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Gao Y, Barton JP. A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583183. [PMID: 38464239 PMCID: PMC10925374 DOI: 10.1101/2024.03.03.583183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Natural selection often acts on multiple traits simultaneously. For example, the virus HIV-1 faces pressure to evade host immunity while also preserving replicative fitness. While past work has studied selection during HIV-1 evolution, it is challenging to quantitatively separate different contributions to fitness. This task is made more difficult because a single mutation can affect both immune escape and replication. Here, we develop an evolutionary model that disentangles the effects of escaping CD8+ T cell-mediated immunity, which we model as a binary trait, from other contributions to fitness. After validation in simulations, we applied this model to study within-host HIV-1 evolution in a clinical data set. We observed strong selection for immune escape, sometimes greatly exceeding past estimates, especially early in infection. Conservative estimates suggest that roughly half of HIV-1 fitness gains during the first months to years of infection can be attributed to T cell escape. Our approach is not limited to HIV-1 or viruses, and could be adapted to study the evolution of quantitative traits in other contexts.
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Affiliation(s)
- Yirui Gao
- Department of Physics and Astronomy, University of California, Riverside, USA
| | - John P. Barton
- Department of Physics and Astronomy, University of California, Riverside, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, USA
- Department of Physics and Astronomy, University of Pittsburgh, USA
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2
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Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
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Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
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3
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Navarrete-Muñoz MA, Ramos R, Holguín Á, Cabello A, Górgolas M, Benito JM, Rallón N. High frequency of CD8 escape mutations in elite controllers as new obstacle for HIV cure. Virulence 2022; 13:1713-1719. [PMID: 36190143 PMCID: PMC9543107 DOI: 10.1080/21505594.2022.2129353] [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] [Indexed: 10/30/2022] Open
Abstract
Accumulation of mutations in epitopes of cytolytic-T-lymphocytes immune response (CTL) in HIV-reservoir seems to be one of the reasons for shock-and-kill strategy failure. Ten non-controller patients on successful cART (TX) and seven elite controllers (EC) were included. HIV-Gag gene from purified resting memory CD4+ T-cells was sequenced by Next-Generation-Sequencing. HLA class-I alleles were typed to predict optimal HIV-Gag CTL epitopes. For each subject, the frequency of mutated epitopes in the HIV-Gag gene, the proportion of them considered as CTL-escape variants as well as their effect on antigen recognition by HLA were assessed. The proportion (%) of mutated HIV-Gag CTL epitopes in the reservoir was high and similar in EC and TX (86%[50-100] and 57%[48-82] respectively, p=0.315). Many of them were predicted to negatively impact antigen recognition. Moreover, the proportion of mutated epitopes considered to be CTL-escape variants was also similar in TX and EC (77%[49-92] vs. 50%[33-75] respectively, p=0.117). Thus, the most relevant finding of our study was the high and similar proportions of HIV-Gag CTL-escape mutations in the reservoir of both HIV-noncontroller patients with cART (TX) and patients with spontaneous HIV-control (EC). Our findings suggest that escape mutations of CTL-response may be another obstacle to eliminate the HIV reservoir and constitute a proof of concept that challenges HIV cure strategies focused on the reactivation of reservoirs. Due to the small sample size that could impact the robustness of the study, further studies with larger cohorts of elite controller patients are needed to confirm these results.
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Affiliation(s)
- María A Navarrete-Muñoz
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Ricardo Ramos
- Unidad de Genómica, Scientific Park of Madrid, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Instituto Ramón y Cajal de Investigación Sanitaria(IRYCIS), Madrid, Spain
| | - Alfonso Cabello
- Division of Infectious Diseases, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Miguel Górgolas
- Division of Infectious Diseases, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José M Benito
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Norma Rallón
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
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4
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Moyano A, Blanch-Lombarte O, Tarancon-Diez L, Pedreño-Lopez N, Arenas M, Alvaro T, Casado C, Olivares I, Vera M, Rodriguez C, Del Romero J, López-Galíndez C, Ruiz-Mateos E, Prado JG, Pernas M. Immunoescape of HIV-1 in Env-EL9 CD8 + T cell response restricted by HLA-B*14:02 in a Non progressor who lost twenty-seven years of HIV-1 control. Retrovirology 2022; 19:6. [PMID: 35346235 PMCID: PMC8962528 DOI: 10.1186/s12977-022-00591-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/16/2022] Open
Abstract
Background Long-Term Non-Progressors (LTNPs) are untreated Human Immunodeficiency virus type 1 (HIV-1) infected individuals able to control disease progression for prolonged periods. However, the LTNPs status is temporary, as viral load increases followed by decreases in CD4 + T-cell counts. Control of HIV-1 infection in LTNPs viremic controllers, have been associated with effective immunodominant HIV-1 Gag-CD8 + T-cell responses restricted by protective HLA-B alleles. Individuals carrying HLA-B*14:02 control HIV-1 infection is related to an immunodominant Env-CD8 + T-cell response. Limited data are available on the contribution of HLA-B*14:02 CD8 + T -cells in LTNPs. Results In this study, we performed a virological and immunological detailed analysis of an HLA-B*14:02 LNTP individual that lost viral control (LVC) 27 years after HIV-1 diagnosis. We analysed viral evolution and immune escape in HLA-B*14:02 restricted CD8 + T -cell epitopes and identified viral evolution at the Env-EL9 epitope selecting the L592R mutation. By IFN-γ ELISpot and immune phenotype, we characterized HLA- B*14:02 HIV-1 CD8 + T cell responses targeting, Gag-DA9 and Env-EL9 epitopes before and after LVC. We observed an immunodominant response against the Env-EL9 epitope and a decreased of the CD8 T + cell response over time with LVC. Loss of Env-EL9 responses was concomitant with selecting K588R + L592R mutations at Env-EL9. Finally, we evaluated the impact of Env-EL9 escape mutations on HIV-1 infectivity and Env protein structure. The K588R + L592R escape variant was directly related to HIV-1 increase replicative capacity and stability of Env at the LVC. Conclusions These findings support the contribution of immunodominant Env-EL9 CD8 + T-cell responses and the imposition of immune escape variants with higher replicative capacity associated with LVC in this LNTP. These data highlight the importance of Env-EL9 specific-CD8 + T-cell responses restricted by the HLA-B*14:02 and brings new insights into understanding long-term HIV-1 control mediated by Env mediated CD8 + T-cell responses. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-022-00591-7.
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Affiliation(s)
- Ana Moyano
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain.,Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Oscar Blanch-Lombarte
- IrsiCaixa AIDS Research Institute, Crta Canyet SN, Badalona, 08916, Barcelona, Spain.,Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Laura Tarancon-Diez
- Institute of Biomedicine of Seville (IBiS)/Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain.,Molecular Immunobiology Laboratory, Immunology Section, Hospital Gregorio Marañón, Madrid, Spain
| | - Nuria Pedreño-Lopez
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain.,IrsiCaixa AIDS Research Institute, Crta Canyet SN, Badalona, 08916, Barcelona, Spain
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.,CINBIO, University of Vigo, 36310, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Tamara Alvaro
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Concepción Casado
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Isabel Olivares
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval. Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Carmen Rodriguez
- Centro Sanitario Sandoval. Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Jorge Del Romero
- Centro Sanitario Sandoval. Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Cecilio López-Galíndez
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville (IBiS)/Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Crta Canyet SN, Badalona, 08916, Barcelona, Spain. .,Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain.
| | - María Pernas
- Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Carretera de Pozuelo a Majadahonda Km 2, 28220, Madrid, Spain.
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5
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Evolution during primary HIV infection does not require adaptive immune selection. Proc Natl Acad Sci U S A 2022; 119:2109172119. [PMID: 35145025 PMCID: PMC8851487 DOI: 10.1073/pnas.2109172119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 01/20/2023] Open
Abstract
Modern HIV research depends crucially on both viral sequencing and population measurements. To directly link mechanistic biological processes and evolutionary dynamics during HIV infection, we developed multiple within-host phylodynamic models of HIV primary infection for comparative validation against viral load and evolutionary dynamics data. The optimal model of primary infection required no positive selection, suggesting that the host adaptive immune system reduces viral load but surprisingly does not drive observed viral evolution. Rather, the fitness (infectivity) of mutant variants is drawn from an exponential distribution in which most variants are slightly less infectious than their parents (nearly neutral evolution). This distribution was not largely different from either in vivo fitness distributions recorded beyond primary infection or in vitro distributions that are observed without adaptive immunity, suggesting the intrinsic viral fitness distribution may drive evolution. Simulated phylogenetic trees also agree with independent data and illuminate how phylogenetic inference must consider viral and immune-cell population dynamics to gain accurate mechanistic insights.
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6
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Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time. Genes (Basel) 2022; 13:genes13020170. [PMID: 35205215 PMCID: PMC8872422 DOI: 10.3390/genes13020170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/08/2022] [Accepted: 01/12/2022] [Indexed: 02/07/2023] Open
Abstract
Mutation is the driving force of species evolution, which may change the genetic information of organisms and obtain selective competitive advantages to adapt to environmental changes. It may change the structure or function of translated proteins, and cause abnormal cell operation, a variety of diseases and even cancer. Therefore, it is particularly important to identify gene regions with high mutations. Mutations will cause changes in nucleotide distribution, which can be characterized by natural vectors globally. Based on natural vectors, we propose a mathematical formula for measuring the difference in nucleotide distribution over time to investigate the mutations of human immunodeficiency virus. The studied dataset is from public databases and includes gene sequences from twenty HIV-infected patients. The results show that the mutation rate of the nine major genes or gene segment regions in the genome exhibits discrepancy during the infected period, and the Env gene has the fastest mutation rate. We deduce that the peak of virus mutation has a close temporal relationship with viral divergence and diversity. The mutation study of HIV is of great significance to clinical diagnosis and drug design.
