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Phillips KA, Bales KL, Capitanio JP, Conley A, Czoty PW, ‘t Hart BA, Hopkins WD, Hu SL, Miller LA, Nader MA, Nathanielsz PW, Rogers J, Shively CA, Voytko ML. Why primate models matter. Am J Primatol 2014; 76:801-27. [PMID: 24723482 PMCID: PMC4145602 DOI: 10.1002/ajp.22281] [Citation(s) in RCA: 391] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/01/2014] [Accepted: 03/02/2014] [Indexed: 12/13/2022]
Abstract
Research involving nonhuman primates (NHPs) has played a vital role in many of the medical and scientific advances of the past century. NHPs are used because of their similarity to humans in physiology, neuroanatomy, reproduction, development, cognition, and social complexity-yet it is these very similarities that make the use of NHPs in biomedical research a considered decision. As primate researchers, we feel an obligation and responsibility to present the facts concerning why primates are used in various areas of biomedical research. Recent decisions in the United States, including the phasing out of chimpanzees in research by the National Institutes of Health and the pending closure of the New England Primate Research Center, illustrate to us the critical importance of conveying why continued research with primates is needed. Here, we review key areas in biomedicine where primate models have been, and continue to be, essential for advancing fundamental knowledge in biomedical and biological research.
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Affiliation(s)
- Kimberley A. Phillips
- Department of Psychology, Trinity University, San Antonio TX 78212
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio TX
| | - Karen L. Bales
- Department of Psychology, University of California, Davis CA 95616
- California National Primate Research Center, Davis CA 95616
| | - John P. Capitanio
- Department of Psychology, University of California, Davis CA 95616
- California National Primate Research Center, Davis CA 95616
| | - Alan Conley
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis CA 95616
| | - Paul W. Czoty
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem NC 27157
| | - Bert A. ‘t Hart
- Department of Immunobiology, Biomedical Primate Research Center, Rijswick, The Netherlands
| | - William D. Hopkins
- Neuroscience Institute and Language Research Center, Georgia State University, Atlanta GA 30302
- Division of Cognitive and Developmental Neuroscience, Yerkes National Primate Research Center, Atlanta GA 30030
| | - Shiu-Lok Hu
- Department of Pharmaceutics and Washington National Primate Research Center, University of Washington, Seattle WA
| | - Lisa A. Miller
- California National Primate Research Center, Davis CA 95616
- Department of Anatomy, Physiology and Cell Biology, University of California, Davis CA 95616
| | - Michael A. Nader
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Winston-Salem NC 27157
| | - Peter W. Nathanielsz
- Center for Pregnancy and Newborn Research, University of Texas Health Science Center, San Antonio TX 78229
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston TX
- Wisconsin National Primate Research Center, Madison, WI
| | - Carol A. Shively
- Department of Pathology, Section on Comparative Medicine, Wake Forest University School of Medicine, Winston-Salem NC 27157
| | - Mary Lou Voytko
- Department of Neurobiology and Anatomy, Wake Forest University School of Medicine, Winston-Salem NC 27157
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Prentice HA, Pajewski NM, He D, Zhang K, Brown EE, Kilembe W, Allen S, Hunter E, Kaslow RA, Tang J. Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort. Genes Immun 2014; 15:275-81. [PMID: 24784026 PMCID: PMC4111776 DOI: 10.1038/gene.2014.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 03/28/2014] [Accepted: 03/28/2014] [Indexed: 12/31/2022]
Abstract
Multiple MHC loci encoding human leukocyte antigens (HLA) have allelic variants unequivocally associated with differential immune control of HIV-1 infection. Fine mapping based on single nucleotide polymorphisms (SNPs) in the extended MHC (xMHC) region is expected to reveal causal or novel factors and to justify a search for functional mechanisms. We have tested the utility of a custom fine-mapping platform (the ImmunoChip) for 172 HIV-1 seroconverters (SCs) and 449 seroprevalent individuals (SPs) from Lusaka, Zambia, with a focus on more than 6,400 informative xMHC SNPs. When conditioned on HLA and non-genetic factors previously associated with HIV-1 viral load (VL) in the study cohort, penalized approaches (HyperLasso models) identified an intergenic SNP (rs3094626 between RPP21 and HLA-E) and an intronic SNP (rs3134931 in NOTCH4) as novel correlates of early set-point VL in SCs. The minor allele of rs2857114 (downstream from HLA-DOB) was an unfavorable factor in SPs. Joint models based on demographic features, HLA alleles and the newly identified SNP variants could explain 29% and 15% of VL variance in SCs and SPs, respectively. These findings and bioinformatics strongly suggest that both classic and non-classic MHC genes deserve further investigation, especially in Africans with relatively short haplotype blocks.
