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Mantel N, Piras-Douce F, Chautard E, Marcos-Lopez E, Bodinham CL, Cosma A, Courtois V, Dhooge N, Gautheron S, Kaufmann SHE, Pizzoferro K, Lewis DJM, Martinon F, Pagnon A, Raynal F, Dereuddre-Bosquet N, Le Grand R. Cynomolgus macaques as a translational model of human immune responses to yellow fever 17D vaccination. J Virol 2024; 98:e0151623. [PMID: 38567951 PMCID: PMC11092345 DOI: 10.1128/jvi.01516-23] [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: 10/11/2023] [Accepted: 12/22/2023] [Indexed: 05/15/2024] Open
Abstract
The non-human primate (NHP) model (specifically rhesus and cynomolgus macaques) has facilitated our understanding of the pathogenic mechanisms of yellow fever (YF) disease and allowed the evaluation of the safety and efficacy of YF-17D vaccines. However, the accuracy of this model in mimicking vaccine-induced immunity in humans remains to be fully determined. We used a systems biology approach to compare hematological, biochemical, transcriptomic, and innate and antibody-mediated immune responses in cynomolgus macaques and human participants following YF-17D vaccination. Immune response progression in cynomolgus macaques followed a similar course as in adult humans but with a slightly earlier onset. Yellow fever virus neutralizing antibody responses occurred earlier in cynomolgus macaques [by Day 7[(D7)], but titers > 10 were reached in both species by D14 post-vaccination and were not significantly different by D28 [plaque reduction neutralization assay (PRNT)50 titers 3.6 Log vs 3.5 Log in cynomolgus macaques and human participants, respectively; P = 0.821]. Changes in neutrophils, NK cells, monocytes, and T- and B-cell frequencies were higher in cynomolgus macaques and persisted for 4 weeks versus less than 2 weeks in humans. Low levels of systemic inflammatory cytokines (IL-1RA, IL-8, MIP-1α, IP-10, MCP-1, or VEGF) were detected in either or both species but with no or only slight changes versus baseline. Similar changes in gene expression profiles were elicited in both species. These included enriched and up-regulated type I IFN-associated viral sensing, antiviral innate response, and dendritic cell activation pathways D3-D7 post-vaccination in both species. Hematological and blood biochemical parameters remained relatively unchanged versus baseline in both species. Low-level YF-17D viremia (RNAemia) was transiently detected in some cynomolgus macaques [28% (5/18)] but generally absent in humans [except one participant (5%; 1/20)].IMPORTANCECynomolgus macaques were confirmed as a valid surrogate model for replicating YF-17D vaccine-induced responses in humans and suggest a key role for type I IFN.
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Affiliation(s)
| | | | | | - Ernesto Marcos-Lopez
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | - Caroline L. Bodinham
- Surrey Clinical Research Centre, University of Surrey, Guildford, Surrey, United Kingdom
| | - Antonio Cosma
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | | | - Nina Dhooge
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | | | - Stefan H. E. Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany; Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, Texas, USA
| | - Kathleen Pizzoferro
- Surrey Clinical Research Centre, University of Surrey, Guildford, Surrey, United Kingdom
| | - David J. M. Lewis
- Surrey Clinical Research Centre, University of Surrey, Guildford, Surrey, United Kingdom
| | - Frédéric Martinon
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | - Anke Pagnon
- Research and Development, Sanofi, Marcy L'Etoile, France
| | - Franck Raynal
- Research and Development, Sanofi, Marcy L'Etoile, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
| | - Roger Le Grand
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay aux Roses, France
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Uno Y, Uehara S, Yamazaki H. Polymorphic cytochromes P450 in non-human primates. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:329-364. [PMID: 35953160 DOI: 10.1016/bs.apha.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cynomolgus macaques (Macaca fascicularis, an Old World monkey) are widely used in drug development because of their genetic and physiological similarities to humans, and this trend has continued with the use of common marmosets (Callithrix jacchus, a New World monkey). Information on the major drug-metabolizing cytochrome P450 (CYP, P450) enzymes of these primate species indicates that multiple forms of their P450 enzymes have generally similar substrate selectivities to those of human P450 enzymes; however, some differences in isoform, activity, and substrate specificity account for limited species differences in drug oxidative metabolism. This review provides information on the P450 enzymes of cynomolgus macaques and marmosets, including cDNA, tissue expression, substrate specificity, and genetic variants, along with age differences and induction. Typical examples of important P450s to be considered in drug metabolism studies include cynomolgus CYP2C19, which is expressed abundantly in liver and metabolizes numerous drugs. Moreover, genetic variants of cynomolgus CYP2C19 affect the individual pharmacokinetic data of drugs such as R-warfarin. These findings provide a foundation for understanding each P450 enzyme and the individual pharmacokinetic and toxicological results in cynomolgus macaques and marmosets as preclinical models. In addition, the effects of induction on some drug clearances mediated by P450 enzymes are also described. In summary, this review describes genetic and acquired individual differences in cynomolgus and marmoset P450 enzymes involved in drug oxidation that may be associated with pharmacological and/or toxicological effects.
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Affiliation(s)
- Yasuhiro Uno
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.
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Gupta A, Galinski MR, Voit EO. Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. Front Mol Biosci 2022; 8:800721. [PMID: 35242812 PMCID: PMC8886244 DOI: 10.3389/fmolb.2021.800721] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria has a complex pathology with varying manifestations and symptoms, effects on host tissues, and different degrees of severity and ultimate outcome, depending on the causative Plasmodium pathogen and host species. Previously, we compared the peripheral blood transcriptomes of two macaque species (Macaca mulatta and Macaca fascicularis) in response to acute primary infection by Plasmodium knowlesi. Although these two species are very closely related, the infection in M. mulatta is fatal, unless aggressively treated, whereas M. fascicularis develops a chronic, but tolerable infection in the blood. As a reason for this stark difference, our analysis suggests delayed pathogen detection in M. mulatta followed by extended inflammation that eventually overwhelms this monkey’s immune response. By contrast, the natural host M. fascicularis detects the pathogen earlier and controls the inflammation. Additionally, M. fascicularis limits cell proliferation pathways during the log phase of infection, presumably in an attempt to control inflammation. Subsequent cell proliferation suggests a cell-mediated adaptive immune response. Here, we focus on molecular mechanisms underlying the key differences in the host and parasite responses and their coordination. SICAvar Type 1 surface antigens are highly correlated with pattern recognition receptor signaling and important inflammatory genes for both hosts. Analysis of pathogen detection pathways reveals a similar signaling mechanism, but with important differences in the glutamate G-protein coupled receptor (GPCR) signaling pathway. Furthermore, differences in inflammasome assembly processes suggests an important role of S100 proteins in balancing inflammation and cell proliferation. Both differences point to the importance of Ca2+ homeostasis in inflammation. Additionally, the kynurenine-to-tryptophan ratio, a known inflammatory biomarker, emphasizes higher inflammation in M. mulatta during log phase. Transcriptomics-aided metabolic modeling provides a functional method for evaluating these changes and understanding downstream changes in NAD metabolism and aryl hydrocarbon receptor (AhR) signaling, with enhanced NAD metabolism in M. fascicularis and stronger AhR signaling in M. mulatta. AhR signaling controls important immune genes like IL6, IFNγ and IDO1. However, direct changes due to AhR signaling could not be established due to complicated regulatory feedback mechanisms associated with the AhR repressor (AhRR). A complete understanding of the exact dynamics of the immune response is difficult to achieve. Nonetheless, our comparative analysis provides clear suggestions of processes that underlie an effective immune response. Thus, our study identifies multiple points of intervention that are apparently responsible for a balanced and effective immune response and thereby paves the way toward future immune strategies for treating malaria.
