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Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel. Heredity (Edinb) 2022; 128:88-96. [PMID: 34857925 PMCID: PMC8813985 DOI: 10.1038/s41437-021-00477-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 02/03/2023] Open
Abstract
Identification of genetic structure within wildlife populations have implications in their conservation and management. Accurately inferring population genetic structure requires whole-genome data across the geographical range of the species, which can be resource-intensive. A cheaper strategy is to employ a subset of markers that can efficiently recapitulate the population genetic structure inferred by the whole genome data. Such ancestry informative markers (AIMs), have rarely been developed for endangered species such as tigers utilizing single nucleotide polymorphisms (SNPs). Here, we first identify the population structure of the Indian tiger using whole-genome sequences and then develop an AIMs panel with a minimum number of SNPs that can recapitulate this structure. We identified four population clusters of Indian tigers with North-East, North-West, and South Indian tigers forming three separate groups, and Terai and Central Indian tigers forming a single cluster. To evaluate the robustness of our AIMs, we applied it to a separate dataset of tigers from across India. Out of 92 SNPs present in our AIMs panel, 49 were present in the new dataset. These 49 SNPs were sufficient to recapitulate the population genetic structure obtained from the whole genome data. To the best of our knowledge, this is the first-ever SNP-based AIMs panel for big cats, which can be used as a cost-effective alternative to whole-genome sequencing for detecting the biogeographical origin of Indian tigers. Our study can be used as a guideline for developing an AIMs panel for the management of other endangered species where obtaining whole genome sequences are difficult.
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Phadphon P, Kanthaswamy S, Oldt RF, Hamada Y, Malaivijitnond S. Population Structure of Macaca fascicularis aurea, and their Genetic Relationships with M. f. fascicularis and M. mulatta Determined by 868 RADseq-Derived Autosomal SNPs-A consideration for biomedical research. J Med Primatol 2022; 51:33-44. [PMID: 34825374 PMCID: PMC8849537 DOI: 10.1111/jmp.12554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND This study examined the population structure of Macaca fascicularis aurea and their genetic relationships with M. f. fascicularis and M. mulatta. METHODS The study analyzed 868 RADseq-derived SNPs from samples representing the entire distribution range of M. f. aurea, including their inter- and intraspecific hybrid zones. RESULTS The study supports a M. mulatta/Indochinese M. f. fascicularis, Sundaic M. f. fascicularis, and M. f. aurea trichotomy; M. f. aurea was genetically distinct from both forms of M. f. fascicularis and M. mulatta. Hybridization between M. f. aurea and M. f. fascicularis occurred in two directions: south-north (8°25' to 15°56') and west-east (98°28' to 99°02'). Low levels of M. mulatta introgression were also detected in M. f. aurea. CONCLUSION This study showcases a complicated scenario of genetic relationships between the M. fascicularis subspecies and between M. fascicularis and M. mulatta and underscores the importance of these taxa's population structure and genetic relationships for biomedical research.
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Affiliation(s)
- Poompat Phadphon
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA,California National Primate Research Center, University of California, Davis, CA, USA,Correspondence to: Suchinda Malaivijitnond, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. Tel./Fax: +66-2-2185275; ; Sree Kanthaswamy, School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA. Tel.: (602) 543-3405;
| | - Robert F. Oldt
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Yuzuru Hamada
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand,Correspondence to: Suchinda Malaivijitnond, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. Tel./Fax: +66-2-2185275; ; Sree Kanthaswamy, School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA. Tel.: (602) 543-3405;
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Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome 2022; 33:91-99. [PMID: 34999909 PMCID: PMC8742695 DOI: 10.1007/s00335-021-09922-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022]
Abstract
Rhesus macaques (Macaca mulatta) are among the most extensively studied of nonhuman primates. This species has been the subject of many investigations concerning basic primate biology and behavior, including studies of social organization, developmental psychology, physiology, endocrinology, and neurodevelopment. Rhesus macaques are also critically important as a nonhuman primate model of human health and disease, including use in studies of infectious diseases, metabolic diseases, aging, and drug or alcohol abuse. Current research addressing fundamental biological and/or applied biomedical questions benefits from various genetic and genomic analyses. As a result, the genome of rhesus macaques has been the subject of more study than most nonhuman primates. This paper briefly discusses a number of information resources that can provide interested researchers with access to genetic and genomic data describing the content of the rhesus macaque genome, available information regarding genetic variation within the species, results from studies of gene expression, and other aspects of genomic analysis. Specific online databases are discussed, including the US National Center for Biotechnology Information, the University of California Santa Cruz genome browser, Ensembl genome browser, the Macaque Genotype and Phenotype database (mGAP), Rhesusbase, and others.
