1
|
Siddiqui S, Perez S, Gao Y, Doyle-Meyers L, Foley BT, Li Q, Ling B. Persistent Viral Reservoirs in Lymphoid Tissues in SIV-Infected Rhesus Macaques of Chinese-Origin on Suppressive Antiretroviral Therapy. Viruses 2019; 11:v11020105. [PMID: 30691203 PMCID: PMC6410399 DOI: 10.3390/v11020105] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 12/13/2022] Open
Abstract
Understanding HIV latent reservoirs in tissues is essential for the development of new strategies targeting these sites for eradication. Here, we assessed the size of latent reservoirs and the source of residual viruses in multiple lymphoid tissues of SIV-infected and fully suppressed rhesus macaques of Chinese-origin (cRMs). Eight cRMs were infected with SIVmac251 and treated with tenofovir and emtricitabine daily for 24 weeks initiated 4 weeks post-infection. Four of the eight animals reached sustained full viral suppression with undetectable viremia. The levels of cell-associated SIV DNA varied in peripheral blood mononuclear cells (PBMCs) and multiple lymphoid tissues, but with higher levels in the mesenteric lymph nodes (MesLNs). The levels of cell-associated SIV RNA also varied in different tissues. The higher frequency of viral RNA detection in the MesLNs was also observed by in situ hybridization. Consistently, the infection unit per million cells (IUPM) in the MesLNs was higher than in PBMCs and other tested lymphoid tissues by quantitative viral outgrowth assay (QVOA). Furthermore, env gp120 from tissue SIV RNA was amplified by single genome amplification. Phylogenetic analysis revealed diverse variants from tissues parallel to the viral inoculum in all viral suppressed animals. These results demonstrate that the latency and viral reservoirs in the lymphoid tissues still exist in aviremic macaques under full suppressive therapy. Moreover, the size of viral latent reservoirs differs in various lymphoid tissues with a relatively larger size in the MesLNs.
Collapse
Affiliation(s)
- Summer Siddiqui
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA.
| | - Stefanie Perez
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA.
| | - Yong Gao
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Lara Doyle-Meyers
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA 70433, USA.
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA.
| | - Brian T Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Binhua Ling
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA.
- Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA 70112, USA.
- Department of Microbiology & Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
| |
Collapse
|
2
|
Bissel SJ, Gurnsey K, Jedema HP, Smith NF, Wang G, Bradberry CW, Wiley CA. Aged Chinese-origin rhesus macaques infected with SIV develop marked viremia in absence of clinical disease, inflammation or cognitive impairment. Retrovirology 2018; 15:17. [PMID: 29391069 PMCID: PMC5796498 DOI: 10.1186/s12977-018-0400-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Damage to the central nervous system during HIV infection can lead to variable neurobehavioral dysfunction termed HIV-associated neurocognitive disorders (HAND). There is no clear consensus regarding the neuropathological or cellular basis of HAND. We sought to study the potential contribution of aging to the pathogenesis of HAND. Aged (range = 14.7-24.8 year) rhesus macaques of Chinese origin (RM-Ch) (n = 23) were trained to perform cognitive tasks. Macaques were then divided into four groups to assess the impact of SIVmac251 infection (n = 12) and combined antiretroviral therapy (CART) (5 infected; 5 mock-infected) on the execution of these tasks. RESULTS Aged SIV-infected RM-Ch demonstrated significant plasma viremia and modest CSF viral loads but showed few clinical signs, no elevations of systemic temperature, and no changes in activity levels, platelet counts or weight. Concentrations of biomarkers of acute and chronic inflammation such as soluble CD14, CXCL10, IL-6 and TNF-α are known to be elevated following SIV infection of young adult macaques of several species, but concentrations of these biomarkers did not shift after SIV infection in aged RM-Ch and remained similar to mock-infected macaques. Neither acute nor chronic SIV infection or CART had a significant impact on accuracy, speed or percent completion in a sensorimotor test. CONCLUSIONS Viremia in the absence of a chronic elevated inflammatory response seen in some aged RM-Ch is reminiscent of SIV infection in natural disease resistant hosts. The absence of cognitive impairment during SIV infection in aged RM-Ch might be in part attributed to diminishment of some facets of the immunological response. Additional study encompassing species and age differences is necessary to substantiate this hypothesis.
