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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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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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3
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Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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4
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Na HS, Lee SY, Min HK, Park WJ, Lee JH, Cho KH, Hong SH, Kim DH, Jhun J, Choi JW, Kim SM, Kwok SK, Cho ML, Park SH. The establishment of a rheumatoid arthritis primate model in Macaca fascicularis. J Transl Med 2020; 18:264. [PMID: 32605610 PMCID: PMC7329448 DOI: 10.1186/s12967-020-02402-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a long-term autoimmune disorder that mostly affects the joints and leads to the destruction of cartilage. An RA model in non-human primates is especially useful because of their close phylogenetic relationship to humans in terms of cross-reactivity to compounds developed using modern drug technologies. Methods We used a collagen-induced arthritis (CIA) model in Macaca fascicularis. CIA was induced by the immunization of chicken type II collagen. Swelling was measured as the longitudinal and transverse axes of 16 proximal interphalangeal joints. Results A new system for visual evaluation was created, with a perfect score of 16. Individual behavioral analysis was also conducted. Serum was collected once a week after the first immunization. Blood chemistry and inflammatory cytokine parameters were higher in the CIA group than in the wild type group. Conclusion In conclusion, we established CIA in M. fascicularis, and the results can be used for drug evaluation models.
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Affiliation(s)
- Hyun Sik Na
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seon-Yeong Lee
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong Ki Min
- Division of Rheumatology, Department of Internal Medicine, Konkuk University Medical Center, Seoul, Republic of Korea
| | - Wan-Je Park
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Jung-Hwan Lee
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Ka-Hee Cho
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Shin-Hee Hong
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Dae-Hoon Kim
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Jooyeon Jhun
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong-Won Choi
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung-Min Kim
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Ki Kwok
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Mi-La Cho
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea. .,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea. .,Department of Medical Lifescience, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea. .,Conversant Research Consortium in Immunologic Disease, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-Ku, 137-040, Seoul, Korea.
| | - Sung-Hwan Park
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea.
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5
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KANTHASWAMY SREETHARAN, OLDT ROBERTF, NG JILLIAN, SMITH DAVIDGLENN, MARTÍNEZ MELWEENI, SARIOL CARLOSA. Determination of major histocompatibility class I and class II genetic composition of the Caribbean Primate Center specific pathogen-free rhesus macaque (Macaca mulatta) colony based on massively parallel sequencing. J Med Primatol 2018; 47:379-387. [PMID: 29971797 PMCID: PMC6234078 DOI: 10.1111/jmp.12353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND Knowledge of major histocompatibility complex (MHC) composition and distribution in rhesus macaque colonies is critical for management strategies that maximize the utility of this model for biomedical research. METHODS Variation within the Mamu-A and Mamu-B (class I) and DRB, DQA/B, and DPA/B (class II) regions of 379 animals from the Caribbean Primate Research Center's (CPRC) specific pathogen free (SPF) colony was examined using massively parallel sequencing. RESULTS Analyses of the 7 MHC loci revealed a background of Indian origin with high levels of variation despite past genetic bottlenecks. All loci exhibited mutual linkage disequilibria while conforming to Hardy-Weinberg expectations suggesting the achievement of mutation-selection balance. CONCLUSION The CPRC's SPF colony is a significant resource for research on AIDS and other infectious agents. Characterizing colony-wide MHC variability facilitates the breeding and selection of animals bearing desired haplotypes and increases the investigator's ability to understand the immune responses mounted by these animals.
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Affiliation(s)
- SREETHARAN KANTHASWAMY
- California National Primate Research Center, University of
California, Davis, CA, USA
- School of Mathematics and Natural Sciences, Arizona State University
(ASU) at the West Campus, Glendale, AZ, USA
| | - ROBERT F. OLDT
- School of Mathematics and Natural Sciences, Arizona State University
(ASU) at the West Campus, Glendale, AZ, USA
| | - JILLIAN NG
- California National Primate Research Center, University of
California, Davis, CA, USA
| | - DAVID GLENN SMITH
- California National Primate Research Center, University of
California, Davis, CA, USA
| | - MELWEEN I. MARTÍNEZ
- Caribbean Primate Research Center, University of Puerto Rico-Medical
Sciences Campus, San Juan, Puerto Rico
| | - CARLOS A. SARIOL
- Caribbean Primate Research Center, University of Puerto Rico-Medical
Sciences Campus, San Juan, Puerto Rico
- Department of Microbiology and Medical Zoology, University of Puerto
Rico-Medical Sciences Campus, San Juan, Puerto Rico
- Department of Medicine, University of Puerto Rico-Medical Sciences
Campus, San Juan, Puerto Rico
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6
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Walter L, Ansari AA. MHC and KIR Polymorphisms in Rhesus Macaque SIV Infection. Front Immunol 2015; 6:540. [PMID: 26557119 PMCID: PMC4617107 DOI: 10.3389/fimmu.2015.00540] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/08/2015] [Indexed: 02/04/2023] Open
Abstract
Natural killer lymphocytes are essentially involved as the first line of defense against agents such as viruses and malignant cells. The activity of these cells is regulated via interaction of specific and diverse killer cell immunoglobulin-like receptors (KIR) with the highly polymorphic cognate MHC class I proteins on target cells. Genetic variability of both KIR and MHC-I ligands has been shown to be associated with resistance to many diseases, including infection with the immunodeficiency virus. Disease course and progression to AIDS after infection with human immunodeficiency virus-1 (HIV-1) is essentially influenced by the presence of the stimulatory KIR3DS1 receptor in combination with HLA-Bw4. Knowledge of such genetic interactions that contribute to not only disease resistance but also susceptibility are just as important. Such combined genetic factors were recently reported in the rhesus macaque AIDS model. Here, we review the rhesus macaque MHC class I and KIR gene systems and the role of their polymorphisms in the SIV infection model.
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Affiliation(s)
- Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research , Göttingen , Germany
| | - Aftab A Ansari
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
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7
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Mothé BR, Lindestam Arlehamn CS, Dow C, Dillon MBC, Wiseman RW, Bohn P, Karl J, Golden NA, Gilpin T, Foreman TW, Rodgers MA, Mehra S, Scriba TJ, Flynn JL, Kaushal D, O'Connor DH, Sette A. The TB-specific CD4(+) T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans. Tuberculosis (Edinb) 2015; 95:722-735. [PMID: 26526557 DOI: 10.1016/j.tube.2015.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/23/2015] [Accepted: 07/26/2015] [Indexed: 01/05/2023]
Abstract
Non-human primate (NHP) models of tuberculosis (TB) immunity and pathogenesis, especially rhesus and cynomolgus macaques, are particularly attractive because of the high similarity of the human and macaque immune systems. However, little is known about the MHC class II epitopes recognized in macaques, thus hindering the establishment of immune correlates of immunopathology and protective vaccination. We characterized immune responses in rhesus macaques vaccinated against and/or infected with Mycobacterium tuberculosis (Mtb), to a panel of antigens currently in human vaccine trials. We defined 54 new immunodominant CD4(+) T cell epitopes, and noted that antigens immunodominant in humans are also immunodominant in rhesus macaques, including Rv3875 (ESAT-6) and Rv3874 (CFP10). Pedigree and inferred restriction analysis demonstrated that this phenomenon was not due to common ancestry or inbreeding, but rather presentation by common alleles, as well as, promiscuous binding. Experiments using a second cohort of rhesus macaques demonstrated that a pool of epitopes defined in the previous experiments can be used to detect T cell responses in over 75% of individual monkeys. Additionally, 100% of cynomolgus macaques, irrespective of their latent or active TB status, responded to rhesus and human defined epitope pools. Thus, these findings reveal an unexpected general repertoire overlap between MHC class II epitopes recognized in both species of macaques and in humans, showing that epitope pools defined in humans can also be used to characterize macaque responses, despite differences in species and antigen exposure. The results have general implications for the evaluation of new vaccines and diagnostics in NHPs, and immediate applicability in the setting of macaque models of TB.
