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Effect of Difference in Consensus Sequence between HIV-1 Subtype A/E and Subtype B Viruses on Elicitation of Gag-Specific CD8 + T Cells and Accumulation of HLA-Associated Escape Mutations. J Virol 2021; 95:JVI.02061-20. [PMID: 33361435 PMCID: PMC8094948 DOI: 10.1128/jvi.02061-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/09/2020] [Indexed: 01/14/2023] Open
Abstract
The Gag280 mutation is associated with HLA-C*01:02 but not with HLA-B*52:01 in subtype A/E-infected individuals, whereas this mutation is associated with HLA-B*52:01 but not with HLA-C*01:02 in subtype B infections. Although it is known that the Gag280 mutant is selected by HLA-B*52:01-restricted GagRI8 (Gag275-282)-specific T cells in subtype B infections, it remains unknown why this Gag280 mutation is associated with HLA-C*01:02 rather than HLA-B*52:01 in subtype A/E infections. The subtype B and A/E viruses have different consensus sequence, with Thr and Val at Gag280, respectively. To clarify the effect of this difference in Gag280 consensus sequence, we investigated the role of HLA-C*01:02-restricted GagYI9 (Gag277-285)-specific T cells in selection of Gag280 mutations in subtype A/E-infected Vietnamese and subtype B-infected Japanese individuals. GagYI9-4V-specific T cells, which were frequently elicited in Vietnamese individuals infected with the consensus-type A/E virus, failed to recognize GagV280T mutant A/E virus-infected cells. GagYI9-4T mutant epitope-specific T cells, which were weakly elicited in individuals infected with the mutant A/E virus, had weak or no ability to recognize the mutant virus. These results account for the mechanism for selection and accumulation of GagV280T mutants in the case of subtype A/E infections. In contrast, HLA-C*01:02-restricted GagYI9-4T-specific T cells were weakly elicited in Japanese individuals infected with the subtype B virus, explaining why HLA-C*01:02-restricted Gag280 mutations are not accumulated in the case of a subtype B infection. The present study demonstrated that a difference in the Gag280 consensus sequence influenced the elicitation of the GagYI9-specific T cells involved in the accumulation of HLA-C*01:02-associated Gag280 mutations.IMPORTANCE HIV-1 mutations escaped from HIV-specific CD8+ T cells are mostly detected as HLA-associated mutations. A diversity of HLA-associated mutations is somewhat distinct to each race and region, since HLA allele distribution differs among them. A difference in the consensus sequence among HIV-1 subtypes may also influence the diversity of HLA-associated mutations. HLA-C*01:02-associated GagV280T and HLA-B*52:01-associated GagT280A/S mutations were previously identified in HIV-1 subtype A/E-infected and subtype B-infected individuals, respectively, though these subtype viruses have a different consensus sequence at Gag280. We demonstrated that the GagV280T mutant virus was selected by HLA-C*01:02-restricted GagYI9-4V-specific T cells in subtype A/E-infected Vietnamese but that HLA-C*01:02-restricted GagYI9-4T-specific T cells were weakly elicited in subtype B-infected Japanese. Together with our recent study which demonstrated the mechanism for the accumulation of HLA-B*52:01-associated mutations, we clarified the mechanism for the accumulation of different Gag280 mutations and the effect of the difference in the consensus sequence on the accumulation of escape mutations.
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Garcia-Bates TM, Palma ML, Anderko RR, Hsu DC, Ananworanich J, Korber BT, Gaiha GD, Phanuphak N, Thomas R, Tovanabutra S, Walker BD, Mellors JW, Piazza PA, Kroon E, Riddler SA, Michael NL, Rinaldo CR, Mailliard RB. Dendritic cells focus CTL responses toward highly conserved and topologically important HIV-1 epitopes. EBioMedicine 2021; 63:103175. [PMID: 33450518 PMCID: PMC7811131 DOI: 10.1016/j.ebiom.2020.103175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/05/2022] Open
Abstract
Background During early HIV-1 infection, immunodominant T cell responses to highly variable epitopes lead to the establishment of immune escape virus variants. Here we assessed a type 1-polarized monocyte-derived dendritic cell (MDC1)-based approach to selectively elicit cytotoxic T lymphocyte (CTL) responses against highly conserved and topologically important HIV-1 epitopes in HIV-1-infected individuals from the Thailand RV254/SEARCH 010 cohort who initiated antiretroviral therapy (ART) during early infection (Fiebig stages I-IV). Methods Autologous MDC1 were used as antigen presenting cells to induce in vitro CTL responses against HIV-1 Gag, Pol, Env, and Nef as determined by flow cytometry and ELISpot assay. Ultra-conserved or topologically important antigens were respectively identified using the Epigraph tool and a structure-based network analysis approach and compared to overlapping peptides spanning the Gag proteome. Findings MDC1 presenting either the overlapping Gag, Epigraph, or Network 14–21mer peptide pools consistently activated and expanded HIV-1-specific T cells to epitopes identified at the 9–13mer peptide level. Interestingly, some CTL responses occurred outside known or expected HLA associations, providing evidence of new HLA-associated CTL epitopes. Comparative analyses demonstrated more sequence conservation among Epigraph antigens but a higher magnitude of CTL responses to Network and Gag peptide groups. Importantly, CTL responses against topologically constrained Gag epitopes contained in both the Network and Gag peptide pools were selectively enhanced in the Network pool-initiated cultures. Interpretation Our study supports the use of MDC1 as a therapeutic strategy to induce and focus CTL responses toward putative fitness-constrained regions of HIV-1 to prevent immune escape and control HIV-1 infection. Funding A full list of the funding sources is detailed in the Acknowledgment section of the manuscript.
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Affiliation(s)
- Tatiana M Garcia-Bates
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Mariana L Palma
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Renee R Anderko
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Denise C Hsu
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States; SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States; SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand; Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM, New Mexico Consortium, Los Alamos, NM, United States
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, United States
| | | | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - John W Mellors
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, United States
| | - Paolo A Piazza
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Eugene Kroon
- SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Sharon A Riddler
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robbie B Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States.
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