation, differential segregation of genes/alleles present on a haplotype (diversity) and transcription level differences. A combination of techniques was implemented to screen a large panel of pedigreed Indian rhesus macaques (1,384 individuals representing the offspring of 137 founding animals) for haplotype diversity in an efficient and inexpensive manner. This approach allowed the definition of 140 haplotypes that display a relatively low degree of region variation as reflected by the presence of only 17 A, 18 B and 22 DRB types, respectively, exhibiting a global linkage disequilibrium comparable to that in humans. This finding contrasts with the situation observed in rhesus macaques from other geographic origins and in cynomolgus monkeys from Indonesia. In these latter populations, nearly every haplotype appears to be characterised by a unique A, B and DRB region. In the Indian population, however, a reshuffling of existing segments generated “new” haplotypes. Since the recombination frequency within the core MHC of the Indian rhesus macaques is relatively low, the various haplotypes were most probably produced by recombination events that accumulated over a long evolutionary time span. This idea is in accord with the notion that Indian rhesus macaques experienced a severe reduction in population during the Pleistocene due to a bottleneck caused by geographic changes. Thus, recombination-like processes appear to be a way to expand a diminished genetic repertoire in an isolated and relatively small founder population.
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17
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Huchard E, Albrecht C, Schliehe-Diecks S, Baniel A, Roos C, Kappeler PM, Peter PMK, Brameier M. Large-scale MHC class II genotyping of a wild lemur population by next generation sequencing. Immunogenetics 2012; 64:895-913. [PMID: 22948859 PMCID: PMC3496554 DOI: 10.1007/s00251-012-0649-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 08/13/2012] [Indexed: 12/23/2022]
Abstract
The critical role of major histocompatibility complex (MHC) genes in disease resistance, along with their putative function in sexual selection, reproduction and chemical ecology, make them an important genetic system in evolutionary ecology. Studying selective pressures acting on MHC genes in the wild nevertheless requires population-wide genotyping, which has long been challenging because of their extensive polymorphism. Here, we report on large-scale genotyping of the MHC class II loci of the grey mouse lemur (Microcebus murinus) from a wild population in western Madagascar. The second exons from MHC-DRB and -DQB of 772 and 672 individuals were sequenced, respectively, using a 454 sequencing platform, generating more than 800,000 reads. Sequence analysis, through a stepwise variant validation procedure, allowed reliable typing of more than 600 individuals. The quality of our genotyping was evaluated through three independent methods, namely genotyping the same individuals by both cloning and 454 sequencing, running duplicates, and comparing parent-offspring dyads; each displaying very high accuracy. A total of 61 (including 20 new) and 60 (including 53 new) alleles were detected at DRB and DQB genes, respectively. Both loci were non-duplicated, in tight linkage disequilibrium and in Hardy-Weinberg equilibrium, despite the fact that sequence analysis revealed clear evidence of historical selection. Our results highlight the potential of 454 sequencing technology in attempts to investigate patterns of selection shaping MHC variation in contemporary populations. The power of this approach will nevertheless be conditional upon strict quality control of the genotyping data.
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Affiliation(s)
- Elise Huchard
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, Göttingen, Germany.
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18
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Li W, Wang T, Ling F, Zhao H, Wei L, Zhuo M, Du H, Wang X. Identification of MhcMafa-DRB alleles in a cohort of cynomolgus macaques of Vietnamese origin. Am J Primatol 2012; 74:958-66. [PMID: 22903750 DOI: 10.1002/ajp.22048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/04/2012] [Accepted: 05/23/2012] [Indexed: 11/11/2022]
Abstract
Cynomolgus macaques have been used widely to build a research model of infectious and chronic diseases, as well as in transplantation studies, where disease susceptibility and/or resistance are associated with the major histocompatibility complex (MHC). To better elucidate polymorphisms and genetic differences in the Mafa-DRB locus, and facilitate the experimental use of cynomolgus macaques, we used pool screening combined with cloning and direct sequencing of polymerase chain reaction products to characterize MhcMafa-DRB gene alleles in 153 Vietnamese cynomolgus macaques. We identified 30 Mafa-DRB alleles belonging to 17 allelic lineages, including four novel sequences that had not been documented in earlier reports. The highest frequency allele was Mafa-DRB*W27:04, which was present in 7 of 35 (20%) monkeys. The next most frequent alleles were Mafa-DRB*3:07 and Mafa-DRB*W7:01, which were detected in 5 of 35 (14.3%) and 4 of 35 (11.4%) of the monkeys, respectively. The high-frequency alleles in this Vietnamese population may be high priority targets for additional characterization of immune functions. Only the DRB1*03 and DRB1*10 lineages were also present in humans, whereas the remaining alleles were monkey-specific lineages. We found 25 variable sites by aligning the deduced amino acid sequences of 29 identified alleles. Evolutionary and population analyses based on these sequences showed that human, rhesus, and cynomolgus macaques share several Mhc-DRB lineages and the shared polymorphisms in the DRB region may be attributable to the existence of interbreeding between rhesus and cynomolgus macaques. This information will promote the understanding of MHC diversity and polymorphism in cynomolgus macaques and increase the value of this species as a model for biomedical research.
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Affiliation(s)
- Wai Li
- School of Life Science, General Hospital of PLA T, Beijing, PR China
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19
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't Hart BA, Abbott DH, Nakamura K, Fuchs E. The marmoset monkey: a multi-purpose preclinical and translational model of human biology and disease. Drug Discov Today 2012; 17:1160-5. [PMID: 22728226 DOI: 10.1016/j.drudis.2012.06.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 05/31/2012] [Accepted: 06/13/2012] [Indexed: 01/13/2023]
Abstract
The development of biologic molecules (monoclonal antibodies, cytokines, soluble receptors) as specific therapeutics for human disease creates a need for animal models in which safety and efficacy can be tested. Models in lower animal species are precluded when the reagents fail to recognize their targets, which is often the case in rats and mice. In this Feature article we will highlight the common marmoset, a small-bodied nonhuman primate (NHP), as a useful model in biomedical and preclinical translational research.