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Affiliation(s)
- Bianca R Mothé
- Department of Biology, CSUSM, San Marcos, CA 92096, USA; La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.
| | | | - Courtney Dow
- Department of Biology, CSUSM, San Marcos, CA 92096, USA
| | - Myles B C Dillon
- La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA
| | - Patrick Bohn
- Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA
| | - Julie Karl
- Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA
| | - Nadia A Golden
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Trey Gilpin
- Department of Biology, CSUSM, San Marcos, CA 92096, USA
| | - Taylor W Foreman
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Mark A Rodgers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15216, USA
| | - Smriti Mehra
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University Baton Rouge, LA 70803, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Department of Pediatrics and Child Health, University of Cape Town, Cape Town 7925, South Africa
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15216, USA
| | - Deepak Kaushal
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center and Department of Pathology and Laboratory Medicine, UW-Madison, Madison, WI 53706, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
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8
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Albrecht C, Malzahn D, Brameier M, Hermes M, Ansari AA, Walter L. Progression to AIDS in SIV-Infected Rhesus Macaques is Associated with Distinct KIR and MHC class I Polymorphisms and NK Cell Dysfunction. Front Immunol 2014; 5:600. [PMID: 25506344 PMCID: PMC4246914 DOI: 10.3389/fimmu.2014.00600] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/07/2014] [Indexed: 12/21/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIR) regulate the activity of natural killer (NK) cells and have been shown to be associated with susceptibility to a number of human infectious diseases. Here, we analyzed NK cell function and genetic associations in a cohort of 52 rhesus macaques experimentally infected with SIVmac and subsequently stratified into high viral load (HVL) and low viral load (LVL) plasma viral loads at set point. This stratification coincided with fast (HVL) and slow (LVL) disease progression indicated by the disease course and critical clinical parameters including CD4+ T cell counts. HVL animals revealed sustained proliferation of NK cells but distinct loss of peripheral blood NK cell numbers and lytic function. Genetic analyses revealed that KIR genes 3DL05, 3DS05, and 3DL10 as well as 3DSW08, 3DLW03, and 3DSW09 are correlated, most likely due to underlying haplotypes. SIV-infection outcome associated with presence of transcripts for two inhibitory KIR genes (KIR3DL02, KIR3DL10) and three activating KIR genes (KIR3DSW08, KIR3DS02, KIR3DS05). Presence of KIR3DL02 and KIR3DSW08 was associated with LVL outcome, whereas presence of KIR3DS02 was associated with HVL outcome. Furthermore, we identified epistasis between KIR and MHC class I alleles as the transcript presence of the correlated genes KIR3DL05, KIR3DS05, and KIR3DL10 increased HVL risk when Mamu-B*012 transcripts were also present or when Mamu-A1*001 transcripts were absent. These genetic associations were mirrored by changes in the numbers, the level of proliferation, and lytic capabilities of NK cells as well as overall survival time and gastro-intestinal tissue viral load.
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Affiliation(s)
- Christina Albrecht
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research , Göttingen , Germany
| | - Dörthe Malzahn
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University , Göttingen , Germany
| | - Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research , Göttingen , Germany
| | - Meike Hermes
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research , Göttingen , Germany
| | - Aftab A Ansari
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine , Atlanta, GA , USA
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research , Göttingen , Germany
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9
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Identification of MHC class I sequences in four species of Macaca of China. Immunogenetics 2013; 65:851-9. [PMID: 24045838 DOI: 10.1007/s00251-013-0735-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
Abstract
Tibetan macaques (Macaca thibetana), stump-tailed macaques (M. arctoides), Assamese macaques (M. assamensis), and northern pig-tailed macaques (M. leonina) are four major species of Macaca in China. In order to effectively use these species in biomedical research, thorough investigations of their MHC immunogenetics are required. In this study, we identified MHC class I sequences using cDNA cloning and sequencing on a cohort of six M. thibetana, three M. arctoides, three M. assamensis, and three M. leonina derived from Sichuan and Yunnan provinces of China. Eighty new alleles were identified, including 26 MHC-A alleles, 46 MHC-B alleles, and 8 MHC-I alleles. Among them, Math-A1*126:01, Math-B*190:01, Math-B*191:01, Math-B*192:01, Maar-A1*127:01, Maar-A1*129:01, and Maas-A1*128:01 represent lineages that had not been reported earlier in Macaca. Phylogenetic analyses show that no obvious separation of lineages among these species of Macaca. This study provides important information about the MHC immunogenetics for the four major species of Chinese macaques and adds value to these species as model organisms in biomedical research.
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10
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Karl JA, Bohn PS, Wiseman RW, Nimityongskul FA, Lank SM, Starrett GJ, O’Connor DH. Major histocompatibility complex class I haplotype diversity in Chinese rhesus macaques. G3 (BETHESDA, MD.) 2013; 3:1195-201. [PMID: 23696100 PMCID: PMC3704247 DOI: 10.1534/g3.113.006254] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/14/2013] [Indexed: 12/28/2022]
Abstract
The use of Chinese-origin rhesus macaques (Macaca mulatta) for infectious disease immunity research is increasing despite the relative lack of major histocompatibility complex (MHC) class I immunogenetics information available for this population. We determined transcript-based MHC class I haplotypes for 385 Chinese rhesus macaques from five different experimental cohorts, providing a concise representation of the full complement of MHC class I major alleles expressed by each animal. In total, 123 Mamu-A and Mamu-B haplotypes were defined in the full Chinese rhesus macaque cohort. We then performed an analysis of haplotype frequencies across the experimental cohorts of Chinese rhesus macaques, as well as a comparison against a group of 96 Indian rhesus macaques. Notably, 35 of the 51 Mamu-A and Mamu-B haplotypes observed in Indian rhesus macaques were also detected in the Chinese population, with 85% of the 385 Chinese-origin rhesus macaques expressing at least one of these class I haplotypes. This unexpected conservation of Indian rhesus macaque MHC class I haplotypes in the Chinese rhesus macaque population suggests that immunologic insights originally gleaned from studies using Indian rhesus macaques may be more applicable to Chinese rhesus macaques than previously appreciated and may provide an opportunity for studies of CD8(+) T-cell responses between populations. It may also be possible to extend these studies across multiple species of macaques, as we found evidence of shared ancestral haplotypes between Chinese rhesus and Mauritian cynomolgus macaques.
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Affiliation(s)
- Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Patrick S. Bohn
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | | | - Simon M. Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Gabriel J. Starrett
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705
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11
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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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12
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Expression patterns of killer cell immunoglobulin-like receptors (KIR) of NK-cell and T-cell subsets in Old World monkeys. PLoS One 2013; 8:e64936. [PMID: 23717676 PMCID: PMC3661512 DOI: 10.1371/journal.pone.0064936] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 04/23/2013] [Indexed: 02/04/2023] Open
Abstract
The expression of killer cell immunoglobulin-like receptors (KIR) on lymphocytes of rhesus macaques and other Old World monkeys was unknown so far. We used our recently established monoclonal anti-rhesus macaque KIR antibodies in multicolour flow cytometry for phenotypic characterization of KIR protein expression on natural killer (NK) cells and T cell subsets of rhesus macaques, cynomolgus macaques, hamadryas baboons, and African green monkeys. Similar to human KIR, we found clonal expression patterns of KIR on NK and T cell subsets in rhesus macaques and differences between individuals using pan-KIR3D antibody 1C7 and antibodies specific for single KIR. Similar results were obtained with lymphocytes from the other studied species. Notably, African green monkeys show only a low frequency of KIR3D expressed on CD8+ αβT cells. Contrasting human NK cells are KIR-positive CD56bright NK cells and frequencies of KIR-expressing NK cells that are independent of the presence of their cognate MHC class I ligands in rhesus macaques. Interestingly, the frequency of KIR-expressing cells and the expression strength of KIR3D are correlated in γδ T cells of rhesus macaques and CD8+ αβT cells of baboons.
