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Arman MS, Hasan MZ. A computational exploration of global and temporal dynamics of selection pressure on HIV-1 Vif polymorphism. Virus Res 2024; 341:199323. [PMID: 38237808 PMCID: PMC10831783 DOI: 10.1016/j.virusres.2024.199323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Virion infectivity factor (Vif), an accessory protein of HIV-1 (human immunodeficiency virus type 1), antagonizes host APOBEC3 protein (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3) or A3 via proteasomal degradation, facilitating viral replication. HLA (Human leukocyte antigens) alleles, host restriction factors, and error-prone reverse transcription contribute to the global polymorphic dynamics of HIV, impacting effective vaccine design. Our computational analysis of over 50,000 HIV-1 M vif sequences from the Los Alamos National Laboratory (LANL) database (1998-2021) revealed positive selection pressure on the vif gene (nonsynonymous to synonymous ratio, dn/ds=1.58) and an average entropy score of 0.372 in protein level. Interestingly, over the years (1998-2021), a decreasing trend of dn/ds (1.68 to 1.47) and an increasing trend of entropy (0.309 to 0.399) was observed. The predicted mutational frequency against Vif consensus sequence decreased over time (slope = -0.00024, p < 0.0001). Sequence conservation was observed in Vif functional motifs F1, F2, F3, G, BC box, and CBF β binding region, while variability was observed mainly in N- and C- terminal and Zinc finger region, which were dominantly under immune pressure by host HLA-I-restricted CD8+ T cell. Computational analysis of ∆∆Gstability through protein stability prediction tools suggested that missense mutation may affect Vif stability, especially in the Vif-A3 binding interface. Notably, mutations R17K and Y44F in F1 and G box were predicted to destabilize the Vif-A3 binding interface by altering bond formations with adjacent amino acids. Therefore, our analysis demonstrates Vif adaptation with host physiology by maintaining sequence conservation, especially in A3 interacting functional motifs, highlighting important therapeutic candidate regions of Vif against HIV-1 infections.
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Affiliation(s)
- Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Zafrul Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
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2
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Su Y, Qi M, Zhong M, Yu N, Chen C, Ye Z, Cheng C, Hu Z, Zhang H, Wei H. Prevalence of HIV Transmitted Drug Resistance in Nanjing from 2018 to 2021. Infect Drug Resist 2023; 16:735-745. [PMID: 36756611 PMCID: PMC9901445 DOI: 10.2147/idr.s391296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/16/2022] [Indexed: 02/05/2023] Open
Abstract
Background Transmitted drug resistance (TDR) is a major challenge in the clinical management of acquired immunodeficiency syndrome (AIDS). Therefore, this study aimed to investigate the epidemic characteristics of and risk factors for human immunodeficiency virus (HIV)-1 TDR in Nanjing from 2018 to 2021 to provide support for clinical management. Methods The HIV-1 Pol gene was amplified by nested reverse transcription polymerase chain reaction from venous blood of 1190 HIV-infected patients who did not receive antiviral therapy, and the amplified product was sequenced using an in-house sequencing method. The sequencing result was compared with the HIV drug resistance database from Stanford University to elucidate the rates of antiviral drug resistance and distribution of drug-resistant mutation sites. Factors associated with TDR were evaluated using a logistic regression model. Results Detection of drug resistance at the gene level was successful in 1138 of 1190 HIV-1-infected patients (95.6%), and the overall 4-year drug resistance rate was 8.2% (93/1138). The drug resistance rate was higher for non-nucleoside reverse transcriptase inhibitors (NNRTIs; 6.7%) than for nucleoside reverse transcriptase inhibitors (NRTIs; 2.5%) or protease inhibitors (PIs; 0.1%) (χ 2 = 83.907, P<0.0001). The most common NNRTI-related mutation was V179D/E followed by K103N. M184V was the dominant NRTI-associated mutation, and M46L/I was the most prevalent PI-associated mutation. A CD4+ T cell count of <50 cells/μL was significantly associated with an increased risk of TDR (OR=3.62, 95% CI: 1.38-9.51, P=0.009). Conclusion The prevalence of TDR in the city of Nanjing from 2018 to 2021 was at a moderate epidemic risk according to World Health Organization standards. Continuous monitoring of TDR can inform clinical diagnosis and treatment. Patients with advanced disease and a low CD4+ T lymphocyte count are more likely to have TDR in Nanjing.
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Affiliation(s)
- Yifan Su
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Mingxue Qi
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Mingli Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Nawei Yu
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Chen Chen
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Zi Ye
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Cong Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Hongying Zhang
- Nanjing Center for Disease Control and Prevention Affiliated with Nanjing Medical University, Nanjing, People’s Republic of China,Hongying Zhang, Email
| | - Hongxia Wei
- Department of Infectious Disease, The Second Hospital of Nanjing Affiliated to Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China,Correspondence: Hongxia Wei, Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China, Email
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3
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Habermann D, Kharimzadeh H, Walker A, Li Y, Yang R, Kaiser R, Brumme ZL, Timm J, Roggendorf M, Hoffmann D. HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations. Bioinformatics 2022; 38:2428-2436. [PMID: 35238330 DOI: 10.1093/bioinformatics/btac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/21/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION A key process in anti-viral adaptive immunity is that the Human Leukocyte Antigen system (HLA) presents epitopes as Major Histocompatibility Complex I (MHC I) protein-peptide complexes on cell surfaces and in this way alerts CD8+ cytotoxic T-Lymphocytes (CTLs). This pathway exerts strong selection pressure on viruses, favoring viral mutants that escape recognition by the HLA/CTL system. Naturally, such immune escape mutations often emerge in highly variable viruses, e.g. HIV or HBV, as HLA-associated mutations (HAMs), specific to the hosts MHC I proteins. The reliable identification of HAMs is not only important for understanding viral genomes and their evolution, but it also impacts the development of broadly effective anti-viral treatments and vaccines against variable viruses. By their very nature, HAMs are amenable to detection by statistical methods in paired sequence/HLA data. However, HLA alleles are very polymorphic in the human host population which makes the available data relatively sparse and noisy. Under these circumstances, one way to optimize HAM detection is to integrate all relevant information in a coherent model. Bayesian inference offers a principled approach to achieve this. RESULTS We present a new Bayesian regression model for the detection of HAMs that integrates a sparsity-inducing prior, epitope predictions, and phylogenetic bias assessment, and that yields easily interpretable quantitative information on HAM candidates. The model predicts experimentally confirmed HAMs as having high posterior probabilities, and it performs well in comparison to state-of-the-art models for several data sets from individuals infected with HBV, HDV, and HIV. AVAILABILITY The source code of this software is available at https://github.com/HAMdetector/Escape.jl under a permissive MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Habermann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, 45117, Germany
| | - Hadi Kharimzadeh
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany
| | - Andreas Walker
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, 40225, Germany
| | - Yang Li
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology,Chinese Academy of Science, Wuhan, P. R. China
| | - Rongge Yang
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology,Chinese Academy of Science, Wuhan, P. R. China
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, 50935, Germany
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jörg Timm
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, 40225, Germany
| | - Michael Roggendorf
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, 45117, Germany.,Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.,Center for Computational Sciences and Simulation, University of Duisburg-Essen, Essen, Germany
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4
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Kamori D, Hasan Z, Carlson J, Kawana-Tachikawa A, Gatanaga H, Oka S, Ueno T. Impact of Human Leukocyte Antigen-Associated Polymorphisms on Variability of HIV-1 Accessory and Regulatory Proteins. AIDS Res Hum Retroviruses 2021; 37:962-966. [PMID: 33757299 DOI: 10.1089/aid.2021.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 escapes by acquiring mutations that differentially influence the course of infection. Unlike HIV-1 structural and enzymatic proteins, it remains elusive what extent the host immune-mediated selection pressure influences the variability of the accessory (Vif, Vpu, Vpr, and Nef) and regulatory (Tat and Rev) proteins. To address this, we analyzed the viral sequences encoding accessory and regulatory proteins from 446 human leukocyte antigen (HLA)-typed, chronically HIV-1 subtype B-infected, and treatment-naive individuals in Japan. We observed that Vpu and Vpr were the most and least polymorphic proteins with the average Shannon entropy scores of 0.63 and 0.38, respectively. Phylogenetically corrected methods identified a total of 161 HLA-associated polymorphisms; whereby Nef and Vpu had the highest (26.6%) and lowest (1.2%) proportion of amino acid sites associated with HLA-class I alleles, respectively. These results add further insight on the role of HLA-mediated selection pressure on HIV-1 sequence polymorphisms of HIV-1 accessory and regulatory proteins.
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Affiliation(s)
- Doreen Kamori
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Zafrul Hasan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Jonathan Carlson
- Department of Immunomics, Microsoft Research, Los Angeles, California, USA
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Gatanaga
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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5
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Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021; 13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
Abstract
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic.
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Affiliation(s)
| | - Dominique Fournelle
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jana Schockaert
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | | | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Fatima Mostefai
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - Frederic Saab
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | | | - Martin A Smith
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Sofie Pattijn
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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6
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CONNOLLY S, CARLSON JM, SCHAEFER M, BERE A, KILEMBE W, ALLEN S, HUNTER E. HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs. AIDS 2021; 35:1157-1165. [PMID: 33710015 PMCID: PMC8546905 DOI: 10.1097/qad.0000000000002868] [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] [Indexed: 11/27/2022]
Abstract
OBJECTIVE S We investigated the relationship between human leukocyte antigen (HLA)-associated preadaptation for the entire subtype C HIV-1 proteome of the transmitted founder virus and subsequent HIV-1 disease progression in a cohort of heterosexual linked transmission pairs in Zambia. DESIGN An adaptation model was used to calculate an adaptation score for each virus-HLA combination in order to quantify the degree of preadaptation of the transmitted virus to the linked recipient's HLA alleles. These scores were then assessed for their relationship to viral load and longitudinal CD4+ decline in the recipient. METHODS Viral RNA was extracted from the plasma of the donor partner and the linked recipient near the time of transmission, as well as longitudinally from the linked recipient. Viral adaptation scores were calculated for each individual and each protein in the subtype C HIV-1 proteome. RESULTS The majority of HLA-associated sites were located in Gag, Pol and Nef; however, proportional to protein length, the accessory and regulatory proteins contained a relatively high proportion of HLA-associated sites. Over the course of infection, HLA-mediated immune adaptation increased for all proteins except Vpu and gp120. Preadaptation was positively associated with higher early set point viral load and faster CD4+ decline. When examined by protein, preadaptation in Pol and Vif were statistically significantly associated with these markers of disease progression. CONCLUSION Adaptation in Pol had the greatest impact on viral control. Despite containing a large proportion of HLA-associated sites, Vif was the only regulatory or accessory protein for which preadaptation significantly correlated with disease progression.