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Affiliation(s)
- Bert A 't Hart
- Department of Immunobiology, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
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20
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Creager HM, Becker EA, Sandman KK, Karl JA, Lank SM, Bimber BN, Wiseman RW, Hughes AL, O’Connor SL, O’Connor DH. Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques. Immunogenetics 2011; 63:611-8. [PMID: 21614582 PMCID: PMC3156323 DOI: 10.1007/s00251-011-0537-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/10/2011] [Indexed: 01/09/2023]
Abstract
In recent years, the use of cynomolgus macaques in biomedical research has increased greatly. However, with the exception of the Mauritian population, knowledge of the MHC class II genetics of the species remains limited. Here, using cDNA cloning and Sanger sequencing, we identified 127 full-length MHC class II alleles in a group of 12 Indonesian and 12 Vietnamese cynomolgus macaques. Forty two of these were completely novel to cynomolgus macaques while 61 extended the sequence of previously identified alleles from partial to full length. This more than doubles the number of full-length cynomolgus macaque MHC class II alleles available in GenBank, significantly expanding the allele library for the species and laying the groundwork for future evolutionary and functional studies.
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Affiliation(s)
- Hannah M Creager
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Ericka A. Becker
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Kelly K. Sandman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Simon M. Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Benjamin N. Bimber
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA 53705
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA 53715
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA 53705
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Schad J, Dechmann DKN, Voigt CC, Sommer S. MHC class II DRB diversity, selection pattern and population structure in a neotropical bat species, Noctilio albiventris. Heredity (Edinb) 2011; 107:115-26. [PMID: 21245894 DOI: 10.1038/hdy.2010.173] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) have a crucial role in the immune response of vertebrates, alter the individual odour and are involved in shaping mating preferences. Pathogen-mediated selection, sexual selection and maternal-fetal interactions have been proposed as the main drivers of frequently observed high levels of polymorphism in functionally important parts of the MHC. Bats constitute the second largest mammalian order and have recently emerged as important vectors of infectious diseases. In addition, Chiroptera are interesting study subjects in evolutionary ecology in the context of olfactory communication, mate choice and associated fitness benefits. Thus, it is surprising that they belong to the least studied mammalian taxa in terms of their MHC diversity. In this study, we investigated the variability in the functionally important MHC class II gene DRB, evidence for selection and population structure in the group-living lesser bulldog bat, Noctilio albiventris, in Panama. We found a single expressed, polymorphic Noal-DRB gene. The substitution pattern of the nucleotide sequences of the 18 detected alleles provided evidence for positive selection acting above the evolutionary history of the species in shaping MHC diversity. Roosting colonies were not genetically differentiated but females showed lower levels of heterozygosity than males, which might be a sign that the sexes differ in the selection pressures acting on the MHC. This study provides the prerequisites for further investigations of the role of the individual MHC constitution in parasite resistance, olfactory communication and mate choice in N. albiventris and other bats.
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Affiliation(s)
- J Schad
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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Genomic plasticity of the MHC class I A region in rhesus macaques: extensive haplotype diversity at the population level as revealed by microsatellites. Immunogenetics 2010; 63:73-83. [PMID: 20949353 PMCID: PMC3019358 DOI: 10.1007/s00251-010-0486-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 09/30/2010] [Indexed: 12/11/2022]
Abstract
The Mamu-A genes of the rhesus macaque show different degrees of polymorphism, transcription level variation, and differential haplotype distribution. Per haplotype, usually one “major” transcribed gene is present, A1 (A7), in various combinations with “minor” genes, A2 to A6. In silico analysis of the physical map of a heterozygous animal revealed the presence of similar Mamu-A regions consisting of four duplication units, but with dissimilar positions of the A1 genes on both haplotypes, and in combination with different minor genes. Two microsatellites, D6S2854 and D6S2859, have been selected as potential tools to characterize this complex region. Subsequent analysis of a large breeding colony resulted in the description of highly discriminative patterns, displaying copy number variation in concert with microsatellite repeat length differences. Sequencing and segregation analyses revealed that these patterns are unique for each Mamu-A haplotype. In animals of Indian, Burmese, and Chinese origin, 19, 15, or 9 haplotypes, respectively, could be defined, illustrating the occurrence of differential block duplications and subsequent rearrangements by recombination. The haplotypes can be assigned to 12 unique combinations of genes (region configurations). Although most configurations harbor two transcribed A genes, one or three genes per haplotype are also present. Additionally, haplotypes lacking an A1 gene or with an A1 duplication appear to exist. The presence of different transcribed A genes/alleles in monkeys from various origins may have an impact on differential disease susceptibilities. The high-throughput microsatellite technique will be a valuable tool in animal selection for diverse biomedical research projects.
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Averdam A, Kuschal C, Otto N, Westphal N, Roos C, Reinhardt R, Walter L. Sequence analysis of the grey mouse lemur (Microcebus murinus) MHC class II DQ and DR region. Immunogenetics 2010; 63:85-93. [PMID: 20938657 DOI: 10.1007/s00251-010-0487-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 10/01/2010] [Indexed: 11/29/2022]
Abstract
We here report the genomic organisation of the grey mouse lemur (Microcebus murinus) MHC class II DQ and DR region based on BAC clone analysis. The sequenced Mimu-MHC haplotype spans 343 kb and encompasses the genes TAP2, DOB, DQB, DQA, DRB, DRA, BTNL2 and a further BTNL gene. The DQ and DR genes of this haplotype are not duplicated. Mimu-DOB is not transcribed and represents a pseudogene due to deletions and premature stop codons. Analysis of BAC clone DNA, a cDNA sample and eight genomic DNA samples suggests that Mimu-DRB, Mimu-DQA and Mimu-DQB are highly polymorphic with the majority of peptide-binding residues being affected by polymorphisms. In contrast, Mimu-DRA is moderately polymorphic, and the variable amino acid positions are not part of the peptide-binding region. Phylogenetic analysis of Mimu-DQA and Mimu-DQB and other primate DQA and DQB genes indicates that duplication of DQA and DQB loci occurred in Anthropoidea after the split from Strepsirrhini.
