1
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Miner MD, deCamp A, Grunenberg N, De Rosa SC, Fiore-Gartland A, Bar K, Spearman P, Allen M, Yu PC, Manso B, Frahm N, Kalams S, Baden L, Keefer MC, Scott HM, Novak R, Van Tieu H, Tomaras GD, Kublin JG, McElrath MJ, Corey L, Frank I. Polytopic fractional delivery of an HIV vaccine alters cellular responses and results in increased epitope breadth in a phase 1 randomized trial. EBioMedicine 2024; 100:104987. [PMID: 38306894 PMCID: PMC10847480 DOI: 10.1016/j.ebiom.2024.104987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/20/2023] [Accepted: 01/15/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Elicitation of broad immune responses is understood to be required for an efficacious preventative HIV vaccine. This Phase 1 randomized controlled trial evaluated whether administration of vaccine antigens separated at multiple injection sites vs combined, fractional delivery at multiple sites affected T-cell breadth compared to standard, single site vaccination. METHODS We randomized 90 participants to receive recombinant adenovirus 5 (rAd5) vector with HIV inserts gag, pol and env via three different strategies. The Standard group received vaccine at a single anatomic site (n = 30) compared to two polytopic (multisite) vaccination groups: Separated (n = 30), where antigens were separately administered to four anatomical sites, and Fractioned (n = 30), where fractions of each vaccine component were combined and administered at four sites. All groups received the same total dose of vaccine. FINDINGS CD8 T-cell response rates and magnitudes were significantly higher in the Fractioned group than Standard for several antigen pools tested. CD4 T-cell response magnitudes to Pol were higher in the Separated than Standard group. T-cell epitope mapping demonstrated greatest breadth in the Fractioned group (median 8.0 vs 2.5 for Standard, Wilcoxon p = 0.03; not significant after multiplicity adjustment for co-primary endpoints). IgG binding antibody response rates to Env were higher in the Standard and Fractioned groups vs Separated group. INTERPRETATION This study shows that the number of anatomic sites for which a vaccine is delivered and distribution of its antigenic components influences immune responses in humans. FUNDING National Institute of Allergy and Infectious Diseases, NIH.
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Affiliation(s)
- Maurine D Miner
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA.
| | - Allan deCamp
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Paul Spearman
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mary Allen
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pei-Chun Yu
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Bryce Manso
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Spyros Kalams
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Michael C Keefer
- Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - Hyman M Scott
- San Francisco Department of Public Health, San Francisco, CA, USA
| | | | - Hong Van Tieu
- Laboratory of Infectious Disease Prevention, Lindsley F. Kimball Research Institute, New York Blood Center, New York City, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York City, NY, USA
| | | | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Ian Frank
- University of Pennsylvania, Philadelphia, PA, USA
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2
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA. .,Department of Medicine, Duke University School of Medicine, Durham, NC, USA. .,Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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3
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Files JK, Sterrett S, Henostroza S, Fucile C, Maroney K, Fram T, Mallal S, Kalams S, Carlson J, Rosenberg A, Erdmann N, Bansal A, Goepfert PA. HLA-II-Associated HIV-1 Adaptation Decreases CD4 + T-Cell Responses in HIV-1 Vaccine Recipients. J Virol 2022; 96:e0119122. [PMID: 36000845 PMCID: PMC9472760 DOI: 10.1128/jvi.01191-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Epitopes with evidence of HLA-II-associated adaptation induce poorly immunogenic CD4+ T-cell responses in HIV-positive (HIV+) individuals. Many such escaped CD4+ T-cell epitopes are encoded by HIV-1 vaccines being evaluated in clinical trials. Here, we assessed whether this viral adaptation adversely impacts CD4+ T-cell responses following HIV-1 vaccination, thereby representing escaped epitopes. When evaluated in separate peptide pools, vaccine-encoded adapted epitopes (AE) induced CD4+ T-cell responses less frequently than nonadapted epitopes (NAE). We also demonstrated that in a polyvalent vaccine, where both forms of the same epitope were encoded, AE were less immunogenic. NAE-specific CD4+ T cells had increased, albeit low, levels of interferon gamma (IFN-γ) cytokine production. Single-cell transcriptomic analyses showed that NAE-specific CD4+ T cells expressed interferon-related genes, while AE-specific CD4+ T cells resembled a Th2 phenotype. Importantly, the magnitude of NAE-specific CD4+ T-cell responses, but not that of AE-specific responses, was found to positively correlate with Env-specific antibodies in a vaccine efficacy trial. Together, these findings show that HLA-II-associated viral adaptation reduces CD4+ T-cell responses in HIV-1 vaccine recipients and suggest that vaccines encoding a significant number of AE may not provide optimal B-cell help for HIV-specific antibody production. IMPORTANCE Despite decades of research, an effective HIV-1 vaccine remains elusive. Vaccine strategies leading to the generation of broadly neutralizing antibodies are likely needed to provide the best opportunity of generating a protective immune response against HIV-1. Numerous studies have demonstrated that T-cell help is necessary for effective antibody generation. However, immunogen sequences from recent HIV-1 vaccine efficacy trials include CD4+ T-cell epitopes that have evidence of immune escape. Our study shows that these epitopes, termed adapted epitopes, elicit lower frequencies of CD4+ T-cell responses in recipients from multiple HIV-1 vaccine trials. Additionally, the counterparts to these epitopes, termed nonadapted epitopes, elicited CD4+ T-cell responses that correlated with Env-specific antibodies in one efficacy trial. These results suggest that vaccine-encoded adapted epitopes dampen CD4+ T-cell responses, potentially impacting both HIV-specific antibody production and efficacious vaccine efforts.