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Affiliation(s)
- Sarah CONNOLLY
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
| | | | - Malinda SCHAEFER
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
| | - Alfred BERE
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
| | | | - Susan ALLEN
- Zambia–Emory HIV Research Project, Lusaka, Zambia
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
| | - Eric HUNTER
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
- Zambia–Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
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7
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Akahoshi T, Gatanaga H, Kuse N, Chikata T, Koyanagi M, Ishizuka N, Brumme CJ, Murakoshi H, Brumme ZL, Oka S, Takiguchi M. T-cell responses to sequentially emerging viral escape mutants shape long-term HIV-1 population dynamics. PLoS Pathog 2020; 16:e1009177. [PMID: 33370400 PMCID: PMC7833229 DOI: 10.1371/journal.ppat.1009177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/25/2021] [Accepted: 11/18/2020] [Indexed: 11/18/2022] Open
Abstract
HIV-1 strains harboring immune escape mutations can persist in circulation, but the impact of selection by multiple HLA alleles on population HIV-1 dynamics remains unclear. In Japan, HIV-1 Reverse Transcriptase codon 135 (RT135) is under strong immune pressure by HLA-B*51:01-restricted and HLA-B*52:01-restricted T cells that target a key epitope in this region (TI8; spanning RT codons 128-135). Major population-level shifts have occurred at HIV-1 RT135 during the Japanese epidemic, which first affected hemophiliacs (via imported contaminated blood products) and subsequently non-hemophiliacs (via domestic transmission). Specifically, threonine accumulated at RT135 (RT135T) in hemophiliac and non-hemophiliac HLA-B*51:01+ individuals diagnosed before 1997, but since then RT135T has markedly declined while RT135L has increased among non-hemophiliac individuals. We demonstrated that RT135V selection by HLA-B*52:01-restricted TI8-specific T-cells led to the creation of a new HLA-C*12:02-restricted epitope TN9-8V. We further showed that TN9-8V-specific HLA-C*12:02-restricted T cells selected RT135L while TN9-8T-specific HLA-C*12:02-restricted T cells suppressed replication of the RT135T variant. Thus, population-level accumulation of the RT135L mutation over time in Japan can be explained by initial targeting of the TI8 epitope by HLA-B*52:01-restricted T-cells, followed by targeting of the resulting escape mutant by HLA-C*12:02-restricted T-cells. We further demonstrate that this phenomenon is particular to Japan, where the HLA-B*52:01-C*12:02 haplotype is common: RT135L did not accumulate over a 15-year longitudinal analysis of HIV sequences in British Columbia, Canada, where this haplotype is rare. Together, our observations reveal that T-cell responses to sequentially emerging viral escape mutants can shape long-term HIV-1 population dynamics in a host population-specific manner.
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Affiliation(s)
| | - Hiroyuki Gatanaga
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Shinichi Oka
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- Division of International Collaboration Research, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Tokyo, Japan
- * E-mail:
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8
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Li Z, Khanna M, Grimley SL, Ellenberg P, Gonelli CA, Lee WS, Amarasena TH, Kelleher AD, Purcell DFJ, Kent SJ, Ranasinghe C. Mucosal IL-4R antagonist HIV vaccination with SOSIP-gp140 booster can induce high-quality cytotoxic CD4 +/CD8 + T cells and humoral responses in macaques. Sci Rep 2020; 10:22077. [PMID: 33328567 PMCID: PMC7744512 DOI: 10.1038/s41598-020-79172-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/02/2020] [Indexed: 11/09/2022] Open
Abstract
Inducing humoral, cellular and mucosal immunity is likely to improve the effectiveness of HIV-1 vaccine strategies. Here, we tested a vaccine regimen in pigtail macaques using an intranasal (i.n.) recombinant Fowl Pox Virus (FPV)-gag pol env-IL-4R antagonist prime, intramuscular (i.m.) recombinant Modified Vaccinia Ankara Virus (MVA)-gag pol-IL-4R antagonist boost followed by an i.m SOSIP-gp140 boost. The viral vector-expressed IL-4R antagonist transiently inhibited IL-4/IL-13 signalling at the vaccination site. The SOSIP booster not only induced gp140-specific IgG, ADCC (antibody-dependent cellular cytotoxicity) and some neutralisation activity, but also bolstered the HIV-specific cellular and humoral responses. Specifically, superior sustained systemic and mucosal HIV Gag-specific poly-functional/cytotoxic CD4+ and CD8+ T cells were detected with the IL-4R antagonist adjuvanted strategy compared to the unadjuvanted control. In the systemic compartment elevated Granzyme K expression was linked to CD4+ T cells, whilst Granzyme B/TIA-1 to CD8+ T cells. In contrast, the cytotoxic marker expression by mucosal CD4+ and CD8+ T cells differed according to the mucosal compartment. This vector-based mucosal IL-4R antagonist/SOSIP booster strategy, which promotes cytotoxic mucosal CD4+ T cells at the first line of defence, and cytotoxic CD4+ and CD8+ T cells plus functional antibodies in the blood, may prove valuable in combating mucosal infection with HIV-1 and warrants further investigation.
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Affiliation(s)
- Z Li
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - M Khanna
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - S L Grimley
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - P Ellenberg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - C A Gonelli
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - T H Amarasena
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - A D Kelleher
- Immunovirology and Pathogenesis Program, Kirby Institute, University of New South Wales, Sydney, NSW, 2052, Australia
| | - D F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - S J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - C Ranasinghe
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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9
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Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals. Sci Rep 2020; 10:19416. [PMID: 33173092 PMCID: PMC7656250 DOI: 10.1038/s41598-020-76375-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 01/23/2023] Open
Abstract
HIV-1 Nef plays an essential role in enhancing virion infectivity by antagonizing the host restriction molecule SERINC5. Because Nef is highly polymorphic due to the selective forces of host cellular immunity, we hypothesized that certain immune-escape polymorphisms may impair Nef’s ability to antagonize SERINC5 and thereby influence viral fitness in vivo. To test this hypothesis, we identified 58 Nef polymorphisms that were overrepresented in HIV-infected patients in Japan sharing the same HLA genotypes. The number of immune-associated Nef polymorphisms was inversely correlated with the plasma viral load. By breaking down the specific HLA allele-associated mutations, we found that a number of the HLA-B*51:01-associated Y120F and Q125H mutations were most significantly associated with a reduced plasma viral load. A series of biochemical experiments showed that the double mutations Y120F/Q125H, but not either single mutation, impaired Nef’s ability to antagonize SERINC5 and was associated with decreasing virion infectivity and viral replication in primary lymphocytes. In contrast, other Nef functions such as CD4, CCR5, CXCR4 and HLA class I downregulation and CD74 upregulation remained unchanged. Taken together, our results suggest that the differential ability of Nef to counteract SERINC5 by naturally occurring immune-associated mutations was associated with the plasma viral load in vivo.
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10
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Jin SW, Alsahafi N, Kuang XT, Swann SA, Toyoda M, Göttlinger H, Walker BD, Ueno T, Finzi A, Brumme ZL, Brockman MA. Natural HIV-1 Nef Polymorphisms Impair SERINC5 Downregulation Activity. Cell Rep 2020; 29:1449-1457.e5. [PMID: 31693887 PMCID: PMC6925589 DOI: 10.1016/j.celrep.2019.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/26/2019] [Accepted: 10/01/2019] [Indexed: 11/30/2022] Open
Abstract
HIV-1 Nef enhances virion infectivity by counteracting host restriction factor SERINC5; however, the impact of natural Nef polymorphisms on this function is largely unknown. We characterize SERINC5 downregulation activity of 91 primary HIV-1 subtype B nef alleles, including isolates from 45 elite controllers and 46 chronic progressors. Controller-derived Nef clones display lower ability to downregulate SERINC5 (median 80% activity) compared with progressor-derived clones (median 96% activity) (p = 0.0005). We identify 18 Nef polymorphisms associated with differential function, including two CTL escape mutations that contribute to lower SERINC5 downregulation: K94E, driven by HLA-B∗08, and H116N, driven by the protective allele HLA-B∗57. HIV-1 strains encoding Nef K94E and/or H116N display lower infectivity and replication capacity in the presence of SERINC5. Our results demonstrate that natural polymorphisms in HIV-1 Nef can impair its ability to internalize SERINC5, indicating that variation in this recently described function may contribute to differences in viral pathogenesis.
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Affiliation(s)
- Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Xiaomei T Kuang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Shayda A Swann
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Mako Toyoda
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Department of Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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11
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Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung’u T, Brumme ZL, Brockman MA. Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. PLoS Pathog 2020; 16:e1008813. [PMID: 32925973 PMCID: PMC7515180 DOI: 10.1371/journal.ppat.1008813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis.
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Affiliation(s)
- Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mwebesa Bosco Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q. Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter W. Hunt
- School of Medicine, University of California, San Francisco, United States of America
| | - Jeff N. Martin
- School of Medicine, University of California, San Francisco, United States of America
| | - David R. Bangsberg
- School of Public Health, Oregon Health Science University, Portland, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, United States of America
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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12
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Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure. Curr Opin HIV AIDS 2020; 14:194-204. [PMID: 30925534 DOI: 10.1097/coh.0000000000000541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent advances in our understanding of HIV adaptation to human leukocyte antigen (HLA)-associated immune pressures and its relevance to HIV prevention and cure research. RECENT FINDINGS Recent research has confirmed that HLA is a major driver of individual and population-level HIV evolution, that HIV strains are adapting to the immunogenetic profiles of the different human ethnic groups in which they circulate, and that HIV adaptation has substantial clinical and immunologic consequences. As such, adaptation represents a major challenge to HIV prevention and cure. At the same time, there are opportunities: Studies of HIV adaptation are revealing why certain HLA alleles are protective in some populations and not others; they are identifying immunogenic viral epitopes that harbor high mutational barriers to escape, and they may help illuminate novel, vaccine-relevant HIV epitopes in regions where circulating adaptation is extensive. Elucidation of HLA-driven adapted and nonadapted viral forms in different human populations and HIV subtypes also renders 'personalized' immunogen selection, as a component of HIV cure strategies, conceptually feasible. SUMMARY Though adaptation represents a major challenge to HIV prevention and cure, achieving an in-depth understanding of this phenomenon can help move the design of such strategies forward.
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13
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Sudderuddin H, Kinloch NN, Jin SW, Miller RL, Jones BR, Brumme CJ, Joy JB, Brockman MA, Brumme ZL. Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study. Retrovirology 2020; 17:3. [PMID: 31918727 PMCID: PMC6953280 DOI: 10.1186/s12977-019-0510-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/26/2019] [Indexed: 11/29/2022] Open
Abstract
The HIV accessory protein Nef downregulates the viral entry receptor CD4, the Human Leukocyte Antigen (HLA)-A and -B molecules, the Serine incorporator 5 (SERINC5) protein and other molecules from the infected cell surface, thereby promoting viral infectivity, replication and immune evasion. The nef locus also represents one of the most genetically variable regions in the HIV genome, and nef sequences undergo substantial evolution within a single individual over the course of infection. Few studies however have simultaneously characterized the impact of within-host nef sequence evolution on Nef protein function over prolonged timescales. Here, we isolated 50 unique Nef clones by single-genome amplification over an 11-year period from the plasma of an individual who was largely naïve to antiretroviral treatment during this time. Together, these clones harbored nonsynonymous substitutions at 13% of nef’s codons. We assessed their ability to downregulate cell-surface CD4, HLA and SERINC5 and observed that all three Nef functions declined modestly over time, where the reductions in CD4 and HLA downregulation (an average of 0.6% and 2.0% per year, respectively) achieved statistical significance. The results from this case study support all three Nef activities as being important to maintain throughout untreated HIV infection, but nevertheless suggest that, despite nef’s mutational plasticity, within-host viral evolution can compromise Nef function, albeit modestly, over prolonged periods.
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Affiliation(s)
- Hanwei Sudderuddin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Rachel L Miller
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | | | - Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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14
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Fellay J, Pedergnana V. Exploring the interactions between the human and viral genomes. Hum Genet 2019; 139:777-781. [PMID: 31729546 DOI: 10.1007/s00439-019-02089-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/31/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, genome-wide association studies led to major advances in identifying human genetic variants associated with infectious disease susceptibility. On the pathogen side, comparable methods are now applied to identify disease-modulating pathogen variants. As host and pathogen variants jointly determine disease outcomes, the most recent development has been to explore simultaneously host and pathogen genomes, through so-called genome-to-genome studies. In this review, we provide some background on the development of genome-to-genome analysis and we detail the first wave of studies in this emerging field, which focused on patients chronically infected with HIV and hepatitis C virus. We also discuss the need for novel statistical methods to better tackle the issues of population stratification and multiple testing. Finally, we speculate on future research areas where genome-to-genome analysis may prove to be particularly effective.