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Affiliation(s)
- Anuj Gupta
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Mary R. Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, United States
| | - Eberhard O. Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
- *Correspondence: Eberhard O. Voit,
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Kumpai P, Hamada Y, Kanthaswamy S, Malaivijitnond S. Gene flow from rhesus (Macaca mulatta) to cynomolgus macaques (M. fascicularis) and effects of introgressive hybridization on reproduction in two biomedically relevant non-human primate species. J Med Primatol 2022; 51:108-118. [PMID: 35132636 DOI: 10.1111/jmp.12570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND We compared the reproductive patterns of wild Indochinese and Sundaic cynomolgus macaques (Mf) exhibiting different levels of genetic admixture with rhesus macaques (Mm). METHODS Ten adult females from each Indochinese (WHM) and Sundaic (KN/KTK) Mf populations, which exhibited 50% and 15% of Mm autosomal SNPs, were selected as focal animals. Animals were observed for 12 months, and the frequencies of sexual proceptivity, attractivity and receptivity, number of newborns, and changes in sex skin were recorded. RESULTS Both populations showed all three sexual behaviors throughout the year, but they were classified as moderately seasonal breeders because their 3-month birth counts were as high as ~50%. The fecundity of WHM was lower than the KN/KTK. Changes in sex skin of WHM were more prone to Mm's pattern than the KN/KTK. CONCLUSION The introgressive gene flow from Mm to Mf does not affect Mf's sexual behaviors; however, it can impact fecundity and physiological (sex skin) changes.
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Affiliation(s)
- Prangmas Kumpai
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Yuzuru Hamada
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, Arizona, USA.,California National Primate Research Center, University of California, Davis, California, USA
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
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5
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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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Genetic variation in the Mauritian cynomolgus macaque population reflects variation in the human population. Gene 2021; 787:145648. [PMID: 33848572 DOI: 10.1016/j.gene.2021.145648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/23/2021] [Accepted: 04/07/2021] [Indexed: 11/21/2022]
Abstract
The cynomolgus macaque is an important species for preclinical research, however the extent of genetic variation in this population and its similarity to the human population is not well understood. Exome sequencing was conducted for 101 cynomolgus macaques to characterize genetic variation. The variant distribution frequency was 7.81 variants per kilobase across the sequenced regions, with a total of 2,770,009 single nucleotide variants identified from 2,996,041 loci. A large portion (85.6%) had minor allele frequencies greater than 5%. Enriched pathways for genes with high genetic diversity (≥10 variants per kilobase) were those involving signaling peptides and immune response. Compared to human, the variant distribution frequency and nucleotide diversity in the macaque exome was approximately 4 times greater; however the ratio of non-synonymous to synonymous variants was similar (0.735 and 0.831, respectively). Understanding genetic variability in cynomolgus macaques will enable better interpretation and human translation of phenotypic variability in this species.
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7
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Kawamoto Y. Genetic Assessment on the Origin of Alien Macaques in the Boso Peninsula in Japan. MAMMAL STUDY 2021. [DOI: 10.3106/ms2020-0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yoshi Kawamoto
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
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8
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Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles. Immunity 2021; 54:355-366.e4. [PMID: 33484642 DOI: 10.1016/j.immuni.2020.12.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/19/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022]
Abstract
Definition of the specific germline immunoglobulin (Ig) alleles present in an individual is a critical first step to delineate the ontogeny and evolution of antigen-specific antibody responses. Rhesus and cynomolgus macaques are important animal models for pre-clinical studies, with four main sub-groups being used: Indian- and Chinese-origin rhesus macaques and Mauritian and Indonesian cynomolgus macaques. We applied the (Ig) gene inference tool IgDiscover and performed extensive Sanger sequencing-based genomic validation to define germline VDJ alleles in these 4 sub-groups, comprising 45 macaques in total. There was allelic overlap between Chinese- and Indian-origin rhesus macaques and also between the two macaque species, which is consistent with substantial admixture. The island-restricted Mauritian cynomolgus population displayed the lowest number of alleles of the sub-groups, yet maintained high individual allelic diversity. These comprehensive databases of germline IGH alleles for rhesus and cynomolgus macaques provide a resource toward the study of B cell responses in these important pre-clinical models.
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9
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Ito T, Kanthaswamy S, Bunlungsup S, Oldt RF, Houghton P, Hamada Y, Malaivijitnond S. Secondary contact and genomic admixture between rhesus and long-tailed macaques in the Indochina Peninsula. J Evol Biol 2020; 33:1164-1179. [PMID: 33448526 DOI: 10.1111/jeb.13681] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/11/2020] [Accepted: 07/08/2020] [Indexed: 01/07/2023]
Abstract
Understanding the process and consequences of hybridization is one of the major challenges in evolutionary biology. A growing body of literature has reported evidence of ancient hybridization events or natural hybrid zones in primates, including humans; however, we still have relatively limited knowledge about the pattern and history of admixture because there have been little studies that simultaneously achieved genome-scale analysis and a geographically wide sampling of wild populations. Our study applied double-digest restriction site-associated DNA sequencing to samples from the six localities in and around the provisional hybrid zone of rhesus and long-tailed macaques and evaluated population structure, phylogenetic relationships, demographic history, and geographic clines of morphology and allele frequencies. A latitudinal gradient of genetic components was observed, highlighting the transition from rhesus (north) to long-tailed macaque distribution (south) as well as the presence of one northern population of long-tailed macaques exhibiting unique genetic structure. Interspecific gene flow was estimated to have recently occurred after an isolation period, and the migration rate from rhesus to long-tailed macaques was slightly greater than in the opposite direction. Although some rhesus macaque-biased alleles have widely introgressed into long-tailed macaque populations, the inflection points of allele frequencies have been observed as concentrated around the traditionally recognized interspecific boundary where morphology discontinuously changed; this pattern was more pronounced in the X chromosome than in autosomes. Thus, due to geographic separation before secondary contact, reproductive isolation could have evolved, contributing to the maintenance of an interspecific boundary and species-specific morphological characteristics.
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Affiliation(s)
- Tsuyoshi Ito
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Sreetharan Kanthaswamy
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA
| | - Srichan Bunlungsup
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Robert F Oldt
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University West Campus, Glendale, AZ, USA
| | | | - Yuzuru Hamada
- Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
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10
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De Witte C, Berlamont H, Smet A, Ducatelle R, Haesebrouck F. Rhesus macaques are most likely the ancestral source of Helicobacter suis infection in pigs and not cynomolgus macaques. Helicobacter 2020; 25:e12689. [PMID: 32219893 DOI: 10.1111/hel.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Helena Berlamont
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Annemieke Smet
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Antwerp University, Antwerp, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Ramsay L, Quillé ML, Orset C, de la Grange P, Rousselet E, Férec C, Le Gac G, Génin E, Timsit S. Blood transcriptomic biomarker as a surrogate of ischemic brain gene expression. Ann Clin Transl Neurol 2019; 6:1681-1695. [PMID: 31400065 PMCID: PMC6764628 DOI: 10.1002/acn3.50861] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/18/2023] Open
Abstract
Objectives Blood biomarkers for cerebral tissue ischemia are lacking. The goal was to identify a blood transcriptomic signature jointly identified in the ischemic brain. Methods A nonhuman primate model with middle cerebral artery (MCA) territory infarction was used to study gene expression by microarray during acute ischemic cerebral stroke in the brain and the blood. Brain samples were collected in the infarcted and contralateral non‐infarcted cortex as well as blood samples before and after occlusion. Gene expression was compared between the two brain locations to find differentially expressed genes. The expressions of these genes were then compared in the blood pre‐ and post‐occlusion. Results Hierarchical clustering of brain expression data revealed strong independent clustering of ischemic and nonischemic brain samples. The top five enriched, up‐regulated gene sets in the brain were TNF α signaling, apoptosis, P53 pathway, hypoxia, and UV response up. A comparison of differentially expressed genes in the brain and blood revealed a significant overlap of gene expression patterns. Stringent analysis of blood expression data from pre‐ and post‐occlusion samples in each monkey identified nine genes highly differentially expressed in both the brain and the blood. Many of these up‐regulated genes belong to pathways involved in cell death and DNA damage repair. Interpretation Common gene expression profile can be identified in the brain and blood and clearly differentiates ischemic from nonischemic conditions. Therefore, specific blood transcriptomic signature may represent a surrogate for brain ischemic gene expression.