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7
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Lewitus E, Sanders-Buell E, Bose M, O'Sullivan AM, Poltavee K, Li Y, Bai H, Mdluli T, Donofrio G, Slike B, Zhao H, Wong K, Chen L, Miller S, Lee J, Ahani B, Lepore S, Muhammad S, Grande R, Tran U, Dussupt V, Mendez-Rivera L, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Rerks-Ngarm S, O'Connell RJ, Janes H, Gilbert PB, Gramzinski R, Vasan S, Robb ML, Michael NL, Krebs SJ, Herbeck JT, Edlefsen PT, Mullins JI, Kim JH, Tovanabutra S, Rolland M. RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection. Virus Evol 2021; 7:veab057. [PMID: 34532060 PMCID: PMC8438874 DOI: 10.1093/ve/veab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 02/01/2023] Open
Abstract
The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1’s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.
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Affiliation(s)
- Eric Lewitus
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Meera Bose
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Kultida Poltavee
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Yifan Li
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Hongjun Bai
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Thembi Mdluli
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Gina Donofrio
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Bonnie Slike
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Kim Wong
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Shana Miller
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Jenica Lee
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Bahar Ahani
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Steven Lepore
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Sevan Muhammad
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Rebecca Grande
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Ursula Tran
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Vincent Dussupt
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Sorachai Nitayaphan
- US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jaranit Kaewkungwal
- US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Robert J O'Connell
- US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Holly Janes
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Peter B Gilbert
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Robert Gramzinski
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Merlin L Robb
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Nelson L Michael
- Center for Infectious Disease Research, WRAIR, Silver Spring, MD 20910, USA
| | - Shelly J Krebs
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Paul T Edlefsen
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Jerome H Kim
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
| | | | - Morgane Rolland
- US Military HIV Research Program, WRAIR, Silver Spring, MD 20910, USA
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8
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Nguyen H, Thorball CW, Fellay J, Böni J, Yerly S, Perreau M, Hirsch HH, Kusejko K, Thurnheer MC, Battegay M, Cavassini M, Kahlert CR, Bernasconi E, Günthard HF, Kouyos RD. Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link. eLife 2021; 10:67388. [PMID: 34061023 PMCID: PMC8169104 DOI: 10.7554/elife.67388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
Background: Considering the remaining threat of drug-resistantmutations (DRMs) to antiretroviral treatment (ART) efficacy, we investigated how the selective pressure of human leukocyte antigen (HLA)-restricted cytotoxic T lymphocytes drives certain DRMs’ emergence and retention. Methods: We systematically screened DRM:HLA class I allele combinations in 3997 ART-naïve Swiss HIV Cohort Study (SHCS) patients. For each pair, a logistic regression model preliminarily tested for an association with the DRM as the outcome. The three HLA:DRM pairs remaining after multiple testing adjustment were analyzed in three ways: cross-sectional logistic regression models to determine any HLA/infection time interaction, survival analyses to examine if HLA type correlated with developing specific DRMs, and via NetMHCpan to find epitope binding evidence of immune escape. Results: Only one pair, RT-E138:HLA-B18, exhibited a significant interaction between infection duration and HLA. The survival analyses predicted two pairs with an increased hazard of developing DRMs: RT-E138:HLA-B18 and RT-V179:HLA-B35. RT-E138:HLA-B18 exhibited the greatest significance in both analyses (interaction term odds ratio [OR] 1.169 [95% confidence interval (CI) 1.075–1.273]; p-value<0.001; survival hazard ratio 12.211 [95% CI 3.523–42.318]; p-value<0.001). The same two pairs were also predicted by netMHCpan to have epitopic binding. Conclusions: We identified DRM:HLA pairs where HLA presence is associated with the presence or emergence of the DRM, indicating that the selective pressure for these mutations alternates direction depending on the presence of these HLA alleles. Funding: Funded by the Swiss National Science Foundation within the framework of the SHCS, and the University of Zurich, University Research Priority Program: Evolution in Action: From Genomes Ecosystems, in Switzerland.
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Affiliation(s)
- Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Christian Wandell Thorball
- School of Life Sciences, École Polytechnique, Fédérale de Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique, Fédérale de Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Hans H Hirsch
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, Department of Medicine, University Hospital Basel, Basel, Switzerland.,Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Maria Christine Thurnheer
- University Clinic of Infectious Diseases, University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Manuel Battegay
- Infectious Diseases and Hospital Epidemiology, Department of Medicine, University Hospital Basel, Basel, Switzerland
| | - Matthias Cavassini
- Department of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital, Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
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9
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Sohail MS, Louie RHY, McKay MR, Barton JP. MPL resolves genetic linkage in fitness inference from complex evolutionary histories. Nat Biotechnol 2021; 39:472-479. [PMID: 33257862 PMCID: PMC8044047 DOI: 10.1038/s41587-020-0737-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Genetic linkage causes the fate of new mutations in a population to be contingent on the genetic background on which they appear. This makes it challenging to identify how individual mutations affect fitness. To overcome this challenge, we developed marginal path likelihood (MPL), a method to infer selection from evolutionary histories that resolves genetic linkage. Validation on real and simulated data sets shows that MPL is fast and accurate, outperforming existing inference approaches. We found that resolving linkage is crucial for accurately quantifying selection in complex evolving populations, which we demonstrate through a quantitative analysis of intrahost HIV-1 evolution using multiple patient data sets. Linkage effects generated by variants that sweep rapidly through the population are particularly strong, extending far across the genome. Taken together, our results argue for the importance of resolving linkage in studies of natural selection.
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Affiliation(s)
- Muhammad Saqib Sohail
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - Raymond H Y Louie
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, China
- Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China.
| | - John P Barton
- Department of Physics and Astronomy, University of California, Riverside, Riverside, CA, USA.
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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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11
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Gomes STM, da Silva Graça Amoras E, Gomes ÉR, Queiroz MAF, Júnior ECS, de Vasconcelos Massafra JM, da Silva Lemos P, Júnior JLV, Ishak R, Vallinoto ACR. Immune escape mutations in HIV-1 controllers in the Brazilian Amazon region. BMC Infect Dis 2020; 20:546. [PMID: 32711474 PMCID: PMC7382849 DOI: 10.1186/s12879-020-05268-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV-1) infection is characterized by high viral replication and a decrease in CD4+ T cells (CD4+TC), resulting in AIDS, which can lead to death. In elite controllers and viremia controllers, viral replication is naturally controlled, with maintenance of CD4+TC levels without the use of antiretroviral therapy (ART). METHODS The aim of the present study was to describe virological and immunological risk factors among HIV-1-infected individuals according to characteristics of progression to AIDS. The sample included 30 treatment-naive patients classified into three groups based on infection duration (> 6 years), CD4+TC count and viral load: (i) 2 elite controllers (ECs), (ii) 7 viremia controllers (VCs) and (iii) 21 nonviremia controllers (NVCs). Nested PCR was employed to amplify the virus genome, which was later sequenced using the Ion PGM platform for subtyping and analysis of immune escape mutations. RESULTS Viral samples were classified as HIV-1 subtypes B and F. Greater selection pressure on mutations was observed in the group of viremia controllers, with a higher frequency of immunological escape mutations in the genes investigated, including two new mutations in gag. The viral sequences of viremia controllers and nonviremia controllers did not differ significantly regarding the presence of immune escape mutations. CONCLUSION The results suggest that progression to AIDS is not dependent on a single variable but rather on a set of characteristics and pressures exerted by virus biology and interactions with immunogenetic host factors.
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Affiliation(s)
- Samara Tatielle Monteiro Gomes
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Biological Science Institute, Federal University of Pará, Ananindeua, Brazil
| | | | - Érica Ribeiro Gomes
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
| | - Maria Alice Freitas Queiroz
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
| | - Edivaldo Costa Sousa Júnior
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Poliana da Silva Lemos
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | - João Lídio Vianez Júnior
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | - Ricardo Ishak
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
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12
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Immunization of BLT Humanized Mice Redirects T Cell Responses to Gag and Reduces Acute HIV-1 Viremia. J Virol 2019; 93:JVI.00814-19. [PMID: 31375576 DOI: 10.1128/jvi.00814-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
BLT (bone marrow-liver-thymus) humanized mice, which reconstitute a functional human immune system, develop prototypic human virus-specific CD8+ T cell responses following infection with human immunodeficiency virus type 1 (HIV-1). We explored the utility of the BLT model for HIV-1 vaccine development by immunizing BLT mice against the conserved viral Gag protein, utilizing a rapid prime-boost protocol of poly(lactic-co-glycolic) acid microparticles and a replication-defective herpes simplex virus (HSV) recombinant vector. After HIV-1 challenge, the mice developed broad, proteome-wide gamma interferon-positive (IFN-γ+) T cell responses against HIV-1 that reached magnitudes equivalent to what is observed in HIV-1-infected individuals. The functionality of these responses was underscored by the consistent emergence of escape mutations in multiple CD8+ T cell epitopes during the course of infection. Although prechallenge vaccine-induced responses were largely undetectable, the Gag immunization increased both the magnitude and the kinetics of anamnestic Gag-specific T cell responses following HIV-1 infection, and the magnitude of these postchallenge Gag-specific responses was inversely correlated with acute HIV-1 viremia. Indeed, Gag immunization was associated with a modest but significant 0.5-log reduction in HIV-1 viral load when analyzed across four experimental groups of BLT mice. Notably, the HSV vector induced elevated plasma concentrations of polarizing cytokines and chemotactic factors, including interleukin-12p70 (IL-12p70) and MIP-1α, which were positively correlated with the magnitude of Gag-specific responses. Overall, these results support the ability of BLT mice to recapitulate human pathogen-specific T cell responses and to respond to immunization; however, additional improvements to the model are required to develop a robust system for testing HIV-1 vaccine efficacy.IMPORTANCE Advances in the development of humanized mice have raised the possibility of a small-animal model for preclinical testing of an HIV-1 vaccine. Here, we describe the capacity of BLT humanized mice to mount broadly directed HIV-1-specific human T cell responses that are functionally active, as indicated by the rapid emergence of viral escape mutations. Although immunization of BLT mice with the conserved viral Gag protein did not result in detectable prechallenge responses, it did increase the magnitude and kinetics of postchallenge Gag-specific T cell responses, which was associated with a modest but significant reduction in acute HIV-1 viremia. Additionally, the BLT model revealed immunization-associated increases in the plasma concentrations of immunomodulatory cytokines and chemokines that correlated with more robust T cell responses. These data support the potential utility of the BLT humanized mouse for HIV-1 vaccine development but suggest that additional improvements to the model are warranted.