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13
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Wiseman RW, Karl JA, Bohn PS, Nimityongskul FA, Starrett GJ, O'Connor DH. Haplessly hoping: macaque major histocompatibility complex made easy. ILAR J 2013; 54:196-210. [PMID: 24174442 PMCID: PMC3814398 DOI: 10.1093/ilar/ilt036] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Major histocompatibility complex (MHC) gene products control the repertoire of T cell responses that an individual may create against pathogens and foreign tissues. This text will review the current understanding of MHC genetics in nonhuman primates, with a focus on Mauritian-origin cynomolgus macaques (Macaca fascicularis) and Indian-origin rhesus macaques (Macaca mulatta). These closely related macaque species provide important experimental models for studies of infectious disease pathogenesis, vaccine development, and transplantation research. Recent advances resulting from the application of several cost effective, high-throughput approaches, with deep sequencing technologies have revolutionized our ability to perform MHC genotyping of large macaque cohorts. Pyrosequencing of cDNA amplicons with a Roche/454 GS Junior instrument, provides excellent resolution of MHC class I allelic variants with semi-quantitative estimates of relative levels of transcript abundance. Introduction of the Illumina MiSeq platform significantly increased the sample throughput, since the sample loading workflow is considerably less labor intensive, and each instrument run yields approximately 100-fold more sequence data. Extension of these sequencing methods from cDNA to genomic DNA amplicons further streamlines the experimental workflow and opened opportunities for retrospective MHC genotyping of banked DNA samples. To facilitate the reporting of MHC genotypes, and comparisons between groups of macaques, this text also introduces an intuitive series of abbreviated rhesus MHC haplotype designations based on a major Mamu-A or Mamu-B transcript characteristic for ancestral allele combinations. The authors believe that the use of MHC-defined macaques promises to improve the reproducibility, and predictability of results from pre-clinical studies for translation to humans.
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Affiliation(s)
- Roger W. Wiseman
- Address correspondence and reprint requests to Dr. Roger Wiseman, Wisconsin National Primate Research Center, University of Wisconsin-Madison, 555 Science Drive, Madison, WI 53711 or email
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14
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Liu Y, Li A, Wang X, Sui L, Li M, Zhao Y, Liu B, Zeng L, Sun Z. Mamu-B genes and their allelic repertoires in different populations of Chinese-origin rhesus macaques. Immunogenetics 2012; 65:273-80. [PMID: 23271617 DOI: 10.1007/s00251-012-0673-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 12/11/2012] [Indexed: 11/24/2022]
Abstract
Since rhesus monkeys of Chinese origin have gained greater utilization in recent years, it is urgent to investigate the major histocompatibility complex (MHC) immunogenetics of Chinese rhesus macaques. In this study, we identified 81 Mamu-B sequences using complementary DNA cloning and sequencing on a cohort of 58 rhesus monkeys derived from three local populations of China. Twenty of these Mamu-B alleles are novel and four of them represent new lineages. Although more alleles are shared among different populations than Mamu-A locus, the Mamu-B allelic repertoires found in these three populations of Chinese macaques are largely independent, which underscores the MHC polymorphism among different populations of Chinese rhesus macaques. Our results are an important addition to the limited MHC immunogenetic information available for rhesus macaques of Chinese origin.
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Affiliation(s)
- Yi Liu
- Laboratory Animal Center of the Academy of Military Medical Science, Beijing, 100071, China
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15
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Li A, Wang X, Liu Y, Zhao Y, Liu B, Sui L, Zeng L, Sun Z. Preliminary observations of MHC class I A region polymorphism in three populations of Chinese-origin rhesus macaques. Immunogenetics 2012; 64:887-94. [PMID: 22940774 DOI: 10.1007/s00251-012-0645-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/05/2012] [Indexed: 02/06/2023]
Abstract
Rhesus macaques are an animal model for the study of a variety of human diseases. The Chinese rhesus macaques have been widely used in biomedical research in recent years. However, the polymorphism of major histocompatibility complex (MHC) class I A region among different local populations of Chinese rhesus macaques has never been investigated. In this study, we identified 46 Mamu-A alleles by cDNA cloning and sequencing on a cohort of 53 Chinese rhesus monkeys including Zhiming, Chuanxi, and Fujian populations, of which 5 were first reported in rhesus monkeys. The frequencies of alleles were identified for each population. The result suggests that the repertoire of allelic variants of MHC class I A region found in different populations of Chinese macaques is largely non-overlapping. The frequencies of alleles and the popular allele are also different for different populations. PCR-SSP experiment further confirms the different frequencies of two alleles, Mamu-A*026:01 and Mamu-A*022:01, in additional 99 Zhiming monkeys and 191 Chuanxi monkeys. Our findings have important practical implications in that the origin of the individuals and the genetic polymorphism of the monkeys need to be considered at the level of local populations for Chinese rhesus monkeys in biomedical research. Further immunogenetic work is needed to investigate the MHC polymorphism among different populations of Chinese rhesus macaques and to reveal the functional implication of such polymorphism and disease outcome correlations.
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Affiliation(s)
- Aixue Li
- Laboratory Animal Center of the Academy of Military Medical Science, Beijing, 100071, China
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16
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Orysiuk D, Lawrence J, Prashar T, Spangelo L, Pilon R, Fournier J, Rud E, Sandstrom P, Plummer FA, Luo M. Evidence of recombination producing allelic diversity in MHC class I Mafa-B and -A alleles in cynomolgus macaques. ACTA ACUST UNITED AC 2012; 79:351-8. [PMID: 22489944 DOI: 10.1111/j.1399-0039.2012.01867.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MHC class I-A and -B genes of cynomolgus macaques are highly polymorphic. These genes encode proteins presenting peptides to CD8+ T cells to initiate adaptive immune response. Recombination events are one way the diversity of these alleles can be increased. Such events have been well characterized in humans, but have not been as well characterized in macaques. In order to identify and examine recombinations that create new alleles, it is important to analyze intron sequences. Intron sequences have been shown to be important to understand the evolutionary mechanisms involved in the generation of major histocompatibility complex (MHC) alleles and loci. Thus far, there have been relatively few intron sequences reported for MHC class I alleles in macaques, and this has hampered the understanding of MHC organization and evolution in macaques. In this study, we present evidence of a gene conversion event generating the Mafa-B*099 allele lineage by the combination of Mafa-B*054 and Mafa-B*095 allele lineages. A potential recombination between the Mafa-A3*13 and Mafa-A4:14 lineages was also observed, but it is less clear due to lack of intron 2 sequence. This report stresses the role that recombination can play in MHC class I diversity in cynomologus macaques, and the importance of introns in identifying and analyzing such events.