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Affiliation(s)
- LeeAnn Ramsay
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Marie-Lise Quillé
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Cyrille Orset
- Department of Physiopathology and Imaging of Neurological Disorders, INSERM U1237, University Caen Normandie, GIP Cyceron, Caen, France
| | | | - Estelle Rousselet
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Claude Férec
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Gérald Le Gac
- Inserm U1078, Université Bretagne Loire Université de Bretagne Occidentale, IBSAM, Laboratoire de Genetique Moleculaire et Histocompatibilité, CHRU de Brest, Hopital Morvan, Brest, France
| | - Emmanuelle Génin
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Serge Timsit
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France.,Neurology and Stroke Department, Centre Hospitalier Régional Universitaire (CHRU), Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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12
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Day GQ, Ng J, Oldt RF, Houghton PW, Smith DG, Kanthaswamy S. DNA-based Determination of Ancestry in Cynomolgus Macaques ( Macaca fascicularis). JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2018; 57:432-442. [PMID: 30165920 PMCID: PMC6159685 DOI: 10.30802/aalas-jaalas-17-000147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/29/2017] [Accepted: 02/26/2018] [Indexed: 11/05/2022]
Abstract
Interest in the genetic composition of cynomolgus macaques (Macaca fascicularis) has increased due to the rising demand for NHP models in human biomedical research. Significant genetic differences among regional populations of cynomolgus macaques can confound interpretations of research results because they do not solely reflect differences in experimental treatment effects. Therefore, the common origin of cynomolgus macaques used as research subjects should be verified by using region-specific genetic markers to minimize the influence of underlying genetic variation among animals selected as research subjects on phenotypes under study. We compared the effectiveness of 18 short tandem repeat (STR) markers with that of 83 single-nucleotide polymorphism (SNP) markers to differentiate the ancestry of cynomolgus macaques from 6 different populations (Cambodia, Sumatra, Mauritius, Singapore, and the islands of Luzon and Zamboanga in the Philippines). Genetic diversity indices such as allele numbers and expected heterozygosity based on SNP were lower and exhibited lower standard errors than those provided by STR, probably because, unlike STR, most SNP are biallelic and consequently exhibit maximal expected heterozygosity values of 0.50. However, the standard error of estimates of observed heterozygosity based on SNP was higher than that for STR, perhaps reflecting sampling errors. Only 27 SNP were required to match the resolving power of 17 STR to detect population structure, that is, 1.6 SNP:1 STR. Whereas STR only differentiated the Mauritian population from all other populations, SNP detected 4 genetically distinct groups (Cambodia, Singapore-Sumatra, Mauritius, and Zamboanga). SNP are poised to become as valuable as STR for understanding and detecting genetic structure among cynomolgus macaques. Although STR will remain an important tool for cynomolgus macaque population studies, SNP have the potential to become the mainstream marker type.
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Affiliation(s)
- George Q Day
- Molecular Anthropology Laboratory, University of California, Davis, California
| | - Jillian Ng
- Molecular Anthropology Laboratory, University of California, Davis, California
| | - Robert F Oldt
- Molecular Anthropology Laboratory, University of California, Davis, California, School of Mathematics and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona
| | | | - David Glenn Smith
- Molecular Anthropology Laboratory, California National Primate Research Center, University of California, Davis, California
| | - Sree Kanthaswamy
- California National Primate Research Center, University of California, Davis, California, School of Mathematics and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona;,
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13
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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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14
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Koyama S, Fukuda K, Watanabe S, Matsushita A, Tsuchiya H, Fujinami N, Kohara S, Murayama N, Nagano M, Yamazaki H, Fukuzaki K, Uno Y, Hosoi Y. CYP2C76 deficiency is embryonic lethal in cynomolgus macaques: The potential role of CYP2C76 in early embryogenesis. Drug Metab Pharmacokinet 2017; 32:112-115. [PMID: 28153493 DOI: 10.1016/j.dmpk.2016.10.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
Cynomolgus macaques are an important primate species for drug metabolism studies; however cynomolgus CYP2C76, an important drug-metabolizing enzyme, accounts for drug metabolism differences to humans, so that CYP2C76-null animals might show drug-metabolizing properties more similar to humans. In this study, attempts were made to produce CYP2C76-null animals by assisted reproduction technology. Oocytes and sperm collected from the heterozygotes for the null allele (c.449TG > A) were subjected to intracytoplasmic sperm injection, and the embryos produced were cultured in vitro through the blastocyst stage. Preimplantation genetic diagnosis using a biopsied portion of the blastocyst revealed that none of the 32 blastocysts analyzed were homozygotes. In contrast, 2 of the 20 embryos analyzed were homozygotes at the 8-cell stage, indicating that CYP2C76-null embryos most likely stop developing between the 8-cell and blastocyst stage. By polymerase chain reaction, expression of CYP2C76 mRNA was detected in oocytes and blastocysts, but not in 2-, 4-, 8-, or 16/32-cell stage embryos. Metabolic assays showed that CYP2C76 metabolized progesterone. These results indicated that CYP2C76 null was likely embryonic lethal, suggesting its potential role during early embryogenesis in cynomolgus macaques.
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Affiliation(s)
- Shuzo Koyama
- Drug Safety Research Center (DSR), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kagoshima, Japan; SNBL USA, Ltd., Everett, WA, USA
| | - Koji Fukuda
- Drug Safety Research Center (DSR), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kagoshima, Japan; SNBL USA, Ltd., Everett, WA, USA
| | - Sho Watanabe
- Drug Safety Research Center (DSR), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kagoshima, Japan; SNBL USA, Ltd., Everett, WA, USA
| | - Akinori Matsushita
- Drug Safety Research Center (DSR), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kagoshima, Japan; Pharmacokinetics and Bioanalysis Center (PBC), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kainan, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Nahoko Fujinami
- Graduate School of Biology-Oriented Science and Technology, Kinki University, Kinokawa, Japan
| | - Sakae Kohara
- Pharmacokinetics and Bioanalysis Center (PBC), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kainan, Japan
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Japan
| | - Masashi Nagano
- Laboratory of Theriogenology, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Japan
| | - Koichiro Fukuzaki
- Drug Safety Research Center (DSR), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kagoshima, Japan; SNBL USA, Ltd., Everett, WA, USA
| | - Yasuhiro Uno
- Pharmacokinetics and Bioanalysis Center (PBC), Shin Nippon Biomedical Laboratories (SNBL), Ltd., Kainan, Japan.
| | - Yoshihiko Hosoi
- Graduate School of Biology-Oriented Science and Technology, Kinki University, Kinokawa, Japan.
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15
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Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta). Sci Rep 2016; 6:32598. [PMID: 27600022 PMCID: PMC5013489 DOI: 10.1038/srep32598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/10/2016] [Indexed: 11/13/2022] Open
Abstract
Retroposition is an RNA-mediated mechanism to generate gene duplication, and is believed to play an important role in genome evolution and phenotypic adaptation in various species including primates. Previous studies suggested an elevated rate of recent retroposition in the rhesus macaque genome. To better understand the impact of retroposition on macaque species which have undergone an adaptive radiation approximately 3–6 million years ago, we developed a bioinformatics pipeline to identify recently derived retrocopies in cynomolgus monkeys. As a result, we identified seven experimentally validated young retrocopies, all of which are polymorphic in cynomolgus monkeys. Unexpectedly, five of them are also present in rhesus monkeys and are still segregating. Molecular evolutionary analysis indicates that the observed inter-specific polymorphism is attribute to ancestral polymorphism. Further population genetics analysis provided strong evidence of balancing selection on at least one case (Crab-eating monkey retrocopy 6, or CER6) in both species. CER6 is in adjacent with an immunoglobulin related gene and may be involved in host-pathogen interaction, a well-known target of balancing selection. Altogether, our data support that retroposition is an important force to shape genome evolution and species adaptation.