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Affiliation(s)
- Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Vincent Pedergnana
- French National Center for Scientific Research (CNRS), Laboratory MIVEGEC (CNRS, IRD, UM), Montpellier, France
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15
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Hanke T. Aiming for protective T-cell responses: a focus on the first generation conserved-region HIVconsv vaccines in preventive and therapeutic clinical trials. Expert Rev Vaccines 2019; 18:1029-1041. [PMID: 31613649 DOI: 10.1080/14760584.2019.1675518] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: Despite life-saving antiretroviral drugs, an effective HIV-1 vaccine is the best solution and likely a necessary component of any strategy for halting the AIDS epidemic. The currently prevailing aim is to pursue antibody-mediated vaccine protection. With ample evidence for the ability of T cells to control HIV-1 replication, their protective potential should be also harnessed by vaccination. The challenge is to elicit not just any, but protective T cells.Areas covered: This article reviews the clinical experience with the first-generation conserved-region immunogen HIVconsv delivered by combinations of plasmid DNA, simian adenovirus, and poxvirus MVA. The aim of our strategy is to induce strong and broad T cells targeting functionally important parts of HIV-1 proteins common to global variants. These vaccines were tested in eight phase 1/2 preventive and therapeutic clinical trials in Europe and Africa, and induced high frequencies of broadly specific CD8+ T cells capable of in vitro inhibition of four major HIV-1 clades A, B, C and D, and in combination with latency-reactivating agent provided a signal of drug-free virological control in early treated patients.Expert opinion: A number of critical T-cell traits have to come together at the same time to achieve control over HIV-1.
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Affiliation(s)
- Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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16
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Shadabi E, Liang B, Plummer F, Luo M. Identification and Characterization of Positively Selected Mutations in Nef of Four HIV-1 Major Subtypes from Los Alamos National Laboratory. Curr HIV Res 2019; 16:130-142. [PMID: 29600767 DOI: 10.2174/1570162x16666180330140807] [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: 10/23/2017] [Revised: 03/07/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human immunodeficiency virus-1 (HIV-1) mutates rapidly to escape host immune pressure. This results in the generation of positively selected mutations (PSM) throughout the viral genome. Escape mutations in Nef, one of the accessory proteins of HIV-1, which plays an important role in viral pathogenicity have previously been identified in several large cohort studies, but the evolution of PSMs overtime in various HIV-1 subtypes remains unknown. METHODS 161 clade A1, 3093 clade B, 647 clade C and 115 clade D HIV-1 nef sequences were obtained from the HIV Database of Los Alamos National Laboratory and aligned using MEGA 6.0. The sequences from each clade were grouped based on the year of collection. Quasi analysis was used to identify PSMs and the number and locations of PSMs were compared among different subtypes. RESULTS PSMs for all four subtypes were distributed across the sequence of Nef, and conserved residues F90, W113, PxxPxR (a.a 72-77) remain unaltered overtime. The frequency of PSMs was stable among subtype B sequences but increased overtime for other subtypes. Phylogenetic analysis shows that sequences containing PSMs tend to cluster together at both inter and intra- subtype levels. CONCLUSION Identification of PSMs and their changes overtime within various subtypes of HIV-1 is important in defining global viral evolutionary patterns that can provide insights for designing therapeutic strategies.
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Affiliation(s)
- Elnaz Shadabi
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Frank Plummer
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ma Luo
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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17
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Kinloch NN, Lee GQ, Carlson JM, Jin SW, Brumme CJ, Byakwaga H, Muzoora C, Bwana MB, Cobarrubias KD, Hunt PW, Martin JN, Carrington M, Bangsberg DR, Harrigan PR, Brockman MA, Brumme ZL. Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity. J Virol 2019; 93:e01502-18. [PMID: 30305354 PMCID: PMC6288327 DOI: 10.1128/jvi.01502-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/28/2018] [Indexed: 11/20/2022] Open
Abstract
The extent to which viral genetic context influences HIV adaptation to human leukocyte antigen (HLA) class I-restricted immune pressures remains incompletely understood. The Ugandan HIV epidemic, where major pandemic group M subtypes A1 and D cocirculate in a single host population, provides an opportunity to investigate this question. We characterized plasma HIV RNA gag, pol, and nef sequences, along with host HLA genotypes, in 464 antiretroviral-naive individuals chronically infected with HIV subtype A1 or D. Using phylogenetically informed statistical approaches, we identified HLA-associated polymorphisms and formally compared their strengths of selection between viral subtypes. A substantial number (32%) of HLA-associated polymorphisms identified in subtype A1 and/or D had previously been reported in subtype B, C, and/or circulating recombinant form 01_AE (CRF01_AE), confirming the shared nature of many HLA-driven escape pathways regardless of viral genetic context. Nevertheless, 34% of the identified HLA-associated polymorphisms were significantly differentially selected between subtypes A1 and D. Experimental investigation of select examples of subtype-specific escape revealed distinct underlying mechanisms with important implications for vaccine design: whereas some were attributable to subtype-specific sequence variation that influenced epitope-HLA binding, others were attributable to differential mutational barriers to immune escape. Overall, our results confirm that HIV genetic context is a key modulator of viral adaptation to host cellular immunity and highlight the power of combined bioinformatic and mechanistic studies, paired with knowledge of epitope immunogenicity, to identify appropriate viral regions for inclusion in subtype-specific and universal HIV vaccine strategies.IMPORTANCE The identification of HIV polymorphisms reproducibly selected under pressure by specific HLA alleles and the elucidation of their impact on viral function can help identify immunogenic viral regions where immune escape incurs a fitness cost. However, our knowledge of HLA-driven escape pathways and their functional costs is largely limited to HIV subtype B and, to a lesser extent, subtype C. Our study represents the first characterization of HLA-driven adaptation pathways in HIV subtypes A1 and D, which dominate in East Africa, and the first statistically rigorous characterization of differential HLA-driven escape across viral subtypes. The results support a considerable impact of viral genetic context on HIV adaptation to host HLA, where HIV subtype-specific sequence variation influences both epitope-HLA binding and the fitness costs of escape. Integrated bioinformatic and mechanistic characterization of these and other instances of differential escape could aid rational cytotoxic T-lymphocyte-based vaccine immunogen selection for both subtype-specific and universal HIV vaccines.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Guinevere Q Lee
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, USA
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, San Francisco, California, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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18
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Abstract
Supplemental Digital Content is available in the text Objective: HIV incidence in the Canadian province of Saskatchewan, where Indigenous persons make up 80% of those infected, are among the highest on the continent. Reports of accelerated HIV progression, associated with carriage of certain human leukocyte antigen (HLA) alleles (including the typically protective HLA-B∗51) have also emerged from the region. Given that acquisition of HIV preadapted to host HLA negatively impacts clinical outcome, we hypothesized that HIV-host adaptation may be elevated in Saskatchewan. Design: Comparative analysis of population-level HIV sequence datasets from Saskatchewan and elsewhere in Canada/USA. Methods: We analyzed 1144 HIV subtype B Pol sequences collected in Saskatchewan between 2000 and 2016, comprising ∼65% of cumulative provincial HIV cases, for the presence of 70 HLA-associated Pol mutations. Sequences from British Columbia (N = 6525) and elsewhere in Canada/USA (N = 6517) were used for comparison. HIV adaptation levels to 34 HLA alleles were also computed. Putative HIV transmission clusters were identified, and the prevalence of HLA-associated adaptations within and outside these clusters was investigated. Results: Analyses confirmed significantly elevated and temporally increasing levels of HIV adaptation to commonly expressed HLA alleles, in particular B∗51. Notably, HLA-adapted HIV strains were significantly enriched among phylogenetic clusters in Saskatchewan. Conclusion: Extensive circulating HIV adaptation to HLA in Saskatchewan provides a plausible explanation for accelerated progression, while enrichment of adapted variants in phylogenetic clusters suggests they are being widely transmitted. Results highlight the utility of Pol sequences, routinely collected for drug resistance monitoring, for surveillance of HIV-host adaptation, and underscore the urgent need to expand HIV prevention and treatment programmes in Saskatchewan.
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Potential immune escape mutations under inferred selection pressure in HIV-1 strains circulating in Medellín, Colombia. INFECTION GENETICS AND EVOLUTION 2018; 69:267-278. [PMID: 30808498 DOI: 10.1016/j.meegid.2018.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/22/2018] [Accepted: 07/02/2018] [Indexed: 11/20/2022]
Abstract
The introduction of highly active antiretroviral therapy (HAART) has significantly improved life expectancy of HIV-infected patients; nevertheless, it does not eliminate the virus from hosts, so a cure for this infection is crucial. Some strategies have employed the induction of anti-HIV CD8+ T cells. However, the high genetic variability of HIV-1 represents the biggest obstacle for these strategies, since immune escape mutations within epitopes restricted by Human Leukocyte Antigen class I molecules (HLA-I) abrogate the antiviral activity of these cells. We used a bioinformatics pipeline for the determination of such mutations, based on selection pressure and docking/refinement analyses. Fifty HIV-1 infected patients were recruited; HLA-A and HLA-B alleles were typified using sequence-specific oligonucleotide approach, and viral RNA was extracted for the amplification of HIV-1 gag, which was bulk sequenced and aligned to perform selection pressure analysis, using Single Likelihood Ancestor Counting (SLAC) and Fast Unconstrained Bayesian Approximation (FUBAR) algorithms. Positively selected sites were mapped into HLA-I-specific epitopes, and both mutated and wild type epitopes were modelled using PEP-FOLD. Molecular docking and refinement assays were carried out using AutoDock Vina 4 and FlexPepDock. Five positively selected sites were found: S54 at HLA-A*02 GC9, T84 at HLA-A*02 SL9, S125 at HLA-B*35 HY9, S173 at HLA-A*02/B*57 KS12 and I223 at HLA-B*35 HA9. Although some mutations have been previously described as immune escape mutations, the majority of them have not been reported. Molecular docking/refinement analysis showed that one combination of mutations at GC9, one at SL9, and eight at HY9 epitopes could act as immune escape mutations. Moreover, HLA-A*02-positive patients harbouring mutations at KS12, and HLA-B*35-positive patients with mutations at HY9 have significantly higher plasma viral loads than patients lacking such mutations. Thus, HLA-A and -B alleles could be shaping the genetic diversity of HIV-1 through the selection of potential immune escape mutations.