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Affiliation(s)
- D Orysiuk
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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17
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Otting N, de Groot N, de Vos-Rouweler AJM, Louwerse A, Doxiadis GGM, Bontrop RE. Multilocus definition of MHC haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis). Immunogenetics 2012; 64:755-65. [PMID: 22772814 PMCID: PMC3438390 DOI: 10.1007/s00251-012-0632-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/06/2012] [Indexed: 12/20/2022]
Abstract
Cynomolgus macaques (Macaca fascicularis) are used widely in biomedical research, and the genetics of their MHC (Mhc-Mafa) has become the focus of considerable attention in recent years. The cohort of Indonesian pedigreed macaques that we present here was typed for Mafa-A, -B, and -DR, by sequencing, as described in earlier studies. Additionally, the DRB region of these animals was characterised by microsatellite analyses. In this study, full-length sequencing of Mafa-DPA/B and -DQA/B in these animals was performed. A total of 75 different alleles were observed; 22 of which have not previously been reported, plus 18 extended exon 2 alleles that were already known. Furthermore, two microsatellites, D6S2854 and D6S2859, were used to characterise the complex Mafa-A region. Sequencing and segregation analyses revealed that the length patterns of these microsatellites are unique for each Mafa-A haplotype. In this work, we present a pedigreed colony of approximately 120 cynomolgus macaques; all of which are typed for the most significant polymorphic MHC class I and class II markers. Offspring of these pedigreed animals are easily characterised for their MHC by microsatellite analyses on the Mafa-A and -DRB regions, which makes the cumbersome sequencing analyses redundant.
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Affiliation(s)
- Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288GJ, Rijswijk, The Netherlands.
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18
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Kean LS, Singh K, Blazar BR, Larsen CP. Nonhuman primate transplant models finally evolve: detailed immunogenetic analysis creates new models and strengthens the old. Am J Transplant 2012; 12:812-9. [PMID: 22177005 PMCID: PMC3482466 DOI: 10.1111/j.1600-6143.2011.03873.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nonhuman primate (NHP) models play a critical role in the translation of novel therapies for transplantation to the clinic. However, although MHC disparity significantly affects the outcome of transplantation, until recently, experiments using NHP models were performed without the ability to rigorously control the degree of MHC disparity in transplant cohorts. In this review, we discuss several key technical breakthroughs in the field, which have finally enabled detailed immunogenetic data to be incorporated into NHP transplantation studies. These advances have created a new gold-standard for NHP transplantation research, which incorporates detailed information regarding the degree of relatedness and the degree of MHC haplotype disparity between transplant pairs and the precise MHC alleles that both donors and recipients express. The adoption of this new standard promises to increase the rigor of NHP transplantation studies and to ensure that these experiments are optimally translatable to patient care.
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Affiliation(s)
- L S Kean
- Aflac Cancer Center and Blood Disorders Service, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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19
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Liao Q, Strong AJ, Liu Y, Liu Y, Meng P, Fu Y, Touzjian N, Shao Y, Zhao Z, Lu Y. HIV vaccine candidates generate in vitro T cell response to putative epitopes in Chinese-origin rhesus macaques. Vaccine 2012; 30:1601-8. [PMID: 22261410 DOI: 10.1016/j.vaccine.2011.12.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 12/16/2011] [Accepted: 12/23/2011] [Indexed: 11/30/2022]
Abstract
The Indian rhesus macaque is the established animal model for HIV infection and vaccine research. Growing evidence suggests that the more readily available Chinese rhesus macaque may be a more relevant option. As increasing numbers of novel Chinese rhesus MHC alleles are reported, we decided to explore potential HIV vaccine epitopes in this model. We immunized forty Chinese rhesus macaques with three different HIV vaccine candidates either individually or following a prime/boost strategy. We used ELISPOT to measure immune response in vitro to HIV-1 p24C and HIV-1 gp160 peptide libraries. We identified five putative epitopes with associations to HLA-I alleles including HLA*B-2705 and HLA-B*5101 (associated with slow disease progression and low viral set point) and HLA-B*18 (associated with rapid disease progression and high viral set point). This suggests the possible use of Chinese rhesus macaques to model different disease progressions. We also explored the use of fusion proteins as stimulators in ELISPOT assays. While PBMCs from 6 monkeys responded to peptide stimulation, PBMCs from 28 monkeys responded to the anthrax lethal factor fusion proteins LFn p24C and/or LFn gp140C. Our results support the use of Chinese rhesus macaques in HIV vaccine studies.
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Affiliation(s)
- Qi Liao
- Vaccine Laboratory, NanKai University, Tianjin, China
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20
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Wambua D, Henderson R, Solomon C, Hunter M, Marx P, Sette A, Mothé BR. SIV-infected Chinese-origin rhesus macaques express specific MHC class I alleles in either elite controllers or normal progressors. J Med Primatol 2011; 40:244-7. [PMID: 21781132 DOI: 10.1111/j.1600-0684.2011.00487.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Daniel Wambua
- Department of Biology, California State University, San Marcos, USA
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21
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Lang Kuhs KA, Ginsberg AA, Yan J, Wiseman RW, Khan AS, Sardesai NY, O'Connor DH, Weiner DB. Hepatitis C virus NS3/NS4A DNA vaccine induces multiepitope T cell responses in rhesus macaques mimicking human immune responses [corrected]. Mol Ther 2011; 20:669-78. [PMID: 21952169 DOI: 10.1038/mt.2011.188] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Numerous studies have suggested that an effective hepatitis C virus (HCV) vaccine must induce a strong T helper 1 (Th1) T cell response. While several therapeutic vaccine candidates have shown promise in clinical trials, response rates have been low suggesting that further optimization is important. However, such optimization has been hindered by a lack of a benchmark animal model in which to test vaccine-induced immune responses before clinical evaluation. The goal of this study was to analyze the utility of the rhesus macaque vaccination model in assessing HCV vaccine-induced T cell responses. To test this, we employed the use of a novel HCV genotype 1a/1b consensus DNA vaccine encoding both HCV nonstructural protein 3 (NS3) and nonstructural protein 4A (NS4A) proteins. Following immunization, rhesus macaques mounted HCV-specific responses strikingly similar to those reported in resolving patients, including strong NS3-specific interferon-γ (IFN-γ) responses, robust CD4(+) and CD8(+) T cell proliferation, and induction of polyfunctional T cells. Additionally, fine epitope mapping revealed one animal that mounted a T cell response against a known HCV NS3 human leukocyte antigen A2 (HLA-A2) epitope previously identified in humans. Taken together our findings suggest that the rhesus macaque vaccination model is a useful tool in the evaluation of immune responses induced by HCV immunogens.
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Affiliation(s)
- Krystle A Lang Kuhs
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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22
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Saito Y, Naruse TK, Akari H, Matano T, Kimura A. Diversity of MHC class I haplotypes in cynomolgus macaques. Immunogenetics 2011; 64:131-41. [PMID: 21881951 DOI: 10.1007/s00251-011-0568-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Accepted: 08/19/2011] [Indexed: 12/01/2022]
Abstract
Cynomolgus macaques are widely used as a primate model for human diseases associated with an immunological process. Because there are individual differences in immune responsiveness, which are controlled by the polymorphic nature of the major histocompatibility (MHC) locus, it is important to reveal the diversity of MHC in the model animal. In this study, we analyzed 26 cynomolgus macaques from five families for MHC class I genes. We identified 32 Mafa-A, 46 Mafa-B, 6 Mafa-I, and 3 Mafa-AG alleles in which 14, 20, 3, and 3 alleles were novel. There were 23 MHC class I haplotypes and each haplotype was composed of one to three Mafa-A alleles and one to five Mafa-B alleles. Family studies revealed that there were two haplotypes which contained two Mafa-A1 alleles. These observations demonstrated further the complexity of MHC class I locus in the Old World monkey.