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16
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Ng J, Trask JS, Smith DG, Kanthaswamy S. Heterospecific SNP diversity in humans and rhesus macaque (Macaca mulatta). J Med Primatol 2015; 44:194-201. [PMID: 25963897 DOI: 10.1111/jmp.12174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND Conservation of single nucleotide polymorphisms (SNPs) between human and other primates (i.e., heterospecific SNPs) in candidate genes can be used to assess the utility of those organisms as models for human biomedical research. METHODS A total of 59,691 heterospecific SNPs in 22 rhesus macaques and 20 humans were analyzed for human trait associations and 4207 heterospecific SNPs biallelic in both taxa were compared for genetic variation. RESULTS Variation comparisons at the 4207 SNPs showed that humans were more genetically diverse than rhesus macaques with observed and expected heterozygosities of 0.337 and 0.323 vs. 0.119 and 0.102, and minor allele frequencies of 0.239 and 0.063, respectively. In total, 431 of the 59,691 heterospecific SNPs are reportedly associated with human-specific traits. CONCLUSION While comparisons between human and rhesus macaque genomes are plausible, functional studies of heterospecific SNPs are necessary to determine whether rhesus macaque alleles are associated with the same phenotypes as their corresponding human alleles.
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Affiliation(s)
- Jillian Ng
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA
| | - Jessica Satkoski Trask
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.,California National Primate Research Center, University of California, Davis, CA, USA
| | - David Glenn Smith
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.,California National Primate Research Center, University of California, Davis, CA, USA
| | - Sree Kanthaswamy
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA.,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.,Department of Environmental Toxicology, University of California, Davis, CA, USA
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17
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Shorey-Kendrick LE, Ford MM, Allen DC, Kuryatov A, Lindstrom J, Wilhelm L, Grant KA, Spindel ER. Nicotinic receptors in non-human primates: Analysis of genetic and functional conservation with humans. Neuropharmacology 2015; 96:263-73. [PMID: 25661700 PMCID: PMC4486519 DOI: 10.1016/j.neuropharm.2015.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 01/18/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are highly conserved between humans and non-human primates. Conservation exists at the level of genomic structure, protein structure and epigenetics. Overall homology of nAChRs at the protein level is 98% in macaques versus 89% in mice, which is highly relevant for evaluating subtype-specific ligands that have different affinities in humans versus rodents. In addition to conservation at the protein level, there is high conservation of genomic structure in terms of intron and exon size and placement of CpG sites that play a key role in epigenetic regulation. Analysis of single nucleotide polymorphisms (SNPs) shows that while the majority of SNPs are not conserved between humans and macaques, some functional polymorphisms are. Most significantly, cynomolgus monkeys express a similar α5 nAChR Asp398Asn polymorphism to the human α5 Asp398Asn polymorphism that has been linked to greater nicotine addiction and smoking related disease. Monkeys can be trained to readily self-administer nicotine, and in an initial study we have demonstrated that cynomolgus monkeys bearing the α5 D398N polymorphism show a reduced behavioral sensitivity to oral nicotine and tend to consume it in a different pattern when compared to wild-type monkeys. Thus the combination of highly homologous nAChR, higher cortical functions and capacity for complex training makes non-human primates a unique model to study in vivo functions of nicotinic receptors. In particular, primate studies on nicotine addiction and evaluation of therapies to prevent or overcome nicotine addiction are likely to be highly predictive of treatment outcomes in humans.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Matthew M Ford
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Daicia C Allen
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Alexander Kuryatov
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jon Lindstrom
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Larry Wilhelm
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health &, Science University, Beaverton, OR 97006, USA.
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18
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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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19
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Abstract
Because of their strong similarities to humans across physiologic, developmental, behavioral, immunologic, and genetic levels, nonhuman primates are essential models for a wide spectrum of biomedical research. But unlike other animal models, nonhuman primates possess substantial outbred genetic variation, reducing statistical power and potentially confounding interpretation of results in research studies. Although unknown genetic variation is a hindrance in studies that allocate animals randomly, taking genetic variation into account in study design affords an opportunity to transform the way that nonhuman primates are used in biomedical research. New understandings of how the function of individual genes in rhesus macaques mimics that seen in humans are greatly advancing the rhesus macaques utility as research models, but epistatic interaction, epigenetic regulatory mechanisms, and the intricacies of gene networks limit model development. We are now entering a new era of nonhuman primate research, brought on by the proliferation and rapid expansion of genomic data. Already the cost of a rhesus macaque genome is dwarfed by its purchase and husbandry costs, and complete genomic datasets will inevitably encompass each rhesus macaque used in biomedical research. Advancing this outcome is paramount. It represents an opportunity to transform the way animals are assigned and used in biomedical research and to develop new models of human disease. The genetic and genomic revolution brings with it a paradigm shift for nonhuman primates and new mandates on how nonhuman primates are used in biomedical research.
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20
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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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21
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Abdul-Latiff MAB, Ruslin F, Fui VV, Abu MH, Rovie-Ryan JJ, Abdul-Patah P, Lakim M, Roos C, Yaakop S, Md-Zain BM. Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences. Zookeys 2014; 407:121-40. [PMID: 24899832 PMCID: PMC4042704 DOI: 10.3897/zookeys.407.6982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/22/2014] [Indexed: 12/03/2022] Open
Abstract
Phylogenetic relationships among Malaysia's long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo's population was distinguished from Peninsula's population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia's M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.
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Affiliation(s)
- Muhammad Abu Bakar Abdul-Latiff
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farhani Ruslin
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Vun Vui Fui
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- UCSI University, 1, Jalan Menara Gading, UCSI Heights, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Mohd-Hashim Abu
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | | | - Pazil Abdul-Patah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Wildlife and National Parks, Km 10, Jalan Cheras, 50664, Kuala Lumpur, Malaysia
| | - Maklarin Lakim
- Sabah Parks, Research and Education Division, PO Box 10626, 88806, Kota Kinabalu, Sabah, Malaysia
| | - Christian Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Salmah Yaakop
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Badrul Munir Md-Zain
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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22
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Fawcett GL, Dettmer AM, Kay D, Raveendran M, Higley JD, Ryan ND, Cameron JL, Rogers J. Quantitative Genetics of Response to Novelty and Other Stimuli by Infant Rhesus Macaques ( Macaca mulatta) Across Three Behavioral Assessments. INT J PRIMATOL 2014; 35:325-339. [PMID: 24701001 DOI: 10.1007/s10764-014-9750-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Primate behavior is influenced by both heritable factors and environmental experience during development. Previous studies of rhesus macaques (Macaca mulatta) examined the effects of genetic variation on expressed behavior and related neurobiological traits (heritability and/or genetic association) using a variety of study designs. Most of these prior studies examined genetic effects on the behavior of adults or adolescent rhesus macaques, not in young macaques early in development. To assess environmental and additive genetic variation in behavioral reactivity and response to novelty among infants, we investigated a range of behavioral traits in a large number (N = 428) of pedigreed infants born and housed in large outdoor corrals at the Oregon National Primate Research Center (ONPRC). We recorded the behavior of each subject during a series of brief tests, involving exposure of each infant to a novel environment, to a social threat without the mother present, and to a novel environment with its mother present but sedated. We found significant heritability (h2 ) for willingness to move away from the mother and explore a novel environment (h2 = 0.25 ± 0.13; P = 0.003). The infants also exhibited a range of heritable behavioral reactions to separation stress or to threat when the mother was not present (h2 = 0.23 ± 0.13-0.24 ± 0.15, P < 0.01). We observed no evidence of maternal environmental effects on these traits. Our results extend knowledge of genetic influences on temperament and reactivity in nonhuman primates by demonstrating that several measures of behavioral reactivity among infant rhesus macaques are heritable.