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Affiliation(s)
- Anne Averdam
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
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24
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Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0093-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Simian immunodeficiency virus-specific CD4+ T cells from successful vaccinees target the SIV Gag capsid. Immunogenetics 2010; 62:701-7. [PMID: 20812010 DOI: 10.1007/s00251-010-0473-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
Abstract
We recently demonstrated that vaccinated rhesus macaques controlled viral replication of a heterologous SIV challenge. Here, we analyzed anamnestic SIV-specific CD4+ T-cell responses expanding immediately after challenge and show that successful vaccinees consistently targeted a short region of the Gag-p27 Capsid (amino acids 249-291). We have also defined the major histocompatibility complex class II (MHC-II) restricting alleles for several of these responses and show that DQ-restricted CD4+ T-cells depend on unique combinations of both the DQA and DQB alleles. Analysis of SIV-specific CD4+ T-cell responses elicited by a successful vaccine may have important implications in the understanding of vaccine design.
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26
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Affiliation(s)
- W. BABIK
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30‐387 Kraków, Poland
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27
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Doxiadis GGM, de Groot N, de Groot NG, Rotmans G, de Vos-Rouweler AJM, Bontrop RE. Extensive DRB region diversity in cynomolgus macaques: recombination as a driving force. Immunogenetics 2010; 62:137-47. [PMID: 20131048 PMCID: PMC2827794 DOI: 10.1007/s00251-010-0422-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 01/08/2010] [Indexed: 12/21/2022]
Abstract
The DR region of primate species is generally complex and displays diversity concerning the number and combination of distinct types of DRB genes present per region configuration. A highly variable short tandem repeat (STR) present in intron 2 of nearly all primate DRB genes can be utilized as a quick and accurate high through-put typing procedure. This approach resulted previously in the description of unique and haplotype-specific DRB-STR length patterns in humans, chimpanzees, and rhesus macaques. For the present study, a cohort of 230 cynomolgus monkeys, including self-sustaining breeding groups, has been examined. MtDNA analysis showed that most animals originated from the Indonesian islands, but some are derived from the mainland, south and north of the Isthmus of Kra. Haplotyping and subsequent sequencing resulted in the detection of 118 alleles, including 28 unreported ones. A total of 49 Mafa-DRB region configurations were detected, of which 28 have not yet been described. Humans and chimpanzees possess a low number of different DRB region configurations in concert with a high degree of allelic variation. In contrast, however, allelic heterogeneity within a given Mafa-DRB configuration is even less frequently observed than in rhesus macaques. Several of these region configurations appear to have been generated by recombination-like events, most probably propagated by a retroviral element mapping within DRB6 pseudogenes, which are present on the majority of haplotypes. This undocumented high level of DRB region configuration-associated diversity most likely represents a species-specific strategy to cope with various pathogens.
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Affiliation(s)
- Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands.
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Lenz TL, Wells K, Pfeiffer M, Sommer S. Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the Long-tailed giant rat (Leopoldamys sabanus). BMC Evol Biol 2009; 9:269. [PMID: 19930637 PMCID: PMC2788554 DOI: 10.1186/1471-2148-9-269] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 11/23/2009] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Genes of the major histocompatibility complex (MHC) code for key functions in the adaptive immune response of vertebrates and most of them show exceptionally high polymorphism. This polymorphism has been associated with the selection by diverse and changing parasite communities. We analysed MHC class IIB diversity, gastrointestinal parasite load and body condition in the wild ranging tropical rat Leopoldamys sabanus (Thomas, 1887) under natural selection conditions in a highly variable rainforest environment in Borneo to explore the mechanisms that maintain these high levels of genetic polymorphism. RESULTS Allelic diversity was determined via SSCP and sequencing, and parasite screening was done through non-invasive faecal egg count. The detected alleles showed expected high levels of polymorphism and balancing selection. Besides a clear advantage for more diverse MHC genotypes in terms of number of alleles, reflected in better body condition and resistance against helminth infection, our data also suggested a positive effect of MHC allele divergence within an individual on these parameters. CONCLUSION In accordance with the heterozygote advantage hypothesis, this study provides evidence for an advantage of more diverse MHC genotypes. More specifically, the potential negative relation between individual allele divergence and number of parasite species is in line with the 'divergent allele advantage' hypothesis.
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Affiliation(s)
- Tobias L Lenz
- Department of Animal Ecology and Animal Conservation, University of Hamburg, 20146 Hamburg, Germany
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Konstans Wells
- Institute of Experimental Ecology, University of Ulm, 89069 Ulm, Germany
| | - Martin Pfeiffer
- Institute of Experimental Ecology, University of Ulm, 89069 Ulm, Germany
| | - Simone Sommer
- Department of Animal Ecology and Animal Conservation, University of Hamburg, 20146 Hamburg, Germany
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Postfach 601103, D-10252 Berlin, Germany
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Bonhomme M, Doxiadis GGM, Heijmans CMC, Vervoort V, Otting N, Bontrop RE, Crouau-Roy B. Genomic plasticity of the immune-related Mhc class I B region in macaque species. BMC Genomics 2008; 9:514. [PMID: 18973694 PMCID: PMC2584111 DOI: 10.1186/1471-2164-9-514] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 10/30/2008] [Indexed: 11/12/2022] Open
Abstract
Background In sharp contrast to humans and great apes, the expanded Mhc-B region of rhesus and cynomolgus macaques is characterized by the presence of differential numbers and unique combinations of polymorphic class I B genes per haplotype. The MIB microsatellite is closely linked to the single class I B gene in human and in some great apes studied. The physical map of the Mhc of a heterozygous rhesus monkey provides unique material to analyze MIB and Mamu-B copy number variation and then allows one to decipher the compound evolutionary history of this region in primate species. Results In silico research pinpointed 12 MIB copies (duplicons), most of which are associated with expressed B-genes that cluster in a separate clade in the phylogenetic tree. Generic primers tested on homozygous rhesus and pedigreed cynomolgus macaques allowed the identification of eight to eleven MIB copies per individual. The number of MIB copies present per haplotype varies from a minimum of three to six in cynomolgus macaques and from five to eight copies in rhesus macaques. Phylogenetic analyses highlight a strong transpecific sharing of MIB duplicons. Using the physical map, we observed that, similar to MIB duplicons, highly divergent Mamu-B genes can be present on the same haplotype. Haplotype variation as reflected by the copy number variation of class I B loci is best explained by recombination events, which are found to occur between MIBs and Mamu-B. Conclusion The data suggest the existence of highly divergent MIB and Mamu-B lineages on a given haplotype, as well as variable MIB and B copy numbers and configurations, at least in rhesus macaque. Recombination seems to occur between MIB and Mamu-B loci, and the resulting haplotypic plasticity at the individual level may be a strategy to better cope with pathogens. Therefore, evolutionary inferences based on the multiplicated MIB loci but also other markers close to B-genes appear to be promising for the study of B-region organization and evolution in primates.