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Oldt RF, Bussey KJ, Settles ML, Fass JN, Roberts JA, Reader JR, Komandoor S, Abrich VA, Kanthaswamy S. MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques ( Macaca mulatta). Comp Med 2020; 70:358-367. [PMID: 32753092 PMCID: PMC7574221 DOI: 10.30802/aalas-cm-19-000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/13/2020] [Accepted: 02/07/2020] [Indexed: 11/05/2022]
Abstract
In humans, abnormal thickening of the left ventricle of the heart clinically defines hypertrophic cardiomyopathy (HCM), a common inherited cardiovascular disorder that can precede a sudden cardiac death event. The wide range of clinical presentations in HCM obscures genetic variants that may influence an individual's susceptibility to sudden cardiac death. Although exon sequencing of major sarcomere genes can be used to detect high-impact causal mutations, this strategy is successful in only half of patient cases. The incidence of left ventricular hypertrophy (LVH) in a managed research colony of rhesus macaques provides an excellent comparative model in which to explore the genomic etiology of severe HCM and sudden cardiac death. Because no rhesus HCM-associated mutations have been reported, we used a next-generation genotyping assay that targets 7 sarcomeric rhesus genes within 63 genomic sites that are orthologous to human genomic regions known to harbor HCM disease variants. Amplicon sequencing was performed on 52 macaques with confirmed LVH and 42 unrelated, unaffected animals representing both the Indian and Chinese rhesus macaque subspecies. Bias-reduced logistic regression uncovered a risk haplotype in the rhesus MYBPC3 gene, which is frequently disrupted in both human and feline HCM; this haplotype implicates an intronic variant strongly associated with disease in either homozygous or carrier form. Our results highlight that leveraging evolutionary genomic data provides a unique, practical strategy for minimizing population bias in complex disease studies.
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Affiliation(s)
- Robert F Oldt
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University at the West Campus, Glendale, Arizona;,
| | - Kimberly J Bussey
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; BEYOND Center for Fundamental Concepts in Science, Arizona State University at the West Campus, Glendale, Arizona
| | - Matthew L Settles
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, California
| | - Joseph N Fass
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, California
| | - Jeffrey A Roberts
- California National Primate Research Center, University of California, Davis, California
| | - J Rachel Reader
- California National Primate Research Center, University of California, Davis, California
| | | | - Victor A Abrich
- Division of Cardiovascular Diseases, Mayo Clinic, Scottsdale, Arizona
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona; Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University at the West Campus, Glendale, Arizona; California National Primate Research Center, University of California, Davis, California
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5
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Developing ancestry informative marker panel for Nigeria-Cameroonian chimpanzees. J Genet 2020. [DOI: 10.1007/s12041-020-01192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Martin ML, Bitzer AA, Schrader A, Bergmann-Leitner ES, Soto K, Zou X, Beck Z, Matyas GR, Dutta S. Comparison of immunogenicity and safety outcomes of a malaria vaccine FMP013/ALFQ in rhesus macaques (Macaca mulatta) of Indian and Chinese origin. Malar J 2019; 18:377. [PMID: 31775762 PMCID: PMC6880475 DOI: 10.1186/s12936-019-3014-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
Background Indian-origin rhesus (InR) are preferred for research, but strict export restrictions continue to limit their use. Chinese-origin rhesus (ChR), although easier to procure, are genetically distinct from InR and differ in their immune response to infectious agents, such as the Simian Immunodeficiency Virus. The most advanced malaria vaccine, RTS,S (GlaxoSmithKline), is based on the circumsporozoite protein (CSP) of Plasmodium falciparum. The efficacy of RTS,S vaccine in the field remains low and short-lived; efforts are underway to improve CSP-based vaccines. Rhesus models can accelerate preclinical down-selection of the next generation of malaria vaccines. This study was used to determine if the safety and immunogenicity outcomes following vaccination with a CSP vaccine would differ in the InR and ChR models, given the genetic differences between the two sub-populations of rhesus. Methods The FMP013 vaccine, was composed of nearly full-length soluble P. falciparum CSP produced in Escherichia coli and was adjuvanted with the Army liposomal formulation (ALFQ). Three doses of the vaccine were administered in InR and ChR (n = 6) at 1-month intervals and the antibody and T cell responses were assessed. Results Local and systemic toxicity profile of FMP013 vaccine in InR and ChR were similar and they revealed that the FMP013 vaccine was safe and caused only mild and transient inflammatory adverse reactions. Following the first 2 vaccines, there was a slower acquisition of antibodies to the CSP repeat region in ChR. However after the 3rd vaccination the titers in the two models were comparable. The ChR group repeat-specific antibodies had higher avidity and ChR group showed higher inhibition of liver stage development activity compared to InR. There was no difference in T-cell responses to the FMP013 vaccine between the two models. Conclusions A difference in the quality of serological responses was detected between the two sub-populations of rhesus. However, both models confirmed that FMP013/ALFQ vaccine was safe, highly immunogenic, elicited functional antibodies and T-cell responses. Overall, the data suggests that rhesus of Indian and Chinese origins can be interchangeably used to compare the safety and immunogenicity of next-generation of malaria vaccines and adjuvants.