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Affiliation(s)
- G L Fawcett
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - A M Dettmer
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - D Kay
- Department of Clinical and Health Psychology, University of Florida, Gainesville, Florida 32610
| | - M Raveendran
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - J D Higley
- Department of Psychology, Brigham Young University, Provo, Utah 84602
| | - N D Ryan
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - J L Cameron
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon 97006
| | - J Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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23
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Goswami DB, Ogawa LM, Ward JM, Miller GM, Vallender EJ. Large-scale polymorphism discovery in macaque G-protein coupled receptors. BMC Genomics 2013; 14:703. [PMID: 24119066 PMCID: PMC3907043 DOI: 10.1186/1471-2164-14-703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/04/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis). RESULTS Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals. CONCLUSIONS In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease.
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Affiliation(s)
- Dharmendra B Goswami
- New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, Southborough, MA 01772, USA.
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24
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Kanthaswamy S, Ng J, Satkoski Trask J, George DA, Kou AJ, Hoffman LN, Doherty TB, Houghton P, Smith DG. The genetic composition of populations of cynomolgus macaques (Macaca fascicularis) used in biomedical research. J Med Primatol 2013; 42:120-31. [PMID: 23480663 PMCID: PMC3651788 DOI: 10.1111/jmp.12043] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2013] [Indexed: 12/01/2022]
Abstract
BACKGROUND The genetic composition of cynomolgus macaques used in biomedical research is not as well-characterized as that of rhesus macaques. METHODS Populations of cynomolgus macaques from Sumatra, Corregidor, Mauritius, Singapore, Cambodia, and Zamboanga were analyzed using 24 STRs. RESULTS The Sumatran and Cambodian populations exhibited the highest allelic diversity, while the Mauritian population exhibited the lowest. Sumatran cynomolgus macaques were the most genetically similar to all others, consistent with an Indonesian origin of the species. The high diversity among Cambodian animals may result from interbreeding with rhesus macaques. The Philippine and Mauritian samples were the most divergent from other populations, the former due to separation from the Sunda Shelf by deepwater and the latter due to anthropogenic translocation and extreme founder effects. CONCLUSIONS Investigators should verify their research subjects' origin, ancestry, and pedigree to minimize risks to biomedical experimentation from genetic variance stemming from close kinship and mixed ancestry as these can obscure treatment effects.
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Affiliation(s)
- S Kanthaswamy
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA.
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25
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Víquez-Zamora M, Vosman B, van de Geest H, Bovy A, Visser RGF, Finkers R, van Heusden AW. Tomato breeding in the genomics era: insights from a SNP array. BMC Genomics 2013; 14:354. [PMID: 23711327 PMCID: PMC3680325 DOI: 10.1186/1471-2164-14-354] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/20/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. RESULTS From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoes earlier results. CONCLUSIONS Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome.
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Affiliation(s)
- Marcela Víquez-Zamora
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen Campus, PB Wageningen, 6807, The Netherlands
| | - Ben Vosman
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Henri van de Geest
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
- Bioscience, Plant Research International, P.O. Box 619, AP Wageningen, 6700, The Netherlands
| | - Arnaud Bovy
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Richard GF Visser
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Richard Finkers
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
| | - Adriaan W van Heusden
- Wageningen UR Plant Breeding, P.O. Box 16, AJ, Wageningen, 6700, The Netherlands
- Centre for Biosystems Genomics, P.O. Box 98, AB, Wageningen, 6700, The Netherlands
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Wu SJ, Luo J, Li QQ, Wang YQ, Murphy RW, Blair C, Wu SF, Yue BS, Zhang YP. Ecological genetics of Chinese rhesus macaque in response to mountain building: all things are not equal. PLoS One 2013; 8:e55315. [PMID: 23405134 PMCID: PMC3566204 DOI: 10.1371/journal.pone.0055315] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/21/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pliocene uplifting of the Qinghai-Tibetan Plateau (QTP) and Quaternary glaciation may have impacted the Asian biota more than any other events. Little is documented with respect to how the geological and climatological events influenced speciation as well as spatial and genetic structuring, especially in vertebrate endotherms. Macaca mulatta is the most widely distributed non-human primate. It may be the most suitable model to test hypotheses regarding the genetic consequences of orogenesis on an endotherm. METHODOLOGY AND PRINCIPAL FINDINGS Using a large dataset of maternally inherited mitochondrial DNA gene sequences and nuclear microsatellite DNA data, we discovered two maternal super-haplogroups exist, one in western China and the other in eastern China. M. mulatta formed around 2.31 Ma (1.51-3.15, 95%), and divergence of the two major matrilines was estimated at 1.15 Ma (0.78-1.55, 95%). The western super-haplogroup exhibits significant geographic structure. In contrast, the eastern super-haplogroup has far greater haplotypic variability with little structure based on analyses of six variable microsatellite loci using Structure and Geneland. Analysis using Migrate detected greater gene flow from WEST to EAST than vice versa. We did not detect signals of bottlenecking in most populations. CONCLUSIONS Analyses of the nuclear and mitochondrial datasets obtained large differences in genetic patterns for M. mulatta. The difference likely reflects inheritance mechanisms of the maternally inherited mtDNA genome versus nuclear biparentally inherited STRs and male-mediated gene flow. Dramatic environmental changes may be responsible for shaping the matrilineal history of macaques. The timing of events, the formation of M. mulatta, and the divergence of the super-haplogroups, corresponds to both the uplifting of the QTP and Quaternary climatic oscillations. Orogenesis likely drove divergence of western populations in China, and Pleistocene glaciations are likely responsible for genetic structuring in the eastern super-haplogroup via geographic isolation and secondary contact.
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Affiliation(s)
- Shan-Jin Wu
- Laboratory for Conservation and Utilization of Bio-resources, School of Life Science, Yunnan University, Kunming, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Jing Luo
- Laboratory for Conservation and Utilization of Bio-resources, School of Life Science, Yunnan University, Kunming, China
| | - Qing-Qing Li
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yan-Qin Wang
- Laboratory for Conservation and Utilization of Bio-resources, School of Life Science, Yunnan University, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Christopher Blair
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Bi-Song Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
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Kanthaswamy S, Ng J, Ross CT, Trask JS, Smith DG, Buffalo VS, Fass JN, Lin D. Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Genomics 2012; 101:30-7. [PMID: 22982528 DOI: 10.1016/j.ygeno.2012.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 07/27/2012] [Accepted: 09/04/2012] [Indexed: 02/07/2023]
Abstract
We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes. Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes.
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Affiliation(s)
- Sree Kanthaswamy
- Molecular Anthropology Lab., Dept. of Anthropology, UC Davis, CA, USA.
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Higashino A, Sakate R, Kameoka Y, Takahashi I, Hirata M, Tanuma R, Masui T, Yasutomi Y, Osada N. Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome. Genome Biol 2012; 13:R58. [PMID: 22747675 PMCID: PMC3491380 DOI: 10.1186/gb-2012-13-7-r58] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 07/02/2012] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The genetic background of the cynomolgus macaque (Macaca fascicularis) is made complex by the high genetic diversity, population structure, and gene introgression from the closely related rhesus macaque (Macaca mulatta). Herein we report the whole-genome sequence of a Malaysian cynomolgus macaque male with more than 40-fold coverage, which was determined using a resequencing method based on the Indian rhesus macaque genome. RESULTS We identified approximately 9.7 million single nucleotide variants (SNVs) between the Malaysian cynomolgus and the Indian rhesus macaque genomes. Compared with humans, a smaller nonsynonymous/synonymous SNV ratio in the cynomolgus macaque suggests more effective removal of slightly deleterious mutations. Comparison of two cynomolgus (Malaysian and Vietnamese) and two rhesus (Indian and Chinese) macaque genomes, including previously published macaque genomes, suggests that Indochinese cynomolgus macaques have been more affected by gene introgression from rhesus macaques. We further identified 60 nonsynonymous SNVs that completely differentiated the cynomolgus and rhesus macaque genomes, and that could be important candidate variants for determining species-specific responses to drugs and pathogens. The demographic inference using the genome sequence data revealed that Malaysian cynomolgus macaques have experienced at least three population bottlenecks. CONCLUSIONS This list of whole-genome SNVs will be useful for many future applications, such as an array-based genotyping system for macaque individuals. High-quality whole-genome sequencing of the cynomolgus macaque genome may aid studies on finding genetic differences that are responsible for phenotypic diversity in macaques and may help control genetic backgrounds among individuals.