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Affiliation(s)
- Maxime Bonhomme
- Université Paul Sabatier, Laboratoire Evolution et Diversité Biologique UMR5174 UPS/CNRS, 118 Route de Narbonne, Toulouse 31062 cedex 9, France.
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Comparative genetics of a highly divergent DRB microsatellite in different macaque species. Immunogenetics 2008; 60:737-48. [PMID: 18956179 PMCID: PMC4629986 DOI: 10.1007/s00251-008-0333-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 09/29/2008] [Indexed: 12/11/2022]
Abstract
The DRB region of the major histocompatibility complex (MHC) of cynomolgus and rhesus macaques is highly plastic, and extensive copy number variation together with allelic polymorphism makes it a challenging enterprise to design a typing protocol. All intact DRB genes in cynomolgus monkeys (Mafa) appear to possess a compound microsatellite, DRB-STR, in intron 2, which displays extensive length polymorphism. Therefore, this STR was studied in a large panel of animals, comprising pedigreed families as well. Sequencing analysis resulted in the detection of 60 Mafa-DRB exon 2 sequences that were unambiguously linked to the corresponding microsatellite. Its length is often allele specific and follows Mendelian segregation. In cynomolgus and rhesus macaques, the nucleotide composition of the DRB-STR is in concordance with the phylogeny of exon 2 sequences. As in humans and rhesus monkeys, this protocol detects specific combinations of different DRB-STR lengths that are unique for each haplotype. In the present panel, 22 Mafa-DRB region configurations could be defined, which exceeds the number detected in a comparable cohort of Indian rhesus macaques. The results suggest that, in cynomolgus monkeys, even more frequently than in rhesus macaques, new haplotypes are generated by recombination-like events. Although both macaque species are known to share several identical DRB exon 2 sequences, the lengths of the corresponding microsatellites often differ. Thus, this method allows not only fast and accurate DRB haplotyping but may also permit discrimination between highly related macaque species.
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Huchard E, Weill M, Cowlishaw G, Raymond M, Knapp LA. Polymorphism, haplotype composition, and selection in the Mhc-DRB of wild baboons. Immunogenetics 2008; 60:585-98. [DOI: 10.1007/s00251-008-0319-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 06/30/2008] [Indexed: 11/25/2022]
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Lutz W. Pas de deux: natural killer receptors and MHC class I ligands in primates. Curr Genomics 2008; 8:51-7. [PMID: 18645628 PMCID: PMC2474688 DOI: 10.2174/138920207780076974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 12/06/2006] [Accepted: 12/18/2006] [Indexed: 11/22/2022] Open
Abstract
Major histocompatibility complex (MHC) class I and NK cell receptor gene regions are a paradigm of genomic plasticity as they reveal a considerable degree of diversity, exemplified by high allelic polymorphism, genomic duplications and contractions, and formation of gene families. Both genetic components show signs of rapid evolution due to strong selective pressure to combat pathogens. Comparative analyses of these genomic regions in various primates revealed considerable differences, reflecting species-specific adaptations to pathogenic threat or different strategies to combat infections. MHC and NK receptor genomic diversity in populations are important factors that determine susceptibility or resistance to a variety of diseases including autoimmune and infectious diseases as well as reproductive success.
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Affiliation(s)
- Walter Lutz
- Department of Primate Genetics, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany.
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Meyer-Lucht Y, Otten C, Püttker T, Sommer S. Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials. BMC Genet 2008; 9:39. [PMID: 18534008 PMCID: PMC2442840 DOI: 10.1186/1471-2156-9-39] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 06/05/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined. RESULTS G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species. CONCLUSION Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism.
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Affiliation(s)
- Yvonne Meyer-Lucht
- Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str, 17, D-10315 Berlin, Germany.
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Impact of endogenous intronic retroviruses on major histocompatibility complex class II diversity and stability. J Virol 2008; 82:6667-77. [PMID: 18448532 DOI: 10.1128/jvi.00097-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major histocompatibility complex (MHC) represents a multigene family that is known to display allelic and gene copy number variations. Primate species such as humans, chimpanzees (Pan troglodytes), and rhesus macaques (Macaca mulatta) show DRB region configuration polymorphism at the population level, meaning that the number and content of DRB loci may vary per haplotype. Introns of primate DRB alleles differ significantly in length due to insertions of transposable elements as long endogenous retrovirus (ERV) and human ERV (HERV) sequences in the DRB2, DRB6, and DRB7 pseudogenes. Although the integration of intronic HERVs resulted sooner or later in the inactivation of the targeted genes, the fixation of these endogenous retroviral segments over long time spans seems to have provided evolutionary advantage. Intronic HERVs may have integrated in a sense or an antisense manner. On the one hand, antisense-oriented retroelements such as HERV-K14I, observed in intron 2 of the DRB7 genes in humans and chimpanzees, seem to promote stability, as configurations/alleles containing these hits have experienced strong conservative selection during primate evolution. On the other hand, the HERVK3I present in intron 1 of all DRB2 and/or DRB6 alleles tested so far integrated in a sense orientation. The data suggest that multigenic regions in particular may benefit from sense introgressions by HERVs, as these elements seem to promote and maintain the generation of diversity, whereas these types of integrations may be lethal in monogenic systems, since they are known to influence transcript regulation negatively.
