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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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Michelo CM, Fiore-Gartland A, Dalel JA, Hayes P, Tang J, McGowan E, Kilembe W, Fernandez N, Gilmour J, Hunter E. Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes. Vaccines (Basel) 2023; 11:472. [PMID: 36851349 PMCID: PMC9961105 DOI: 10.3390/vaccines11020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.
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Affiliation(s)
- Clive M. Michelo
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jama A. Dalel
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - William Kilembe
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Eric Hunter
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
- Emory Vaccine Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
- Emory National Primate Research Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
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3
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Cohen KW, Fiore-Gartland A, Walsh SR, Yusim K, Frahm N, Elizaga ML, Maenza J, Scott H, Mayer KH, Goepfert PA, Edupuganti S, Pantaleo G, Hutter J, Morris DE, De Rosa SC, Geraghty DE, Robb ML, Michael NL, Fischer W, Giorgi EE, Malhi H, Pensiero MN, Ferrari G, Tomaras GD, Montefiori DC, Gilbert PB, McElrath MJ, Haynes BF, Korber BT, Baden LR. Trivalent mosaic or consensus HIV immunogens prime humoral and broader cellular immune responses in adults. J Clin Invest 2023; 133:e163338. [PMID: 36787249 PMCID: PMC9927951 DOI: 10.1172/jci163338] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/27/2022] [Indexed: 02/15/2023] Open
Abstract
BACKGROUNDMosaic and consensus HIV-1 immunogens provide two distinct approaches to elicit greater breadth of coverage against globally circulating HIV-1 and have shown improved immunologic breadth in nonhuman primate models.METHODSThis double-blind randomized trial enrolled 105 healthy HIV-uninfected adults who received 3 doses of either a trivalent global mosaic, a group M consensus (CON-S), or a natural clade B (Nat-B) gp160 env DNA vaccine followed by 2 doses of a heterologous modified vaccinia Ankara-vectored HIV-1 vaccine or placebo. We performed prespecified blinded immunogenicity analyses at day 70 and day 238 after the first immunization. T cell responses to vaccine antigens and 5 heterologous Env variants were fully mapped.RESULTSEnv-specific CD4+ T cell responses were induced in 71% of the mosaic vaccine recipients versus 48% of the CON-S recipients and 48% of the natural Env recipients. The mean number of T cell epitopes recognized was 2.5 (95% CI, 1.2-4.2) for mosaic recipients, 1.6 (95% CI, 0.82-2.6) for CON-S recipients, and 1.1 (95% CI, 0.62-1.71) for Nat-B recipients. Mean breadth was significantly greater in the mosaic group than in the Nat-B group using overall (P = 0.014), prime-matched (P = 0.002), heterologous (P = 0.046), and boost-matched (P = 0.009) measures. Overall T cell breadth was largely due to Env-specific CD4+ T cell responses.CONCLUSIONPriming with a mosaic antigen significantly increased the number of epitopes recognized by Env-specific T cells and enabled more, albeit still limited, cross-recognition of heterologous variants. Mosaic and consensus immunogens are promising approaches to address global diversity of HIV-1.TRIAL REGISTRATIONClinicalTrials.gov NCT02296541.FUNDINGUS NIH grants UM1 AI068614, UM1 AI068635, UM1 AI068618, UM1 AI069412, UL1 RR025758, P30 AI064518, UM1 AI100645, and UM1 AI144371, and Bill & Melinda Gates Foundation grant OPP52282.