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Yuan Q, Zhou Z, Lindell SG, Higley JD, Ferguson B, Thompson RC, Lopez JF, Suomi SJ, Baghal B, Baker M, Mash DC, Barr CS, Goldman D. The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human. BMC Genet 2012; 13:52. [PMID: 22747632 PMCID: PMC3426462 DOI: 10.1186/1471-2156-13-52] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 05/18/2012] [Indexed: 11/23/2022] Open
Abstract
Background As a model organism in biomedicine, the rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate. Although a draft genome sequence was completed in 2007, there has been no systematic genome-wide comparison of genetic variation of this species to humans. Comparative analysis of functional and nonfunctional diversity in this highly abundant and adaptable non-human primate could inform its use as a model for human biology, and could reveal how variation in population history and size alters patterns and levels of sequence variation in primates. Results We sequenced the mRNA transcriptome and H3K4me3-marked DNA regions in hippocampus from 14 humans and 14 rhesus macaques. Using equivalent methodology and sampling spaces, we identified 462,802 macaque SNPs, most of which were novel and disproportionately located in the functionally important genomic regions we had targeted in the sequencing. At least one SNP was identified in each of 16,797 annotated macaque genes. Accuracy of macaque SNP identification was conservatively estimated to be >90%. Comparative analyses using SNPs equivalently identified in the two species revealed that rhesus macaque has approximately three times higher SNP density and average nucleotide diversity as compared to the human. Based on this level of diversity, the effective population size of the rhesus macaque is approximately 80,000 which contrasts with an effective population size of less than 10,000 for humans. Across five categories of genomic regions, intergenic regions had the highest SNP density and average nucleotide diversity and CDS (coding sequences) the lowest, in both humans and macaques. Although there are more coding SNPs (cSNPs) per individual in macaques than in humans, the ratio of dN/dS is significantly lower in the macaque. Furthermore, the number of damaging nonsynonymous cSNPs (have damaging effects on protein functions from PolyPhen-2 prediction) in the macaque is more closely equivalent to that of the human. Conclusions This large panel of newly identified macaque SNPs enriched for functionally significant regions considerably expands our knowledge of genetic variation in the rhesus macaque. Comparative analysis reveals that this widespread, highly adaptable species is approximately three times as diverse as the human but more closely equivalent in damaging variation.
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Affiliation(s)
- Qiaoping Yuan
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
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Identification of polymorphisms in genes of the immune system in cynomolgus macaques. Mamm Genome 2012; 23:467-77. [DOI: 10.1007/s00335-012-9399-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/26/2012] [Indexed: 11/30/2022]
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Knapp LA, Innocent SHS. Molecules and mating: positive selection and reproductive behaviour in primates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 739:218-36. [PMID: 22399405 DOI: 10.1007/978-1-4614-1704-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sexual reproduction is generally thought to be more costly than asexual reproduction. However, it does have the advantage of accelerating rates of adaptation through processes such as recombination and positive selection. Comparative studies of the human and nonhuman primate genomes have demonstrated that positive selection has played an important role in the evolutionary history of humans and other primates. To date, many dozens of genes, thought to be affected by positive selection, have been identified. In this chapter, we will focus on genes that are associated with mating behaviours and reproductive processes, concentrating on genes that are most likely to enhance reproductive success and that also show evidence of positive selection. The genes encode phenotypic features that potentially influence mate choice decisions or impact the evolution and function of genes involved in the perception and regulation of, and the response to, phenotypic signals. We will also consider genes that influence precopulatory behavioural traits in humans and nonhuman primates, such as social bonding and aggression. The evolution of post-copulatory strategies such as sperm competition and selective abortion may also evolve in the presence of intense competition and these adaptations will also be considered. Although behaviour may not be solely determined by genes, the evidence suggests that the genes discussed in this chapter have some influence on human and nonhuman primate behaviour and that positive selection on these genes results in some degree of population differentiation and diversity.
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Affiliation(s)
- Leslie A Knapp
- Primate Immunogenetics and Molecular Ecology Research Group, Department of Biological Anthropology, University of Cambridge, Cambridge, UK.
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Uehara S, Murayama N, Yamazaki H, Uno Y. CYP2C76 Non-synonymous Variants in Cynomolgus and Rhesus Macaques. Drug Metab Pharmacokinet 2012; 27:344-8. [DOI: 10.2133/dmpk.dmpk-11-nt-118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ise R, Nakanishi Y, Kohara S, Yamashita H, Yoshikawa T, Iwasaki K, Nagata R, Fukuzaki K, Utoh M, Nakamura C, Yamazaki H, Uno Y. Expression profile of hepatic genes in cynomolgus macaques bred in Cambodia, China, and Indonesia: implications for cytochrome P450 genes. Drug Metab Pharmacokinet 2011; 27:307-16. [PMID: 22166892 DOI: 10.2133/dmpk.dmpk-11-rg-133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cynomolgus macaques, frequently used in drug metabolism studies, are bred mainly in the countries of Asia; however, comparative studies of drug metabolism between cynomolgus macaques bred in these countries have not been conducted. In this study, hepatic gene expression profiles of cynomolgus macaques bred in Cambodia (mfCAM), China (mfCHN), and Indonesia (mfIDN) were analyzed. Microarray analysis revealed that expression of most hepatic genes, including drug-metabolizing enzyme genes, was not substantially different between mfCAM, mfCHN, and mfIDN; only 1.1% and 3.0% of all the gene probes detected differential expression (>2.5-fold) in mfCAM compared with mfCHN and mfIDN, respectively. Quantitative polymerase chain reaction showed that the expression levels of 14 cytochromes P450 (P450s) important for drug metabolism did not differ (>2.5-fold) in mfCAM, mfCHN, and mfIDN, validating the microarray data. In contrast, expression of CYP2B6 and CYP3A4 differed (>2.5-fold, p < 0.05) between cynomolgus (mfCAM, mfCHN, or mfIDN) and rhesus macaques, indicating greater differences in expression of P450 genes between the two lineages. Moreover, metabolic activities measured using 14 P450 substrates did not differ substantially (<1.5-fold) between mfCAM and mfCHN. These results suggest that gene expression profiles, including drug-metabolizing enzyme genes such as P450 genes, are similar in mfCAM, mfCHN, and mfIDN.
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Affiliation(s)
- Ryota Ise
- Drug Safety Research Center, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
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Ebeling M, Küng E, See A, Broger C, Steiner G, Berrera M, Heckel T, Iniguez L, Albert T, Schmucki R, Biller H, Singer T, Certa U. Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment. Genome Res 2011; 21:1746-56. [PMID: 21862625 PMCID: PMC3202291 DOI: 10.1101/gr.123117.111] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 07/11/2011] [Indexed: 01/04/2023]
Abstract
The long-tailed macaque, also referred to as cynomolgus monkey (Macaca fascicularis), is one of the most important nonhuman primate animal models in basic and applied biomedical research. To improve the predictive power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy that uses either the rhesus or the human genome to assemble sequence reads. The sixfold sequence coverage of the draft genome sequence enabled discovery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. Homology-based annotation allowed us to identify 17,387 orthologs of human protein-coding genes in the M. fascicularis draft genome, and the predicted transcripts enabled the design of a M. fascicularis-specific gene expression microarray. Using liver samples from 36 individuals of different geographic origin we identified 718 genes with highly variable expression in liver, whereas the majority of the transcriptome shows relatively stable and comparable expression. Knowledge of the M. fascicularis draft genome is an important contribution to both the use of this animal in disease models and the safety assessment of drugs and their metabolites. In particular, this information allows high-resolution genotyping and microarray-based gene-expression profiling for animal stratification, thereby allowing the use of well-characterized animals for safety testing. Finally, the genome sequence presented here is a significant contribution to the global "3R" animal welfare initiative, which has the goal to reduce, refine, and replace animal experiments.