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Affiliation(s)
- Yusuke Saito
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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23
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Maness NJ, Walsh AD, Rudersdorf RA, Erickson PA, Piaskowski SM, Wilson NA, Watkins DI. Chinese origin rhesus macaque major histocompatibility complex class I molecules promiscuously present epitopes from SIV associated with molecules of Indian origin; implications for immunodominance and viral escape. Immunogenetics 2011; 63:587-97. [PMID: 21626440 DOI: 10.1007/s00251-011-0538-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 05/19/2011] [Indexed: 01/21/2023]
Abstract
The presentation of identical peptides by different major histocompatibility complex class I (MHC-I) molecules, termed promiscuity, is a controversial feature of T cell-mediated immunity to pathogens. The astounding diversity of MHC-I molecules in human populations, presumably to enable binding of equally diverse peptides, implies promiscuity would be a rare phenomenon. However, if it occurs, it would have important implications for immunity. We screened 77 animals for responses to peptides known to bind MHC-I molecules that were not expressed by these animals. Some cases of supposed promiscuity were determined to be the result of either non-identical optimal peptides or were simply not mapped to the correct MHC-I molecule in previous studies. Cases of promiscuity, however, were associated with alterations of immunodominance hierarchies, either in terms of the repertoire of peptides presented by the different MHC-I molecules or in the magnitude of the responses directed against the epitopes themselves. Specifically, we found that the Mamu-B*017:01-restricted peptides Vif HW8 and cRW9 were also presented by Mamu-A2*05:26 and targeted by an animal expressing that allele. We also found that the normally subdominant Mamu-A1*001:01 presented peptide Gag QI9 was also presented by Mamu-B*056:01. Both A2*05:26 and B*056:01 are molecules typically or exclusively expressed by animals of Chinese origin. These data clearly demonstrate that MHC-I epitope promiscuity, though rare, might have important implications for immunodominance and for the transmission of escape mutations, depending on the relative frequencies of the given alleles in a population.
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Affiliation(s)
- Nicholas James Maness
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, WI 53711, USA.
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24
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Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities. Immunogenetics 2011; 63:275-90. [PMID: 21274527 PMCID: PMC3068250 DOI: 10.1007/s00251-010-0502-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/07/2010] [Indexed: 01/15/2023]
Abstract
The Simian immunodeficiency virus (SIV)-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection and AIDS-related research, despite the potential that macaques of Chinese origin is a more relevant model. Ongoing efforts to further characterize the Chinese rhesus macaques' major histocompatibility complex (MHC) for composition and function should facilitate greater utilization of the species. Previous studies have demonstrated that Chinese-origin M. mulatta (Mamu) class I alleles are more polymorphic than their Indian counterparts, perhaps inferring a model more representative of human MHC, human leukocyte antigen (HLA). Furthermore, the Chinese rhesus macaque class I allele Mamu-A1*02201, the most frequent allele thus far identified, has recently been characterized and shown to be an HLA-B7 supertype analog, the most frequent supertype in human populations. In this study, we have characterized two additional alleles expressed with high frequency in Chinese rhesus macaques, Mamu-A1*02601 and Mamu-B*08301. Upon the development of MHC-peptide-binding assays and definition of their associated motifs, we reveal that these Mamu alleles share peptide-binding characteristics with the HLA-A2 and HLA-A3 supertypes, respectively, the next most frequent human supertypes after HLA-B7. These data suggest that Chinese rhesus macaques may indeed be a more representative model of HLA gene diversity and function as compared to the species of Indian origin and therefore a better model for investigating human immune responses.
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25
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Rosner C, Kruse PH, Hermes M, Otto N, Walter L. Rhesus macaque inhibitory and activating KIR3D interact with Mamu-A-encoded ligands. THE JOURNAL OF IMMUNOLOGY 2011; 186:2156-63. [PMID: 21257962 DOI: 10.4049/jimmunol.1002634] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Specific interactions between killer cell Ig-like receptors (KIRs) and MHC class I ligands have not been described in rhesus macaques despite their importance in biomedical research. Using KIR-Fc fusion proteins, we detected specific interactions for three inhibitory KIRs (3DLW03, 3DL05, 3DL11) and one activating KIR (3DS05). As ligands we identified Macaca mulatta MHC (Mamu)-A1- and Mamu-A3-encoded allotypes, among them Mamu-A1*001:01, which is well known for association with slow progression to AIDS in the rhesus macaque experimental SIV infection model. Interactions with Mamu-B or Mamu-I molecules were not found. KIR3DLW03 and KIR3DL05 differ in their binding sites to their shared ligand Mamu-A1*001:01, with 3DLW03 depending on presence of the α1 domain, whereas 3DL05 depends on both the α1 and α2 domains. Fine-mapping studies revealed that binding of KIR3DLW03 is influenced by presence of the complete Bw4 epitope (positions 77, 80-83), whereas that of KIR3DL05 is mainly influenced by amino acid position 77 of Bw4 and positions 80-83 of Bw6. Our findings allowed the successful prediction of a further ligand of KIR3DL05, Mamu-A1*002:01. These functional differences of rhesus macaque KIR3DL molecules are in line with the known genetic diversification of lineage II KIRs in macaques.
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Affiliation(s)
- Cornelia Rosner
- Primate Genetics Laboratory, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
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26
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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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27
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Xu HL, Wang YT, Cheng AC, Yao YF, Ni QY, Zeng W, Bi FJ, Yang ZX, Chen XY. [Polymorphism of MHC-DPB1 gene exon 2 in rhesus macaques (Macaca mulatta)]. YI CHUAN = HEREDITAS 2010; 32:588-98. [PMID: 20566463 DOI: 10.3724/sp.j.1005.2010.00588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rhesus macaque (Macaca mulatta) has long been used as an experimental model animal for biomedical research and was under the key state protection (class II) from Chinese government. In order to facilitate the use of Chinese rhesus macaques in biomedical research and their protection based on better understanding of the major mistocompability complex (MHC) genes in these macaques, the exon 2 of Mamu-DPB1 genes were determined in 106 wild rhesus macaques using DGGE, cloning and sequencing. A total of 21 Mamu-DPB1 alleles were obtained, of which 15 alleles were novel sequences that had not been documented previously. Mamu-DPB1 30 was the most frequent allele in the whole large population comprising all 106 rhesus macaque individuals (0.1120) and in Xiaojin population (0.1120), Mamu-DPB1 04 in Heishui (0.1702), -DPB1 32 in Bazhong (0.1613), -DPB1 30 in Hanyuan (0.1120), and -DPB1 04 in Jiulong (0.1139). The alignment of the amino acids sequences showed that 12 variable sites were species-specific, of which 9 sites occurred in the putative amino acids sequences of the 15 novel Mamu-DPB1 alleles. Trans-species polymorphism was observed on the phylogenetic tree based on the DPB1 alleles of rhesus macaques and cynomolgus (Macaca fascicularis). In addition, these results also demonstrated that significant genetic differentiation has occurred between Chinese and Indian rhesus macaque population.
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Affiliation(s)
- Huai-Liang Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, China.
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28
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Otting N, Mörner A, Bontrop RE. Novel major histocompatibility complex class I alleles extracted from two rhesus macaque populations. ACTA ACUST UNITED AC 2010; 77:79-80. [PMID: 20946193 DOI: 10.1111/j.1399-0039.2010.01565.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here the novel Mamu-A and -B alleles that were detected in two groups of rhesus monkeys.
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Affiliation(s)
- N Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.