Collapse
Affiliation(s)
- Stephanie J. Bissel
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
| | - Kate Gurnsey
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
| | - Hank P. Jedema
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
- Present Address: National Institute on Drug Abuse, 251 Bayview Boulevard, Baltimore, MD 21224 USA
| | - Nicholas F. Smith
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
| | - Guoji Wang
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
| | - Charles W. Bradberry
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
- Veterans Affairs Pittsburgh Healthcare System, 4100 Allequippa Street, Pittsburgh, PA 15213 USA
- Present Address: National Institute on Drug Abuse, 251 Bayview Boulevard, Baltimore, MD 21224 USA
| | - Clayton A. Wiley
- University of Pittsburgh, 3550 Terrace Street, S758 Scaife Hall, Pittsburgh, PA 15261 USA
| |
Collapse
|
3
|
Perez S, Johnson AM, Xiang SH, Li J, Foley BT, Doyle-Meyers L, Panganiban A, Kaur A, Veazey RS, Wu Y, Ling B. Persistence of SIV in the brain of SIV-infected Chinese rhesus macaques with or without antiretroviral therapy. J Neurovirol 2017; 24:62-74. [PMID: 29181724 DOI: 10.1007/s13365-017-0594-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/27/2017] [Accepted: 10/23/2017] [Indexed: 02/06/2023]
Abstract
Persistence of HIV-1 reservoirs in the central nervous system (CNS) is an obstacle to cure strategies. However, little is known about residual viral distribution, viral replication levels, and genetic diversity in different brain regions of HIV-infected individuals on combination antiretroviral therapy (cART). Because myeloid cells particularly microglia are likely major reservoirs in the brain, and more microglia exist in white matter than gray matter in a human brain, we hypothesized the major viral reservoirs in the brain are the white matter reflected by higher levels of viral DNA. To address the issue, we used the Chinese rhesus macaque (ChRM) model of SIV infection, and treated 11 SIVmac251-infected animals including long-term nonprogressors with cART for up to 24 weeks. SIV reservoirs were assessed by SIV DNA levels in 16 specific regions of the brain and 4 regions of spinal cord. We found relatively high frequencies of SIV in basal ganglia and brain stem compared to other regions. cART-receiving animals had significantly lower SIV DNA levels in the gray matter than white matter. Moreover, a shortened envelope gp120 with 21 nucleotide deletions and guanine-to-adenine hypermutations were observed. These results demonstrate that SIV enters the CNS in SIV-infected ChRM with a major reservoir in the white matter after cART; the SIV/ChRM/cART is an appropriate model for studying HIV CNS reservoirs and testing new eradication strategies. Further, examining multiple regions of the CNS may be needed when assessing whether an agent is successful in reducing the size of SIV reservoirs in the CNS.