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13
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Palmer DS, Turner I, Fidler S, Frater J, Goedhals D, Goulder P, Huang KHG, Oxenius A, Phillips R, Shapiro R, Vuuren CV, McLean AR, McVean G. Mapping the drivers of within-host pathogen evolution using massive data sets. Nat Commun 2019; 10:3017. [PMID: 31289267 PMCID: PMC6616926 DOI: 10.1038/s41467-019-10724-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 05/20/2019] [Indexed: 11/09/2022] Open
Abstract
Differences among hosts, resulting from genetic variation in the immune system or heterogeneity in drug treatment, can impact within-host pathogen evolution. Genetic association studies can potentially identify such interactions. However, extensive and correlated genetic population structure in hosts and pathogens presents a substantial risk of confounding analyses. Moreover, the multiple testing burden of interaction scanning can potentially limit power. We present a Bayesian approach for detecting host influences on pathogen evolution that exploits vast existing data sets of pathogen diversity to improve power and control for stratification. The approach models key processes, including recombination and selection, and identifies regions of the pathogen genome affected by host factors. Our simulations and empirical analysis of drug-induced selection on the HIV-1 genome show that the method recovers known associations and has superior precision-recall characteristics compared to other approaches. We build a high-resolution map of HLA-induced selection in the HIV-1 genome, identifying novel epitope-allele combinations.
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Affiliation(s)
- Duncan S Palmer
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK.
| | - Isaac Turner
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Sarah Fidler
- Division of Medicine, Wright Fleming Institute, Imperial College, London, W2 1PG, UK
| | - John Frater
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK
- Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Dominique Goedhals
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4013, South Africa
| | - Philip Goulder
- Division of Infectious Diseases, University of the Free State, and 3 Military Hospital, Bloemfontein, 9300, South Africa
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
| | - Kuan-Hsiang Gary Huang
- Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
- Einstein Medical Center Philadelphia, 5501 Old York Road, PA, 19141, USA
| | - Annette Oxenius
- Institute of Microbiology, Swiss Federal Institute of Technology Zurich, 8093, Zurich, Switzerland
| | - Rodney Phillips
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK
- Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LE, UK
- Faculty of Medicine, UNSW Sydney, NSW, 2052, Australia
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, BO 320, Botswana
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02215, USA
| | - Cloete van Vuuren
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4013, South Africa
| | - Angela R McLean
- Institute for Emerging Infections, The Oxford Martin School, Oxford, OX1 3BD, UK
- Zoology Department, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Gil McVean
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
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14
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Kim J, De La Cruz J, Lam K, Ng H, Daar ES, Balamurugan A, Yang OO. CD8 + Cytotoxic T Lymphocyte Responses and Viral Epitope Escape in Acute HIV-1 Infection. Viral Immunol 2018; 31:525-536. [PMID: 30059271 DOI: 10.1089/vim.2018.0040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epitope escape from HIV-1-targeted CD8+ cytotoxic T lymphocyte (CTL) responses occurs rapidly after acute infection and contributes to the eventual failure of effective immune control of HIV-1 infection. Because the early CTL response is key in determining HIV-1 disease outcome, studying the process of epitope escape is crucial for understanding what leads to failure of immune control in acute HIV-1 infection and will provide important implications for HIV-1 vaccine design. HIV-1-specific CD8+ T lymphocyte responses against viral epitopes were mapped in six acutely infected individuals, and the magnitudes of these responses were measured longitudinally during acute infection. The evolution of autologous circulating viral epitopes was determined in four of these subjects. In-depth testing of CD8+ T lymphocyte responses against index and all autologous-detected variant epitopes was performed in one subject. Among the four individuals examined, 10 of a total of 35 CD8+ T cell responses within Gag, Pol, and Nef showed evidence of epitope escape. CTL responses with viral epitope variant evolution were shown in one subject, and this evolution occurred with and without measurable CTL responses against epitope variants. These results demonstrate a dynamic period of viral epitope evolution in early HIV-1 infection due to CD8+ CTL response pressure.
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Affiliation(s)
- Joseph Kim
- 1 Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Justin De La Cruz
- 1 Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Karen Lam
- 2 Department of Microbiology, Immunology, and Molecular Genetics, University of California , Los Angeles, California
| | - Hwee Ng
- 1 Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Eric S Daar
- 3 Los Angeles Biomedical Research Institute , Harbor-UCLA Medical Center, Torrance, California
| | - Arumugam Balamurugan
- 1 Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California , Los Angeles, California
| | - Otto O Yang
- 1 Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California , Los Angeles, California.,2 Department of Microbiology, Immunology, and Molecular Genetics, University of California , Los Angeles, California.,4 AIDS Healthcare Foundation , Los Angeles, California
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15
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Abstract
The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance. We highlight the multiple ways in which the neutral theory has had an impact, which has been accelerated in the age of high-throughput, high-resolution genomics.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge,
United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Brittany Rife Magalis
- Institute for Genomics and Evolutionary Medicine, Temple University,
Philadelphia, PA
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16
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Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Pond SLK, Chung YS, Penugonda S, Chipman JG, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, Wolinsky SM. Lorenzo-Redondo et al. reply. Nature 2017; 551:E10. [PMID: 29168807 PMCID: PMC10851914 DOI: 10.1038/nature24635] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60011, USA
| | - Helen R Fryer
- Institute for Emerging Infections, Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60011, USA
| | - John Archer
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas 4485-661 Vairão, Portugal
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Yoon-Seok Chung
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju-si, Chungcheongbuk-do, 28159, South Korea
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60011, USA
| | - Jeffrey G Chipman
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Courtney V Fletcher
- Antiviral Pharmacology Laboratory, University of Nebraska Medical Center, College of Pharmacy, Omaha, Nebraska 68198, USA
| | - Timothy W Schacker
- Division of Infectious Diseases, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ashley T Haase
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Angela R McLean
- Institute for Emerging Infections, Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60011, USA
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17
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Rosenbloom DIS, Hill AL, Laskey SB, Siliciano RF. Re-evaluating evolution in the HIV reservoir. Nature 2017; 551:E6-E9. [PMID: 29168805 DOI: 10.1038/nature24634] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/23/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel I S Rosenbloom
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
| | - Alison L Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA
| | - Sarah B Laskey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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18
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Dapp MJ, Kober KM, Chen L, Westfall DH, Wong K, Zhao H, Hall BM, Deng W, Sibley T, Ghorai S, Kim K, Chen N, McHugh S, Au L, Cohen M, Anastos K, Mullins JI. Patterns and rates of viral evolution in HIV-1 subtype B infected females and males. PLoS One 2017; 12:e0182443. [PMID: 29045410 PMCID: PMC5646779 DOI: 10.1371/journal.pone.0182443] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/18/2017] [Indexed: 12/18/2022] Open
Abstract
Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6–11 years of infection from 8 Women’s Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men.
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Affiliation(s)
- Michael J. Dapp
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kord M. Kober
- Department of Physiological Nursing, University of California at San Francisco, California, United States of America
| | - Lennie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Dylan H. Westfall
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kim Wong
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hong Zhao
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Breana M. Hall
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Wenjie Deng
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Thomas Sibley
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Suvankar Ghorai
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Katie Kim
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Natalie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Sarah McHugh
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lily Au
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Mardge Cohen
- The Core Center, Bureau of Health Services of Cook County, Chicago, Illinois, United States of America
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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19
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Rosás-Umbert M, Mothe B, Noguera-Julian M, Bellido R, Puertas MC, Carrillo J, Rodriguez C, Perez-Alvarez N, Cobarsí P, Gomez CE, Esteban M, Jímenez JL, García F, Blanco J, Martinez-Picado J, Paredes R, Brander C. Virological and immunological outcome of treatment interruption in HIV-1-infected subjects vaccinated with MVA-B. PLoS One 2017; 12:e0184929. [PMID: 28953921 PMCID: PMC5617163 DOI: 10.1371/journal.pone.0184929] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/13/2017] [Indexed: 01/02/2023] Open
Abstract
The most relevant endpoint in therapeutic HIV vaccination is the assessment of time to viral rebound or duration of sustained control of low-level viremia upon cART treatment cessation. Structured treatment interruptions (STI) are however not without risk to the patient and reliable predictors of viral rebound/control after therapeutic HIV-1 vaccination are urgently needed to ensure patient safety and guide therapeutic vaccine development. Here, we integrated immunological and virological parameters together with viral rebound dynamics after STI in a phase I therapeutic vaccine trial of a polyvalent MVA-B vaccine candidate to define predictors of viral control. Clinical parameters, proviral DNA, host HLA genetics and measures of humoral and cellular immunity were evaluated. A sieve effect analysis was conducted comparing pre-treatment viral sequences to breakthrough viruses after STI. Our results show that a reduced proviral HIV-1 DNA at study entry was independently associated with two virological parameters, delayed HIV-1 RNA rebound (p = 0.029) and lower peak viremia after treatment cessation (p = 0.019). Reduced peak viremia was also positively correlated with a decreased number of HLA class I allele associated polymorphisms in Gag sequences in the rebounding virus population (p = 0.012). Our findings suggest that proviral DNA levels and the number of HLA-associated Gag polymorphisms may have an impact on the clinical outcome of STI. Incorporation of these parameters in future therapeutic vaccine trials may guide refined immunogen design and help conduct safer STI approaches.