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de Groot NG, Heijmans CMC, de Groot N, Otting N, de Vos-Rouweller AJM, Remarque EJ, Bonhomme M, Doxiadis GGM, Crouau-Roy B, Bontrop RE. Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics. Mol Ecol 2008; 17:2074-88. [PMID: 18346126 DOI: 10.1111/j.1365-294x.2008.03716.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep.
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Affiliation(s)
- Natasja G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 139, 2288 GJ Rijswijk, The Netherlands.
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Doxiadis GGM, de Groot N, Claas FHJ, Doxiadis IIN, van Rood JJ, Bontrop RE. A highly divergent microsatellite facilitating fast and accurate DRB haplotyping in humans and rhesus macaques. Proc Natl Acad Sci U S A 2007; 104:8907-12. [PMID: 17502594 PMCID: PMC1868589 DOI: 10.1073/pnas.0702964104] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DRB region of the MHC in primate species is known to display abundant region configuration polymorphism with regard to the number and content of genes present per haplotype. Furthermore, depending on the species studied, the different DRB genes themselves may display varying degrees of allelic polymorphism. Because of this combination of diversity (differential gene number) and polymorphism (allelic variation), molecular typing methods for the primate DRB region are cumbersome. All intact DRB genes present in humans and rhesus macaques appear to possess, however, a complex and highly divergent microsatellite. Microsatellite analysis of a sizeable panel of outbred rhesus macaques, covering most of the known Mamu-DRB haplotypes, resulted in the definition of unique genotyping patterns that appear to be specific for a given haplotype. Subsequent examination of a representative panel of human cells illustrated that this approach also facilitates high-resolution HLA-DRB typing in an easy, quick, and reproducible fashion. The genetic composition of this complex microsatellite is shown to be in concordance with the phylogenetic relationships of various HLA-DRB and Mamu-DRB exon 2 gene/lineage sequences. Moreover, its length variability segregates with allelic variation of the respective gene. This simple protocol may find application in a variety of research avenues such as transplantation biology, disease association studies, molecular ecology, paternity testing, and forensic medicine.
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Affiliation(s)
- Gaby G. M. Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands; and
- To whom correspondence may be addressed. E-mail: or
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands; and
| | - Frans H. J. Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, E3-Q, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Ilias I. N. Doxiadis
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, E3-Q, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Jon J. van Rood
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, E3-Q, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
- To whom correspondence may be addressed. E-mail: or
| | - Ronald E. Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands; and
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Abstract
One of the most important assumptions of kin selection theory is that individuals behave differently towards kin than non-kin. In mammals, there is strong evidence that maternal kin are distinguished from non-kin via familiarity. However, little is known about whether or not mammals can also recognize paternal kin as many female mammals, including primates, mate with multiple males near the time of conception, potentially concealing paternal kinship. Genetic data in several mammalian species with a promiscuous mating system and male-biased dispersal reveal a high skew in male reproduction which leads to co-residing paternal half-siblings. In most primates, individuals also form stable bisexual groups creating opportunities for males to interact with their offspring. Here I consider close paternal kin co-resident in the same social group, such as father-offspring and paternal half-siblings (i.e. animals sharing the same father but who were born to different mothers) and review mammalian studies of paternal kin discrimination. Furthermore, I summarize the most likely mechanisms of paternal kin discrimination (familiarity and phenotype matching). When familiarity is the underlying mechanism, mothers and/or the sire could mediate familiarity among paternal half-siblings as well as between fathers and offspring assuming mothers and/or fathers can assess paternity. When animals use phenotype matching, they might use their fathers' template (when the father is present) or self (when the father is absent) to assess paternal kinship in others. Available evidence suggests that familiarity and phenotype matching might be used for paternal kin discrimination and that both mechanisms might apply to a wide range of social mammals characterized by a high skew in male reproduction and co-residence of paternal kin. Among primates, suggested evidence for phenotype matching can often have an alternative explanation, which emphasizes the crucial importance of controlling for familiarity as a potential confounding variable. However, the mechanism/s used to identify paternal kin might differ within a species (as a function of each individual's specific circumstances) as well as among species (depending upon the key sensory modalities of the species considered). Finally, I discuss the possible cues used in paternal kin discrimination and offer suggestions for future studies.
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Affiliation(s)
- Anja Widdig
- Max Planck Institute for Evolutionary Anthropology, Department of Primatology, Deutscher Platz 6, D-04103 Leipzig, Germany.
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Otting N, de Vos-Rouweler AJM, Heijmans CMC, de Groot NG, Doxiadis GGM, Bontrop RE. MHC class I A region diversity and polymorphism in macaque species. Immunogenetics 2007; 59:367-75. [PMID: 17334754 PMCID: PMC1914291 DOI: 10.1007/s00251-007-0201-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 02/01/2007] [Indexed: 12/04/2022]
Abstract
The HLA-A locus represents a single copy gene that displays abundant allelic polymorphism in the human population, whereas, in contrast, a nonhuman primate species such as the rhesus macaque (Macaca mulatta) possesses multiple HLA-A-like (Mamu-A) genes, which parade varying degrees of polymorphism. The number and combination of transcribed Mamu-A genes present per chromosome display diversity in a population of Indian animals. At present, it is not clearly understood whether these different A region configurations are evolutionarily stable entities. To shed light on this issue, rhesus macaques from a Chinese population and a panel of cynomolgus monkeys (Macaca fascicularis) were screened for various A region-linked variations. Comparisons demonstrated that most A region configurations are old entities predating macaque speciation, whereas most allelic variation (>95%) is of more recent origin. The latter situation contrasts the observations of the major histocompatibility complex class II genes in rhesus and cynomolgus macaques, which share a high number of identical alleles (>30%) as defined by exon 2 sequencing.