Collapse
Affiliation(s)
- Stefanie Perez
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA.,Hayward Genetics Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Ann-Marie Johnson
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Shi-Hua Xiang
- Nebraska Center for Virology, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, 68583, USA
| | - Jian Li
- Department of Statistics, Tulane University School of Public Health and Tropic Medicine, New Orleans, LA, 70112, USA
| | - Brian T Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Lara Doyle-Meyers
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Antonito Panganiban
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA.,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Amitinder Kaur
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA.,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA.,Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yuntao Wu
- National Center for Biodefense and Infectious Diseases, Department of Molecular and Microbiology, George Mason University, Manassas, VA, 20110, USA
| | - Binhua Ling
- Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA. .,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| |
Collapse
|
4
|
Zhang GH, Han JB, Zhu L, Luo RH, Zhang XH, Chen X, Hu YJ, Fu LC, Zheng YT. Aikeqing decreases viral loads in SHIV89.6-infected Chinese rhesus macaques. Chin Med 2016; 11:31. [PMID: 27375770 PMCID: PMC4930622 DOI: 10.1186/s13020-016-0105-x] [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: 08/25/2014] [Accepted: 06/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aikeqing (AKQ) has been shown in clinical studies to improve quality of life of HIV/AIDS patients, but anti-HIV activity has not been determined. The SHIV-infected macaque is an important animal model for testing antiviral drugs. This study aimed to determine the anti-HIV activity of AKQ in chronically SHIV89.6-infected Chinese rhesus macaques. METHODS Nine Chinese rhesus macaques were inoculated intravenously with SHIV89.6 virus. At 11 weeks post-infection, the animals were arbitrarily divided into three groups: high-dose (AKQ 1.65 g/kg; n = 3), low-dose (AKQ 0.55 g/kg; n = 3), and control (water 1 mL/kg; n = 3). Treatment was administered by the intragastric gavage route once-daily for 8 weeks. Blood (5 mL) was collected biweekly. Viral loads were analyzed by real-time quantitative RT-PCR assays, and T cell counts were monitored by FACS analyses throughout the treatment. RESULTS AKQ induced a persistent decline (P = 0.02) in plasma viral loads during treatment in the high-dose group compared with their baseline levels, and cessation of the therapy caused viral load rebound to the pretreatment levels. No significant difference (P = 0.06) was found in the plasma viral loads during treatment in the low-dose group. The CD4(+) T cell counts and CD4/CD8 ratios remained at stable high levels during the treatment period. CONCLUSION AKQ reduced plasma viral loads in the SHIV89.6-infected Chinese rhesus macaque model.
Collapse
Affiliation(s)
- Gao-Hong Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Jian-Bao Han
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Lin Zhu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China ; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 Yunnan China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Xi-He Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China ; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 Yunnan China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China ; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 Yunnan China
| | - Ying-Jie Hu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Lin-Chun Fu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China ; Kunming Primate Research Center of the Chinese Academy of Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| |
Collapse
|
5
|
Policicchio BB, Pandrea I, Apetrei C. Animal Models for HIV Cure Research. Front Immunol 2016; 7:12. [PMID: 26858716 PMCID: PMC4729870 DOI: 10.3389/fimmu.2016.00012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/12/2016] [Indexed: 12/17/2022] Open
Abstract
The HIV-1/AIDS pandemic continues to spread unabated worldwide, and no vaccine exists within our grasp. Effective antiretroviral therapy (ART) has been developed, but ART cannot clear the virus from the infected patient. A cure for HIV-1 is badly needed to stop both the spread of the virus in human populations and disease progression in infected individuals. A safe and effective cure strategy for human immunodeficiency virus (HIV) infection will require multiple tools, and appropriate animal models are tools that are central to cure research. An ideal animal model should recapitulate the essential aspects of HIV pathogenesis and associated immune responses, while permitting invasive studies, thus allowing a thorough evaluation of strategies aimed at reducing the size of the reservoir (functional cure) or eliminating the reservoir altogether (sterilizing cure). Since there is no perfect animal model for cure research, multiple models have been tailored and tested to address specific quintessential questions of virus persistence and eradication. The development of new non-human primate and mouse models, along with a certain interest in the feline model, has the potential to fuel cure research. In this review, we highlight the major animal models currently utilized for cure research and the contributions of each model to this goal.