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Affiliation(s)
- Miriam Rosás-Umbert
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
| | - Rocío Bellido
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Maria C. Puertas
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - C. Rodriguez
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Núria Perez-Alvarez
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Patricia Cobarsí
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
| | | | | | | | - Felipe García
- Hospital Clinic–HIVACAT, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
- Health Sciences Research Institute Germans Trias i Pujol, IGTP, Badalona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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20
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Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity. J Virol 2017. [PMID: 28637761 DOI: 10.1128/jvi.00518-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In the large majority of cases, HIV infection is established by a single variant, and understanding the characteristics of successfully transmitted variants is relevant to prevention strategies. Few studies have investigated the viral determinants of mother-to-child transmission. To determine the impact of Gag-protease-driven viral replication capacity on mother-to-child transmission, the replication capacities of 148 recombinant viruses encoding plasma-derived Gag-protease from 53 nontransmitter mothers, 48 transmitter mothers, and 47 infected infants were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. All study participants were infected with HIV-1 subtype C. There was no significant difference in replication capacities between the nontransmitter (n = 53) and transmitter (n = 44) mothers (P = 0.48). Infant-derived Gag-protease NL4-3 recombinant viruses (n = 41) were found to have a significantly lower Gag-protease-driven replication capacity than that of viruses derived from the mothers (P < 0.0001 by a paired t test). High percent similarities to consensus subtype C Gag, p17, p24, and protease sequences were also found in the infants (n = 28) in comparison to their mothers (P = 0.07, P = 0.002, P = 0.03, and P = 0.02, respectively, as determined by a paired t test). These data suggest that of the viral quasispecies found in mothers, the HIV mother-to-child transmission bottleneck favors the transmission of consensus-like viruses with lower viral replication capacities.IMPORTANCE Understanding the characteristics of successfully transmitted HIV variants has important implications for preventative interventions. Little is known about the viral determinants of HIV mother-to-child transmission (MTCT). We addressed the role of viral replication capacity driven by Gag, a major structural protein that is a significant determinant of overall viral replicative ability and an important target of the host immune response, in the MTCT bottleneck. This study advances our understanding of the genetic bottleneck in MTCT by revealing that viruses transmitted to infants have a lower replicative ability as well as a higher similarity to the population consensus (in this case HIV subtype C) than those of their mothers. Furthermore, the observation that "consensus-like" virus sequences correspond to lower in vitro replication abilities yet appear to be preferentially transmitted suggests that viral characteristics favoring transmission are decoupled from those that enhance replicative capacity.
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21
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Gorin AM, Du Y, Liu FY, Zhang TH, Ng HL, Hofmann C, Cumberland WG, Sun R, Yang OO. HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes. PLoS Pathog 2017; 13:e1006541. [PMID: 28787455 PMCID: PMC5560751 DOI: 10.1371/journal.ppat.1006541] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/17/2017] [Accepted: 07/19/2017] [Indexed: 01/11/2023] Open
Abstract
Certain Major Histocompatibility-I (MHC-I) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes (CTLs), but the mechanisms mediating this containment are difficult to elucidate in vivo. Here we provide controlled assessments of fitness landscapes and CTL-imposed constraints for immunodominant epitopes presented by two protective (B*57 and B*27) and one non-protective (A*02) MHC-I types. Libraries of HIV-1 with saturation mutagenesis of CTL epitopes are propagated with and without CTL selective pressure to define the fitness landscapes for epitope mutation and escape from CTLs via deep sequencing. Immunodominant B*57- and B*27- present epitopes are highly limited in options for fit mutations, with most viable variants recognizable by CTLs, whereas an immunodominant A*02 epitope-presented is highly permissive for mutation, with many options for CTL evasion without loss of viability. Generally, options for evasion overlap considerably between CTL clones despite highly distinct T cell receptors. Finally, patterns of variant recognition suggest population-wide CTL selection for the A*02-presented epitope. Overall, these findings indicate that these protective MHC-I types yield CTL targeting of highly constrained epitopes, and underscore the importance of blocking public escape pathways for CTL-based interventions against HIV-1. Certain MHC class I types are associated with superior immune containment of HIV-1, underscoring the importance of CD8+ cytotoxic T lymphocytes (CTLs). Epitope escape mutations for these types is limited, indicating reduced immune evasion. Two proposed mechanisms are: 1) CTL targeting of highly sequence-constrained epitopes, or 2) more promiscuous CTLs for epitope variation. However, the in vivo complexity of undefined starting virus, multiple targeted epitopes, polyclonal CTL responses against each epitope, and post-hoc evaluation of the interaction renders examination of mechanisms difficult. Here we approach this question with controlled prospective in vitro experiments using saturation mutagenesis of epitopes in clonal HIV-1, propagated in the absence or presence of CTL clones to define the options for epitope mutation and immune evasion by deep sequencing. We find that two immunodominant epitopes presented by protective MHC types are highly mutation-constrained compared to one presented by a non-protective MHC type, whereas CTL promiscuity for epitope variation is not appreciably different. These results suggest that these protective MHC types are associated with limited HIV-1 escape predominately due to intrinsic constraints on epitope mutation, and underscore the importance of focusing the CTL response on highly conserved epitopes for immunotherapies and vaccines.
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Affiliation(s)
- Aleksandr M. Gorin
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Franklin Y. Liu
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tian-Hao Zhang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Hwee L. Ng
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Christian Hofmann
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - William G. Cumberland
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, United States of America
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Otto O. Yang
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- AIDS Healthcare Foundation, Los Angeles, California, United States of America
- * E-mail:
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22
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Park SY, Love TMT, Reynell L, Yu C, Kang TM, Anastos K, DeHovitz J, Liu C, Kober KM, Cohen M, Mack WJ, Lee HY. The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards. Sci Rep 2017; 7:7480. [PMID: 28785052 PMCID: PMC5547093 DOI: 10.1038/s41598-017-07490-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/29/2017] [Indexed: 11/09/2022] Open
Abstract
HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment. HIV incidence assay performance is evaluated via false recency rate (FRR) and mean duration of recent infection (MDRI). We conducted a meta-analysis of 438 incident and 305 chronic specimens' HIV envelope genes from a diverse global cohort. The genome similarity index (GSI) accurately characterized infection stage across diverse host and viral factors. All except one chronic specimen had GSIs below 0.67, yielding a FRR of 0.33 [0-0.98] %. We modeled the incidence assay biomarker dynamics with a logistic link function assuming individual variabilities in a Beta distribution. The GSI probability density function peaked close to 1 in early infection and 0 around two years post infection, yielding MDRI of 420 [361, 467] days. We tested the assay by newly sequencing 744 envelope genes from 59 specimens of 21 subjects who followed from HIV negative status. Both standardized residuals and Anderson-Darling tests showed that the test dataset was statistically consistent with the model biomarker dynamics. This is the first reported incidence assay meeting the optimal FRR and MDRI performance standards. Signatures of HIV gene diversification can allow precise cross-sectional surveillance with a desirable temporal range of incidence detection.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Lucy Reynell
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Carl Yu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Tina Manzhu Kang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Kathryn Anastos
- Department of Medicine, and Epidemiology & Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States
| | - Jack DeHovitz
- Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Chenglong Liu
- Department of Medicine, Georgetown University, Washington, DC, United States
| | - Kord M Kober
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, United States
| | - Mardge Cohen
- Department of Medicine, Stroger Hospital, Chicago, IL, United States
| | - Wendy J Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
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23
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Kijak GH, Sanders-Buell E, Chenine AL, Eller MA, Goonetilleke N, Thomas R, Leviyang S, Harbolick EA, Bose M, Pham P, Oropeza C, Poltavee K, O’Sullivan AM, Billings E, Merbah M, Costanzo MC, Warren JA, Slike B, Li H, Peachman KK, Fischer W, Gao F, Cicala C, Arthos J, Eller LA, O’Connell RJ, Sinei S, Maganga L, Kibuuka H, Nitayaphan S, Rao M, Marovich MA, Krebs SJ, Rolland M, Korber BT, Shaw GM, Michael NL, Robb ML, Tovanabutra S, Kim JH. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog 2017; 13:e1006510. [PMID: 28759651 PMCID: PMC5552316 DOI: 10.1371/journal.ppat.1006510] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/10/2017] [Accepted: 07/03/2017] [Indexed: 01/12/2023] Open
Abstract
In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.
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Affiliation(s)
- Gustavo H. Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- * E-mail:
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Michael A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Nilu Goonetilleke
- School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States of America
| | - Elizabeth A. Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Celina Oropeza
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Kultida Poltavee
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Anne Marie O’Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Erik Billings
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Melanie Merbah
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Margaret C. Costanzo
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Joanna A. Warren
- School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Bonnie Slike
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Kristina K. Peachman
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Will Fischer
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Claudia Cicala
- Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - James Arthos
- Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Leigh A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | | | | | | | - Hannah Kibuuka
- Makerere University-Walter Reed Project, Kampala, Uganda
| | | | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Mary A. Marovich
- Vaccine Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States of America
| | - Shelly J. Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Bette T. Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
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24
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HIV-1 Epitope Variability Is Associated with T Cell Receptor Repertoire Instability and Breadth. J Virol 2017; 91:JVI.00771-17. [PMID: 28592539 DOI: 10.1128/jvi.00771-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 05/31/2017] [Indexed: 12/31/2022] Open
Abstract
Mutational escape of HIV-1 from HIV-1-specific CD8+ T lymphocytes (CTLs) is a major barrier for effective immune control. Each epitope typically is targeted by multiple clones with distinct T cell receptors (TCRs). While the clonal repertoire may be important for containing epitope variation, determinants of its composition are poorly understood. We investigate the clonal repertoire of 29 CTL responses against 23 HIV-1 epitopes longitudinally in nine chronically infected untreated subjects with plasma viremia of <3,000 RNA copies/ml over 17 to 179 weeks. The composition of TCRs targeting each epitope varied considerably in stability over time, although clonal stability (Sorensen index) was not significantly time dependent within this interval. However, TCR stability inversely correlated with epitope variability in the Los Alamos HIV-1 Sequence Database, consistent with TCR evolution being driven by epitope variation. Finally, a robust inverse correlation of TCR breadth against each epitope versus epitope variability further suggested that this variability drives TCR repertoire diversification. In the context of studies demonstrating rapidly shifting HIV-1 sequences in vivo, our findings support a variably dynamic process of shifting CTL clonality lagging in tandem with viral evolution and suggest that preventing escape of HIV-1 may require coordinated direction of the CTL clonal repertoire to simultaneously block escape pathways.IMPORTANCE Mutational escape of HIV-1 from HIV-1-specific CD8+ T lymphocytes (CTLs) is a major barrier to effective immune control. The number of distinct CTL clones targeting each epitope is proposed to be an important factor, but the determinants are poorly understood. Here, we demonstrate that the clonal stability and number of clones for the CTL response against an epitope are inversely associated with the general variability of the epitope. These results show that CTLs constantly lag epitope mutation, suggesting that preventing HIV-1 escape may require coordinated direction of the CTL clonal repertoire to simultaneously block escape pathways.