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20
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Valenzuela-Ponce H, Alva-Hernández S, Garrido-Rodríguez D, Soto-Nava M, García-Téllez T, Escamilla-Gómez T, García-Morales C, Quiroz-Morales VS, Tapia-Trejo D, Del Arenal-Sánchez S, Prado-Galbarro FJ, Hernández-Juan R, Rodríguez-Aguirre E, Murakami-Ogasawara A, Mejía-Villatoro C, Escobar-Urias IY, Pinzón-Meza R, Pascale JM, Zaldivar Y, Porras-Cortés G, Quant-Durán C, Lorenzana I, Meza RI, Palou EY, Manzanero M, Cedillos RA, Aláez C, Brockman MA, Harrigan PR, Brumme CJ, Brumme ZL, Ávila-Ríos S, Reyes-Terán G. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 2018; 8:6111. [PMID: 29666450 PMCID: PMC5904102 DOI: 10.1038/s41598-018-23849-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/21/2018] [Indexed: 12/26/2022] Open
Abstract
Associations between HLA class I alleles and HIV progression in populations exhibiting Amerindian and Caucasian genetic admixture remain understudied. Using univariable and multivariable analyses we evaluated HLA associations with five HIV clinical parameters in 3,213 HIV clade B-infected, ART-naïve individuals from Mexico and Central America (MEX/CAM cohort). A Canadian cohort (HOMER, n = 1622) was used for comparison. As expected, HLA allele frequencies in MEX/CAM and HOMER differed markedly. In MEX/CAM, 13 HLA-A, 24 HLA-B, and 14 HLA-C alleles were significantly associated with at least one clinical parameter. These included previously described protective (e.g. B*27:05, B*57:01/02/03 and B*58:01) and risk (e.g. B*35:02) alleles, as well as novel ones (e.g. A*03:01, B*15:39 and B*39:02 identified as protective, and A*68:03/05, B*15:30, B*35:12/14, B*39:01/06, B*39:05~C*07:02, and B*40:01~C*03:04 identified as risk). Interestingly, both protective (e.g. B*39:02) and risk (e.g. B*39:01/05/06) subtypes were identified within the common and genetically diverse HLA-B*39 allele group, characteristic to Amerindian populations. While HLA-HIV associations identified in MEX and CAM separately were similar overall (Spearman's rho = 0.33, p = 0.03), region-specific associations were also noted. The identification of both canonical and novel HLA/HIV associations provides a first step towards improved understanding of HIV immune control among unique and understudied Mestizo populations.
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Affiliation(s)
- Humberto Valenzuela-Ponce
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Selma Alva-Hernández
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Daniela Garrido-Rodríguez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Maribel Soto-Nava
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Thalía García-Téllez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.,Institut Pasteur, Unité HIV, Inflammation and Persistence, Paris, France
| | - Tania Escamilla-Gómez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | - Daniela Tapia-Trejo
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Silvia Del Arenal-Sánchez
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | - Ramón Hernández-Juan
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Edna Rodríguez-Aguirre
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico
| | | | | | | | | | - Yamitzel Zaldivar
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | | | | | - Ivette Lorenzana
- Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Rita I Meza
- Honduras HIV National Laboratory, Tegucigalpa, Honduras
| | - Elsa Y Palou
- Hospital Escuela Universitario, Tegucigalpa, Honduras
| | | | | | - Carmen Aláez
- National Institute of Genomic Medicine, Translational Medicine Laboratory, Mexico City, Mexico
| | - Mark A Brockman
- Simon Fraser University, Faculty of Health Sciences, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | | | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Zabrina L Brumme
- Simon Fraser University, Faculty of Health Sciences, Burnaby, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Santiago Ávila-Ríos
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.
| | - Gustavo Reyes-Terán
- National Institute of Respiratory Diseases, CIENI Center for Research in Infectious Diseases, Mexico City, Mexico.
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Subtle differences in selective pressures applied on the envelope gene of HIV-1 in pregnant versus non-pregnant women. INFECTION GENETICS AND EVOLUTION 2018; 62:141-150. [PMID: 29678797 DOI: 10.1016/j.meegid.2018.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 04/09/2018] [Accepted: 04/15/2018] [Indexed: 10/17/2022]
Abstract
Pregnancy is associated with modulations of maternal immunity that contribute to foeto-maternal tolerance. To understand whether and how these alterations impact antiviral immunity, a detailed cross-sectional analysis of selective pressures exerted on HIV-1 envelope amino-acid sequences was performed in a group of pregnant (n = 32) and non-pregnant (n = 44) HIV-infected women in absence of treatment with antiretroviral therapy (ART). Independent of HIV-1 subtype, p-distance, dN and dS were all strongly correlated with one another but were not significantly different in pregnant as compared to non-pregnant patients. Differential levels of selective pressure applied on different Env subdomains displayed similar yet non-identical patterns between the two groups, with pressure applied on C1 being significantly lower in constant regions C1 and C2 than in V1, V2, V3 and C3. To draw a general picture of the selection applied on the envelope and compensate for inter-individual variations, we performed a binomial test on selection frequency data pooled from pregnant and non-pregnant women. This analysis uncovered 42 positions, present in both groups, exhibiting statistically-significant frequency of selection that invariably mapped to the surface of the Env protein, with the great majority located within epitopes recognized by Env-specific antibodies or sites associated with the development of cross-reactive neutralizing activity. The median frequency of occurrence of positive selection per site was significantly lower in pregnant versus non-pregnant women. Furthermore, examination of the distribution of positively selected sites using a hypergeometric test revealed that only 2 positions (D137 and S142) significantly differed between the 2 groups. Taken together, these result indicate that pregnancy is associated with subtle yet distinctive changes in selective pressures exerted on the HIV-1 Env protein that are compatible with transient modulations of maternal immunity.
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22
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Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico. J Virol 2018; 92:JVI.01128-17. [PMID: 29093100 PMCID: PMC5752930 DOI: 10.1128/jvi.01128-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/27/2017] [Indexed: 01/24/2023] Open
Abstract
HIV circumvents HLA class I-restricted CD8+ T-cell responses through selection of escape mutations that leave characteristic mutational “footprints,” also known as HLA-associated polymorphisms (HAPs), on HIV sequences at the population level. While many HLA footprints are universal across HIV subtypes and human populations, others can be region specific as a result of the unique immunogenetic background of each host population. Using a published probabilistic phylogenetically informed model, we compared HAPs in HIV Gag and Pol (PR-RT) in 1,612 subtype B-infected, antiretroviral treatment-naive individuals from Mexico and 1,641 individuals from Canada/United States. A total of 252 HLA class I allele subtypes were represented, including 140 observed in both cohorts, 67 unique to Mexico, and 45 unique to Canada/United States. At the predefined statistical threshold of a q value of <0.2, 358 HAPs (201 in Gag, 157 in PR-RT) were identified in Mexico, while 905 (534 in Gag and 371 in PR-RT) were identified in Canada/United States. HAPs identified in Mexico included both canonical HLA-associated escape pathways and novel associations, in particular with HLA alleles enriched in Amerindian and mestizo populations. Remarkably, HLA footprints on HIV in Mexico were not only fewer but also, on average, significantly weaker than those in Canada/United States, although some exceptions were noted. Moreover, exploratory analyses suggested that the weaker HLA footprint on HIV in Mexico may be due, at least in part, to weaker and/or less reproducible HLA-mediated immune pressures on HIV in this population. The implications of these differences for natural and vaccine-induced anti-HIV immunity merit further investigation. IMPORTANCE HLA footprints on HIV identify viral regions under intense and consistent pressure by HLA-restricted immune responses and the common mutational pathways that HIV uses to evade them. In particular, HLA footprints can identify novel immunogenic regions and/or epitopes targeted by understudied HLA alleles; moreover, comparative analyses across immunogenetically distinct populations can illuminate the extent to which HIV immunogenic regions and escape pathways are shared versus population-specific pathways, information which can in turn inform the design of universal or geographically tailored HIV vaccines. We compared HLA-associated footprints on HIV in two immunogenetically distinct North American populations, those of Mexico and Canada/United States. We identify both shared and population-specific pathways of HIV adaptation but also make the surprising observation that HLA footprints on HIV in Mexico overall are fewer and weaker than those in Canada/United States, raising the possibility that HLA-restricted antiviral immune responses in Mexico are weaker, and/or escape pathways somewhat less consistent, than those in other populations.
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Resistance of Major Histocompatibility Complex Class B (MHC-B) to Nef-Mediated Downregulation Relative to that of MHC-A Is Conserved among Primate Lentiviruses and Influences Antiviral T Cell Responses in HIV-1-Infected Individuals. J Virol 2017; 92:JVI.01409-17. [PMID: 29046444 DOI: 10.1128/jvi.01409-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 10/03/2017] [Indexed: 12/19/2022] Open
Abstract
Patient-derived HIV-1 subtype B Nef clones downregulate HLA-A more efficiently than HLA-B. However, it remains unknown whether this property is common to Nef proteins across primate lentiviruses and how antiviral immune responses may be affected. We examined 263 Nef clones from diverse primate lentiviruses including different pandemic HIV-1 group M subtypes for their ability to downregulate major histocompatibility complex class A (MHC-A) and MHC-B from the cell surface. Though lentiviral Nef proteins differed markedly in their absolute MHC-A and MHC-B downregulation abilities, all lentiviral Nef lineages downregulated MHC-A, on average, 11 to 32% more efficiently than MHC-B. Nef genotype/phenotype analyses in a cohort of HIV-1 subtype C-infected patients (n = 168), together with site-directed mutagenesis, revealed Nef position 9 as a subtype-specific determinant of differential HLA-A versus HLA-B downregulation activity. Nef clones harboring nonconsensus variants at codon 9 downregulated HLA-B (though not HLA-A) significantly better than those harboring the consensus sequence at this site, resulting in reduced recognition of infected target cells by HIV-1-specific CD8+ effector cells in vitro Among persons expressing protective HLA class I alleles, carriage of Nef codon 9 variants was also associated with reduced ex vivo HIV-specific T cell responses. Our results demonstrate that Nef's inferior ability to downregulate MHC-B compared to that of MHC-A is conserved across primate lentiviruses and suggest that this property influences antiviral cellular immune responses.IMPORTANCE Primate lentiviruses encode the Nef protein that plays an essential role in establishing persistent infection in their respective host species. Nef interacts with the cytoplasmic region of MHC-A and MHC-B molecules and downregulates them from the infected cell surface to escape recognition by host cellular immunity. Using a panel of Nef alleles isolated from diverse primate lentiviruses including pandemic HIV-1 group M subtypes, we demonstrate that Nef proteins across all lentiviral lineages downregulate MHC-A approximately 20% more effectively than MHC-B. We further identify a naturally polymorphic site at Nef position 9 that contributes to the MHC-B downregulation function in HIV-1 subtype C and show that carriage of Nef variants with enhanced MHC-B downregulation ability is associated with reduced breadth and magnitude of MHC-B-restricted cellular immune responses in HIV-infected individuals. Our study underscores an evolutionarily conserved interaction between lentiviruses and primate immune systems that may contribute to pathogenesis.
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Naranbhai V, Carrington M. Host genetic variation and HIV disease: from mapping to mechanism. Immunogenetics 2017; 69:489-498. [PMID: 28695282 PMCID: PMC5537324 DOI: 10.1007/s00251-017-1000-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Abstract
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era. Nevertheless, genome-wide evaluations have nicely validated the impact of HLA and CCR5 variants on HIV disease, and importantly, made clear the many false positive associations that were previously suggested by studies using the candidate gene approach. We describe how multiple HIV outcome measures such as acquisition, viral control, and immune decline have been studied in adults and in children, but that collectively these identify only the two replicable loci responsible for modifying HIV disease, CCR5, and HLA. Recent heritability estimates in this disease corroborate the modest impact of genetic determinants and their oligogenic nature. While the mechanism of protection afforded by genetic variants that diminish CCR5 expression is clear, new aspects of HLA class I-mediated protection continue to be uncovered. We describe how these genetic findings have enhanced insights into immunobiology, been clinically translated into CCR5 antagonists, allowed prioritization of antigens for vaccination efforts, and identified targets for genome-editing interventions. Finally, we describe how studies of genetically complex parts of the genome using new tools may begin revealing additional correlates.