Collapse
Affiliation(s)
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh , Pittsburgh, PA , USA
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh , Pittsburgh, PA , USA
| |
Collapse
|
6
|
Vaccine-induced plasmablast responses in rhesus macaques: phenotypic characterization and a source for generating antigen-specific monoclonal antibodies. J Immunol Methods 2014; 416:69-83. [PMID: 25445326 DOI: 10.1016/j.jim.2014.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/09/2014] [Accepted: 11/03/2014] [Indexed: 12/25/2022]
Abstract
Over 100 broadly neutralizing antibodies have been isolated from a minority of HIV infected patients, but the steps leading to the selection of plasma cells producing such antibodies remain incompletely understood, hampering the development of vaccines able to elicit them. Rhesus macaques have become a preferred animal model system used to study SIV/HIV, for the characterization and development of novel therapeutics and vaccines as well as to understand pathogenesis. However, most of our knowledge about the dynamics of antibody responses is limited to the analysis of serum antibodies or monoclonal antibodies generated from memory B cells. In a vaccine setting, relatively little is known about the early cellular responses that elicit long-lived plasma cells and memory B cells and the tools to dissect plasmablast responses are not available in macaques. In the current study, we show that the majority (>80%) of the vaccine-induced plasmablast response are antigen-specific by functional ELISPOT assays. While plasmablasts are easily defined and isolated in humans, those same phenotypic markers have not been useful for identifying macaque plasmablasts. Here we describe an approach that allows for the isolation and single cell sorting of vaccine-induced plasmablasts. Finally, we show that isolated plasmablasts can be used to efficiently recover antigen-specific monoclonal antibodies through single cell expression cloning. This will allow detailed studies of the early plasmablast responses in rhesus macaques, enabling the characterization of both their repertoire breadth as well as the epitope specificity and functional qualities of the antibodies they produce, not only in the context of SIV/HIV vaccines but for many other pathogens/vaccines as well.
Collapse
|
7
|
Ling B, Piatak M, Rogers L, Johnson AM, Russell-Lodrigue K, Hazuda DJ, Lifson JD, Veazey RS. Effects of treatment with suppressive combination antiretroviral drug therapy and the histone deacetylase inhibitor suberoylanilide hydroxamic acid; (SAHA) on SIV-infected Chinese rhesus macaques. PLoS One 2014; 9:e102795. [PMID: 25033210 PMCID: PMC4102539 DOI: 10.1371/journal.pone.0102795] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/23/2014] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Viral reservoirs-persistent residual virus despite combination antiretroviral therapy (cART)-remain an obstacle to cure of HIV-1 infection. Difficulty studying reservoirs in patients underscores the need for animal models that mimics HIV infected humans on cART. We studied SIV-infected Chinese-origin rhesus macaques (Ch-RM) treated with intensive combination antiretroviral therapy (cART) and 3 weeks of treatment with the histone deacetyalse inhibitor, suberoylanilide hydroxamic acid (SAHA). METHODS SIVmac251 infected Ch-RM received reverse transcriptase inhibitors PMPA and FTC and integrase inhibitor L-870812 beginning 7 weeks post infection. Integrase inhibitor L-900564 and boosted protease inhibitor treatment with Darunavir and Ritonavir were added later. cART was continued for 45 weeks, with daily SAHA administered for the last 3 weeks, followed by euthanasia/necropsy. Plasma viral RNA and cell/tissue-associated SIV gag RNA and DNA were quantified by qRT-PCR/qPCR, with flow cytometry monitoring changes in immune cell populations. RESULTS Upon cART initiation, plasma viremia declined, remaining <30 SIV RNA copy Eq/ml during cART, with occasional blips. Decreased viral replication was associated with decreased immune activation and partial restoration of intestinal CD4+ T cells. SAHA was well tolerated but did not result in demonstrable treatment-associated changes in plasma or cell associated viral parameters. CONCLUSIONS The ability to achieve and sustain virological suppression makes cART-suppressed, SIV-infected Ch-RM a potentially useful model to evaluate interventions targeting residual virus. However, despite intensive cART over one year, persistent viral DNA and RNA remained in tissues of all three animals. While well tolerated, three weeks of SAHA treatment did not demonstrably impact viral RNA levels in plasma or tissues; perhaps reflecting dosing, sampling and assay limitations.