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Affiliation(s)
- Martin Ebeling
- Translational Research Sciences, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Erich Küng
- Global Non-clinical Safety, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Angela See
- Roche NimbleGen, Inc., Madison, Wisconsin 53719, USA
| | - Clemens Broger
- Research Informatics, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Guido Steiner
- Translational Research Sciences, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Marco Berrera
- Translational Research Sciences, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Tobias Heckel
- Global Non-clinical Safety, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | | | - Thomas Albert
- Roche NimbleGen, Inc., Madison, Wisconsin 53719, USA
| | - Roland Schmucki
- Translational Research Sciences, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Hermann Biller
- Research Informatics, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Thomas Singer
- Global Non-clinical Safety, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
| | - Ulrich Certa
- Global Non-clinical Safety, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland
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Variable prevalence and functional diversity of the antiretroviral restriction factor TRIMCyp in Macaca fascicularis. J Virol 2011; 85:9956-63. [PMID: 21795330 DOI: 10.1128/jvi.00097-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The retroviral restriction factor TRIMCyp, derived from the TRIM5 gene, blocks replication at a postentry step. TRIMCyp has so far been found in four species of Asian macaques, Macaca fascicularis, M. mulatta, M. nemestrina, and M. leonina. M. fascicularis is commonly used as a model for AIDS research, but TRIMCyp has not been analyzed in detail in this species. We analyzed the prevalence of TRIMCyp in samples from Indonesia, Indochina, the Philippines, and Mauritius. We found that TRIMCyp is present at a higher frequency in Indonesian than in Indochinese M. fascicularis macaques and is also present in samples from the Philippines. TRIMCyp is absent in Mauritian M. fascicularis macaques. We then analyzed the restriction specificity of TRIMCyp derived from three animals of Indonesian origin. One allele, like the prototypic TRIMCyp alleles described for M. mulatta and M. nemestrina, restricts human immunodeficiency virus type 2 (HIV-2) and feline immunodeficiency virus (FIV) but not HIV-1. The others restrict HIV-1 and FIV but not HIV-2. Mutagenesis studies confirmed that polymorphisms at amino acid residues 369 and 446 in TRIMCyp (or residues 66 and 143 in the cyclophilin A [CypA] domain) confer restriction specificity. Additionally, we identified a polymorphism in the coiled-coil domain that appears to affect TRIMCyp expression or stability. Taken together, these data show that M. fascicularis has the most diverse array of TRIM5 restriction factors described for any primate species to date. These findings are relevant to our understanding of the evolution of retroviral restriction factors and the use of M. fascicularis models in AIDS research.
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Fawcett GL, Raveendran M, Deiros DR, Chen D, Yu F, Harris RA, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs R, Rogers J. Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). BMC Genomics 2011; 12:311. [PMID: 21668978 PMCID: PMC3141668 DOI: 10.1186/1471-2164-12-311] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 06/13/2011] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies. RESULTS We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiD™ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease. CONCLUSIONS Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.
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Affiliation(s)
- Gloria L Fawcett
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
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Uno Y, Iwasaki K, Yamazaki H, Nelson DR. Macaque cytochromes P450: nomenclature, transcript, gene, genomic structure, and function. Drug Metab Rev 2011; 43:346-61. [DOI: 10.3109/03602532.2010.549492] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Uno Y, Uehara S, Yamazaki H. Discovery of Genetic Variants in CYP1D1: Implication for Functional Integrity of CYP1D1 in Cynomolgus Macaques and Rhesus Macaques. Drug Metab Pharmacokinet 2011; 26:627-31. [DOI: 10.2133/dmpk.dmpk-11-nt-026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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UNO Y, MATSUSHITA A, YAMAZAKI H. CYP1B1 is Polymorphic in Cynomolgus and Rhesus Macaques. J Vet Med Sci 2011; 73:1229-31. [DOI: 10.1292/jvms.11-0137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Yasuhiro UNO
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories
| | - Akinori MATSUSHITA
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories
| | - Hiroshi YAMAZAKI
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University
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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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Nakanishi Y, Matsushita A, Matsuno K, Iwasaki K, Utoh M, Nakamura C, Uno Y. Regional distribution of cytochrome p450 mRNA expression in the liver and small intestine of cynomolgus monkeys. Drug Metab Pharmacokinet 2010; 25:290-7. [PMID: 20610888 DOI: 10.2133/dmpk.25.290] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cynomolgus monkey is used to study drug metabolism because of its evolutionary closeness to humans. Despite their importance, regional distribution of cytochrome P450 (CYP) enzymes including CYP3As in the liver and small intestine, the major sites of drug metabolism, has not been fully investigated in cynomolgus monkeys. In this study, we measured mRNA expression levels of 14 CYPs in the CYP1, 2, and 3 subfamilies, including orthologs of human CYP3A4 and CYP3A5, in the liver and small intestine of cynomolgus monkeys. Expression levels of each CYP mRNA in various regions of the liver were quantified and comparisons were made between the right lobe, quadrate lobe, left medial lobe, left lateral lobe, and caudate lobe and with four different sections of the right lobe. In the small intestine, the same mRNAs were measured in the duodenum and six different sections from the proximal jejunum to the distal ileum. Expression levels of the CYP mRNAs were not substantially different between liver samples, but varied between the different sections of the small intestine, including CYP3A4. These results suggest that analysis of distinct sections is required for a better understanding of cynomolgus monkey CYPs in the small intestine.
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Affiliation(s)
- Yasuharu Nakanishi
- Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories Ltd., 16-1 Minami-Akasaka, Kainan, Wakayama, Japan
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Zao CL, Armstrong K, Tomanek L, Cooke A, Berger R, Estep JS, Marx PA, Trask JS, Smith DG, Yee JL, Lerche NW. The complete genome and genetic characteristics of SRV-4 isolated from cynomolgus monkeys (Macaca fascicularis). Virology 2010; 405:390-6. [PMID: 20615522 DOI: 10.1016/j.virol.2010.06.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 04/15/2010] [Accepted: 06/14/2010] [Indexed: 11/28/2022]
Abstract
At least 5 serotypes of exogenous simian retrovirus type D (SRV/D) have been found in nonhuman primates, but only SRV-1, 2 and 3 have been completely sequenced. SRV-4 was recovered once from cynomolgus macaques in California in 1984, but its genome sequences are unknown. Here we report the second identification of SRV-4 and its complete genome from infected cynomolgus macaques with Indochinese and Indonesian/Indochinese mixed ancestry. Phylogenetic analysis demonstrated that SRV-4 was distantly related to SRV-1, 2, 3, 5, 6 and 7. SRV/D-T, a new SRV/D recovered in 2005 from cynomolgus monkeys at Tsukuba Primate Center in Japan, clustered with the SRV-4 isolates from California and Texas and was shown to be another occurrence of SRV-4 infection. The repeated occurrence of SRV-4 in cynomolgus monkeys in different areas of the world and across 25years suggests that this species is the natural host of SRV-4.