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29
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Nieuwenhuis I, Beenhakker N, Bogers WMJM, Otting N, Bontrop RE, Dubois P, Mooij P, Heeney JL, Koopman G. No difference in Gag and Env immune-response profiles between vaccinated and non-vaccinated rhesus macaques that control immunodeficiency virus replication. J Gen Virol 2010; 91:2974-84. [PMID: 20826621 DOI: 10.1099/vir.0.022772-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Recent advances in human immunodeficiency virus (HIV) vaccine design have resulted in induction of strong CD4 T-cell proliferative and polyfunctional cytokine responses, which are also characteristic for long-term non-progressing (LTNP) HIV-infected individuals. However, limited information is available on the persistence of these responses after infection. Results from studies in non-human primates indicate that vaccine-induced immune responses are partially maintained upon viral infection and differ from the responses seen in non-vaccinated animals that typically progress to disease. However, it is unclear how these partially preserved responses compare to immune responses that are acquired naturally by LTNP animals. In this study, immune-response profiles were compared between vaccinated animals that, upon SHIV₈₉.₆ challenge, became infected but were able to control virus replication, and a group of animals having spontaneous control of this viral infection. Both groups were found to develop very similar immune responses with regard to induction of CD4 and CD8 T-cell polyfunctional cytokine responses, proliferative capacity and cytotoxic capacity, as measured by a standard ₅₁Cr release assay and more direct ex vivo and in vivo CTL assays. Hence, vaccinated animals that become infected, but control infection, appear to establish immune responses that are similar to those elicited by long-term non-progressors.
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Affiliation(s)
- Ivonne Nieuwenhuis
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
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30
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Diversity of MHC class I genes in Burmese-origin rhesus macaques. Immunogenetics 2010; 62:601-11. [PMID: 20640416 DOI: 10.1007/s00251-010-0462-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 06/24/2010] [Indexed: 01/05/2023]
Abstract
Rhesus macaques (Macaca mulatta) are widely used in developing a strategy for vaccination against human immunodeficiency virus by using simian immunodeficiency virus infection as a model system. Because the genome diversity of major histocompatibility complex (MHC) is well known to control the immune responsiveness to foreign antigens, MHC loci in Indian- and Chinese-origin macaques used in the experiments have been characterized, and it was revealed that the diversity of MHC in macaques was larger than the human MHC. To further characterize the diversity of Mamu-A and Mamu-B loci, we investigated a total of 73 different sequences of Mamu-A, 83 sequences of Mamu-B, and 15 sequences of Mamu-I cDNAs isolated from Burmese-origin macaques. It was found that there were one to five expressing genes in each locus. Among the Mamu-A, Mamu-B, and Mamu-I sequences, 44 (60.2%), 45 (54.2%), and 8 (53.3%), respectively, were novel, and most of the other known alleles were identical to those reported from Chinese- or Indian-origin macaques, demonstrating a genetic mixture between the geographically distinct populations of present day China and India. In addition, it was found that a Mamu haplotype contained at least two highly transcribed Mamu-A genes, because multiple Mamu-A1 cDNAs were obtained from one haplotype. These findings further revealed the diversity and complexity of MHC locus in the rhesus macaques.
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31
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Rosner C, Kruse PH, Lübke T, Walter L. Erratum to: rhesus macaque MHC class I molecules show differential subcellular localizations. Immunogenetics 2010; 62:409-18. [PMID: 20445972 PMCID: PMC3128699 DOI: 10.1007/s00251-010-0447-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MHC class I gene family of rhesus macaques is characterised by considerable gene duplications. While a HLA-C-orthologous gene is absent, the Mamu-A and in particular the Mamu-B genes have expanded, giving rise to plastic haplotypes with differential gene content. Although some of the rhesus macaque MHC class I genes are known to be associated with susceptibility/resistance to infectious diseases, the functional significance of duplicated Mamu-A and Mamu-B genes and the expression pattern of their encoded proteins are largely unknown. Here, we present data of the subcellular localization of AcGFP-tagged Mamu-A and Mamu-B molecules. We found strong cell surface and low intracellular expression for Mamu-A1, Mamu-A2 and Mamu-A3-encoded molecules as well as for Mamu-B*01704, Mamu-B*02101, Mamu-B*04801, Mamu-B*06002 and Mamu-B*13401. In contrast, weak cell surface and strong intracellular expression was seen for Mamu-A4*1403, Mamu-B*01202, Mamu-B*02804, Mamu-B*03002, Mamu-B*05704, Mamu-I*010201 and Mamu-I*0121. The different expression patterns were assigned to the antigen-binding alpha1 and alpha2 domains, suggesting failure of peptide binding is responsible for retaining 'intracellular' Mamu class I molecules in the endoplasmic reticulum. These findings indicate a diverse functional role of the duplicated rhesus macaque MHC class I genes.
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Affiliation(s)
- Cornelia Rosner
- Abteilung Primatengenetik, Deutsches Primatenzentrum-Leibniz, Institut für Primatenforschung, Kellnerweg 4, 37077, Göttingen, Germany
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32
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The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype. Immunogenetics 2010; 62:451-64. [PMID: 20480161 PMCID: PMC2890073 DOI: 10.1007/s00251-010-0450-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Accepted: 04/19/2010] [Indexed: 01/30/2023]
Abstract
Of the two rhesus macaque subspecies used for AIDS studies, the Simian immunodeficiency virus-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection, providing both insight into pathogenesis and a system for testing novel vaccines. Despite the Chinese rhesus macaque potentially being a more relevant model for AIDS outcomes than the Indian rhesus macaque, the Chinese-origin rhesus macaques have not been well-characterized for their major histocompatibility complex (MHC) composition and function, reducing their greater utilization. In this study, we characterized a total of 50 unique Chinese rhesus macaques from several varying origins for their entire MHC class I allele composition and identified a total of 58 unique complete MHC class I sequences. Only nine of the sequences had been associated with Indian rhesus macaques, and 28/58 (48.3%) of the sequences identified were novel. From all MHC alleles detected, we prioritized Mamu-A1*02201 for functional characterization based on its higher frequency of expression. Upon the development of MHC/peptide binding assays and definition of its associated motif, we revealed that this allele shares peptide binding characteristics with the HLA-B7 supertype, the most frequent supertype in human populations. These studies provide the first functional characterization of an MHC class I molecule in the context of Chinese rhesus macaques and the first instance of HLA-B7 analogy for rhesus macaques.
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Blokhuis JH, van der Wiel MK, Doxiadis GGM, Bontrop RE. The mosaic of KIR haplotypes in rhesus macaques. Immunogenetics 2010; 62:295-306. [PMID: 20204612 PMCID: PMC2858804 DOI: 10.1007/s00251-010-0434-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 02/08/2010] [Indexed: 12/24/2022]
Abstract
To further refine and improve biomedical research in rhesus macaques, it is necessary to increase our knowledge concerning both the degree of allelic variation (polymorphism) and diversity (gene copy number variation) in the killer cell immunoglobulin-like receptor (KIR) gene cluster. Pedigreed animals in particular should be studied, as segregation data will provide clues to the linkage of particular KIR genes/alleles segregating on a haplotype and to its gene content as well. A dual strategy allowed us to screen the presence and absence of genes and the corresponding transcripts, as well as to track differences in transcription levels. On the basis of this approach, 14 diverse KIR haplotypes have been described. These haplotypes consist of multiple inhibitory and activating Mamu-KIR genes, and any gene present on one haplotype may be absent on another. This suggests that the cost of accelerated evolution by recombination may be the loss of certain framework genes on a haplotype.