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Affiliation(s)
- Jacob K. Files
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sarah Sterrett
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sebastian Henostroza
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher Fucile
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin Maroney
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tim Fram
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Simon Mallal
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Spyros Kalams
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Alexander Rosenberg
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathan Erdmann
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anju Bansal
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul A. Goepfert
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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4
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The Use of Molecular Dynamics Simulation Method to Quantitatively Evaluate the Affinity between HBV Antigen T Cell Epitope Peptides and HLA-A Molecules. Int J Mol Sci 2022; 23:ijms23094629. [PMID: 35563019 PMCID: PMC9105472 DOI: 10.3390/ijms23094629] [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: 03/04/2022] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 12/10/2022] Open
Abstract
Chronic hepatitis B virus (HBV), a potentially life-threatening liver disease, makes people vulnerable to serious diseases such as cancer. T lymphocytes play a crucial role in clearing HBV virus, while the pathway depends on the strong binding of T cell epitope peptide and HLA. However, the experimental identification of HLA-restricted HBV antigenic peptides is extremely time-consuming. In this study, we provide a novel prediction strategy based on structure to assess the affinity between the HBV antigenic peptide and HLA molecule. We used residue scanning, peptide docking and molecular dynamics methods to obtain the molecular docking model of HBV peptide and HLA, and then adopted the MM-GBSA method to calculate the binding affinity of the HBV peptide–HLA complex. Overall, we collected 59 structures of HLA-A from Protein Data Bank, and finally obtained 352 numerical affinity results to figure out the optimal bind choice between the HLA-A molecules and 45 HBV T cell epitope peptides. The results were highly consistent with the qualitative affinity level determined by the competitive peptide binding assay, which confirmed that our affinity prediction process based on an HLA structure is accurate and also proved that the homologous modeling strategy for HLA-A molecules in this study was reliable. Hence, our work highlights an effective way by which to predict and screen for HLA-peptide binding that would improve the treatment of HBV infection.
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5
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Currenti J, Law BM, Qin K, John M, Pilkinton MA, Bansal A, Leary S, Ram R, Chopra A, Gangula R, Yue L, Warren C, Barnett L, Alves E, McDonnell WJ, Sooda A, Heath SL, Mallal S, Goepfert P, Kalams SA, Gaudieri S. Cross-Reactivity to Mutated Viral Immune Targets Can Influence CD8 + T Cell Functionality: An Alternative Viral Adaptation Strategy. Front Immunol 2021; 12:746986. [PMID: 34764960 PMCID: PMC8577586 DOI: 10.3389/fimmu.2021.746986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022] Open
Abstract
Loss of T cell immunogenicity due to mutations in virally encoded epitopes is a well-described adaptation strategy to limit host anti-viral immunity. Another described, but less understood, adaptation strategy involves the selection of mutations within epitopes that retain immune recognition, suggesting a benefit for the virus despite continued immune pressure (termed non-classical adaptation). To understand this adaptation strategy, we utilized a single cell transcriptomic approach to identify features of the HIV-specific CD8+ T cell responses targeting non-adapted (NAE) and adapted (AE) forms of epitopes containing a non-classical adaptation. T cell receptor (TCR) repertoire and transcriptome were obtained from antigen-specific CD8+ T cells of chronic (n=7) and acute (n=4) HIV-infected subjects identified by either HLA class I tetramers or upregulation of activation markers following peptide stimulation. CD8+ T cells were predominantly dual tetramer+, confirming a large proportion of cross-reactive TCR clonotypes capable of recognizing the NAE and AE form. However, single-reactive CD8+ T cells were identified in acute HIV-infected subjects only, providing the potential for the selection of T cell clones over time. The transcriptomic profile of CD8+ T cells was dependent on the autologous virus: subjects whose virus encoded the NAE form of the epitope (and who transitioned to the AE form at a later timepoint) exhibited an 'effective' immune response, as indicated by expression of transcripts associated with polyfunctionality, cytotoxicity and apoptosis (largely driven by the genes GZMB, IFNɣ, CCL3, CCL4 and CCL5). These data suggest that viral adaptation at a single amino acid residue can provide an alternative strategy for viral survival by modulating the transcriptome of CD8+ T cells and potentially selecting for less effective T cell clones from the acute to chronic phase.