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Affiliation(s)
- Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
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25
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Rossenkhan R, MacLeod IJ, Brumme ZL, Magaret CA, Sebunya TK, Musonda R, Gashe BA, Edlefsen PT, Novitsky V, Essex M. Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection. AIDS Res Hum Retroviruses 2016; 32:1031-1045. [PMID: 27349335 DOI: 10.1089/aid.2015.0330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Viral variants that predominate during early infection may exhibit constrained diversity compared with those found during chronic infection and could contain amino acid signature patterns that may enhance transmission, establish productive infection, and influence early events that modulate the infection course. We compared amino acid distributions in 17 patients recently infected with HIV-1C with patients with chronic infection. We found significantly lower entropy in inferred transmitted/founder (t/f) compared with chronic viruses and identified signature patterns in Vif and Vpr from inferred t/f viruses. We investigated sequence evolution longitudinally up to 500 days postseroconversion and compared the impact of selected substitutions on predicted human leukocyte antigen (HLA) binding affinities of published and predicted cytotoxic T-lymphocyte epitopes. Polymorphisms in Vif and Vpr during early infection occurred more frequently at epitope-HLA anchor residues and significantly decreased predicted epitope-HLA binding. Transmission-associated sequence signatures may have implications for novel strategies to prevent HIV-1 transmission.
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Affiliation(s)
- Raabya Rossenkhan
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Iain J. MacLeod
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Craig A. Magaret
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Theresa K. Sebunya
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Rosemary Musonda
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - Berhanu A. Gashe
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Paul T. Edlefsen
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Vlad Novitsky
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
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Abstract
Human leukocyte antigen class I (HLA)-restricted CD8(+) T lymphocyte (CTL) responses are crucial to HIV-1 control. Although HIV can evade these responses, the longer-term impact of viral escape mutants remains unclear, as these variants can also reduce intrinsic viral fitness. To address this, we here developed a metric to determine the degree of HIV adaptation to an HLA profile. We demonstrate that transmission of viruses that are pre-adapted to the HLA molecules expressed in the recipient is associated with impaired immunogenicity, elevated viral load and accelerated CD4(+) T cell decline. Furthermore, the extent of pre-adaptation among circulating viruses explains much of the variation in outcomes attributed to the expression of certain HLA alleles. Thus, viral pre-adaptation exploits 'holes' in the immune response. Accounting for these holes may be key for vaccine strategies seeking to elicit functional responses from viral variants, and to HIV cure strategies that require broad CTL responses to achieve successful eradication of HIV reservoirs.
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A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection. AIDS 2016; 30:681-9. [PMID: 26595539 DOI: 10.1097/qad.0000000000000969] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Identification of human leukocyte antigen-associated HIV-1 polymorphisms (HLA-APs) in different global populations furthers our understanding of HIV-1 pathogenesis and may help identify candidate immunogens for HIV vaccines targeted to these populations. Although numerous population-based studies identifying HLA-APs have been conducted in HIV-1 subtype B- and subtype C-infected cohorts, few have focused on subtype A/E. DESIGN We investigated HLA-APs in a cohort of chronically HIV-1 subtype A/E-infected Vietnamese individuals. METHODS HLA-APs in HIV-1 Gag, Pol, and Nef regions from 388 treatment-naive individuals chronically infected with HIV-1 subtype A/E were analyzed using phylogenetically informed approaches. RESULTS A total of 303 HLA-APs were identified. HLA-APs occurring at six positions in Gag and six positions in Pol were significantly associated with higher plasma viral load (pVL), whereas HLA-APs occurring at two positions in Gag and 13 positions in Pol were significantly associated with lower CD4 T-cell counts. Furthermore, the proportion of Pol codons harboring an HLA-AP specific to the host's HLA correlated positively with HIV-1 pVL (R = 0.22; P < 0.0001) and inversely with CD4 T-cell counts (R = -0.32; P < 0.0001). Similarly, the proportion of HLA-associated Gag codons harboring host-specific HLA-AP correlated inversely with CD4 T-cell counts (R = -0.13; P = 0.01). CONCLUSION These significant associations between HIV-1 amino acids adapted to Vietnamese HLA alleles and higher pVL and lower CD4 T-cell counts suggests that accumulation of cytotoxic T cells escape mutations may influence clinical outcomes in HIV-1 subtype A/E-infected Vietnamese individuals.
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Katoh J, Kawana-Tachikawa A, Shimizu A, Zhu D, Han C, Nakamura H, Koga M, Kikuchi T, Adachi E, Koibuchi T, Gao GF, Brumme ZL, Iwamoto A. Rapid HIV-1 Disease Progression in Individuals Infected with a Virus Adapted to Its Host Population. PLoS One 2016; 11:e0150397. [PMID: 26953793 PMCID: PMC4783116 DOI: 10.1371/journal.pone.0150397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
HIV-1 escape from CTL is predictable based on the Human Leukocyte Antigen (HLA) class I alleles expressed by the host. As such, HIV-1 sequences circulating in a population of hosts will harbor escape mutations specific to the HLA alleles of that population. In theory, this should increase the frequency of escape mutation transmission to persons expressing the restricting HLA allele, thereby compromising host immunity to the incoming HIV-1 strain. However, the clinical impact of infection with HIV-1 containing immune escape mutations has not conclusively been demonstrated. Japan’s population features limited HLA diversity which is driving population-level HIV adaptation: for example, >60% of Japanese express HLA-A*24:02 and its associated Nef-Y135F escape mutation represents the population consensus. As such, Japan is an ideal population in which to examine this phenomenon. Here, we combine genetic and immunological analyses to identify A*24:02-positive individuals likely to have been infected with Y135F-containing HIV-1. Over a ~5 year follow-up, these individuals exhibited significantly lower CD4 counts compared to individuals inferred to have been infected with wild-type HIV-1. Our results support a significant negative clinical impact of pathogen adaptation to host pressures at the population level.
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Affiliation(s)
- Jiro Katoh
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo. Kashiwa-shi, Chiba, Japan
| | - Ai Kawana-Tachikawa
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Akihisa Shimizu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Dayong Zhu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Chungyong Han
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Hitomi Nakamura
- Department of Infectious Disease Control, the International Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - George F. Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Aikichi Iwamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo. Kashiwa-shi, Chiba, Japan
- Department of Infectious Disease Control, the International Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Asian Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- * E-mail:
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Brockman MA, Jones RB, Brumme ZL. Challenges and Opportunities for T-Cell-Mediated Strategies to Eliminate HIV Reservoirs. Front Immunol 2015; 6:506. [PMID: 26483795 PMCID: PMC4591506 DOI: 10.3389/fimmu.2015.00506] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022] Open
Abstract
HIV's ability to establish latent reservoirs of reactivation-competent virus is the major barrier to cure. "Shock and kill" methods consisting of latency-reversing agents (LRAs) followed by elimination of reactivating cells through cytopathic effects are under active development. However, the clinical efficacy of LRAs remains to be established. Moreover, recent studies indicate that reservoirs may not be reduced efficiently by either viral cytopathic or CD8(+) T-cell-mediated mechanisms. In this perspective, we highlight challenges to T-cell-mediated elimination of HIV reservoirs, including characteristics of responding T cells, aspects of the cellular reservoirs, and properties of the latent virus itself. We also discuss potential strategies to overcome these challenges by targeting the antiviral activity of T cells toward appropriate viral antigens following latency.
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Affiliation(s)
- Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University , Burnaby, BC , Canada ; BC Centre for Excellence in HIV/AIDS , Vancouver, BC , Canada
| | - R Brad Jones
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University , Washington, DC , USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University , Burnaby, BC , Canada ; BC Centre for Excellence in HIV/AIDS , Vancouver, BC , Canada
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Association between a naturally arising polymorphism within a functional region of HIV-1 Nef and disease progression in chronic HIV-1 infection. Arch Virol 2015; 160:2033-41. [PMID: 26060058 DOI: 10.1007/s00705-015-2480-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/31/2015] [Indexed: 01/24/2023]
Abstract
HIV-1 Nef mediates downregulation of HLA class I (HLA-I) through a number of highly conserved sequence motifs. We investigated the in vivo implication(s) of naturally arising polymorphisms in functional motifs in HIV-1 Nef that are associated with HLA-I downregulation, including the acidic cluster, polyproline, di-arginine and Met-20 regions. Plasma samples from treatment-naive, chronically HIV-1 infected subjects were collected after obtaining informed consent, and viral RNA was extracted and amplified by nested RT-PCR. The resultant nef amplicons were sequenced directly, and subtype-B sequences with an intact open reading frame (n = 406) were included in our analyses. There was over-representation of isoleucine at position 20 (Ile-20) in our dataset when compared to sequences in the Los Alamos sequence database (17.7 vs. 6.9 %, p = 0.0309). The presence of having Ile-20 in Nef was found to be associated with higher median plasma viral load (p = 0.013), independent of associated codons or viral lineage effects, whereas no clinical association was found with polymorphisms in the other functional motifs. Moreover, introduction of a Met-20-to-Ile mutation in a laboratory strain SF2 Nef resulted in a modest, albeit not statistically significant, increase in HLA class I downregulation activity (p = 0.06). Taken together, we have identified a naturally arising polymorphism, Ile-20, within HIV-1 subtype B Nef that is associated with poorer disease outcome.
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Grifoni A, Montesano C, Colizzi V, Amicosante M. Key role of human leukocyte antigen in modulating human immunodeficiency virus progression: An overview of the possible applications. World J Virol 2015; 4:124-133. [PMID: 25964877 PMCID: PMC4419116 DOI: 10.5501/wjv.v4.i2.124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 01/20/2015] [Accepted: 02/12/2015] [Indexed: 02/05/2023] Open
Abstract
Host and viral factors deeply influence the human immunodeficiency virus (HIV) disease progression. Among them human leukocyte antigen (HLA) locus plays a key role at different levels. In fact, genes of the HLA locus have shown the peculiar capability to modulate both innate and adaptive immune responses. In particular, HLA class I molecules are recognized by CD8+ T-cells and natural killers (NK) cells towards the interaction with T cell receptor (TCR) and Killer Immunoglobulin Receptor (KIR) 3DL1 respectively. Polymorphisms within the different HLA alleles generate structural changes in HLA class I peptide-binding pockets. Amino acid changes in the peptide-binding pocket lead to the presentation of a different set of peptides to T and NK cells. This review summarizes the role of HLA in HIV progression toward acquired immunodeficiency disease syndrome and its receptors. Recently, many studies have been focused on determining the HLA binding-peptides. The novel use of immune-informatics tools, from the prediction of the HLA-bound peptides to the modification of the HLA-receptor complexes, is considered. A better knowledge of HLA peptide presentation and recognition are allowing new strategies for immune response manipulation to be applied against HIV virus.