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Affiliation(s)
- Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands.
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Haanstra KG, Sick EA, Ringers J, Wubben JAM, Kuhn EM, 't Hart BA, Boon L, Jonker M. No synergy between ATG induction and costimulation blockade induced kidney allograft survival in rhesus monkeys. Transplantation 2007; 82:1194-201. [PMID: 17102771 DOI: 10.1097/01.tp.0000235910.47214.67] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Costimulation blockade with antibodies directed against human CD40 and CD86 leads to prolonged kidney allograft survival in rhesus monkeys, but fails to induce permanent graft acceptance. We have tested whether costimulation blockade is more effective after peripheral T-cell ablation with antithymocyte globulin (ATG), with the aim to remove already primed autoreactive cells present in the normal repertoire. METHODS Rhesus monkeys were transplanted with a mismatched kidney allograft. ATG was given around the time of transplantation (day -1 and 0). Costimulation blockade with anti-CD40+anti-CD86 was given at tapering dosages from day -1 to 56. Cyclosporin A (CsA) was given from day 42 onwards and first rejections occurring after day 42 were treated with prednisone. RESULTS We observed accelerated rejection in ATG-treated monkeys, compared to animals receiving only costimulation blockade. The accelerated rejection of the kidney allograft occurred despite the application of rejection therapy with steroids and CsA. Three of the five ATG-treated animals were found seropositive for donor-specific alloantibodies. Early biopsies (day 21) from animals treated with ATG and anti-CD40+anti-CD86 show substantially reduced expression of cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) and forkhead box P3 (FOXP3) in focal infiltrates as compared to animals treated with only costimulation blockade. Furthermore, we observed the rapid reappearance of CD8 T-cells with a memory phenotype (disappearance of naive CD95/CD11a T-cells) in peripheral blood. CONCLUSION We conclude that (subtotal) T-cell depletion using ATG does not add to costimulation blockade induced kidney allograft survival.
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Affiliation(s)
- Krista G Haanstra
- Department of Immunobiology, Biomedical Primate Research Centre, Rijswijk, the Netherlands.
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Rönn AC, Andrés O, Bruford MW, Crouau-Roy B, Doxiadis G, Domingo-Roura X, Roeder AD, Verschoor E, Zischler H, Syvänen AC. Multiple Displacement Amplification for Generating an Unlimited Source of DNA for Genotyping in Nonhuman Primate Species. INT J PRIMATOL 2006. [DOI: 10.1007/s10764-006-9067-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sano K, Shiina T, Kohara S, Yanagiya K, Hosomichi K, Shimizu S, Anzai T, Watanabe A, Ogasawara K, Torii R, Kulski JK, Inoko H. Novel cynomolgus macaque MHC-DPB1 polymorphisms in three South-East Asian populations. ACTA ACUST UNITED AC 2006; 67:297-306. [PMID: 16634866 DOI: 10.1111/j.1399-0039.2006.00577.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cynomolgus macaques (Macaca fascicularis, Mafa), alias the crab-eating monkeys or long-tailed macaques, live across a vast range of South-East Asia. These non-human primates have emerged as important animal models in infectious and chronic diseases and transplantation studies, necessitating a more extensive characterization of their major histocompatibility complex polymorphic regions. The current information on the polymorphic variation or diversity of the Mafa-DPB1 locus is largely limited in comparison with the more commonly studied rhesus macaque DPB1 locus. In this article, to better elucidate the degree and types of polymorphisms and genetic differences of Mafa-DPB1 locus among three South-East Asian populations and to investigate how the allele differences between macaques and humans might affect their respective immune responses, we identified 40 alleles within exon 2 of the Mafa-DPB1 locus by DNA sequencing using 217 individuals. We also performed evolutionary and population analyses using these sequences to reveal some population-specific alleles and trans-species allelic conservation between the cynomolgus macaques and the rhesus macaques. Of the 40 new alleles, eight belong to a newly identified lineage group not previously found in the rhesus macaque species. This allele information will be useful for medical researchers using the cynomolgus macaques in disease and immunological studies.
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Affiliation(s)
- K Sano
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
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Prasad S, Humphreys I, Kireta S, Gilchrist RB, Bardy P, Russ GR, Coates PTH. MHC Class II DRB genotyping is highly predictive of in-vitro alloreactivity in the common marmoset. J Immunol Methods 2006; 314:153-63. [PMID: 16860822 DOI: 10.1016/j.jim.2006.06.009] [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: 03/27/2006] [Revised: 06/12/2006] [Accepted: 06/15/2006] [Indexed: 11/24/2022]
Abstract
The common marmoset (Callithrix jacchus) is emerging as a promising alternative pre-clinical model for transplantation and immunological research. It is therefore important to establish a rapid and reliable method of confirming alloreactivity between donor-recipient pairs. In this study of a large marmoset colony (n=49), we firstly characterised MHC Class II genes (Caja-DRB*W1201, Caja-DRB1*03, Caja-DRB*W16) using, for the first time in this species, sequence-based allelic typing techniques. Exon 2 was amplified using M13-tailed PCR primers specific for known marmoset alleles, and sequenced using universal M13 sequencing primers and dye terminator cycle sequencing. Twenty-six genotypes involving monomorphic Caja-DRB*W1201, 8 Caja-DRB*W16 and 5 Caja-DRB1*03 alleles were observed. Two new DRB*W16 alleles were identified. Subsequently we investigated whether matching at MHC-DRB loci alone could accurately predict in-vitro alloreactivity as assessed by mixed lymphocyte reactions. Peripheral blood mononuclear cells (PBMC) isolated from fully and partially DRB-matched and fully mismatched animal pairs were mixed and co-cultured for T-cell proliferation. PBMC co-cultured from fully or partially mismatched pairs exhibited significant T cell proliferation above single cell controls (p<0.01). Mixed PBMC from fully DRB-matched pairs exhibited no proliferation over controls (p=0.3). Thus using Caja-DRB genotyping, suitably alloreactive donor-recipient pairs can be rapidly and accurately identified for use in further studies of cellular and solid organ transplantation.