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Affiliation(s)
- Monica L Martin
- Division of Veterinary Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Alexis A Bitzer
- Structural Biologics Laboratory, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Andrew Schrader
- Division of Veterinary Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Elke S Bergmann-Leitner
- Immunology Core, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Kim Soto
- Structural Biologics Laboratory, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Xiaoyan Zou
- Malaria Department, Naval Medical Research Center, Silver Spring, MD, 20910, USA
| | - Zoltan Beck
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.,Henry M. Jackson Foundation, Rockville, MD, 20852, USA
| | - Gary R Matyas
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Sheetij Dutta
- Structural Biologics Laboratory, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
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Bimber BN, Yan MY, Peterson SM, Ferguson B. mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease. BMC Genomics 2019; 20:176. [PMID: 30841849 PMCID: PMC6402181 DOI: 10.1186/s12864-019-5559-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 02/22/2019] [Indexed: 11/17/2022] Open
Abstract
Background Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with parallel genetic risk alleles, underscores the value of macaques in the development of effective treatment strategies. Nonetheless, there are limited genomic resources available to support the exploration and discovery of macaque models of inherited disease. Notably, there are few public databases tailored to searching NHP sequence variants, and no other database making use of centralized variant calling, or providing genotype-level data and predicted pathogenic effects for each variant. Results The macaque Genotype And Phenotype (mGAP) resource is the first public website providing searchable, annotated macaque variant data. The mGAP resource includes a catalog of high confidence variants, derived from whole genome sequence (WGS). The current mGAP release at time of publication (1.7) contains 17,087,212 variants based on the sequence analysis of 293 rhesus macaques. A custom pipeline was developed to enable annotation of the macaque variants, leveraging human data sources that include regulatory elements (ENCODE, RegulomeDB), known disease- or phenotype-associated variants (GRASP), predicted impact (SIFT, PolyPhen2), and sequence conservation (Phylop, PhastCons). Currently mGAP includes 2767 variants that are identical to alleles listed in the human ClinVar database, of which 276 variants, spanning 258 genes, are identified as pathogenic. An additional 12,472 variants are predicted as high impact (SnpEff) and 13,129 are predicted as damaging (PolyPhen2). In total, these variants are predicted to be associated with more than 2000 human disease or phenotype entries reported in OMIM (Online Mendelian Inheritance in Man). Importantly, mGAP also provides genotype-level data for all subjects, allowing identification of specific individuals harboring alleles of interest. Conclusions The mGAP resource provides variant and genotype data from hundreds of rhesus macaques, processed in a consistent manner across all subjects (https://mgap.ohsu.edu). Together with the extensive variant annotations, mGAP presents unprecedented opportunity to investigate potential genetic associations with currently characterized disease models, and to uncover new macaque models based on parallels with human risk alleles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5559-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin N Bimber
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA.,Division of Pathobiology, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA
| | - Melissa Y Yan
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA
| | - Samuel M Peterson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA. .,Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR, 97006, USA. .,Molecular and Medical Genetics Department, Oregon Health and Sciences University, Portland, OR, 97239, USA.
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Ebersole JL, Orraca L, Kensler TB, Gonzalez-Martinez J, Maldonado E, Gonzalez OA. Periodontal disease susceptible matrilines in the Cayo Santiago Macaca mulatta macaques. J Periodontal Res 2018; 54:134-142. [PMID: 30277577 DOI: 10.1111/jre.12610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE AND BACKGROUND The expression of periodontitis, including age of onset, extent, and severity is considered to represent an interaction of the individual's oral microbiome and host response to the microbial challenge that is modified by both genetics and environmental factors. The aim of this study was to determine the distribution of periodontitis in a population of nonhuman primates, to document features of familial distribution that could reflect heritability and transmission of microbes with enhanced virulence. MATERIAL AND METHODS This report presents our findings from evaluation of periodontal disease bone defects in skulls from 569 animals (5-31 years of age) derived from the skeletons of the rhesus monkeys (Macaca mulatta) of Cayo Santiago derived from eight matrilines over 6-9 generations. The distance from the base of alveolar bone to the cemento-enamel junction on 1st /2nd premolars and 1st /2nd molars from all four quadrants was evaluated as a measure of periodontal disease. Additionally, we documented the presence of periodontitis in 79 living descendants within these matrilines. RESULTS The results demonstrated an increased extent and severity of periodontitis with aging across all matrilines. Extensive heterogeneity in disease expression was observed among the animals and this was linked to specific periodontitis susceptible matrilines. Moreover, we identified some matrilines in which the members appeared to show some resistance to more severe disease, even with aging. CONCLUSION Linking these disease variations to multigenerational matriarchal family units supported familial susceptibility of periodontitis. This familial disease relationship was reinforced by the distribution of naturally-occurring periodontitis in the living descendants.