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Newly Exerted T Cell Pressures on Mutated Epitopes following Transmission Help Maintain Consensus HIV-1 Sequences. PLoS One 2015; 10:e0120787. [PMID: 25919393 PMCID: PMC4412704 DOI: 10.1371/journal.pone.0120787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/27/2015] [Indexed: 11/19/2022] Open
Abstract
CD8+ T cells are important for HIV-1 virus control, but are also a major contributing factor that drives HIV-1 virus sequence evolution. Although HIV-1 cytotoxic T cell (CTL) escape mutations are a common aspect during HIV-1 infection, less is known about the importance of T cell pressure in reversing HIV-1 virus back to a consensus sequences. In this study we aimed to assess the frequency with which reversion of transmitted mutations in T cell epitopes were associated with T cell responses to the mutation. This study included 14 HIV-1 transmission pairs consisting of a 'source' (virus-donor) and a 'recipient' (newly infected individual). Non-consensus B sequence amino acids (mutations) in T cell epitopes in HIV-1 gag regions p17, p24, p2 and p7 were identified in each pair and transmission of mutations to the recipient was verified with population viral sequencing. Longitudinal analyses of the recipient's viral sequence were used to identify whether reversion of mutations back to the consensus B sequence occurred. Autologous 12-mer peptides overlapping by 11 were synthesized, representing the sequence region surrounding each reversion and longitudinal analysis of T cell responses to source-derived mutated and reverted epitopes were assessed. We demonstrated that mutations in the source were frequently transmitted to the new host and on an average 17 percent of mutated epitopes reverted to consensus sequence in the recipient. T cell responses to these mutated epitopes were detected in 7 of the 14 recipients in whom reversion occurred. Overall, these findings indicate that transmitted non-consensus B epitopes are frequently immunogenic in HLA-mismatched recipients and new T cell pressures to T cell escape mutations following transmission play a significant role in maintaining consensus HIV-1 sequences.
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Acevedo-Sáenz L, Ochoa R, Rugeles MT, Olaya-García P, Velilla-Hernández PA, Diaz FJ. Selection pressure in CD8⁺ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach. Viruses 2015; 7:1313-31. [PMID: 25803098 PMCID: PMC4379572 DOI: 10.3390/v7031313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 01/24/2023] Open
Abstract
One of the main characteristics of the human immunodeficiency virus is its genetic variability and rapid adaptation to changing environmental conditions. This variability, resulting from the lack of proofreading activity of the viral reverse transcriptase, generates mutations that could be fixed either by random genetic drift or by positive selection. Among the forces driving positive selection are antiretroviral therapy and CD8+ T-cells, the most important immune mechanism involved in viral control. Here, we describe mutations induced by these selective forces acting on the pol gene of HIV in a group of infected individuals. We used Maximum Likelihood analyses of the ratio of non-synonymous to synonymous mutations per site (dN/dS) to study the extent of positive selection in the protease and the reverse transcriptase, using 614 viral sequences from Colombian patients. We also performed computational approaches, docking and algorithmic analyses, to assess whether the positively selected mutations affected binding to the HLA molecules. We found 19 positively-selected codons in drug resistance-associated sites and 22 located within CD8+ T-cell epitopes. A high percentage of mutations in these epitopes has not been previously reported. According to the docking analyses only one of those mutations affected HLA binding. However, algorithmic methods predicted a decrease in the affinity for the HLA molecule in seven mutated peptides. The bioinformatics strategies described here are useful to identify putative positively selected mutations associated with immune escape but should be complemented with an experimental approach to define the impact of these mutations on the functional profile of the CD8+ T-cells.
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Affiliation(s)
- Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | - Rodrigo Ochoa
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, 050010, Colombia.
| | - Maria Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | | | - Paula Andrea Velilla-Hernández
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | - Francisco J Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
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Lourenço L, Samji H, Nohpal A, Chau W, Colley G, Lepik K, Barrios R, Lima V, Hogg RS, Montaner J, Kesselring S, Moore DM. Declines in highly active antiretroviral therapy initiation at CD4 cell counts ≤ 200 cells/μL and the contribution of diagnosis of HIV at CD4 cell counts ≤ 200 cells/μL in British Columbia, Canada. HIV Med 2015; 16:337-45. [PMID: 25721157 DOI: 10.1111/hiv.12212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2014] [Indexed: 12/31/2022]
Abstract
OBJECTIVES The aim of the study was to examine trends in initiating highly active antiretroviral therapy (HAART) with a CD4 count ≤ 200 cells/μL and the contribution of having a CD4 count ≤ 200 cells/μL at the time of diagnosis to these trends, in British Columbia (BC), Canada. METHODS We included in the analysis treatment-naïve BC residents aged ≥ 19 years who initiated HAART from 2003 to 2012. Participants were classified as follows: Group 1: diagnosed and initiated HAART with a CD4 count > 200 cells/μL; Group 2: diagnosed with a CD4 count > 200 cells/μL and initiated HAART with a CD4 count ≤ 200 cells/μL; and Group 3: diagnosed and initiated HAART with a CD4 count ≤ 200 cells/μL. We measured trends in initiating HAART with a CD4 count ≤ 200 cells/μL and used logistic regression models to measure factors associated with initiating HAART with a CD4 count ≤ 200 cells/μL, stratified by having a CD4 count ≤ 200 cells/μL or > 200 cells/μL at the time of diagnosis. RESULTS Between 2003 and 2012, 3506 BC residents initiated HAART. Of these, 44% (1558 of 3506) initiated HAART with a CD4 count ≤ 200 cells/μL. This proportion declined from 69% (198 of 287) in 2003 to 21% (81 of 330) in 2012 (P < 0.001). The proportion of those in Group 3 increased from 49% (97 of 198) in 2003 to 69% (56 of 81) in 2012 (P < 0.001). Overall, 56% (1948), 22% (776) and 22% (782) made up Groups 1, 2, and 3, respectively. In adjusted analyses, seeing a specialist was significantly associated with being in Group 3. Using injection drugs and seeing a specialist were associated with being in Group 2. CONCLUSIONS In recent years, among individuals who ever initiated HAART in BC, being diagnosed with low CD4 cell counts has become a greater contributor to initiating HAART with low CD4 cell counts.
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Affiliation(s)
- L Lourenço
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - H Samji
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - A Nohpal
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - W Chau
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - G Colley
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - K Lepik
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - R Barrios
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - V Lima
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - R S Hogg
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Jsg Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - S Kesselring
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - D M Moore
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol 2015; 23:212-24. [PMID: 25613992 DOI: 10.1016/j.tim.2014.12.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
HIV-1 develops specific mutations within its genome that allow it to escape detection by human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8(+) cytotoxic T lymphocytes (CTL). HLA thus represents a major force driving the evolution and diversification of HIV-1 within individuals and at the population level. Importantly, the study of HIV-1 adaptation to HLA also represents an opportunity to identify what qualities constitute an effective immune response, how the virus in turn adapts to these pressures, and how we may harness this information to design HIV-1 vaccines that stimulate effective cellular immunity.
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Affiliation(s)
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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Grifoni A, Montesano C, Palma P, Giovanetti M, Giovannetti M, Castelli-Gattinara G, Ciccozzi M, Mattei M, Mancino G, Salerno A, Colizzi V, Amicosante M. Role of individual's T-cell immunome in controlling HIV-1 progression. Immunology 2015; 143:631-9. [PMID: 24954875 DOI: 10.1111/imm.12344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/11/2014] [Accepted: 06/17/2014] [Indexed: 02/06/2023] Open
Abstract
Viral and host factors can influence HIV-1 progression, among them human leucocyte antigen (HLA) has shown the strongest effect. However, studies on the functional contribution of HLA in controlling HIV progression toward AIDS are limited by multiple issues, including the viral strain variability within the study subjects. In this study, in a cohort of children infected with a monophyletic strain (CRF02_AG) during an outbreak, we evaluated the HIV-1 Gag, Vif, Vpr, Tat and hepatitis C virus E1/E2 (as control) proteins circulating in a cohort for the capability to be presented by the HLA molecules in the same population. A total of 70 Non-progressors and 37 Progressors to AIDS were evaluated. In the presence of a constant capability of HIV-1 to mutate in the region containing epitopes of Gag protein, the number of epitopes recognized in silico by the combination of the HLA alleles along the Gag consensus sequence is significantly higher in the Non-progressors compared with Progressors (HLA-A: Non-progressors = 1.532 ± 1.211, Progressors = 0.7714 ± 1.031, P = 0.0016; HLA-B: Non-progressors = 1.556 ± 1.298, Progressors = 1.000 ± 0.817, P = 0.0319; HLA-DR: Non-progressors = 13.30 ± 9.488, Progressors = 7.294 ± 6.952, P = 0.0006). Similar results were obtained for the other HIV-1 proteins Vif and Vpr, whereas no differences were obtained in the number of epitopes for the hepatitis C virus E1/E2 protein sequence or for the scrambled HIV-1 sequence. Finally, the results were confirmed also in a subgroup of subjects where both HLA typing and Gag sequence were available. In conclusion, in the absence of bias due to viral strain diversity, it is the overall fitting of the HLA molecules that are capable of better binding HIV-1 proteins in determining the major role in the control of HIV-1 replication and progression to AIDS.
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Affiliation(s)
- Alba Grifoni
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
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Pereyra F, Heckerman D, Carlson JM, Kadie C, Soghoian DZ, Karel D, Goldenthal A, Davis OB, DeZiel CE, Lin T, Peng J, Piechocka A, Carrington M, Walker BD. HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes. J Virol 2014; 88:12937-48. [PMID: 25165115 PMCID: PMC4249072 DOI: 10.1128/jvi.01004-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/19/2014] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED We investigated the hypothesis that the correlation between the class I HLA types of an individual and whether that individual spontaneously controls HIV-1 is mediated by the targeting of specific epitopes by CD8(+) T cells. By measuring gamma interferon enzyme-linked immunosorbent spot (ELISPOT) assay responses to a panel of 257 optimally defined epitopes in 341 untreated HIV-infected persons, including persons who spontaneously control viremia, we found that the correlation between HLA types and control is mediated by the targeting of specific epitopes. Moreover, we performed a graphical model-based analysis that suggested that the targeting of specific epitopes is a cause of such control--that is, some epitopes are protective rather than merely associated with control--and identified eight epitopes that are significantly protective. In addition, we use an in silico analysis to identify protein regions where mutations are likely to affect the stability of a protein, and we found that the protective epitopes identified by the ELISPOT analysis correspond almost perfectly to such regions. This in silico analysis thus suggests a possible mechanism for control and could be used to identify protective epitopes that are not often targeted in natural infection but that may be potentially useful in a vaccine. Our analyses thus argue for the inclusion (and exclusion) of specific epitopes in an HIV vaccine. IMPORTANCE Some individuals naturally control HIV replication in the absence of antiretroviral therapy, and this ability to control is strongly correlated with the HLA class I alleles that they express. Here, in a large-scale experimental study, we provide evidence that this correlation is mediated largely by the targeting of specific CD8(+) T-cell epitopes, and we identify eight epitopes that are likely to cause control. In addition, we provide an in silico analysis indicating that control occurs because mutations within these epitopes change the stability of the protein structures. This in silico analysis also identified additional epitopes that are not typically targeted in natural infection but may lead to control when included in a vaccine, provided that other epitopes that would otherwise distract the immune system from targeting them are excluded from the vaccine.