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25
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Mullins JI, Frenkel LM. Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy. J Infect Dis 2017; 215:S119-S127. [PMID: 28520966 DOI: 10.1093/infdis/jiw636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The latent HIV-1 reservoir in blood decays very slowly, even during prolonged suppression of viral replication by antiretroviral therapy (ART). Mechanisms for reservoir persistence include replenishment through low-level viral replication, longevity and homeostatic proliferation of memory T cells, and most recently appreciated, clonal expansion of HIV-infected cells. Clonally expanded cells make up a large and increasing fraction of the residual infected cell population on ART, and insertion of HIV proviruses into certain host cellular genes has been associated with this proliferation. That the vast majority of proviruses are defective clouds our assessment of the degree to which clonally expanded cells harbor infectious viruses, and thus the extent to which they contribute to reservoirs relevant to curing infection. This review summarizes past studies that have defined our current understanding and the gaps in our knowledge of the mechanisms by which proviral integration and clonal expansion sustain the HIV reservoir.
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Affiliation(s)
- James I Mullins
- Departments of Microbiology, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US
| | - Lisa M Frenkel
- Departments of Pediatrics, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, US
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26
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Kitchen SG, Zack JA. Engineering HIV-Specific Immunity with Chimeric Antigen Receptors. AIDS Patient Care STDS 2016; 30:556-561. [PMID: 27905838 DOI: 10.1089/apc.2016.0239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
HIV remains a highly important public health and clinical issue despite many recent advances in attempting to develop a cure, which has remained elusive for most people infected with HIV. HIV disease can be controlled with pharmacologic therapies; however, these treatments are expensive, may have severe side effects, and are not curative. Consequently, an improved means to control or eliminate HIV replication is needed. Cytotoxic T lymphocytes (CTLs) play a critical role in controlling viral replication and are an important part in the ability of the immune response to eradicate most viral infections. There are considerable efforts to enhance CTL responses in HIV-infected individuals in hopes of providing the immune response with armaments to more effectively control viral replication. In this review, we discuss some of these efforts and focus on the development of a gene therapy-based approach to engineer hematopoietic stem cells with an HIV-1-specific chimeric antigen receptor, which seeks to provide an inexhaustible source of HIV-1-specific immune cells that are MHC unrestricted and superior to natural antiviral T cell responses. These efforts provide the basis for further development of T cell functional enhancement to target and treat chronic HIV infection in hopes of eradicating the virus from the body.
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Affiliation(s)
- Scott G. Kitchen
- Division of Hematology/Oncology, Department of Medicine, and UCLA Center for AIDS Research, UCLA AIDS Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jerome A. Zack
- Division of Hematology/Oncology, Department of Medicine, and UCLA Center for AIDS Research, UCLA AIDS Institute, David Geffen School of Medicine at UCLA, Los Angeles, California
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California
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Angin M, Wong G, Papagno L, Versmisse P, David A, Bayard C, Charmeteau-De Muylder B, Besseghir A, Thiébaut R, Boufassa F, Pancino G, Sauce D, Lambotte O, Brun-Vézinet F, Matheron S, Rowland-Jones SL, Cheynier R, Sáez-Cirión A, Appay V. Preservation of Lymphopoietic Potential and Virus Suppressive Capacity by CD8+ T Cells in HIV-2-Infected Controllers. THE JOURNAL OF IMMUNOLOGY 2016; 197:2787-95. [PMID: 27566819 DOI: 10.4049/jimmunol.1600693] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/23/2016] [Indexed: 12/14/2022]
Abstract
Compared with HIV-1, HIV-2 infection is characterized by a larger proportion of slow or nonprogressors. A better understanding of HIV-2 pathogenesis should open new therapeutic avenues to establish control of HIV-1 replication in infected patients. In this study, we studied the production of CD8(+) T cells and their capacity for viral control in HIV-2 controllers from the French ANRS CO5 HIV-2 cohort. HIV-2 controllers display a robust capacity to support long-term renewal of the CD8(+) T cell compartment by preserving immune resources, including hematopoietic progenitors and thymic activity, which could contribute to the long-term maintenance of the CD8(+) T cell response and the avoidance of premature immune aging. Our data support the presence of HIV-2 Gag-specific CD8(+) T cells that display an early memory differentiation phenotype and robust effector potential in HIV-2 controllers. Accordingly, to our knowledge, we show for the first time that HIV-2 controllers possess CD8(+) T cells that show an unusually strong capacity to suppress HIV-2 infection in autologous CD4(+) T cells ex vivo, an ability that likely depends on the preservation of host immune resources. This effective and durable antiviral response probably participates in a virtuous circle, during which controlled viral replication permits the preservation of potent immune functions, thus preventing HIV-2 disease progression.
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Affiliation(s)
- Mathieu Angin
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Glenn Wong
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France; Nuffield Department of Medicine, Headington, Oxford OX3 7FZ, United Kingdom
| | - Laura Papagno
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France
| | - Pierre Versmisse
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Annie David
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Charles Bayard
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France
| | - Bénédicte Charmeteau-De Muylder
- INSERM U1016, Institut Cochin, Cytokines and Viral Infections Team, Paris 75014, France; CNRS UMR 8104, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Amel Besseghir
- Centre de Méthodologie et de Gestion des Essais Cliniques de l'INSERM U1219, Virus de l'Immunodéficience Humaine, Hépatites Virales et Comorbidités, Épidémiologie Clinique et Santé Publique, Bordeaux 33076, France
| | - Rodolphe Thiébaut
- Centre de Méthodologie et de Gestion des Essais Cliniques de l'INSERM U1219, Virus de l'Immunodéficience Humaine, Hépatites Virales et Comorbidités, Épidémiologie Clinique et Santé Publique, Bordeaux 33076, France
| | - Faroudy Boufassa
- INSERM U1018, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris Sud, Le Kremlin Bicêtre 94270, France
| | - Gianfranco Pancino
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France
| | - Delphine Sauce
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France
| | - Olivier Lambotte
- INSERM UMR 1184, Immunologie des Maladies Virales et Autoimmunes, Le Kremlin Bicêtre 94270, France; Assistance Publique-Hôpitaux de Paris, Service de Médecine Interne, Hôpitaux Universitaires, Le Kremlin Bicêtre 94270, France; Université Paris Sud, Le Kremlin Bicêtre 94270, France
| | - Françoise Brun-Vézinet
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Virologie, Hôpital Bichat, Paris 75018, France
| | - Sophie Matheron
- INSERM UMR 1137, Infections, Antimicrobiens, Modélisation, Evolution, Université Paris Diderot, Sorbonne Paris Cité, Paris 75018, France; and Assistance Publique-Hôpitaux de Paris, Service des Maladies Infectieuses et Tropicales, Hôpital Bichat, Paris 75018, France
| | | | - Rémi Cheynier
- INSERM U1016, Institut Cochin, Cytokines and Viral Infections Team, Paris 75014, France; CNRS UMR 8104, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris 75015, France;
| | - Victor Appay
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, DHU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, Paris 75005, France;
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Goz E, Tuller T. Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions. J Comput Biol 2016; 23:641-50. [PMID: 27347769 DOI: 10.1089/cmb.2016.0052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A large number of studies demonstrated the importance of different HIV RNA structural elements at all stages of the viral life cycle. Nevertheless, the significance of many of these structures is unknown, and plausibly new regions containing RNA structure-mediated regulatory signals remain to be identified. An important characteristic of genomic regions carrying functionally significant secondary structures is their mutational robustness, that is, the extent to which a sequence remains constant in spite of despite mutations in terms of its underlying secondary structure. Structural robustness to mutations is expected to be important in the case of functional RNA structures in viruses with high mutation rate; it may prevent fitness loss due to disruption of possibly functional conformations, pointing to the specific significance of the corresponding genomic region. In the current work, we perform a genome-wide computational analysis to detect signals of a direct evolutionary selection for strong folding and RNA structure-based mutational robustness within HIV coding sequences. We provide evidence that specific regions of HIV structural genes undergo an evolutionary selection for strong folding; in addition, we demonstrate that HIV Rev responsive element seems to undergo a direct evolutionary selection for increased secondary structure robustness to point mutations. We believe that our analysis may enable a better understanding of viral evolutionary dynamics at the RNA structural level and may benefit to practical efforts of engineering antiviral vaccines and novel therapeutic approaches.