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Affiliation(s)
- Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Becker M.P. Law
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Kai Qin
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, WA, Australia
| | - Mark A. Pilkinton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Rama Gangula
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Christian Warren
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Louise Barnett
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Wyatt J. McDonnell
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anuradha Sooda
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Sonya L. Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Spyros A. Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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6
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Bansal A, Gehre MN, Qin K, Sterrett S, Ali A, Dang Y, Abraham S, Costanzo MC, Venegas LA, Tang J, Manjunath N, Brockman MA, Yang OO, Kan-Mitchell J, Goepfert PA. HLA-E-restricted HIV-1-specific CD8+ T cell responses in natural infection. J Clin Invest 2021; 131:148979. [PMID: 34228645 PMCID: PMC8363272 DOI: 10.1172/jci148979] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/01/2021] [Indexed: 01/07/2023] Open
Abstract
CD8+ T cell responses restricted by MHC-E, a nonclassical MHC molecule, have been associated with protection in an SIV/rhesus macaque model. The biological relevance of HLA-E-restricted CD8+ T cell responses in HIV infection, however, remains unknown. In this study, CD8+ T cells responding to HIV-1 Gag peptides presented by HLA-E were analyzed. Using in vitro assays, we observed HLA-E-restricted T cell responses to what we believe to be a newly identified subdominant Gag-KL9 as well as a well-described immunodominant Gag-KF11 epitope in T cell lines derived from chronically HIV-infected patients and also primed from healthy donors. Blocking of the HLA-E/KF11 binding by the B7 signal peptide resulted in decreased CD8+ T cell responses. KF11 presented via HLA-E in HIV-infected cells was recognized by antigen-specific CD8+ T cells. Importantly, bulk CD8+ T cells obtained from HIV-infected individuals recognized infected cells via HLA-E presentation. Ex vivo analyses at the epitope level showed a higher responder frequency of HLA-E-restricted responses to KF11 compared with KL9. Taken together, our findings of HLA-E-restricted HIV-specific immune responses offer intriguing and possibly paradigm-shifting insights into factors that contribute to the immunodominance of CD8+ T cell responses in HIV infection.
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Affiliation(s)
- Anju Bansal
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Mika N. Gehre
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Kai Qin
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Sarah Sterrett
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Ayub Ali
- Department of Medicine and AIDS Institute, UCLA, Los Angeles, California, USA
| | - Ying Dang
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Sojan Abraham
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Margaret C. Costanzo
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Leon A. Venegas
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - N. Manjunath
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | | | - Otto O. Yang
- Department of Medicine and AIDS Institute, UCLA, Los Angeles, California, USA
| | - June Kan-Mitchell
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Paul A. Goepfert
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
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7
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Elevated HIV Infection of CD4 T Cells in MRKAd5 Vaccine Recipients Due to CD8 T Cells Targeting Adapted Epitopes. J Virol 2021; 95:e0016021. [PMID: 34076482 DOI: 10.1128/jvi.00160-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
HIV frequently escapes CD8 T cell responses, leading to the accumulation of viral adaptations. We recently demonstrated that during chronic HIV infection, adapted epitopes can promote maturation of dendritic cells (DCs) through direct CD8 T cell interactions and lead to enhanced HIV trans-infection of CD4 T cells. Here, we sought to determine the role of such adaptations following HIV MRKAd5 vaccination. We observed that vaccine-induced adapted epitope-specific CD8 T cells promoted higher levels of DC maturation than nonadapted ones and that these matured DCs significantly enhanced HIV trans-infection. These matured DCs were associated with higher levels of interleukin 5 (IL-5) and IL-13 and a lower level of CXCL5, which have been shown to impact DC maturation, as well as a lower level of CXCL16. Finally, we observed that vaccine recipients with high HLA-I-associated adaptation became HIV infected more quickly. Our results offer another possible mechanism for enhanced infection among MRKAd5 vaccinees. IMPORTANCE Despite the well-established contribution of CD8 T cells in HIV control, prior CD8 T cell-based HIV vaccines have failed to demonstrate any efficacy in preventing viral infection. One such vaccine, known as the MRKAd5 vaccine, showed a potential increased risk of viral infection among vaccine recipients. However, the underlying mechanism(s) remains unclear. In this study, we observed that vaccine recipients with high adaptation to their HLA-I alleles were associated with an increased HIV infection risk in comparison to the others. Similar to what we observed in HIV infection in the prior study, adapted epitope-specific CD8 T cells obtained from vaccine recipients exhibit a greater capacity in facilitating viral infection by promoting dendritic cell maturation. Our findings provide a possible explanation for the enhanced viral acquisition risk among MRKAd5 vaccine recipients and highlight the importance of optimizing vaccine design with consideration of HLA-I-associated HIV adaptation.