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Affiliation(s)
- Shilpanjali Prasad
- Transplantation Immunology Laboratory and Department of Medicine, University of Adelaide, The Queen Elizabeth Hospital Campus, 28 Woodville Road, Woodville, SA 5011, Australia
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43
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Suárez CF, Patarroyo ME, Trujillo E, Estupiñán M, Baquero JE, Parra C, Rodriguez R. Owl monkey MHC-DRB exon 2 reveals high similarity with several HLA-DRB lineages. Immunogenetics 2006; 58:542-58. [PMID: 16791623 DOI: 10.1007/s00251-006-0127-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 05/03/2006] [Indexed: 10/24/2022]
Abstract
One hundred and ten novel MHC-DRB gene exon 2 nucleotide sequences were sequenced in 96 monkeys from three owl monkey species (67 from Aotus nancymaae, 30 from Aotus nigriceps and 13 from Aotus vociferans). Owl monkeys, like humans, have high MHC-DRB allele polymorphism, revealing a striking similarity with several human allele lineages in the peptide binding region and presenting major convergence with DRB lineages from several Catarrhini (humans, apes and Old World monkeys) rather than with others New World monkeys (Platyrrhini). The parallelism between human and Aotus MHC-DRB reveals additional similarities regarding variability pattern, selection pressure and physicochemical constraints in amino acid replacements. These observations concerning previous findings of similarity between the Aotus immune system molecules and their human counterparts affirm this specie's usefulness as an excellent animal model in biomedical research.
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Affiliation(s)
- Carlos F Suárez
- Fundación Instituto de Inmunmología de Colombia, Carrera 50 No. 26-00, Bogotá, Colombia
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44
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Bak EJ, Ishii Y, Omatsu T, Kyuwa S, Tetsuya T, Hayasaka I, Yoshikawa Y. Identification and analysis of MHC class II DRB1 (Patr-DRB1) alleles in chimpanzees. ACTA ACUST UNITED AC 2006; 67:134-42. [PMID: 16441484 DOI: 10.1111/j.1399-0039.2006.00539.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MHC-DRB1 gene is known to display the most extensive allelic polymorphisms among MHC class II genes. We attempted the selective identification of chimpanzee (Pan troglodytes) DRB1 (Patr-DRB1) alleles using the polymerase chain reaction (PCR) technique in three steps: first, we performed Patr-DRB1*02 lineage-specific 8-kb PCR for *02 lineage detection in each chimpanzee; second, we performed 620-bp PCR for amplification of full-length exon 2; and finally, we carried out an insert check using the pattern of microsatellite repeat length variability. In the genomic DNA of 23 chimpanzees, nine Patr-DRB1 alleles containing two new alleles were detected. Our approach provides a relatively effective method of identifying Patr-DRB1 alleles in individual chimpanzees and should also contribute to our understanding of the features of MHC molecules in non-human primates.
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Affiliation(s)
- E J Bak
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657, Japan.
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45
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Oliver MK, Piertney SB. Isolation and characterization of a MHC class II DRB locus in the European water vole (Arvicola terrestris). Immunogenetics 2006; 58:390-5. [PMID: 16738936 DOI: 10.1007/s00251-006-0121-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
In so-called model species, such as human and mouse, genes of the major histocompatibility complex (MHC) are characterized by extremely high levels of polymorphism, and it is considered that such diversity is maintained by balancing selection. ;There is now a recognized need to expand studies into nonmodel species to examine whether high MHC diversity is mirrored in natural populations, and to determine the ecological, ethological, and evolutionary processes that underpin balancing selection. To address such issues, a necessary prerequisite is the ability to characterize diversity at a single, expressed, polymorphic MHC locus on which selection may be acting. Here, we provide the first description of allelic diversity at exon 2 of an MHC class II DRB locus in the European water vole (Arvicola terrestris), characterize variation across four natural populations, and test whether the patterns of variation are consistent with the effects of balancing selection. Using single-strand conformation polymorphism analysis and subsequent DNA sequencing of gel excisions, five DRB alleles were resolved, each with a unique amino acid sequence, among 100 individuals from four geographically distinct populations. Reverse transcription polymerase chain reaction confirmed that the alleles were products from an expressed locus. Intra-allelic amino acid differences were high (10.5-33.3%), and the nonsynonymous substitution rate exceeded the synonymous substitution rate for the functional peptide-binding region (d (N):d (S)=3.91 and P<0.005). Phylogenetic comparison of resolved alleles with closely related homologues indicated that each allele represented a unique lineage preserved across speciation events. These results indicate that balancing selection has maintained diversity of DRB allelic lineages and amino acid function over evolutionary time scales, but may be less effective at preserving alleles in contemporary populations where stochastic microevolutionary processes may dominate.
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Affiliation(s)
- Matthew K Oliver
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, Scotland, AB24 2TZ, UK.
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46
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Bontrop RE. Comparative genetics of MHC polymorphisms in different primate species: duplications and deletions. Hum Immunol 2006; 67:388-97. [PMID: 16728259 DOI: 10.1016/j.humimm.2006.03.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Indexed: 11/25/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) play a crucial role in the activation of adaptive (antigen-dependent) immune responses. In this paper similarities and dissimilarities among the MHCs of different primate species and their functional implications are reviewed. The human HLA system represents the most thoroughly investigated MHC of any contemporary living primate species, and so it will serve as a reference.
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Affiliation(s)
- Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, GH Rijswijk, The Netherlands.