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Affiliation(s)
- Jeffrey L Ebersole
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, Nevada
| | - Luis Orraca
- School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Terry B Kensler
- Laboratory of Primate Morphology, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Elisabeth Maldonado
- Laboratory of Primate Morphology, University of Puerto Rico, San Juan, Puerto Rico
| | - Octavio A Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, Kentucky.,Division of Periodontology, College of Dentistry, University of Kentucky, Lexington, Kentucky
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Liu Z, Tan X, Orozco-terWengel P, Zhou X, Zhang L, Tian S, Yan Z, Xu H, Ren B, Zhang P, Xiang Z, Sun B, Roos C, Bruford MW, Li M. Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research. Gigascience 2018; 7:5079661. [PMID: 30165519 PMCID: PMC6143732 DOI: 10.1093/gigascience/giy106] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/12/2018] [Indexed: 01/25/2023] Open
Abstract
Background The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species’ natural distribution. Results Populations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125.8 to 51.3 thousand years ago, but feature recent gene flow. Consistent with the expectation of a larger body size in colder climates and smaller body size in warmer climates (Bergman's rule), the northernmost RM lineage (M. m. tcheliensis), possessing the largest body size of all Chinese RMs, and the southernmost lineage (M. m. brevicaudus), with the smallest body size of all Chinese RMs, feature positively selected genes responsible for skeletal development. Further, two candidate selected genes (Fbp1, Fbp2) found in M. m. tcheliensis are involved in gluconeogenesis, potentially maintaining stable blood glucose levels during starvation when food resources are scarce in winter. The tropical subspecies M. m. brevicaudus showed positively selected genes related to cardiovascular function and response to temperature stimuli, potentially involved in tropical adaptation. We found 118 single-nucleotide polymorphisms matching human disease-causing variants with 82 being subspecies specific. Conclusions These data provide a resource for selection of RMs in biomedical experiments. The demographic history of Chinese RMs and their history of local adaption offer new insights into their evolution and provide valuable baseline information for biomedical investigation.
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Affiliation(s)
- Zhijin Liu
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xinxin Tan
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, United Kingdom
| | - Xuming Zhou
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liye Zhang
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Jiuxianqiao North Road, Chaoyang District, Beijing, 100083, China
| | - Zhongze Yan
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China.,Institute of Physical Science and Information Technology, Anhui University, Jiulong Road, Hefei, 230601, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an, 625014, China
| | - Baoping Ren
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Peng Zhang
- School of Sociology and Anthropology, Sun Yat-sen University, Xingang Xi Road, Guang Zhou, 510275, China
| | - Zuofu Xiang
- College of Life Science and Technology, Central South University of Forestry and Technology, Shaoshan South Road, Changsha, 410004, China
| | - Binghua Sun
- School of Life Sciences, Anhui University, Jiulong Road, Hefei, 230601, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, 37077, Germany
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, United Kingdom
| | - Ming Li
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beichen West Road, Chaoyang District, Beijing, 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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Harding JD. Nonhuman Primates and Translational Research: Progress, Opportunities, and Challenges. ILAR J 2017; 58:141-150. [PMID: 29253273 PMCID: PMC5886318 DOI: 10.1093/ilar/ilx033] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 01/15/2023] Open
Abstract
Nonhuman primates (NHPs) are the closest animal models to humans regarding genetics, physiology and behavior. Therefore, NHPs are usually a critical component in translational research projects aimed at developing therapeutics, vaccines, devices or other interventions aimed at preventing, curing or ameliorating human disease. NHPs are often used in conjunction with other animal models, such as rodents, and results obtained using NHPs must often be used as the final criterion for establishing the potential efficacy of a pharmaceutical or vaccine before transition to human clinical trails. In some cases, NHPs may be the only relevant animal models for a particlular translational study. This issue of the ILAR journal brings together, in one place, articles that discuss the use of NHP models for studying human diseases that are highly prevalent and that cause extraordinary human suffering and financial and social burdens. Topics covered in detail include: tuberculosis; viral hepatitis; HIV/AIDS; neurodegenerative disorders; Substance abuse disorders; vision and prevention of blindness; disorder associated with psychosocial processes, such as anxiety, depression and loneliness; cardiovascular disease; metabolic disease, such as obesity and metabolic syndrome; respiratory disease; and female reproduction, prenatal development and women's health. Proper husbandry of NHPs that reduces stress and maintains animal health is critical for the development of NHP models. This issue of the journal includes a review of procedures for environmental enrichment, which helps assure animal health and wellbeing. Taken together, these articles provide detailed reviews of the use of NHP models for translational investigations and discuss successes, limitations, challenges and opportunities associated with this research.