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Osada N, Uno Y, Mineta K, Kameoka Y, Takahashi I, Terao K. Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta. Mol Ecol 2010; 19:2884-95. [PMID: 20579289 DOI: 10.1111/j.1365-294x.2010.04687.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Macaca fascicularis and Macaca mulatta are two of the most commonly used laboratory macaques, yet their genetic differences at a genome-wide level remain unclear. We analysed the multilocus DNA sequence data of 54 autosomal loci obtained from M. fascicularis samples from three different geographic origins and M. mulatta samples of Burmese origin. M. fascicularis shows high nucleotide diversity, four to five times higher than humans, and a strong geographic population structure between Indonesian-Malaysian and Philippine macaques. The pattern of divergence and polymorphism between M. fascicularis and M. mulatta shows a footprint of genetic exchange not only within their current hybrid zone but also across a wider range for more than 1 million years. However, genetic admixture may not be a random event in the genome. Whereas randomly selected genic and intergenic regions have the same evolutionary dynamics between the species, some cytochrome oxidase P450 (CYP) genes (major chemical metabolizing genes and potential target genes for local adaptation) have a significantly larger species divergence than other genes. By surveying CYP3A5 gene sequences of more than a hundred macaques, we identified three nonsynonymous single nucleotide polymorphisms that were highly differentiated between the macaques. The mosaic pattern of species divergence in the genomes may be a consequence of genetic differentiation under ecological adaptation and may be a salient feature in the genomes of nascent species under parapatry.
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Affiliation(s)
- Naoki Osada
- Department of Biomedical Resources, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibraki, Osaka 567-0085, Japan.
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Kanthaswamy S, Capitanio JP, Dubay CJ, Ferguson B, Folks T, Ha JC, Hotchkiss CE, Johnson ZP, Katze MG, Kean LS, Kubisch HM, Lank S, Lyons LA, Miller GM, Nylander J, O'Connor DH, Palermo RE, Smith DG, Vallender EJ, Wiseman RW, Rogers J. Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs). J Med Primatol 2010; 38 Suppl 1:17-23. [PMID: 19863674 DOI: 10.1111/j.1600-0684.2009.00371.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The National Primate Research Centers (NPRCs) established Working Groups (WGs) for developing resources and mechanisms to facilitate collaborations among non-human primate (NHP) researchers. Here we report the progress of the Genome Banking and the Genetics and Genomics WGs in developing resources to advance the exchange, analysis and comparison of NHP genetic and genomic data across the NPRCs. The Genome Banking WG has established a National NHP DNA bank comprising 1250 DNA samples from unrelated animals and family trios from the 10 NHP species housed within the NPRC system. The Genetics and Genomics WG is developing SNP arrays that will provide a uniform, highly informative, efficient and low-cost method for rhesus and long-tailed macaque genotyping across the eight NPRCs. This WG is also establishing a Biomedical Informatics Research Network-based portal for shared bioinformatics resources including vital statistics, genotype and population data and information on the National NHP DNA bank.
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Affiliation(s)
- S Kanthaswamy
- Department of Anthropology, University of California-Davis, CA 95616, USA.
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Aarnink A, Estrade L, Apoil PA, Kita YF, Saitou N, Shiina T, Blancher A. Study of cynomolgus monkey (Macaca fascicularis) DRA polymorphism in four populations. Immunogenetics 2010; 62:123-36. [PMID: 20094710 DOI: 10.1007/s00251-009-0421-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Accepted: 12/21/2009] [Indexed: 12/11/2022]
Abstract
To describe the polymorphism of the DRA gene in Macaca fascicularis, we have studied 141 animals either at cDNA level (78 animals from Mauritius, the Philippines, and Vietnam) or genomic level (63 animals from the Philippines, Indonesia, and Vietnam). In total, we characterized 22 cDNA DRA alleles, 13 of which had not been described until now. In the Mauritius population, we confirmed the presence of three DRA alleles. In the Philippine and Vietnam populations, we observed 11 and 14 DRA alleles, respectively. Only two alleles were present in all three populations. All DRA alleles but one differ from the consensus sequence by one to three mutations, most being synonymous; so, only seven DR alpha proteins were deduced from the 22 cDNA alleles. One DRA cDNA allele, Mafa-DRA*02010101, differs from all other alleles by 11 to 14 mutations of which only four are non-synonymous. The two amino acid changes inside the peptide groove of Mafa-DRA*02010101 are highly conservative. The very low proportion of non-synonymous/synonymous mutations is compatible with a purifying selection which is comparable to all previous observations concerning the evolution of the DRA gene in mammals. Homologues of the allele Mafa-DRA*02010101 are also found in two other Asian macaques (Macaca mulatta and Macaca nemestrina). The forces able to maintain this highly divergent allele in three different macaque species remain hypothetical.
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Affiliation(s)
- Alice Aarnink
- Laboratoire d'immunogénétique moléculaire, EA3034, Faculté de Médecine Purpan, Toulouse 3, France
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Modes of Differentiation in Japanese Macaques: Perspectives from Population Genetics. THE JAPANESE MACAQUES 2010. [DOI: 10.1007/978-4-431-53886-8_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Biomedical researchers studying gene function should consider the impact of variation, even if genetics is not the primary objective of an investigation. Information on genetic variation can provide a valuable insight into the functional range and critical regions of a gene, protein or regulatory element. Genetic variants may be diverse in nature, ranging from single nucleotide variants, tandem repeats, small insertions or deletions to large copy number variants. Until recently, information on genetic variation was quite limited, but now a range of large scale surveys of variation have made plentiful data on common variation and a picture is beginning to emerge from the driving forces in human evolution and population diversification. Next-generation sequencing technologies are moving knowledge into a new phase focused on the individual genome and complete disclosure of individual variation, including the rarest of variants. The consequences of these advances in medicine are unresolved, but it is clear that biomedical researchers cannot afford to ignore this information. This review presents a broad overview of the in silico methods that will allow a researcher to quickly review known variation in a gene of interest, providing some pointers for further investigation.
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Li J, Han K, Xing J, Kim HS, Rogers J, Ryder OA, Disotell T, Yue B, Batzer MA. Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 2009; 448:242-9. [PMID: 19497354 PMCID: PMC2783879 DOI: 10.1016/j.gene.2009.05.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
Genus Macaca (Cercopithecidae: Papionini) is one of the most successful primate radiations. Despite previous studies on morphology and mitochondrial DNA analysis, a number of issues regarding the details of macaque evolution remain unsolved. Alu elements are a class of non-autonomous retroposons belonging to short interspersed elements that are specific to the primate lineage. Because retroposon insertions show very little homoplasy, and because the ancestral state (absence of the SINE) is known, Alu elements are useful genetic markers and have been utilized for analyzing primate phylogenentic relationships and human population genetic relationships. Using PCR display methodology, 298 new Alu insertions have been identified from ten species of macaques. Together with 60 loci reported previously, a total of 358 loci are used to infer the phylogenetic relationships of genus Macaca. With regard to earlier unresolved issues on the macaque evolution, the topology of our tree suggests that: 1) genus Macaca contains four monophyletic species groups; 2) within the Asian macaques, the silenus group diverged first, and members of the sinica and fascicularis groups share a common ancestor; 3) Macaca arctoides are classified in the sinica group. Our results provide a robust molecular phylogeny for genus Macaca with stronger statistical support than previous studies. The present study also illustrates that SINE-based approaches are a powerful tool in primate phylogenetic studies and can be used to successfully resolve evolutionary relationships between taxa at scales from the ordinal level to closely related species within one genus.
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Affiliation(s)
- Jing Li
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kyudong Han
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Jinchuan Xing
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Oliver A. Ryder
- San Diego Zoo's Institute for Conservation Research, San Diego, California 92112, USA
| | - Todd Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York 10003, USA
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Uno Y, Matsushita A, Osada N, Uehara S, Kohara S, Nagata R, Fukuzaki K, Utoh M, Murayamay N, Yamazaki H. Genetic Variants of CYP3A4 and CYP3A5 in Cynomolgus and Rhesus Macaques. Drug Metab Dispos 2009; 38:209-14. [DOI: 10.1124/dmd.109.029710] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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50
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Marques-Bonet T, Ryder OA, Eichler EE. Sequencing primate genomes: what have we learned? Annu Rev Genomics Hum Genet 2009; 10:355-86. [PMID: 19630567 DOI: 10.1146/annurev.genom.9.081307.164420] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.
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Affiliation(s)
- Tomas Marques-Bonet
- Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98105, USA.
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