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Affiliation(s)
- Eli Goz
- 1 Department of Biomedical Engineering, Tel-Aviv University , Ramat Aviv, Israel .,2 SynVaccine Ltd . Ramat Hachayal, Tel Aviv, Israel
| | - Tamir Tuller
- 1 Department of Biomedical Engineering, Tel-Aviv University , Ramat Aviv, Israel .,2 SynVaccine Ltd . Ramat Hachayal, Tel Aviv, Israel .,3 Sagol School of Neuroscience, Tel-Aviv University , Ramat Aviv, Israel
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29
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Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8+ T Cells. mBio 2016; 7:mBio.00473-16. [PMID: 27247230 PMCID: PMC4895106 DOI: 10.1128/mbio.00473-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Curing HIV-1 infection will require elimination of persistent cellular reservoirs that harbor latent virus in the face of combination antiretroviral therapy (cART). Proposed immunotherapeutic strategies to cure HIV-1 infection include enhancing lysis of these infected cells by cytotoxic T lymphocytes (CTL). A major challenge in this strategy is overcoming viral immune escape variants that have evaded host immune control. Here we report that naive CD8+ T cells from chronic HIV-1-infected participants on long-term cART can be primed by dendritic cells (DC). These DC must be mature, produce high levels of interleukin 12p70 (IL-12p70), be responsive to CD40 ligand (CD40L), and be loaded with inactivated, autologous HIV-1. These DC-primed CD8+ T cell responders produced high levels of gamma interferon (IFN-γ) in response to a broad range of both conserved and variable regions of Gag and effectively killed CD4+ T cell targets that were either infected with the autologous latent reservoir-associated virus or loaded with autologous Gag peptides. In contrast, HIV-1-specific memory CD8+ T cells stimulated with autologous HIV-1-loaded DC produced IFN-γ in response to a narrow range of conserved and variable Gag peptides compared to the primed T cells and most notably, displayed significantly lower cytolytic function. Our findings highlight the need to selectively induce new HIV-1-specific CTL from naive precursors while avoiding activation of existing, dysfunctional memory T cells in potential curative immunotherapeutic strategies for HIV-1 infection. Current immunotherapeutic approaches aim to enhance antiviral immunity against the HIV-1 reservoir; however, it has yet to be shown whether T cells from persons on cART can recognize and eliminate virus-infected cells. We show that in persons on cART a personalized medicine approach using their dendritic cells to stimulate their naive T cells induces potent effector CTL in vitro that recognize and eradicate HIV-1-infected CD4+ T cells. Additionally, we show that the same stimulation of existing memory T cells results in cytokine secretion but limited effector function. Our study demonstrates that the naive T cell repertoire can recognize persistent HIV-1 during cART and supports immunotherapy strategies for an HIV-1 cure that targets naive T cells, rather than existing, dysfunctional, memory T cells.
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Tan HX, Gilbertson BP, Jegaskanda S, Alcantara S, Amarasena T, Stambas J, McAuley JL, Kent SJ, De Rose R. Recombinant influenza virus expressing HIV-1 p24 capsid protein induces mucosal HIV-specific CD8 T-cell responses. Vaccine 2016; 34:1172-9. [PMID: 26826545 DOI: 10.1016/j.vaccine.2016.01.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/24/2015] [Accepted: 01/17/2016] [Indexed: 10/22/2022]
Abstract
Influenza viruses are promising mucosal vaccine vectors for HIV but their use has been limited by difficulties in engineering the expression of large amounts of foreign protein. We developed recombinant influenza viruses incorporating the HIV-1 p24 gag capsid into the NS-segment of PR8 (H1N1) and X31 (H3N2) influenza viruses with the use of multiple 2A ribosomal skip sequences. Despite the insertion of a sizable HIV-1 gene into the influenza genome, recombinant viruses were readily rescued to high titers. Intracellular expression of p24 capsid was confirmed by in vitro infection assays. The recombinant influenza viruses were subsequently tested as mucosal vaccines in BALB/c mice. Recombinant viruses were attenuated and safe in immunized mice. Systemic and mucosal HIV-specific CD8 T-cell responses were elicited in mice that were immunized via intranasal route with a prime-boost regimen. Isolated HIV-specific CD8 T-cells displayed polyfunctional cytokine and degranulation profiles. Mice boosted via intravaginal route induced recall responses from the distal lung mucosa and developed heightened HIV-specific CD8 T-cell responses in the vaginal mucosa. These findings demonstrate the potential utility of recombinant influenza viruses as vaccines for mucosal immunity against HIV-1 infection.
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Affiliation(s)
- Hyon-Xhi Tan
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Brad P Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Sinthujan Jegaskanda
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, United States
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - John Stambas
- School of Medicine, Deakin University, Geelong, Victoria, Australia; CSIRO Animal Health Laboratories, Geelong, Victoria, Australia
| | - Julie L McAuley
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Melbourne Sexual Health Centre, Alfred Hospital, Monash University Central Clinical School, Victoria, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Victoria, Australia.
| | - Robert De Rose
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
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Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection. J Virol 2015. [PMID: 26223634 DOI: 10.1128/jvi.01876-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24 gag were generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-γ/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response (r = 0.43; P = 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack. IMPORTANCE Rapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens.
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Roberts HE, Hurst J, Robinson N, Brown H, Flanagan P, Vass L, Fidler S, Weber J, Babiker A, Phillips RE, McLean AR, Frater J. Structured observations reveal slow HIV-1 CTL escape. PLoS Genet 2015; 11:e1004914. [PMID: 25642847 PMCID: PMC4333731 DOI: 10.1371/journal.pgen.1004914] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/23/2014] [Indexed: 01/11/2023] Open
Abstract
The existence of viral variants that escape from the selection pressures imposed by cytotoxic T-lymphocytes (CTLs) in HIV-1 infection is well documented, but it is unclear when they arise, with reported measures of the time to escape in individuals ranging from days to years. A study of participants enrolled in the SPARTAC (Short Pulse Anti-Retroviral Therapy at HIV Seroconversion) clinical trial allowed direct observation of the evolution of CTL escape variants in 125 adults with primary HIV-1 infection observed for up to three years. Patient HLA-type, longitudinal CD8+ T-cell responses measured by IFN-γ ELISpot and longitudinal HIV-1 gag, pol, and nef sequence data were used to study the timing and prevalence of CTL escape in the participants whilst untreated. Results showed that sequence variation within CTL epitopes at the first time point (within six months of the estimated date of seroconversion) was consistent with most mutations being transmitted in the infecting viral strain rather than with escape arising within the first few weeks of infection. Escape arose throughout the first three years of infection, but slowly and steadily. Approximately one third of patients did not drive any new escape in an HLA-restricted epitope in just under two years. Patients driving several escape mutations during these two years were rare and the median and modal numbers of new escape events in each patient were one and zero respectively. Survival analysis of time to escape found that possession of a protective HLA type significantly reduced time to first escape in a patient (p = 0.01), and epitopes escaped faster in the face of a measurable CD8+ ELISpot response (p = 0.001). However, even in an HLA matched host who mounted a measurable, specific, CD8+ response the average time before the targeted epitope evolved an escape mutation was longer than two years.
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Affiliation(s)
- Hannah E. Roberts
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Jacob Hurst
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
| | - Nicola Robinson
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
| | - Helen Brown
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
| | - Peter Flanagan
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Laura Vass
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Sarah Fidler
- Division of Medicine, Wright Fleming Institute, Imperial College, London, United Kingdom
| | - Jonathan Weber
- Division of Medicine, Wright Fleming Institute, Imperial College, London, United Kingdom
| | - Abdel Babiker
- Medical Research Council Clinical Trials Unit, London, United Kingdom
| | - Rodney E. Phillips
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
- * E-mail:
| | - Angela R. McLean
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
- Department of Zoology, Oxford University, Oxford, United Kingdom
| | - John Frater
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The Institute for Emerging Infections, The Oxford Martin School, Oxford, Oxford United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, Oxford, United Kingdom
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Stoll A, Bergmann S, Mummert C, Mueller-Schmucker SM, Spriewald BM, Harrer EG, Harrer T. Identification of HLA-C restricted, HIV-1-specific CTL epitopes by peptide induced upregulation of HLA-C expression. J Immunol Methods 2015; 418:9-18. [PMID: 25633660 DOI: 10.1016/j.jim.2015.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 11/17/2022]
Abstract
HIV-1 negative regulatory factor (Nef) can inhibit CTL recognition by downregulation of HLA-A and HLA-B on the cell surface. In contrast, HLA-C is not affected by Nef and a growing number of studies demonstrate an important role of HLA-C for the control of HIV-1. So far, only a limited number of HLA-C restricted CTL epitopes are known. As the mapping of new CTL epitopes is time and labor intensive, we investigated a novel method for the identification of HLA-C restricted CTL epitopes. B-lymphoblastoid cell lines (B-LCLs) and T2-cells were incubated with HIV-1 specific peptides and subsequently stained for HLA-C surface expression using the HLA-C specific antibody DT9. Peptides that led to increased HLA-C surface expression were used for stimulation of PBMC from HIV-1-infected patients. Subsequently, outgrowing cells were tested for peptide recognition in IFN-γ ELISPOT assays and HLA restriction of the recognized peptides was analyzed in ELISPOT assays using HLA-matched B-LCL. We observed that known HLA-C binding peptides increase HLA-C surface expression on T2-cells and on HLA-C*0102 and HLA-C*0702 homozygous B-LCL. Moreover, screening of HIV-1 Nef with overlapping peptides for potential C*0702 restricted epitopes using this method revealed a total of 8 peptides which considerably increased cell surface expression of HLA-C. By epitope mapping and functional analysis of peptide-stimulated T-cell lines we were able to define the peptide YPLTFGWCY as a new C*0702-restricted CTL epitope. These results show that the analysis of peptide induced HLA-C upregulation on B-LCL and T2-cells enables the efficient identification of new HLA-C restricted CTL epitopes.
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Affiliation(s)
- Andrej Stoll
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Silke Bergmann
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Christiane Mummert
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Sandra M Mueller-Schmucker
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd M Spriewald
- Department of Internal Medicine 5, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ellen G Harrer
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Harrer
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.