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Affiliation(s)
- John D Harding
- John D. Harding, PhD, recently retired after several years of service at the National Institutes of Health in Bethesda, Maryland, where he was program officer for grants funding the US National Primate Research Centers.
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11
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Burwitz BJ, Wu HL, Abdulhaqq S, Shriver-Munsch C, Swanson T, Legasse AW, Hammond KB, Junell SL, Reed JS, Bimber BN, Greene JM, Webb GM, Northrup M, Laub W, Kievit P, MacAllister R, Axthelm MK, Ducore R, Lewis A, Colgin LMA, Hobbs T, Martin LD, Ferguson B, Thomas CR, Panoskaltsis-Mortari A, Meyers G, Stanton JJ, Maziarz RT, Sacha JB. Allogeneic stem cell transplantation in fully MHC-matched Mauritian cynomolgus macaques recapitulates diverse human clinical outcomes. Nat Commun 2017; 8:1418. [PMID: 29127275 PMCID: PMC5681693 DOI: 10.1038/s41467-017-01631-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/04/2017] [Indexed: 12/31/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is a critically important therapy for hematological malignancies, inborn errors of metabolism, and immunodeficiency disorders, yet complications such as graft-vs.-host disease (GvHD) limit survival. Development of anti-GvHD therapies that do not adversely affect susceptibility to infection or graft-vs.-tumor immunity are hampered by the lack of a physiologically relevant, preclinical model of allogeneic HSCT. Here we show a spectrum of diverse clinical HSCT outcomes including primary and secondary graft failure, lethal GvHD, and stable, disease-free full donor engraftment using reduced intensity conditioning and mobilized peripheral blood HSCT in unrelated, fully MHC-matched Mauritian-origin cynomolgus macaques. Anti-GvHD prophylaxis of tacrolimus, post-transplant cyclophosphamide, and CD28 blockade induces multi-lineage, full donor chimerism and recipient-specific tolerance while maintaining pathogen-specific immunity. These results establish a new preclinical allogeneic HSCT model for evaluation of GvHD prophylaxis and next-generation HSCT-mediated therapies for solid organ tolerance, cure of non-malignant hematological disease, and HIV reservoir clearance. Rhesus macaques are not ideal for studying response to allogeneic hematopoietic stem cell transplant (allo-HSCT) owing to complex MHC genetics that prevent full MHC-matching. Here the authors show that inbred Mauritian-origin cynomolgus macaques are a superior preclinical model of allogeneic stem cell transplantation that mimics diverse clinical outcomes of human allo-HSCT.
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Affiliation(s)
- Benjamin J Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Christine Shriver-Munsch
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Tonya Swanson
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Alfred W Legasse
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Katherine B Hammond
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Stephanie L Junell
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Gabriela M Webb
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Mina Northrup
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Wolfram Laub
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Paul Kievit
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Rhonda MacAllister
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Rebecca Ducore
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Anne Lewis
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Lois M A Colgin
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Theodore Hobbs
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Lauren D Martin
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Betsy Ferguson
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Charles R Thomas
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, 2450 Riverside Avenue, Minneapolis, MN, 55454, USA
| | - Gabrielle Meyers
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jeffrey J Stanton
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Richard T Maziarz
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA. .,Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.
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12
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Eberle R, Maxwell LK, Nicholson S, Black D, Jones-Engel L. Genome sequence variation among isolates of monkey B virus (Macacine alphaherpesvirus 1) from captive macaques. Virology 2017; 508:26-35. [PMID: 28494342 PMCID: PMC5535784 DOI: 10.1016/j.virol.2017.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/17/2017] [Accepted: 05/02/2017] [Indexed: 12/15/2022]
Abstract
Complete genome sequences of 19 strains of monkey B virus (Macacine alphaherpesvirus 1; BV) isolated from several macaque species were determined. A low level of sequence variation was present among BV isolates from rhesus macaques. Most variation among BV strains isolated from rhesus macaques was located in regions of repetitive or quasi-repetitive sequence. Variation in coding sequences (polypeptides and miRNAs) was minor compared to regions of non-coding sequences. Non-coding sequences in the long and short repeat regions of the genome did however exhibit islands of conserved sequence. Oral and genital isolates from a single monkey were identical in sequence and varied only in the number of iterations of repeat units in several areas of repeats. Sequence variation between BV isolates from different macaque species (different BV genotypes) was much greater and was spread across the entire genome, confirming the existence of different genotypes of BV in different macaque species.