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Affiliation(s)
- Jeroen H Blokhuis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 139, 2288GJ, Rijswijk, The Netherlands.
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34
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Kruse PH, Rosner C, Walter L. Characterization of rhesus macaque KIR genotypes and haplotypes. Immunogenetics 2010; 62:281-93. [PMID: 20195593 DOI: 10.1007/s00251-010-0433-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 02/08/2010] [Indexed: 12/22/2022]
Abstract
Certain combinations of the killer immunoglobulin-like receptors (KIR) and major histocompatibility complex class I ligands in humans predispose carriers to a variety of diseases, requiring sophisticated genotyping of the highly polymorphic and diverse KIR and HLA genes. Particularly, KIR genotyping is challenging due to polymorphisms (allelic substitutions), genomic diversity (presence/absence of genes), and frequent duplications. Rhesus macaques are often used as important animal models of human diseases such as, e.g. AIDS. However, typing of rhesus macaque KIR genes has not been described so far. In this study, we report the identification of additional novel rhesus macaque KIR cDNA sequences and a sequence-specific KIR genotyping assay. From a cohort of four rhesus macaque families with a total of 70 individuals, we identified 25 distinct KIR genotypes. Segregation analyses of KIR genes and of two polymorphic microsatellite markers allowed the identification of 21 distinct KIR haplotypes in these families, with five to 11 segregating KIR genes per haplotype. Our analyses confirmed and extended knowledge on differential gene KIR gene content in macaques and indicate that rhesus macaque and human KIR haplotypes show a comparable level of diversity and complexity.
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Affiliation(s)
- Philip H Kruse
- Primate Genetics Laboratory, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
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35
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Rosner C, Kruse PH, Lübke T, Walter L. Rhesus macaque MHC class I molecules show differential subcellular localizations. Immunogenetics 2010; 62:149-58. [PMID: 20151120 PMCID: PMC2827799 DOI: 10.1007/s00251-010-0424-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 01/18/2010] [Indexed: 11/16/2022]
Abstract
The MHC class I gene family of rhesus macaques is characterised by considerable gene duplications. While a HLA-C-orthologous gene is absent, the Mamu-A and in particular the Mamu-B genes have expanded, giving rise to plastic haplotypes with differential gene content. Although some of the rhesus macaque MHC class I genes are known to be associated with susceptibility/resistance to infectious diseases, the functional significance of duplicated Mamu-A and Mamu-B genes and the expression pattern of their encoded proteins are largely unknown. Here, we present data of the subcellular localization of AcGFP-tagged Mamu-A and Mamu-B molecules. We found strong cell surface and low intracellular expression for Mamu-A1, Mamu-A2 and Mamu-A3-encoded molecules as well as for Mamu-B*01704, Mamu-B*02101, Mamu-B*04801, Mamu-B*06002 and Mamu-B*13401. In contrast, weak cell surface and strong intracellular expression was seen for Mamu-A4*1403, Mamu-B*01202, Mamu-B*02804, Mamu-B*03002, Mamu-B*05704, Mamu-I*010201 and Mamu-I*0121. The different expression patterns were assigned to the antigen-binding α1 and α2 domains, suggesting failure of peptide binding is responsible for retaining ‘intracellular’ Mamu class I molecules in the endoplasmic reticulum. These findings indicate a diverse functional role of the duplicated rhesus macaque MHC class I genes.
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Affiliation(s)
- Cornelia Rosner
- Abteilung Primatengenetik, Deutsches Primatenzentrum--Leibniz Institut für Primatenforschung, Kellnerweg 4, 37077, Göttingen, Germany
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36
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Abi-Rached L, Kuhl H, Roos C, ten Hallers B, Zhu B, Carbone L, de Jong PJ, Mootnick AR, Knaust F, Reinhardt R, Parham P, Walter L. A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons. THE JOURNAL OF IMMUNOLOGY 2009; 184:1379-91. [PMID: 20026738 DOI: 10.4049/jimmunol.0903016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The killer cell Ig-like receptors (KIRs) of NK cells recognize MHC class I ligands and function in placental reproduction and immune defense against pathogens. During the evolution of monkeys, great apes, and humans, an ancestral KIR3DL gene expanded to become a diverse and rapidly evolving gene family of four KIR lineages. Characterizing the KIR locus are three framework regions, defining two intervals of variable gene content. By analysis of four KIR haplotypes from two species of gibbon, we find that the smaller apes do not conform to these rules. Although diverse and irregular in structure, the gibbon haplotypes are unusually small, containing only two to five functional genes. Comparison with the predicted ancestral hominoid KIR haplotype indicates that modern gibbon KIR haplotypes were formed by a series of deletion events, which created new hybrid genes as well as eliminating ancestral genes. Of the three framework regions, only KIR3DL3 (lineage V), defining the 5' end of the KIR locus, is present and intact on all gibbon KIR haplotypes. KIR2DL4 (lineage I) defining the central framework region has been a major target for elimination or inactivation, correlating with the absence of its putative ligand, MHC-G, in gibbons. Similarly, the MHC-C-driven expansion of lineage III KIR genes in great apes has not occurred in gibbons because they lack MHC-C. Our results indicate that the selective forces shaping the size and organization of the gibbon KIR locus differed from those acting upon the KIR of other hominoid species.
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Affiliation(s)
- Laurent Abi-Rached
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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37
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Definition of Mafa-A and -B haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis). Immunogenetics 2009; 61:745-53. [PMID: 19937015 PMCID: PMC2802488 DOI: 10.1007/s00251-009-0412-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 11/11/2009] [Indexed: 11/02/2022]
Abstract
The major histocompatibility complex (MHC) class I B gene/allelic repertoire was investigated in a pedigreed population of cynomolgus macaques of mixed Indonesian/Malaysian origin. The Mafa-B alleles detected in this cohort are mostly specific for a given geographic area, and only a small number of alleles appears to be shared with other populations. This suggests the fast evolution of Mafa-B alleles due to adaptation to new environments. In contrast to humans, the B locus in Old World monkeys displays extensive copy number variation. The Mafa-B and previously defined -A gene combinations segregate in families and thus allowed the definition of extended haplotypes. In many cases it was possible to assign a particular Mafa-I allele to one of these Mafa-A/B haplotypes as well. The presence of a large number of stable haplotypes in this cohort of animals, which was pedigreed for up to eight generations, looks promising for developing discriminative MHC typing tools that are less cumbersome. Furthermore, the discovery of 53 unreported Mafa-B sequences expands the lexicon of alleles significantly, and may help in understanding the complex organisation of the macaque B region.
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38
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Wiseman RW, Karl JA, Bimber BN, O'Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres E, Wright C, Harkins T, O'Connor DH. Major histocompatibility complex genotyping with massively parallel pyrosequencing. Nat Med 2009; 15:1322-6. [PMID: 19820716 DOI: 10.1038/nm.2038] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Accepted: 05/17/2009] [Indexed: 11/10/2022]
Abstract
Major histocompatibility complex (MHC) genetics dictate adaptive cellular immune responses, making robust MHC genotyping methods essential for studies of infectious disease, vaccine development and transplantation. Nonhuman primates provide essential preclinical models for these areas of biomedical research. Unfortunately, given the unparalleled complexity of macaque MHCs, existing methodologies are inadequate for MHC typing of these key model animals. Here we use pyrosequencing of complementary DNA-PCR amplicons as a general approach to determine comprehensive MHC class I genotypes in nonhuman primates. More than 500 unique MHC class I sequences were resolved by sequence-based typing of rhesus, cynomolgus and pig-tailed macaques, nearly half of which have not been reported previously. The remarkable sensitivity of this approach in macaques demonstrates that pyrosequencing is viable for ultra-high-throughput MHC genotyping of primates, including humans.