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Doxiadis GGM, van der Wiel MKH, Brok HPM, de Groot NG, Otting N, ’t Hart BA, van Rood JJ, Bontrop RE. Reactivation by exon shuffling of a conserved HLA-DR3-like pseudogene segment in a New World primate species. Proc Natl Acad Sci U S A 2006; 103:5864-8. [PMID: 16581907 PMCID: PMC1421335 DOI: 10.1073/pnas.0600643103] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The common marmoset (Callithrix jacchus), a New World monkey species with a limited MHC class II repertoire, is highly susceptible to certain bacterial infections. Genomic analysis of exon 2 sequences documented the existence of only one DRB region configuration harboring three loci. Two of these loci display moderate levels of allelic polymorphism, whereas the -DRB*W12 gene appears to be monomorphic. This study shows that only the Caja-DRB*W16 and -DRB*W12 loci produce functional transcripts. The Caja-DRB1*03 locus is occupied by a pseudogene, given that most of the transcripts, if detected at all, show imperfections and are present at low levels. Moreover, two hybrid transcripts were identified that feature the evolutionarily conserved peptide-binding motif characteristic for the Caja-DRB1*03 gene. Thus, the severely reduced MHC class II repertoire in common marmosets has been expanded by reactivation of a pseudogene segment as a result of exon shuffling.
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Affiliation(s)
- Gaby G. M. Doxiadis
- Departments of Comparative Genetics and Refinement
- To whom correspondence may be addressed at:
Biomedical Primate Research Centre, Lange Kleiweg 139, 2288 GJ, Rijswijk, The Netherlands. E-mail:
| | | | | | | | - Nel Otting
- Departments of Comparative Genetics and Refinement
| | - Bert A. ’t Hart
- Immunobiology, Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands; and
| | - Jon J. van Rood
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, E3-Q, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
- To whom correspondence may be addressed. E-mail:
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Blancher A, Tisseyre P, Dutaur M, Apoil PA, Maurer C, Quesniaux V, Raulf F, Bigaud M, Abbal M. Study of Cynomolgus monkey (Macaca fascicularis) MhcDRB (Mafa-DRB) polymorphism in two populations. Immunogenetics 2006; 58:269-82. [PMID: 16572321 DOI: 10.1007/s00251-006-0102-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 02/06/2006] [Indexed: 12/25/2022]
Abstract
Cynomolgus monkey is one of the macaque species currently used as an animal model for experimental surgery and medicine, in particular, to experiment new drugs or therapy protocols designed for the prevention of allograft rejection. In this field, it is of utmost importance to select histoincompatible recipient-donor pairs. One way to ensure incompatibility between donor and recipient is to check their major histocompatibility complex (MHC) genotypes at the loci playing a determinant role in histocompatibility. We report in this paper on the cynomolgus monkey DRB polymorphism evidenced by sequencing of amplified exon 2 separated either by denaturing gradient gel electrophoresis (DGGE), or by cloning. By the study of 253 unrelated animals from two populations (Mauritius and The Philippines), we characterized 50 exon 2 sequences among which 28 were identical to sequences already reported in Macaca fascicularis or other macaque species (Macaca mulatta, Macaca nemestrina). By cloning and sequencing DRB cDNA, we revealed two additional DRB alleles. Out of the 20 haplotypes that we defined here, only two were found in both populations. The functional impact of DR incompatibility was studied in vitro by mixed lymphocyte culture.
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Affiliation(s)
- Antoine Blancher
- Laboratoire d'Immunogenetique moleculaire, Universite Paul Sabatier, Faculte de Medecine de Rangueil, Batiment A2, 133, Route de Narbonne, 31062, Toulouse cedex 4, France.
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Doxiadis GGM, Rouweler AJM, de Groot NG, Louwerse A, Otting N, Verschoor EJ, Bontrop RE. Extensive sharing of MHC class II alleles between rhesus and cynomolgus macaques. Immunogenetics 2006; 58:259-68. [PMID: 16470376 DOI: 10.1007/s00251-006-0083-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 12/27/2005] [Indexed: 10/25/2022]
Abstract
In contrast to rhesus monkeys, substantial knowledge on cynomolgus monkey major histocompatibility complex (MHC) class II haplotypes is lacking. Therefore, 17 animals, including one pedigreed family, were thoroughly characterized for polymorphic Mhc class II region genes as well as their mitochondrial DNA (mtDNA) sequences. Different cynomolgus macaque populations appear to exhibit unique mtDNA profiles reflecting their geographic origin. Within the present panel, 10 Mafa-DPB1, 14 Mafa-DQA1, 12 Mafa-DQB1, and 35 Mafa-DRB exon 2 sequences were identified. All of these alleles cluster into lineages that were previously described for rhesus macaques. Moreover, about half of the Mafa-DPB1, Mafa-DQA1, and Mafa-DQB1 alleles and one third of the Mafa-DRB exon 2 sequences are identical to rhesus macaque orthologues. Such a high level of Mhc class II allele sharing has not been reported for primate species. Pedigree analysis allowed the characterization of nine distinct Mafa class II haplotypes, and seven additional ones could be deduced. Two of these haplotypes harbor a duplication of the Mafa-DQB1 locus. Despite extensive allele sharing, rhesus and cynomolgus monkeys do not appear to possess identical Mhc class II haplotypes, thus illustrating that new haplotypes were generated after speciation by recombination-like processes.
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Affiliation(s)
- Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
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50
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't Hart BA, Bauer J, Brok HPM, Amor S. Non-human primate models of experimental autoimmune encephalomyelitis: Variations on a theme. J Neuroimmunol 2005; 168:1-12. [PMID: 16023737 DOI: 10.1016/j.jneuroim.2005.05.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 05/26/2005] [Accepted: 05/27/2005] [Indexed: 12/31/2022]
Abstract
Despite years of intensive research into multiple sclerosis (MS) scientists have not yet succeeded in developing an absolute therapy for the treatment of this disabling disease of the human central nervous system. The wide immunological gap between inbred rodent strains and the heterogeneous human population is probably the single most important factor that hampers the translation of scientific principles developed in rodents into effective therapies for MS. Because of the closer immunological proximity to humans, non-human primates provide useful experimental models that may help to bridge this gap. Here we review the models of experimental autoimmune encephalomyelitis in rhesus macaques and common marmosets. We will discuss the salient points of the models and suggest how these may represent the spectrum of inflammatory demyelinating diseases of the central nervous system in humans.
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Affiliation(s)
- Bert A 't Hart
- Department of Immunobiology, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
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