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Affiliation(s)
- R Eberle
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA.
| | - L K Maxwell
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - S Nicholson
- Department of Biochemistry and Molecular Biology, College of Agriculture Sciences and Natural Resources, Oklahoma State University, Stillwater, OK, USA
| | - D Black
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - L Jones-Engel
- Department of Anthropology, University of Washington, Seattle, WA, USA
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13
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Harding JD. Genomic Tools for the Use of Nonhuman Primates in Translational Research. ILAR J 2017; 58:59-68. [PMID: 28838069 PMCID: PMC6279127 DOI: 10.1093/ilar/ilw042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022] Open
Abstract
Nonhuman primates (NHPs) are important preclinical models for understanding the etiology of human diseases and for developing therapies and vaccines to cure or eliminate disease. Most human diseases have genetic components. Therefore, to be of maximal utility, the NHP species used for translational science should be as well characterized in regard to their genome and transcriptome as possible. This article reviews the current status of genomic information for the five NHP species used most often in translational research: rhesus macaque, cynomolgus macaque, vervet (African green) monkey, baboon, and marmoset NHP. These species have published whole genome sequences (with the exception of the baboon) and relatively well-characterized transcriptomes. Some have also been characterized in regard to specific genetic loci that are particularly related to translational concerns, such as the major histocompatability complex and the cytochrome P40 genes. Genomic resources to aid in stratifying captive populations in regard to genetic and phenotypic characteristics have been developed as an aid to enhancing reproducibility and facilitating more efficient use of animals. Taken together, the current genomic resources and numerous studies currently underway to improve them should enhance the value of NHPs as preclinical models of human disease.
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Affiliation(s)
- John D. Harding
- John D. Harding, PhD, recently retired after several years of service at the National Institutes of Health in Bethesda, Maryland, where he was program officer for grants funding the US National Primate Research Centers
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14
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Kanthaswamy S, Ng J, Oldt RF, Phillippi-Falkenstein K, Kubisch HM. SNP-based genetic characterization of the Tulane National Primate Research Center's conventional and specific pathogen-free rhesus macaque (Macaca mulatta) populations. J Med Primatol 2017. [PMID: 28639374 DOI: 10.1111/jmp.12284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The rhesus macaque is an important biomedical model organism, and the Tulane National Primate Research Center (TNPRC) has one of the largest rhesus macaque breeding colonies in the United States. METHODS SNP profiles from 3266 rhesus macaques were used to examine the TNPRC colony genetic composition over time and across conventional or SPF animals of Chinese and Indian ancestry. RESULTS Chinese origin animals were the least genetically diverse and the most inbred; however, since their derivation from their conventional forebearers, neither the Chinese nor the Indian SPF animals exhibit any significant loss of genetic diversity or differentiation. CONCLUSIONS The TNPRC colony managers have successfully minimized loss in genetic variation across generations. Although founder effects and bottlenecks among the Indian animals have been successfully curtailed, the Chinese subpopulation still show some influences from these events.
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Affiliation(s)
- Sree Kanthaswamy
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA.,Julie Ann Wrigley Global Institute of Sustainability, Arizona State University, Tempe, AZ, USA.,Evolutionary Biology PhD program, School of Life Sciences, Arizona State University, Tempe, AZ, USA.,California National Primate Research Center, University of California, Davis, CA, USA
| | - Jillian Ng
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Robert F Oldt
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA.,Evolutionary Biology PhD program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
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15
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Bimber BN, Ramakrishnan R, Cervera-Juanes R, Madhira R, Peterson SM, Norgren RB, Ferguson B. Whole genome sequencing predicts novel human disease models in rhesus macaques. Genomics 2017; 109:214-220. [PMID: 28438488 DOI: 10.1016/j.ygeno.2017.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/10/2017] [Accepted: 04/14/2017] [Indexed: 12/23/2022]
Abstract
Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model. We detected an average of 131 mutations predicted to severely alter protein coding per animal, and identified 45 such variants that coincide with known pathogenic human variants. These data suggest that expanded screening of existing breeding colonies will identify novel models of human disease, and that increased genomic characterization can help inform research studies in macaques.
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Affiliation(s)
- Benjamin N Bimber
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Ranjani Ramakrishnan
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Rita Cervera-Juanes
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Ravi Madhira
- Oregon Health & Sciences University, Portland, OR 97239, United States
| | - Samuel M Peterson
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Robert B Norgren
- Dept. of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Betsy Ferguson
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States.