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34
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Short conserved sequences of HIV-1 are highly immunogenic and shift immunodominance. J Virol 2014; 89:1195-204. [PMID: 25378501 DOI: 10.1128/jvi.02370-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
UNLABELLED Cellular immunity is pivotal in HIV-1 pathogenesis but is hampered by viral sequence diversity. An approach to minimize this diversity is to focus immunity on conserved proteome sequences; therefore, we selected four relatively conserved regions (Gag amino acids 148 to 214 and 250 to 335, Env amino acids 521 to 606, and Nef amino acids 106 to 148), each created in three mosaics, to provide better coverage of M-group HIV-1 sequences. A conserved-region vaccine (CRV) delivering genes for these four regions as equal mixtures of three mosaics each (each region at a separate injection site) was compared to a whole-protein vaccine (WPV) delivering equimolar amounts of genes for whole Gag, Env, and Nef as clade B consensus sequences (separate injection sites). Three rhesus macaques were vaccinated via three DNA primes and a recombinant adenovirus type 5 boost (weeks 0, 4, 8, and 24, respectively). Although CRV inserts were about one-fifth that of WPV, the CRV generated comparable-magnitude blood CD4+ and CD8+ T lymphocyte responses against Gag, Env, and Nef. WPV responses preferentially targeted proteome areas outside the selected conserved regions in direct proportion to sequence lengths, indicating similar immunogenicities for the conserved regions and the outside regions. The CRV yielded a conserved-region targeting density that was approximately 5-fold higher than that of the WPV. A similar pattern was seen for bronchoalveolar lymphocytes, but with quadruple the magnitudes seen in blood. Overall, these findings demonstrate that the selected conserved regions are highly immunogenic and that anatomically isolated vaccinations with these regions focus immunodominance compared to the case for full-length protein vaccination. IMPORTANCE HIV-1 sequence diversity is a major barrier limiting the capability of cellular immunity to contain infection and the ability of vaccines to match circulating viral sequences. To date, vaccines tested in humans have delivered whole proteins or genes for whole proteins, and it is unclear whether including only conserved sequences would yield sufficient cellular immunogenicity. We tested a vaccine delivering genes for four small conserved HIV-1 regions compared to a control vaccine with genes for whole Gag, Env, and Nef. Although the conserved regions ranged from 43 to 86 amino acids and comprised less than one-fifth of the whole Gag/Env/Nef sequence, the vaccines elicited equivalent total magnitudes of both CD4+ and CD8+ T lymphocyte responses. These data demonstrate the immunogenicity of these small conserved regions and the potential for a vaccine to steer immunodominance toward conserved epitopes.
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35
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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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Abstract
UNLABELLED Recall T cell responses to HIV-1 antigens are used as a surrogate for endogenous cellular immune responses generated during infection. Current methods of identifying antigen-specific T cell reactivity in HIV-1 infection use bulk peripheral blood mononuclear cells (PBMC) yet ignore professional antigen-presenting cells (APC) that could reveal otherwise hidden responses. In the present study, peptides representing autologous variants of major histocompatibility complex (MHC) class I-restricted epitopes from HIV-1 Gag and Env were used as antigens in gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) and polyfunctional cytokine assays. Here we show that dendritic cells (DC) enhanced T cell reactivity at all stages of disease progression but specifically restored T cell reactivity after combination antiretroviral therapy (cART) to early infection levels. Type 1 cytokine secretion was also enhanced by DC and was most apparent late post-cART. We additionally show that DC reveal polyfunctional T cell responses after many years of treatment, when potential immunotherapies would be implemented. These data underscore the potential efficacy of DC immunotherapy that aims to awaken a dormant, autologous, HIV-1-specific CD8+ T cell response. IMPORTANCE Assessment of endogenous HIV-1-specific T cell responses is critical for generating immunotherapies for subjects on cART. Current assays ignore the ability of dendritic cells to reveal these responses and may therefore underestimate the breadth and magnitude of T cell reactivity. As DC do not prime new responses in these assays, it can be assumed that the observed responses are not detected without appropriate stimulation. This is important because dogma states that HIV-1 mutates to evade host recognition and that CD8+ cytotoxic T lymphocyte (CTL) failure is due to the inability of T cells to recognize the autologous virus. The results presented here indicate that responses to autologous virus are generated during infection but may need additional stimulation to be effective. Detecting the breadth and magnitude of HIV-1-specific T cell reactivity generated in vivo is of the utmost importance for generating effective DC immunotherapies.
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Romero-Severson E, Skar H, Bulla I, Albert J, Leitner T. Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol Biol Evol 2014; 31:2472-82. [PMID: 24874208 DOI: 10.1093/molbev/msu179] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occur within hosts, not at the moment of transmission, predating the transmission events as described by the pretransmission interval. Second, the order in which nodes in a phylogeny occur may be reflective of the within-host dynamics rather than epidemiologic relationships. To investigate these phenomena, motivated by within-host diversity patterns, we developed a two-phase coalescent model that includes a transmission bottleneck followed by linear outgrowth to a maximum population size followed by either stabilization or decline of the population. The model predicts that the pretransmission interval shrinks compared with predictions based on constant population size or a simple transmission bottleneck. Because lineages coalesce faster in a small population, the probability of a pathogen phylogeny to resemble the transmission history depends on when after infection a donor transmits to a new host. We also show that the probability of inferring the incorrect order of multiple transmissions from the same host is high. Finally, we compare time of HIV-1 infection informed by genetic distances in phylogenies to independent biomarker data, and show that, indeed, the pretransmission interval biases phylogeny-based estimates of when transmissions occurred. We describe situations where caution is needed not to misinterpret which parts of a phylogeny that may indicate outbreaks and tight transmission clusters.
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Affiliation(s)
- Ethan Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Helena Skar
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Ingo Bulla
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, SwedenDepartment of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
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38
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Buggert M, Norström MM, Salemi M, Hecht FM, Karlsson AC. Functional avidity and IL-2/perforin production is linked to the emergence of mutations within HLA-B*5701-restricted epitopes and HIV-1 disease progression. THE JOURNAL OF IMMUNOLOGY 2014; 192:4685-96. [PMID: 24740510 DOI: 10.4049/jimmunol.1302253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Viral escape from HIV-1-specific CD8(+) T cells has been demonstrated in numerous studies previously. However, the qualitative features driving the emergence of mutations within epitopes are still unclear. In this study, we aimed to distinguish whether specific functional characteristics of HLA-B*5701-restricted CD8(+) T cells influence the emergence of mutations in high-risk progressors (HRPs) versus low-risk progressors (LRPs). Single-genome sequencing was performed to detect viral mutations (variants) within seven HLA-B*5701-restricted epitopes in Gag (n = 4) and Nef (n = 3) in six untreated HLA-B*5701 subjects followed from early infection up to 7 y. Several well-characterized effector markers (IFN-γ, IL-2, MIP-1β, TNF, CD107a, and perforin) were identified by flow cytometry following autologous (initial and emerging variant/s) epitope stimulations. This study demonstrates that specific functional attributes may facilitate the outgrowth of mutations within HLA-B*5701-restricted epitopes. A significantly lower fraction of IL-2-producing cells and a decrease in functional avidity and polyfunctional sensitivity were evident in emerging epitope variants compared with the initial autologous epitopes. Interestingly, the HRPs mainly drove these differences, whereas the LRPs maintained a directed and maintained functional response against emerging epitope variants. In addition, LRPs induced improved cell-cycle progression and perforin upregulation after autologous and emerging epitope variant stimulations in contrast to HRPs. The maintained quantitative and qualitative features of the CD8(+) T cell responses in LRPs toward emerging epitope variants provide insights into why HLA-B*5701 subjects have different risks of HIV-1 disease progression.
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Affiliation(s)
- Marcus Buggert
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm S-141 86, Sweden
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39
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Liu Y, Rao U, McClure J, Konopa P, Manocheewa S, Kim M, Chen L, Troyer RM, Tebit DM, Holte S, Arts EJ, Mullins JI. Impact of mutations in highly conserved amino acids of the HIV-1 Gag-p24 and Env-gp120 proteins on viral replication in different genetic backgrounds. PLoS One 2014; 9:e94240. [PMID: 24713822 PMCID: PMC3979772 DOI: 10.1371/journal.pone.0094240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 03/14/2014] [Indexed: 11/24/2022] Open
Abstract
It has been hypothesized that a single mutation at a highly conserved amino acid site (HCS) can be severely deleterious to HIV in most if not all isolate-specific genetic backgrounds. Consequently, potentially universal HIV-1 vaccines exclusively targeting highly conserved regions of the viral proteome have been proposed. To test this hypothesis, we examined the impact of 10 Gag-p24 and 9 Env-gp120 HCS single mutations on viral fitness. In the original founder sequence of the subject in whom these mutations were identified, all Gag-p24 HCS mutations significantly reduced viral replication fitness, including 7 that were lethal. Similar results were obtained at 9/10 sites when the same mutations were introduced into the founder sequences of two epidemiologically unlinked subjects. In contrast, none of the 9 Env-gp120 HCS mutations were lethal in the original founder sequence, and four had no fitness cost. Hence, HCS mutations in Gag-p24 are likely to be severely deleterious in different HIV-1 subtype B backgrounds; however, some HCS mutations in both Gag-p24 and Env-gp120 fragments can be well tolerated. Therefore, when designing HIV-1 immunogens that are intended to force the virus to nonviable escape pathways, the fitness constraints on the HIV segments included should be considered beyond their conservation level.