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Affiliation(s)
- H A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - N M Pajewski
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - D He
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - K Zhang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E E Brown
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Kilembe
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
| | - S Allen
- 1] Zambia-Emory HIV-1 Research Project, Lusaka, Zambia [2] Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - E Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - R A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Tang
- 1] Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA [2] Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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Xu WW, Han MJ, Chen D, Chen L, Guo Y, Willden A, Liu DQ, Zhang HT. Genome-wide search for the genes accountable for the induced resistance to HIV-1 infection in activated CD4+ T cells: apparent transcriptional signatures, co-expression networks and possible cellular processes. BMC Med Genomics 2013; 6:15. [PMID: 23635305 PMCID: PMC3655860 DOI: 10.1186/1755-8794-6-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/23/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Upon co-stimulation with CD3/CD28 antibodies, activated CD4 + T cells were found to lose their susceptibility to HIV-1 infection, exhibiting an induced resistant phenotype. This rather unexpected phenomenon has been repeatedly confirmed but the underlying cell and molecular mechanisms are still unknown. METHODS We first replicated the reported system using the specified Dynal beads with PHA/IL-2-stimulated and un-stimulated cells as controls. Genome-wide expression and analysis were then performed by using Agilent whole genome microarrays and established bioinformatics tools. RESULTS We showed that following CD3/CD28 co-stimulation, a homogeneous population emerged with uniform expression of activation markers CD25 and CD69 as well as a memory marker CD45RO at high levels. These cells differentially expressed 7,824 genes when compared with the controls on microarrays. Series-Cluster analysis identified 6 distinct expression profiles containing 1,345 genes as the representative signatures in the permissive and resistant cells. Of them, 245 (101 potentially permissive and 144 potentially resistant) were significant in gene ontology categories related to immune response, cell adhesion and metabolism. Co-expression networks analysis identified 137 "key regulatory" genes (84 potentially permissive and 53 potentially resistant), holding hub positions in the gene interactions. By mapping these genes on KEGG pathways, the predominance of actin cytoskeleton functions, proteasomes, and cell cycle arrest in induced resistance emerged. We also revealed an entire set of previously unreported novel genes for further mining and functional validation. CONCLUSIONS This initial microarray study will stimulate renewed interest in exploring this system and open new avenues for research into HIV-1 susceptibility and its reversal in target cells, serving as a foundation for the development of novel therapeutic and clinical treatments.
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Affiliation(s)
- Wen-Wen Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Miao-Jun Han
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Dai Chen
- Novel Bioinformatics Co., Ltd, Shanghai, China
| | - Ling Chen
- Yunnan centers for disease control and prevention, Kunming, China
| | - Yan Guo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
| | - Andrew Willden
- Editorial Department, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Di-Qiu Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
| | - Hua-Tang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China
- Chongqing Center for Biomedical Research and Equipment Development, Chongqing Academy of Science and Technology, Chongqing, China
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Abstract
The dynamics of HIV-1 viremia is a complex and evolving landscape with clinical and epidemiological (public health) implications. Most studies have relied on the use of set-point viral load (VL) as a readily available proxy of viral dynamics to assess host and viral correlates. This review highlights recent findings from population-based studies of set-point VL, focusing primarily on robust data related to host genetics. A comprehensive understanding of viral dynamics will clearly need to consider both host and viral characteristics, with close attention to (i) the timing of VL measurements, (ii) the biology of viral evolution, (iii) compartments of active viral replication, (iv) the transmission source partner as the immediate past microenvironment, and (v) proper application of statistical models.
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Affiliation(s)
- Heather A. Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama;
- Author to whom correspondence should be addressed; ; Tel.: +1-720-352-3432
| | - Jianming Tang
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama;
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama;
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Louvain de Souza T, de Souza Campos Fernandes RC, Medina-Acosta E. HIV-1 control in battlegrounds: important host genetic variations for HIV-1 mother-to-child transmission and progression to clinical pediatric AIDS. Future Virol 2012. [DOI: 10.2217/fvl.12.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 mother-to-child transmission (MTCT) is the passing of maternal HIV-1 to the offspring during pregnancy, labor and delivery, and/or breastfeeding. HIV-1 MTCT and the evolution to pediatric AIDS are multifactorial, dynamic and variable phenotypic conditions. Both genetic and nongenetic variables can influence susceptibility to HIV-1 MTCT or the rate of progression to clinical pediatric AIDS. In this review, we summarize the current state of knowledge about the roles of genetic variations seen in host immune response genes, and those that have been independently associated, mostly through population genetics of candidate genes, with interindividual susceptibility to HIV-1 MTCT, and progression to pediatric AIDS. We examine common and rare host genetic variations at coding and noncoding polymorphisms, whether functional or not, in agonists and antagonists of the immune response, which have been implicated in HIV-1 control in battlegrounds of cell entry, replication and evolution to AIDS. Further, we point to over 380 single-nucleotide polymorphisms, mostly within the HLA super region, recently identified in unbiased genome-wide association studies of HIV replication and evolution in adults, still unexplored in the context of HIV-1 MTCT, and which are likely to also influence susceptibility to pediatric HIV-1/AIDS.
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Affiliation(s)
- Thais Louvain de Souza
- Molecular Identification & Diagnosis Unit, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - Regina Célia de Souza Campos Fernandes
- Municipal Program for the Surveillance of Sexually Transmitted Diseases & Acquired Immunodeficiency Syndrome of Campos dos Goytacazes, Brazil
- Faculty of Medicine of Campos, Campos dos Goytacazes, Brazil
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