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16
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Mattison JA, Colman RJ, Beasley TM, Allison DB, Kemnitz JW, Roth GS, Ingram DK, Weindruch R, de Cabo R, Anderson RM. Caloric restriction improves health and survival of rhesus monkeys. Nat Commun 2017; 8:14063. [PMID: 28094793 PMCID: PMC5247583 DOI: 10.1038/ncomms14063] [Citation(s) in RCA: 527] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/24/2016] [Indexed: 12/23/2022] Open
Abstract
Caloric restriction (CR) without malnutrition extends lifespan and delays the onset of age-related disorders in most species but its impact in nonhuman primates has been controversial. In the late 1980s two parallel studies were initiated to determine the effect of CR in rhesus monkeys. The University of Wisconsin study reported a significant positive impact of CR on survival, but the National Institute on Aging study detected no significant survival effect. Here we present a direct comparison of longitudinal data from both studies including survival, bodyweight, food intake, fasting glucose levels and age-related morbidity. We describe differences in study design that could contribute to differences in outcomes, and we report species specificity in the impact of CR in terms of optimal onset and diet. Taken together these data confirm that health benefits of CR are conserved in monkeys and suggest that CR mechanisms are likely translatable to human health. Caloric restriction (CR) delays ageing of model organisms, but whether it works in nonhuman primates has been controversial. Here, the authors pool and reanalyse data from two long-running CR primate studies, concluding that moderate CR indeed improves health and survival of rhesus monkeys.
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Affiliation(s)
- Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Ricki J Colman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - T Mark Beasley
- Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294, USA.,Geriatric Research Education and Clinical Center, Birmingham/Atlanta Veterans Administration Hospital, Birmingham, Alabama 35233, USA
| | - David B Allison
- Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294, USA
| | - Joseph W Kemnitz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53792, USA
| | | | - Donald K Ingram
- Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, USA
| | - Richard Weindruch
- Department of Medicine, University of Wisconsin, Madison, Wisconsin 53792, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Rozalyn M Anderson
- Department of Medicine, University of Wisconsin, Madison, Wisconsin 53792, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin 53705, USA
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17
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Kanthaswamy S, Ng J, Broatch J, Short J, Roberts J. Mitigating Chinese-Indian rhesus macaque (Macaca mulatta) hybridity at the California National Primate Research Center (CNPRC). J Med Primatol 2016; 45:333-335. [PMID: 27466971 PMCID: PMC5274629 DOI: 10.1111/jmp.12231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2016] [Indexed: 11/30/2022]
Abstract
The effectiveness of abating hybridity in a rhesus breeding colony was evaluated. STR data from the 2006 to 2015 newborns were analyzed. Hybridity decreased over successive years. Birth cohorts retained high genetic variability without signs of inbreeding and differentiation. Hybridity was minimized without compromising overall genetic variability.
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Affiliation(s)
- Sree Kanthaswamy
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA
- Julie Ann Wrigley Global Institute of Sustainability, Arizona State University, Tempe, AZ, USA
- Evolutionary Biology PhD program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Jillian Ng
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Jennifer Broatch
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA
| | - Jennifer Short
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Jeffrey Roberts
- California National Primate Research Center, University of California, Davis, CA, USA
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18
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Kanthaswamy S, Ng J, Hernández-Pacheco R, Ruiz-Lambides A, Maldonado E, Martínez MI, Sariol CA. The Population Genetic Composition of Conventional and SPF Colonies of Rhesus Macaques (Macaca mulatta) at the Caribbean Primate Research Center. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2016; 55:147-51. [PMID: 27025804 PMCID: PMC4783631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/22/2015] [Accepted: 07/23/2015] [Indexed: 06/05/2023]
Abstract
The SPF breeding program at the Caribbean Primate Research Center supplies Indian-origin rhesus macaques of known genetic and virologic background for biomedical research. In this study, population genetic analyses using 14 short tandem-repeat sequences showed that the SPF colony has remained genetically homogenous over time, with sufficient amounts of heterozygosity and minimal stratification from its founders. Intergenerational studies indicated that an average of 7 alleles have been retained, inbreeding levels have remained low, and the degree of Indian ancestry is one of the highest among several national primate research centers. The relative low genetic diversity in the free-ranging population as well as in the captive SPF and conventional colonies when compared with that of other primate centers indicates that the free-ranging population, from which the captive-colony animals were derived, has experienced significant founder effects and genetic drift during the years after its establishment. This study supports the historical origin of the free-ranging population and confirms the high value of this resource for biomedical research. Current genetic diversity levels within the SPF colony can be ensured with the practice of colony management approaches such as equalizing male:female ratios in each SPF breeding group and increasing breeding group sizes. Introducing new Indian-origin macaques from other captive colonies might help to maximize the genetic diversity of the breeding stock. Furthermore, genetic estimates must be used to rank breeders according to their genetic value or their genome uniqueness to increase founder-genome representation and curb future genetic bottlenecks and allele loss.