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Affiliation(s)
- Yi Liu
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
| | - Ushnal Rao
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jan McClure
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Philip Konopa
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Siriphan Manocheewa
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Moon Kim
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lennie Chen
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ryan M. Troyer
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Denis M. Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sarah Holte
- Program in Biostatistics and Biomathematics, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eric J. Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
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40
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Leviyang S. Constructing lower-bounds for CTL escape rates in early SIV infection. J Theor Biol 2014; 352:82-91. [PMID: 24603063 DOI: 10.1016/j.jtbi.2014.02.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 01/15/2014] [Accepted: 02/17/2014] [Indexed: 12/30/2022]
Abstract
Intrahost human and simian immunodeficiency virus (HIV and SIV) evolution is marked by repeated viral escape from cytotoxic T-lymphocyte (CTL) response. Typically, the first such CTL escape starts around the time of peak viral load and completes within one or two weeks. Many authors have developed methods to quantify CTL escape rates, but existing methods depend on sampling at two or more timepoints. Since many datasets capture the dynamics of the first CTL escape at a single timepoint, we develop inference methods applicable to single timepoint datasets. To account for model uncertainty, we construct estimators which serve as lower bounds for the escape rate. These lower-bound estimators allow for statistically meaningful comparison of escape rates across different times and different compartments. We apply our methods to two SIV datasets, showing that escape rates are relatively high during the initial days of the first CTL escape and drop to lower levels as the escape proceeds.
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Affiliation(s)
- Sivan Leviyang
- Georgetown University, Department of Mathematics and Statistics, United States
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41
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The impact of viral evolution and frequency of variant epitopes on primary and memory human immunodeficiency virus type 1-specific CD8⁺ T cell responses. Virology 2013; 450-451:34-48. [PMID: 24503065 DOI: 10.1016/j.virol.2013.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/11/2013] [Accepted: 10/08/2013] [Indexed: 12/18/2022]
Abstract
It is unclear if HIV-1 variants lose the ability to prime naïve CD8(+) cytotoxic T lymphocytes (CTL) during progressive, untreated infection. We conducted a comprehensive longitudinal analysis of viral evolution and its impact on primary and memory CD8(+) T cell responses pre-seroconversion (SC), post-SC, and during combination antiretroviral therapy (cART). Memory T cell responses targeting autologous virus variants reached a nadir by 8 years post-SC with development of AIDS, followed by a transient enhancement of anti-HIV-1 CTL responses upon initiation of cART. We show broad and high magnitude primary T cell responses to late variants in pre-SC T cells, comparable to primary anti-HIV-1 responses induced in T cells from uninfected persons. Despite evolutionary changes, CD8(+) T cells could still be primed to HIV-1 variants. Hence, vaccination against late, mutated epitopes could be successful in enhancing primary reactivity of T cells for control of the residual reservoir of HIV-1 during cART.
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42
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Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication. J Virol 2013; 88:1354-65. [PMID: 24227851 DOI: 10.1128/jvi.02361-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major challenge in the development of an HIV vaccine is that of contending with the extensive sequence variability found in circulating viruses. Induction of HIV-specific T-cell responses targeting conserved regions and induction of HIV-specific T-cell responses recognizing a high number of epitope variants have both been proposed as strategies to overcome this challenge. We addressed the ability of cytotoxic T lymphocytes from 30 untreated HIV-infected subjects with and without control of virus replication to recognize all clade B Gag sequence variants encoded by at least 5% of the sequences in the Los Alamos National Laboratory HIV database (1,300 peptides) using gamma interferon and interleukin-2 (IFN-γ/IL-2) FluoroSpot analysis. While targeting of conserved regions was similar in the two groups (P = 0.47), we found that subjects with control of virus replication demonstrated marginally lower recognition of Gag epitope variants than subjects with normal progression (P = 0.05). In viremic controllers and progressors, we found variant recognition to be associated with viral load (r = 0.62, P = 0.001). Interestingly, we show that increased overall sequence coverage, defined as the overall proportion of HIV database sequences targeted through the Gag-specific repertoire, is inversely associated with viral load (r = -0.38, P = 0.03). Furthermore, we found that sequence coverage, but not variant recognition, correlated with increased recognition of a panel of clade B HIV founder viruses (r = 0.50, P = 0.004). We propose sequence coverage by HIV Gag-specific immune responses as a possible correlate of protection that may contribute to control of virus replication. Additionally, sequence coverage serves as a valuable measure by which to evaluate the protective potential of future vaccination strategies.
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43
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Abstract
Intrapatient evolution of human immunodeficiency virus type 1 (HIV-1) is driven by the adaptive immune system resulting in rapid change of HIV-1 proteins. When cytotoxic CD8(+) T cells or neutralizing antibodies target a new epitope, the virus often escapes via nonsynonymous mutations that impair recognition. Synonymous mutations do not affect this interplay and are often assumed to be neutral. We test this assumption by tracking synonymous mutations in longitudinal intrapatient data from the C2-V5 part of the env gene. We find that most synonymous variants are lost even though they often reach high frequencies in the viral population, suggesting a cost to the virus. Using published data from SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) assays, we find that synonymous mutations that disrupt base pairs in RNA stems flanking the variable loops of gp120 are more likely to be lost than other synonymous changes: these RNA hairpins might be important for HIV-1. Computational modeling indicates that, to be consistent with the data, a large fraction of synonymous mutations in this genomic region need to be deleterious with a cost on the order of 0.002 per day. This weak selection against synonymous substitutions does not result in a strong pattern of conservation in cross-sectional data but slows down the rate of evolution considerably. Our findings are consistent with the notion that large-scale patterns of RNA structure are functionally relevant, whereas the precise base pairing pattern is not.
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44
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Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
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45
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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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46
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Gatanaga H, Murakoshi H, Hachiya A, Hayashida T, Chikata T, Ode H, Tsuchiya K, Sugiura W, Takiguchi M, Oka S. Naturally Selected Rilpivirine-Resistant HIV-1 Variants by Host Cellular Immunity. Clin Infect Dis 2013; 57:1051-5. [DOI: 10.1093/cid/cit430] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI. Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PLoS One 2013; 8:e66065. [PMID: 23785468 PMCID: PMC3681919 DOI: 10.1371/journal.pone.0066065] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/03/2013] [Indexed: 12/24/2022] Open
Abstract
The recently available x-ray crystal structure of HIV-1 capsid hexamers has provided insight into the molecular interactions crucial for the virus's mature capsid formation. Amino acid changes at these interaction points are likely to have a strong impact on capsid functionality and, hence, viral infectivity and replication fitness. To test this hypothesis, we introduced the most frequently observed single amino acid substitution at 30 sites: 12 at the capsid hexamerization interface and 18 at non-interface sites. Mutations at the interface sites were more likely to be lethal (Fisher's exact test p = 0.027) and had greater negative impact on viral replication fitness (Wilcoxon rank sum test p = 0.040). Among the interface mutations studied, those located in the cluster of hydrophobic contacts at NTD-NTD interface and those that disrupted NTD-CTD inter-domain helix capping hydrogen bonds were the most detrimental, indicating that these interactions are particularly important for maintaining capsid structure and/or function. These functionally constrained sites provide potential targets for novel HIV drug development and vaccine immunogen design.
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Affiliation(s)
- Siriphan Manocheewa
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - J. Victor Swain
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Erinn Lanxon-Cookson
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Morgane Rolland
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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48
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Munier CML, Kelleher AD, Kent SJ, De Rose R. The role of T cell immunity in HIV-1 infection. Curr Opin Virol 2013; 3:438-46. [PMID: 23747036 DOI: 10.1016/j.coviro.2013.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/07/2013] [Accepted: 05/07/2013] [Indexed: 12/11/2022]
Abstract
The interplay between the T cell immune response and human immunodeficiency virus (HIV)-1 largely determines the outcome of infection. Typically, the virus overcomes the immune defences leading to a gradual decline in function that permits the development of disease. In recent years, a concerted effort in comparing T cell responses between 'controllers' and 'progressors' is beginning to identify the T cell subsets and factors that affect disease progression related to the effector functions of both CD4 and CD8 T cells. These efforts are providing opportunities for development of novel therapies and vaccines.
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Affiliation(s)
- C Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, University of NSW, Sydney, NSW, Australia
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49
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Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, Hertz T, Yu X, Horton H. Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design. PLoS One 2013; 8:e64405. [PMID: 23741326 PMCID: PMC3669284 DOI: 10.1371/journal.pone.0064405] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/12/2013] [Indexed: 12/21/2022] Open
Abstract
A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8+ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8+ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8+ T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8+ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r = - 0.65, p = 0.009). Moreover, subjects possessing CD8+ T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p = 0.021). The association between viral control and the breadth of conserved CD8+ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p = 0.215). The associations with viral control were independent of functional avidity of CD8+ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that can elicit CD8+ T cell responses to multiple conserved epitopes of HIV-1.
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Affiliation(s)
- Pratima Kunwar
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Natalie Hawkins
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Warren L. Dinges
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Polyclinic Infectious Disease, Seattle, Washington, United States of America
| | - Yi Liu
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Erin E. Gabriel
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David A. Swan
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Claire E. Stevens
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Janine Maenza
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ann C. Collier
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Tomer Hertz
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Xuesong Yu
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Helen Horton
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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Abstract
During the first weeks of human immunodeficiency virus-1 (HIV-1) infection, cytotoxic T-lymphocytes (CTLs) select for multiple escape mutations in the infecting HIV population. In recent years, methods that use escape mutation data to estimate rates of HIV escape have been developed, thereby providing a quantitative framework for exploring HIV escape from CTL response. Current methods for escape-rate inference focus on a specific HIV mutant selected by a single CTL response. However, recent studies have shown that during the first weeks of infection, CTL responses occur at one to three epitopes and HIV escape occurs through complex mutation pathways. Consequently, HIV escape from CTL response forms a complex, selective sweep that is difficult to analyze. In this work, we develop a model of initial infection, based on the well-known standard model, that allows for a description of multi-epitope response and the complex mutation pathways of HIV escape. Under this model, we develop Bayesian and hypothesis-test inference methods that allow us to analyze and estimate HIV escape rates. The methods are applied to two HIV patient data sets, concretely demonstrating the utility of our approach.
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