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Affiliation(s)
- Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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39
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Blokhuis JH, van der Wiel MK, Doxiadis GGM, Bontrop RE. Evidence for balancing selection acting on KIR2DL4 genotypes in rhesus macaques of Indian origin. Immunogenetics 2009; 61:503-12. [PMID: 19506858 DOI: 10.1007/s00251-009-0379-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 05/25/2009] [Indexed: 11/30/2022]
Abstract
The interaction of killer-cell immunoglobulin-like receptors (KIR) and their respective major histocompatibility complex (MHC) ligands can alter the activation state of the natural killer (NK) cell. In both humans and rhesus macaques, particular types of non-classical MHC class I molecules are predominantly expressed on the trophoblast. In humans, human leukocyte antigen G has been demonstrated to act as a ligand for KIR2DL4, present on all NK cells, whereas Mamu-AG may execute a similar function in rhesus macaques. During primate evolution, orthologues of KIR2DL4 appear to have been highly conserved, suggesting strong purifying selection. A cohort of 112 related and unrelated rhesus macaques of mostly Indian origin were selected to study their KIR2DL4 genes for the occurrence of polymorphism. Comparison of the proximal region provided evidence for strong conservative selection acting on the exons encoding the Ig domains. As is found in humans, in the Indian rhesus macaque population, two different KIR2DL4 entities are encountered, which differ for their intra-cellular signalling motifs. One genotype contains a complex mutation in the distal region of exon 9, which negates a serine/threonine kinase site. Furthermore, both allelic entities are present in a distribution, which suggests that balancing selection is operating on these two distinct forms of KIR2DL4.
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Affiliation(s)
- Jeroen H Blokhuis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 139, Rijswijk, 2288 GJ, The Netherlands.
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40
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Ouyang DY, Xu LH, Shi HJ, Zheng YT, He XH. Eight novel MHC class I alleles identified in Chinese-origin rhesus macaques. ACTA ACUST UNITED AC 2009; 73:285-7. [PMID: 19254266 DOI: 10.1111/j.1399-0039.2008.01198.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We report here the identification of four Mamu-A1 and four Mamu-B novel alleles of Chinese-origin rhesus macaques.
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Affiliation(s)
- D-Y Ouyang
- Institute of Tissue Transplantation and Immunology, College of Life Science and Technology, Jinan University, Guangzhou, China
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41
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Campbell KJ, Detmer AM, Karl JA, Wiseman RW, Blasky AJ, Hughes AL, Bimber BN, O’Connor SL, O’Connor DH. Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques. Immunogenetics 2009; 61:177-87. [PMID: 19107381 PMCID: PMC2666003 DOI: 10.1007/s00251-008-0351-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 12/08/2008] [Indexed: 11/28/2022]
Abstract
Cynomolgus macaques (Macaca fascicularis) provide increasingly common models for infectious disease research. Several geographically distinct populations of these macaques from Southeast Asia and the Indian Ocean island of Mauritius are available for pathogenesis studies. Though host genetics may profoundly impact results of such studies, similarities and differences between populations are often overlooked. In this study we identified 47 full-length MHC class I nucleotide sequences in 16 cynomolgus macaques of Filipino origin. The majority of MHC class I sequences characterized (39 of 47) were unique to this regional population. However, we discovered eight sequences with perfect identity and six sequences with close similarity to previously defined MHC class I sequences from other macaque populations. We identified two ancestral MHC haplotypes that appear to be shared between Filipino and Mauritian cynomolgus macaques, notably a Mafa-B haplotype that has previously been shown to protect Mauritian cynomolgus macaques against challenge with a simian/human immunodeficiency virus, SHIV(89.6P). We also identified a Filipino cynomolgus macaque MHC class I sequence for which the predicted protein sequence differs from Mamu-B*17 by a single amino acid. This is important because Mamu-B*17 is strongly associated with protection against simian immunodeficiency virus (SIV) challenge in Indian rhesus macaques. These findings have implications for the evolutionary history of Filipino cynomolgus macaques as well as for the use of this model in SIV/SHIV research protocols.
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Affiliation(s)
- Kevin J. Campbell
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Ann M. Detmer
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Alex J. Blasky
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Austin L. Hughes
- Department of Biological Sciences, University of South Carolina, Columbus, SC 29208
| | - Benjamin N. Bimber
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53706
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53706
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53706
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Doxiadis GGM, Heijmans CMC, Bonhomme M, Otting N, Crouau-Roy B, Bontrop RE. Compound evolutionary history of the rhesus macaque MHC class I B region revealed by microsatellite analysis and localization of retroviral sequences. PLoS One 2009; 4:e4287. [PMID: 19172173 PMCID: PMC2625394 DOI: 10.1371/journal.pone.0004287] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 12/19/2008] [Indexed: 12/18/2022] Open
Abstract
In humans, the single polymorphic B locus of the major histocompatibility complex is linked to the microsatellite MIB. In rhesus macaques, however, haplotypes are characterized by the presence of unique combinations of multiple B genes, which may display different levels of polymorphism. The aim of the study was to shed light on the evolutionary history of this highly complex region. First, the robustness of the microsatellite MIB-linked to almost half of the B genes in rhesus macaques (Mamu-B)–for accurate B haplotyping was studied. Based on the physical map of an established haplotype comprising 7 MIB loci, each located next to a certain Mamu-B gene, two MIB loci, MIB1 and MIB6, were investigated in a panel of MHC homozygous monkeys. MIB1 revealed a complex genotyping pattern, whereas MIB6 analysis resulted in the detection of one or no amplicon. Both patterns are specific for a given B haplotype, show Mendelian segregation, and even allow a more precise haplotype definition than do traditional typing methods. Second, a search was performed for retroelements that may have played a role in duplication processes as observed in the macaque B region. This resulted in the description of two types of duplicons. One basic unit comprises an expressed Mamu-B gene, adjacent to an HERV16 copy closely linked to MIB. The second type of duplicon comprises a Mamu-B (pseudo)gene, linked to a truncated HERV16 structure lacking its MIB segment. Such truncation seems to coincide with the loss of B gene transcription. Subsequent to the duplication processes, recombination between MIB and Mamu-B loci appears to have occurred, resulting in a hyperplastic B region. Thus, analysis of MIB in addition to B loci allows deciphering of the compound evolutionary history of the class I B region in Old World monkeys.
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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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Ouyang D, Xu L, Dai Z, Shi H, Zhang G, Zheng Y, He X. Identification of major histocompatibility complex class I alleles in Chinese rhesus macaques. Acta Biochim Biophys Sin (Shanghai) 2008; 40:919-27. [PMID: 18989572 DOI: 10.1111/j.1745-7270.2008.00474.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Major histocompatibility complex (MHC) class I information is vital for understanding variance of immune responses in HIV vaccination and biomedical models. In this study, 9 Mamu-A and 13 Mamu-B alleles were identified from the cDNA products of 10 Chinese-origin rhesus macaques. Except for two alleles that had been reported by others, eight were novel and twelve extended the partial sequences that are available in GenBank. The additional information of MHC class I antigens might be beneficial to the availability of Chinese macaques in human disease studies. Furthermore, the polymorphism of leading peptides and the natural killer receptor recognition motifs in alpha1 domain both implies that Mamu-A and Mamu-B molecules might play key roles in innate immune responses of natural killer cells.
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Affiliation(s)
- Dongyun Ouyang
- Institute of Tissue Transplantation and Immunology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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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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