Collapse
Affiliation(s)
- Binhua Ling
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Michael Piatak
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Linda Rogers
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Ann-Marie Johnson
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Kasi Russell-Lodrigue
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Daria J. Hazuda
- Merck Research Laboratories, West Point, Pennsylvania, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Ronald S. Veazey
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| |
Collapse
|
8
|
Zheng HY, Zhang MX, Pang W, Zheng YT. Aged Chinese rhesus macaques suffer severe phenotypic T- and B-cell aging accompanied with sex differences. Exp Gerontol 2014; 55:113-9. [DOI: 10.1016/j.exger.2014.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/05/2014] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
|
9
|
Dudley DM, Karl JA, Creager HM, Bohn PS, Wiseman RW, O'Connor DH. Full-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one. Immunogenetics 2014; 66:15-24. [PMID: 24241691 PMCID: PMC3910708 DOI: 10.1007/s00251-013-0744-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
Deep sequencing has revolutionized major histocompatibility complex (MHC) class I analysis of nonhuman primates by enabling high-throughput, economical, and comprehensive genotyping. Full-length MHC class I cDNA sequences, which are required to generate reagents such as MHC-peptide tetramers, cannot be directly obtained by short read deep sequencing. We combined data from two next-generation sequencing platforms to discover novel full-length MHC class I mRNA/cDNA transcripts in Chinese rhesus macaques. We first genotyped macaques by Roche/454 pyrosequencing using a 530-bp amplicon spanning the densely polymorphic exons 2 through 4 of the MHC class I loci that encode the peptide-binding region. We then mapped short paired-end 250 bp Illumina sequence reads spanning the full-length transcript to each 530-bp amplicon at high stringency and used paired-end information to reconstruct full-length allele sequences. We characterized 65 full-length sequences from six Chinese rhesus macaques. Overall, approximately 70 % of the alleles distinguished in these six animals contained new sequence information, including 29 novel transcripts. The flexibility of this approach should make full-length MHC class I allele genotyping accessible for any nonhuman primate population of interest. We are currently optimizing this method for full-length characterization of other highly polymorphic, duplicated loci such as the MHC class II DRB and killer immunoglobulin-like receptors. We anticipate that this method will facilitate rapid expansion and near completion of sequence libraries of polymorphic loci, such as MHC class I, within a few years.
Collapse
Affiliation(s)
- Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - Hannah M. Creager
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - Patrick S. Bohn
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| |
Collapse
|
10
|
Karl JA, Bohn PS, Wiseman RW, Nimityongskul FA, Lank SM, Starrett GJ, O’Connor DH. Major histocompatibility complex class I haplotype diversity in Chinese rhesus macaques. G3 (BETHESDA, MD.) 2013; 3:1195-201. [PMID: 23696100 PMCID: PMC3704247 DOI: 10.1534/g3.113.006254] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/14/2013] [Indexed: 12/28/2022]
Abstract
The use of Chinese-origin rhesus macaques (Macaca mulatta) for infectious disease immunity research is increasing despite the relative lack of major histocompatibility complex (MHC) class I immunogenetics information available for this population. We determined transcript-based MHC class I haplotypes for 385 Chinese rhesus macaques from five different experimental cohorts, providing a concise representation of the full complement of MHC class I major alleles expressed by each animal. In total, 123 Mamu-A and Mamu-B haplotypes were defined in the full Chinese rhesus macaque cohort. We then performed an analysis of haplotype frequencies across the experimental cohorts of Chinese rhesus macaques, as well as a comparison against a group of 96 Indian rhesus macaques. Notably, 35 of the 51 Mamu-A and Mamu-B haplotypes observed in Indian rhesus macaques were also detected in the Chinese population, with 85% of the 385 Chinese-origin rhesus macaques expressing at least one of these class I haplotypes. This unexpected conservation of Indian rhesus macaque MHC class I haplotypes in the Chinese rhesus macaque population suggests that immunologic insights originally gleaned from studies using Indian rhesus macaques may be more applicable to Chinese rhesus macaques than previously appreciated and may provide an opportunity for studies of CD8(+) T-cell responses between populations. It may also be possible to extend these studies across multiple species of macaques, as we found evidence of shared ancestral haplotypes between Chinese rhesus and Mauritian cynomolgus macaques.
Collapse
Affiliation(s)
- Julie A. Karl
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Patrick S. Bohn
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | | | - Simon M. Lank
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - Gabriel J. Starrett
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
| | - David H. O’Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705
| |
Collapse
|