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Affiliation(s)
- Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | - Carl Kadie
- Microsoft Research, Redmond, Washington, USA
| | | | - Daniel Karel
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Ariel Goldenthal
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Oliver B Davis
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | | | - Tienho Lin
- Microsoft Research, Los Angeles, California, USA
| | - Jian Peng
- Microsoft Research, Los Angeles, California, USA
| | - Alicja Piechocka
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Martin E, Carlson JM, Le AQ, Chopera DR, McGovern R, Rahman MA, Ng C, Jessen H, Kelleher AD, Markowitz M, Allen TM, Milloy MJ, Carrington M, Wainberg MA, Brumme ZL. Early immune adaptation in HIV-1 revealed by population-level approaches. Retrovirology 2014; 11:64. [PMID: 25212686 PMCID: PMC4190299 DOI: 10.1186/s12977-014-0064-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/24/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The reproducible nature of HIV-1 escape from HLA-restricted CD8+ T-cell responses allows the identification of HLA-associated viral polymorphisms "at the population level" - that is, via analysis of cross-sectional, linked HLA/HIV-1 genotypes by statistical association. However, elucidating their timing of selection traditionally requires detailed longitudinal studies, which are challenging to undertake on a large scale. We investigate whether the extent and relative timecourse of immune-driven HIV adaptation can be inferred via comparative cross-sectional analysis of independent early and chronic infection cohorts. RESULTS Similarly-powered datasets of linked HLA/HIV-1 genotypes from individuals with early (median < 3 months) and chronic untreated HIV-1 subtype B infection, matched for size (N > 200/dataset), HLA class I and HIV-1 Gag/Pol/Nef diversity, were established. These datasets were first used to define a list of 162 known HLA-associated polymorphisms detectable at the population level in cohorts of the present size and host/viral genetic composition. Of these 162 known HLA-associated polymorphisms, 15% (occurring at 14 Gag, Pol and Nef codons) were already detectable via statistical association in the early infection dataset at p ≤ 0.01 (q < 0.2) - identifying them as the most consistently rapidly escaping sites in HIV-1. Among these were known rapidly-escaping sites (e.g. B*57-Gag-T242N) and others not previously appreciated to be reproducibly rapidly selected (e.g. A*31:01-associated adaptations at Gag codons 397, 401 and 403). Escape prevalence in early infection correlated strongly with first-year escape rates (Pearson's R = 0.68, p = 0.0001), supporting cross-sectional parameters as reliable indicators of longitudinally-derived measures. Comparative analysis of early and chronic datasets revealed that, on average, the prevalence of HLA-associated polymorphisms more than doubles between these two infection stages in persons harboring the relevant HLA (p < 0.0001, consistent with frequent and reproducible escape), but remains relatively stable in persons lacking the HLA (p = 0.15, consistent with slow reversion). Published HLA-specific Hazard Ratios for progression to AIDS correlated positively with average escape prevalence in early infection (Pearson's R = 0.53, p = 0.028), consistent with high early within-host HIV-1 adaptation (via rapid escape and/or frequent polymorphism transmission) as a correlate of progression. CONCLUSION Cross-sectional host/viral genotype datasets represent an underutilized resource to identify reproducible early pathways of HIV-1 adaptation and identify correlates of protective immunity.
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Affiliation(s)
- Eric Martin
- />Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
- />British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC Canada
| | | | - Anh Q Le
- />Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
| | - Denis R Chopera
- />Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
- />KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Rachel McGovern
- />British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC Canada
| | - Manal A Rahman
- />Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
| | - Carmond Ng
- />British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC Canada
| | | | | | - Martin Markowitz
- />Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY USA
| | - Todd M Allen
- />Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA USA
| | - M-J Milloy
- />British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC Canada
- />Faculty of Medicine, University of British Columbia, Vancouver, BC Canada
| | - Mary Carrington
- />Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA USA
- />Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | | | - Zabrina L Brumme
- />Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
- />British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC Canada
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Han C, Kawana-Tachikawa A, Shimizu A, Zhu D, Nakamura H, Adachi E, Kikuchi T, Koga M, Koibuchi T, Gao GF, Sato Y, Yamagata A, Martin E, Fukai S, Brumme ZL, Iwamoto A. Switching and emergence of CTL epitopes in HIV-1 infection. Retrovirology 2014; 11:38. [PMID: 24886641 PMCID: PMC4036671 DOI: 10.1186/1742-4690-11-38] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/28/2014] [Indexed: 01/16/2023] Open
Abstract
Background Human Leukocyte Antigen (HLA) class I restricted Cytotoxic T Lymphocytes (CTLs) exert substantial evolutionary pressure on HIV-1, as evidenced by the reproducible selection of HLA-restricted immune escape mutations in the viral genome. An escape mutation from tyrosine to phenylalanine at the 135th amino acid (Y135F) of the HIV-1 nef gene is frequently observed in patients with HLA-A*24:02, an HLA Class I allele expressed in ~70% of Japanese persons. The selection of CTL escape mutations could theoretically result in the de novo creation of novel epitopes, however, the extent to which such dynamic “CTL epitope switching” occurs in HIV-1 remains incompletely known. Results Two overlapping epitopes in HIV-1 nef, Nef126-10 and Nef134-10, elicit the most frequent CTL responses restricted by HLA-A*24:02. Thirty-five of 46 (76%) HLA-A*24:02-positive patients harbored the Y135F mutation in their plasma HIV-1 RNA. Nef codon 135 plays a crucial role in both epitopes, as it represents the C-terminal anchor for Nef126-10 and the N-terminal anchor for Nef134-10. While the majority of patients with 135F exhibited CTL responses to Nef126-10, none harboring the “wild-type” (global HIV-1 subtype B consensus) Y135 did so, suggesting that Nef126-10 is not efficiently presented in persons harboring Y135. Consistent with this, peptide binding and limiting dilution experiments confirmed F, but not Y, as a suitable C-terminal anchor for HLA-A*24:02. Moreover, experiments utilizing antigen specific CTL clones to recognize endogenously-expressed peptides with or without Y135F indicated that this mutation disrupted the antigen expression of Nef134-10. Critically, the selection of Y135F also launched the expression of Nef126-10, indicating that the latter epitope is created as a result of escape within the former. Conclusions Our data represent the first example of the de novo creation of a novel overlapping CTL epitope as a direct result of HLA-driven immune escape in a neighboring epitope. The robust targeting of Nef126-10 following transmission (or in vivo selection) of HIV-1 containing Y135F may explain in part the previously reported stable plasma viral loads over time in the Japanese population, despite the high prevalence of both HLA-A*24:02 and Nef-Y135F in circulating HIV-1 sequences.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aikichi Iwamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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Abstract
UNLABELLED The extent to which HIV-1 clade B strains exhibit population-specific adaptations to host HLA alleles remains incompletely known, in part due to incomplete characterization of HLA-associated HIV-1 polymorphisms (HLA-APs) in different global populations. Moreover, it remains unknown to what extent the same HLA alleles may drive significantly different escape pathways across populations. As the Japanese population exhibits distinctive HLA class I allele distributions, comparative analysis of HLA-APs between HIV-1 clade B-infected Japanese and non-Asian cohorts could shed light on these questions. However, HLA-APs remain incompletely mapped in Japan. In a cohort of 430 treatment-naive Japanese with chronic HIV-1 clade B infection, we identified 284 HLA-APs in Gag, Pol, and Nef using phylogenetically corrected methods. The number of HLA-associated substitutions in Pol, notably those restricted by HLA-B*52:01, was weakly inversely correlated with the plasma viral load (pVL), suggesting that the transmission and persistence of B*52:01-driven Pol mutations could modulate the pVL. Differential selection of HLA-APs between HLA subtype members, including those differing only with respect to substitutions outside the peptide-binding groove, was observed, meriting further investigation as to their mechanisms of selection. Notably, two-thirds of HLA-APs identified in Japan had not been reported in previous studies of predominantly Caucasian cohorts and were attributable to HLA alleles unique to, or enriched in, Japan. We also identified 71 cases where the same HLA allele drove significantly different escape pathways in Japan versus predominantly Caucasian cohorts. Our results underscore the distinct global evolution of HIV-1 clade B as a result of host population-specific cellular immune pressures. IMPORTANCE Cytotoxic T lymphocyte (CTL) escape mutations in HIV-1 are broadly predictable based on the HLA class I alleles expressed by the host. Because HLA allele distributions differ among worldwide populations, the pattern and diversity of HLA-associated escape mutations are likely to be somewhat distinct to each race and region. HLA-associated polymorphisms (HLA-APs) in HIV-1 have previously been identified at the population level in European, North American, Australian, and African cohorts; however, large-scale analyses of HIV-1 clade B-specific HLA-APs in Asians are lacking. Differential intraclade HIV-1 adaptation to global populations can be investigated via comparative analyses of HLA-associated polymorphisms across ethnic groups, but such studies are rare. Here, we identify HLA-APs in a large Japanese HIV-1 clade B cohort using phylogenetically informed methods and observe that the majority of them had not been previously characterized in predominantly Caucasian populations. The results highlight HIV's unique adaptation to cellular immune pressures imposed by different global populations.
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Pey J, Valgepea K, Rubio A, Beasley JE, Planes FJ. Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. BMC SYSTEMS BIOLOGY 2013; 7:134. [PMID: 24314206 PMCID: PMC3878952 DOI: 10.1186/1752-0509-7-134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 11/27/2013] [Indexed: 12/26/2022]
Abstract
Background The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling. Results We present here an in-silico framework to infer relevant metabolic pathways for a particular phenotype under study based on its gene/protein expression data. This framework is based on the Carbon Flux Path (CFP) approach, a mixed-integer linear program that expands classical path finding techniques by considering additional biophysical constraints. In particular, the objective function of the CFP approach is amended to account for gene/protein expression data and influence obtained paths. This approach is termed integrative Carbon Flux Path (iCFP). We show that gene/protein expression data also influences the stoichiometric balancing of CFPs, which provides a more accurate picture of active metabolic pathways. This is illustrated in both a theoretical and real scenario. Finally, we apply this approach to find novel pathways relevant in the regulation of acetate overflow metabolism in Escherichia coli. As a result, several targets which could be relevant for better understanding of the phenomenon leading to impaired acetate overflow are proposed. Conclusions A novel mathematical framework that determines functional pathways based on gene/protein expression data is presented and validated. We show that our approach is able to provide new insights into complex biological scenarios such as acetate overflow in Escherichia coli.
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Affiliation(s)
| | | | | | - John E Beasley
- CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain.
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Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A. Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection. Sci Rep 2013; 3:3097. [PMID: 24192765 PMCID: PMC3818656 DOI: 10.1038/srep03097] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/15/2013] [Indexed: 12/13/2022] Open
Abstract
We investigated the crystal structure of an HLA-A*2402-restricted CTL epitope in the HIV-1 nef gene (Nef134-10) before (pHLA) or after TCR docking. The wild type epitope and two escape mutants were included in the study. Y135F was an early-appearing major mutation, while F139L was a late-appearing mutation which was selected in the patients without Y135F. F139 was an eminent feature of the Nef134-10 epitope. Wild type-specific TCR was less fit to F139L mutant suggesting that F139L is an escape from the CTL against the wild type epitope. Although Y135F mutation disrupted the hydrogen bond to HLA-A*2402 His70, newly formed hydrogen bond between T138 and His70 kept the conformation of the epitope in the reconstituted pMHC. TCR from Y135F- or dually-specific CTL had unique mode of binding to the mutant epitope. Y135F has been reported as a processing mutant but CTL carrying structurally adequate TCR can be found in the patients.
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Affiliation(s)
- Akihisa Shimizu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo. 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O'Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife 2013; 2:e01123. [PMID: 24171102 PMCID: PMC3807812 DOI: 10.7554/elife.01123] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/26/2013] [Indexed: 12/31/2022] Open
Abstract
HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10(-12)). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the 'intermediate phenotype' nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.
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Affiliation(s)
- István Bartha
- School of Life Sciences , École Polytechnique Fédérale de Lausanne , Lausanne , Switzerland ; Institute of Microbiology , University Hospital and University of Lausanne , Lausanne , Switzerland ; Research Group of Theoretical Biology and Evolutionary Ecology , Eötvös Loránd University and the Hungarian Academy of Sciences , Budapest , Hungary ; Swiss Institute of Bioinformatics , Lausanne , Switzerland
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Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJR, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology 2013; 10:100. [PMID: 24041011 PMCID: PMC3849644 DOI: 10.1186/1742-4690-10-100] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022] Open
Abstract
Background The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef’s most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D. Results Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function. Conclusions Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.