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8
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Kist NC, Lambert B, Campbell S, Katzourakis A, Lunn D, Lemey P, Iversen AKN. HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification. Virus Evol 2020; 6:veaa085. [PMID: 33343925 PMCID: PMC7733611 DOI: 10.1093/ve/veaa085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.
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Affiliation(s)
- Nicolaas C Kist
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ben Lambert
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, Medical School Building St Mary’s Campus, Norfolk Place, London W2 1PG, UK
| | - Samuel Campbell
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Daniel Lunn
- Department of Statistics, University of Oxford, St Giles’, Oxford OX1 3LB, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Leuven B-3000, Belgium
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9
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Cross-Reactive CD8 T-Cell Responses Elicited by Adenovirus Type 5-Based HIV-1 Vaccines Contributed to Early Viral Evolution in Vaccine Recipients Who Became Infected. J Virol 2020; 94:JVI.01632-19. [PMID: 31645444 DOI: 10.1128/jvi.01632-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/14/2019] [Indexed: 11/20/2022] Open
Abstract
Because of HIV's vast sequence diversity, the ability of the CD8 T-cell response to recognize several variants of a single epitope is an important consideration for vaccine design. Cross-recognition of viral epitopes by CD8 T cells is associated with viral control during HIV-1 infection, but little is known about CD8 cross-reactivity in the context of HIV-1 vaccination. Here, we evaluated vaccine-induced CD8 cross-reactivity in two preventative HIV-1 vaccine efficacy trials, the MRKAd5 and DNA/rAd5 studies. Cross-reactive CD8 responses elicited by vaccination were similar in magnitude and frequency to those induced during acute HIV-1 infection. Although responses directed against variant epitopes were less avid than responses to vaccine-matched epitopes, we did not detect any difference in response polyfunctionality (the proportion of cells producing multiple effector molecules). And while depth, or the frequency of cross-reactive responses, did not correlate with viral loads in recipients who became infected, cross-reactivity did appear to influence early viral evolution. In comparing viral sequences of placebo versus vaccine recipients, we found that viral sequences from vaccinees encoded CD8 epitopes with more substitutions and greater biochemical dissimilarity. In other words, breakthrough sequences of vaccinees would be less cross-recognized by vaccine-induced responses. Additionally, vaccine-induced CD8 T cells poorly cross-recognized variant epitopes encoding HLA-I-associated adaptations, further supporting our conclusion that these responses play a role in driving early HIV-1 viral evolution.IMPORTANCE HIV-1 has exceptionally high sequence diversity, much of which is found within CD8 epitopes. Therefore, the ability of CD8 T cells to recognize multiple versions of a single epitope could be important for an effective vaccine. Here, we show that two previously tested vaccines induced a similar level of CD8 cross-reactivity to that seen in acute HIV-1 infection. Although this cross-reactivity did not seem to affect viral control in vaccine recipients who became infected, we identified several ways in which CD8 cross-reactivity appeared to influence HIV-1 viral evolution. First, we saw that strains isolated from infected vaccine recipients would likely be poorly cross-recognized by the vaccine-induced response. Second, we saw that adapted CD8 epitopes were poorly cross-recognized in both vaccination and infection. Collectively, we believe these results show that CD8 cross-reactivity could be an important consideration in future HIV-1 vaccine design.
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