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Affiliation(s)
- Sreetharan Kanthaswamy
- California National Primate Research Center, University of California, Davis, California, USA; School of Mathematics and Natural Sciences, West Campus, Arizona State University, Glendale, Arizona, USA.
| | - Jillian Ng
- California National Primate Research Center, University of California, Davis, California, USA
| | - Raisa Hernández-Pacheco
- Caribbean Primate Research Center, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - Angelina Ruiz-Lambides
- Caribbean Primate Research Center, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - Elizabeth Maldonado
- Caribbean Primate Research Center, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
| | - 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, and Internal Medicine, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico
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19
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Haus T, Prinz K, Pauling B, Roos C. Genotyping of non-human primate models: perspectives and challenges for the implementation of the "three R's". Primate Biol 2014. [DOI: 10.5194/pb-1-1-2014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Although non-human primates (NHPs) represent only a minor fraction of all animals used in biomedical research, there is a continuous effort to further reduce, refine and replace research with NHPs in accordance with the principles of the three R's. Most of the NHP model species are genetically highly diverse, and significant variation occurs among populations of different geographic origins, particularly in macaques. Since such differences can considerably affect the outcome of biomedical experiments, genotyping represents a promising tool to refine research approaches and to reduce the number of NHPs in biomedical research. Accordingly, the European Primate Network (EUPRIM-Net) developed an anonymous online survey to evaluate possibilities and potential hindrances for the application of genotyping in NHP research. On the one hand, our results point to the importance of genetic variation in NHPs and the need to consider the genetic background for future research approaches. On the other hand, our survey identified several hindrances and limiting factors for the application of genotyping and its incorporation in research, primate husbandry and breeding. We provide some fundamental recommendations on how to meet these challenges and how genotyping can be efficiently used to refine NHP research and to reduce the number of NHPs in biomedical research in the long term.
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20
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Ogawa LM, Vallender EJ. Genetic substructure in cynomolgus macaques (Macaca fascicularis) on the island of Mauritius. BMC Genomics 2014; 15:748. [PMID: 25174998 PMCID: PMC4167525 DOI: 10.1186/1471-2164-15-748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/21/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Nonhuman primates are commonly used in biomedical research as animal models of human disease and behavior. Compared to common rodent models, nonhuman primates are genetically, physiologically, behaviorally and neurologically more similar to humans owing to more recent shared ancestry and therefore provide the advantage of greater translational validity in preclinical studies. The cynomolgus macaque (Macaca fascicularis) is one of the most commonly used nonhuman primates in academic and industry settings, yet population genetic research has revealed significant substructure throughout the species distribution that may confound studies. Cynomolgus monkeys introduced to Mauritius specifically have previously been thought to maintain the least genetic heterogeneity of all cynomolgus monkeys, although recent work, including work from our lab, suggests macaques from Mauritius too may harbor cryptic substructure. RESULTS To evaluate putative substructure in Mauritian cynomolgus macaques, we designed a panel of 96 single nucleotide polymorphisms based on preliminary findings from previous work to screen 246 of cynomolgus monkeys from two primary suppliers. Results from this study support substructure in Mauritian macaques and suggest a minimum of two populations and maybe three on Mauritius, with moderate admixture. CONCLUSION These findings inform the natural history of these monkeys suggesting either a previously unrecognized physical or ecological barrier to gene flow on Mauritius and/or the breakdown of historic substructure resulting from the history of macaque introduction to the island. These findings are relevant to ongoing research using these models in part because of increased appreciation of segregating common variation with functional effects and may be used to better inform animal selection in preclinical research.
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Affiliation(s)
- Lisa M Ogawa
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772 USA
| | - Eric J Vallender
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772 USA
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21
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Genome typing of nonhuman primate models: implications for biomedical research. Trends Genet 2014; 30:482-7. [PMID: 24954183 DOI: 10.1016/j.tig.2014.05.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 12/18/2022]
Abstract
The success of personalized medicine rests on understanding the genetic variation between individuals. Thus, as medical practice evolves and variation among individuals becomes a fundamental aspect of clinical medicine, a thorough consideration of the genetic and genomic information concerning the animals used as models in biomedical research also becomes critical. In particular, nonhuman primates (NHPs) offer great promise as models for many aspects of human health and disease. These are outbred species exhibiting substantial levels of genetic variation; however, understanding of the contribution of this variation to phenotypes is lagging behind in NHP species. Thus, there is a pivotal need to address this gap and define strategies for characterizing both genomic content and variability within primate models of human disease. Here, we discuss the current state of genomics of NHP models and offer guidelines for future work to ensure continued improvement and utility of this line of biomedical research.
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