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Affiliation(s)
- Jaclyn K Mann
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJR, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Retrovirology 2013. [PMID: 24041011 DOI: 10.1186/742-4690-10-100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND The highly genetically diverse HIV-1 group M subtypes may differ in their biological properties. Nef is an important mediator of viral pathogenicity; however, to date, a comprehensive inter-subtype comparison of Nef in vitro function has not been undertaken. Here, we investigate two of Nef's most well-characterized activities, CD4 and HLA class I downregulation, for clones obtained from 360 chronic patients infected with HIV-1 subtypes A, B, C or D. RESULTS Single HIV-1 plasma RNA Nef clones were obtained from N=360 antiretroviral-naïve, chronically infected patients from Africa and North America: 96 (subtype A), 93 (B), 85 (C), and 86 (D). Nef clones were expressed by transfection in an immortalized CD4+ T-cell line. CD4 and HLA class I surface levels were assessed by flow cytometry. Nef expression was verified by Western blot. Subset analyses and multivariable linear regression were used to adjust for differences in age, sex and clinical parameters between cohorts. Consensus HIV-1 subtype B and C Nef sequences were synthesized and functionally assessed. Exploratory sequence analyses were performed to identify potential genotypic correlates of Nef function. Subtype B Nef clones displayed marginally greater CD4 downregulation activity (p = 0.03) and markedly greater HLA class I downregulation activity (p < 0.0001) than clones from other subtypes. Subtype C Nefs displayed the lowest in vitro functionality. Inter-subtype differences in HLA class I downregulation remained statistically significant after controlling for differences in age, sex, and clinical parameters (p < 0.0001). The synthesized consensus subtype B Nef showed higher activities compared to consensus C Nef, which was most pronounced in cells expressing lower protein levels. Nef clones exhibited substantial inter-subtype diversity: cohort consensus residues differed at 25% of codons, while a similar proportion of codons exhibited substantial inter-subtype differences in major variant frequency. These amino acids, along with others identified in intra-subtype analyses, represent candidates for mediating inter-subtype differences in Nef function. CONCLUSIONS Results support a functional hierarchy of subtype B > A/D > C for Nef-mediated CD4 and HLA class I downregulation. The mechanisms underlying these differences and their relevance to HIV-1 pathogenicity merit further investigation.
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Affiliation(s)
- Jaclyn K Mann
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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Hightower GK, May SJ, Pérez-Santiago J, Pacold ME, Wagner GA, Little SJ, Richman DD, Mehta SR, Smith DM, Pond SLK. HIV-1 clade B pol evolution following primary infection. PLoS One 2013; 8:e68188. [PMID: 23840830 PMCID: PMC3695957 DOI: 10.1371/journal.pone.0068188] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/27/2013] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Characterize intra-individual HIV-1 subtype B pol evolution in antiretroviral naive individuals. DESIGN Longitudinal cohort study of individuals enrolled during primary infection. METHODS Eligible individuals were antiretroviral naïve participants enrolled in the cohort from December 1997-December 2005 and having at least two blood samples available with the first one collected within a year of their estimated date of infection. Population-based pol sequences were generated from collected blood samples and analyzed for genetic divergence over time in respect to dual infection status, HLA, CD4 count and viral load. RESULTS 93 participants were observed for a median of 1.8 years (Mean = 2.2 years, SD =1.9 years). All participants classified as mono-infected had less than 0.7% divergence between any two of their pol sequences using the Tamura-Nei model (TN93), while individuals with dual infection had up to 7.0% divergence. The global substitution rates (substitutions/nucleotide/year) for mono and dually infected individuals were significantly different (p<0.001); however, substitution rates were not associated with HLA haplotype, CD4 or viral load. CONCLUSIONS Even after a maximum of almost 9 years of follow-up, all mono-infected participants had less than 1% divergence between baseline and longitudinal sequences, while participants with dual infection had 10 times greater divergence. These data support the use of HIV-1 pol sequence data to evaluate transmission events, networks and HIV-1 dual infection.
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Affiliation(s)
- George K. Hightower
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Susanne J. May
- Department of Biostatistics, University of Washington, Seattle, Washington United States of America
| | - Josué Pérez-Santiago
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Mary E. Pacold
- Life Technologies, San Francisco, California United States of America
| | - Gabriel A. Wagner
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Susan J. Little
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Douglas D. Richman
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
- Veterans Administration San Diego Healthcare System, San Diego, California, United States of America
| | - Sanjay R. Mehta
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
- Veterans Administration San Diego Healthcare System, San Diego, California, United States of America
- * E-mail:
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California San Diego, La Jolla, California United States of America
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Lamers SL, Fogel GB, Singer EJ, Salemi M, Nolan DJ, Huysentruyt LC, McGrath MS. HIV-1 Nef in macrophage-mediated disease pathogenesis. Int Rev Immunol 2013; 31:432-50. [PMID: 23215766 DOI: 10.3109/08830185.2012.737073] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Combined anti-retroviral therapy (cART) has significantly reduced the number of AIDS-associated illnesses and changed the course of HIV-1 disease in developed countries. Despite the ability of cART to maintain high CD4+ T-cell counts, a number of macrophage-mediated diseases can still occur in HIV-infected subjects. These diseases include lymphoma, metabolic diseases, and HIV-associated neurological disorders. Within macrophages, the HIV-1 regulatory protein "Nef" can modulate surface receptors, interact with signaling pathways, and promote specific environments that contribute to each of these pathologies. Moreover, genetic variation in Nef may also guide the macrophage response. Herein, we review findings relating to the Nef-macrophage interaction and how this relationship contributes to disease pathogenesis.
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48
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Apps R, Qi Y, Carlson JM, Chen H, Gao X, Thomas R, Yuki Y, Del Prete GQ, Goulder P, Brumme ZL, Brumme CJ, John M, Mallal S, Nelson G, Bosch R, Heckerman D, Stein JL, Soderberg KA, Moody MA, Denny TN, Zeng X, Fang J, Moffett A, Lifson JD, Goedert JJ, Buchbinder S, Kirk GD, Fellay J, McLaren P, Deeks SG, Pereyra F, Walker B, Michael NL, Weintrob A, Wolinsky S, Liao W, Carrington M. Influence of HLA-C expression level on HIV control. Science 2013; 340:87-91. [PMID: 23559252 PMCID: PMC3784322 DOI: 10.1126/science.1232685] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression levels of all common HLA-C allotypes and tested directly for effects of HLA-C expression on outcomes of HIV infection in 5243 individuals. Increasing HLA-C expression was associated with protection against multiple outcomes independently of individual HLA allelic effects in both African and European Americans, regardless of their distinct HLA-C frequencies and linkage relationships with HLA-B and HLA-A. Higher HLA-C expression was correlated with increased likelihood of cytotoxic T lymphocyte responses and frequency of viral escape mutation. In contrast, high HLA-C expression had a deleterious effect in Crohn's disease, suggesting a broader influence of HLA expression levels in human disease.
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Affiliation(s)
- Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | | | - Haoyan Chen
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
- Department of Gastroenterology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai 200001, China
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Rasmi Thomas
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Greg Q. Del Prete
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Philip Goulder
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Department of Paediatrics, Oxford University, Oxford OX1 3SY, UK
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada V6Z 1Y6
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada V6Z 1Y6
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, 6150
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, 6150
| | - George Nelson
- Basic Research Program, Center for Cancer Research Genetics Core, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ronald Bosch
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA 02115, USA
| | - David Heckerman
- Microsoft Research, eScience Group, Los Angeles, CA 90024, USA
| | - Judy L. Stein
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | | | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Xue Zeng
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
- Department of Dermatology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Jingyuan Fang
- Department of Gastroenterology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai 200001, China
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, CB2 1QP, UK
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - James J. Goedert
- Infectious and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Susan Buchbinder
- San Francisco Department of Public Health, Bridge HIV, San Francisco, CA 94102, USA
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jacques Fellay
- Institute of Microbiology, University Hospital Lausanne and School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Paul McLaren
- Institute of Microbiology, University Hospital Lausanne and School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, CA 94105, USA
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Amy Weintrob
- Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, 20817, USA
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
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Sanjuán R, Nebot MR, Peris JB, Alcamí J. Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1. PLoS Biol 2013; 11:e1001523. [PMID: 23565057 PMCID: PMC3614509 DOI: 10.1371/journal.pbio.1001523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/14/2013] [Indexed: 01/06/2023] Open
Abstract
HIV, unlike other viruses, may benefit from immune recognition by preserving the sequence of its T cell epitopes, thereby enhancing transmission between cells. The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4+ helper T lymphocytes (TH cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient level can promote either T-cell epitope conservation or escape. We predict greater conservation for epitopes contributing significantly to total immune activation levels (immunodominance), and when TH cell infection is concomitant to epitope recognition (trans-infection). We suggest that HIV-driven immune activation in the lymph nodes during the chronic stage of the disease may offer a favorable scenario for epitope conservation. Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved TH epitopes may be counterproductive. A key component of the immune response against viruses and other pathogens is the recognition of short foreign protein sequences called epitopes. However, viruses can escape the immune system by mutating, so epitopes should accumulate high levels of genetic variability. This has been documented in several human viruses, but in HIV, unexpectedly, epitopes tend to be relatively conserved. Here, we propose that this is a consequence of the peculiar interactions that occur between HIV and the immune system. As with other viruses, recognition of HIV epitopes promotes the activation of cytotoxic and helper T lymphocytes, which then orchestrate a cellular immune response. However, HIV infects helper T lymphocytes as their target cell in the body and does so more efficiently when these cells have been activated to participate in an immune response. Mathematical modeling showed that, in some cases, HIV may take advantage of immune activation, thus favoring epitope conservation. This should be more likely to occur with epitopes that trigger more vigorous T-cell responses, and during the process known as “trans-infection,” in which helper T lymphocytes are infected while being activated. Our results highlight the potential advantages of an HIV vaccination strategy based on epitopes that stimulate cytotoxic T lymphocytes without specifically stimulating helper T lymphocytes.
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Affiliation(s)
- Rafael Sanjuán
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain.
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50
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Distinct HIV-1 escape patterns selected by cytotoxic T cells with identical epitope specificity. J Virol 2012; 87:2253-63. [PMID: 23236061 DOI: 10.1128/jvi.02572-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pol283-8-specific, HLA-B*51:01-restricted, cytotoxic T cells (CTLs) play a critical role in the long-term control of HIV-1 infection. However, these CTLs select for the reverse transcriptase (RT) I135X escape mutation, which may be accumulating in circulating HIV-1 sequences. We investigated the selection of the I135X mutation by CTLs specific for the same epitope but restricted by HLA-B*52:01. We found that Pol283-8-specific, HLA-B*52:01-restricted CTLs were elicited predominantly in chronically HIV-1-infected individuals. These CTLs had a strong ability to suppress the replication of wild-type HIV-1, though this ability was weaker than that of HLA-B*51:01-restricted CTLs. The crystal structure of the HLA-B*52:01-Pol283-8 peptide complex provided clear evidence that HLA-B*52:01 presents the peptide similarly to HLA-B*51:01, ensuring the cross-presentation of this epitope by both alleles. Population level analyses revealed a strong association of HLA-B*51:01 with the I135T mutant and a relatively weaker association of HLA-B*52:01 with several I135X mutants in both Japanese and predominantly Caucasian cohorts. An in vitro viral suppression assay revealed that the HLA-B*52:01-restricted CTLs failed to suppress the replication of the I135X mutant viruses, indicating the selection of these mutants by the CTLs. These results suggest that the different pattern of I135X mutant selection may have resulted from the difference between these two CTLs in the ability to suppress HIV-1 replication.
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