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Affiliation(s)
- Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Stephen R. Walsh
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Karina Yusim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Marnie L. Elizaga
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hyman Scott
- San Francisco Department of Public Health, San Francisco, California, USA
| | - Kenneth H. Mayer
- Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Fenway Health, Boston, Massachusetts, USA
| | | | | | | | - Julia Hutter
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Daryl E. Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Daniel E. Geraghty
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Merlin L. Robb
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Nelson L. Michael
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Will Fischer
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Elena E. Giorgi
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Harmandeep Malhi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael N. Pensiero
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | | | - Bette T. Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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4
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Huang Y, Zhang Y, Seaton KE, De Rosa S, Heptinstall J, Carpp LN, Randhawa AK, McKinnon LR, McLaren P, Viegas E, Gray GE, Churchyard G, Buchbinder SP, Edupuganti S, Bekker LG, Keefer MC, Hosseinipour MC, Goepfert PA, Cohen KW, Williamson BD, McElrath MJ, Tomaras GD, Thakar J, Kobie JJ. Baseline host determinants of robust human HIV-1 vaccine-induced immune responses: A meta-analysis of 26 vaccine regimens. EBioMedicine 2022; 84:104271. [PMID: 36179551 PMCID: PMC9520208 DOI: 10.1016/j.ebiom.2022.104271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/27/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The identification of baseline host determinants that associate with robust HIV-1 vaccine-induced immune responses could aid HIV-1 vaccine development. We aimed to assess both the collective and relative performance of baseline characteristics in classifying individual participants in nine different Phase 1-2 HIV-1 vaccine clinical trials (26 vaccine regimens, conducted in Africa and in the Americas) as High HIV-1 vaccine responders. METHODS This was a meta-analysis of individual participant data, with studies chosen based on participant-level (vs. study-level summary) data availability within the HIV-1 Vaccine Trials Network. We assessed the performance of 25 baseline characteristics (demographics, safety haematological measurements, vital signs, assay background measurements) and estimated the relative importance of each characteristic in classifying 831 participants as High (defined as within the top 25th percentile among positive responders or above the assay upper limit of quantification) versus Non-High responders. Immune response outcomes included HIV-1-specific serum IgG binding antibodies and Env-specific CD4+ T-cell responses assessed two weeks post-last dose, all measured at central HVTN laboratories. Three variable importance approaches based on SuperLearner ensemble machine learning were considered. FINDINGS Overall, 30.1%, 50.5%, 36.2%, and 13.9% of participants were categorized as High responders for gp120 IgG, gp140 IgG, gp41 IgG, and Env-specific CD4+ T-cell vaccine-induced responses, respectively. When including all baseline characteristics, moderate performance was achieved for the classification of High responder status for the binding antibody responses, with cross-validated areas under the ROC curve (CV-AUC) of 0.72 (95% CI: 0.68, 0.76) for gp120 IgG, 0.73 (0.69, 0.76) for gp140 IgG, and 0.67 (95% CI: 0.63, 0.72) for gp41 IgG. In contrast, the collection of all baseline characteristics yielded little improvement over chance for predicting High Env-specific CD4+ T-cell responses [CV-AUC: 0.53 (0.48, 0.58)]. While estimated variable importance patterns differed across the three approaches, female sex assigned at birth, lower height, and higher total white blood cell count emerged as significant predictors of High responder status across multiple immune response outcomes using Approach 1. Of these three baseline variables, total white blood cell count ranked highly across all three approaches for predicting vaccine-induced gp41 and gp140 High responder status. INTERPRETATION The identified features should be studied further in pursuit of intervention strategies to improve vaccine responses and may be adjusted for in analyses of immune response data to enhance statistical power. FUNDING National Institute of Allergy and Infectious Diseases (UM1AI068635 to YH, UM1AI068614 to GDT, UM1AI068618 to MJM, and UM1 AI069511 to MCK), the Duke CFAR P30 AI064518 to GDT, and National Institute of Dental and Craniofacial Research (R01DE027245 to JJK). This work was also supported by the Bill and Melinda Gates Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding sources.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America; Department of Global Health, University of Washington, Seattle, WA, United States of America.
| | - Yuanyuan Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Kelly E Seaton
- Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Stephen De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Jack Heptinstall
- Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - April Kaur Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Lyle R McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MN, Canada; JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MN, Canada; Centre for the AIDS Program of Research in South Africa (CAPRISA), Durban, South Africa
| | - Paul McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MN, Canada; JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MN, Canada
| | - Edna Viegas
- Instituto Nacional de Saúde, Maputo, Mozambique
| | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; South African Medical Research Council, Cape Town, South Africa
| | - Gavin Churchyard
- Aurum Institute, Johannesburg, South Africa; School of Public Health, University of Witwatersrand, Johannesburg, South Africa
| | - Susan P Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, United States of America; Department of Medicine and Department of Epidemiology, University of California, San Francisco, CA, United States of America
| | - Srilatha Edupuganti
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Michael C Keefer
- Department of Medicine, Infectious Diseases Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | - Mina C Hosseinipour
- University of North Carolina Project, Lilongwe, Malawi; Department of Medicine, Institution for Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Brian D Williamson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America; Kaiser Permanente Washington Health Research Institute, Seattle, WA, United States of America
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States of America
| | - Georgia D Tomaras
- Center for Human Systems Immunology, Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | - James J Kobie
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America.
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5
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Oyarzun P, Kashyap M, Fica V, Salas-Burgos A, Gonzalez-Galarza FF, McCabe A, Jones AR, Middleton D, Kobe B. A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. Front Immunol 2021; 12:598778. [PMID: 33717077 PMCID: PMC7952308 DOI: 10.3389/fimmu.2021.598778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/11/2021] [Indexed: 01/06/2023] Open
Abstract
Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccination strategies against EIDs. Human leukocyte antigen (HLA) molecules play a central role in the immune system by determining the peptide repertoire displayed to the T-cell compartment. Genetic polymorphisms of the HLA system thus confer a strong variability in vaccine-induced immune responses and may complicate the selection of vaccine candidates, because the distribution and frequencies of HLA alleles are highly variable among different ethnic groups. Herein, we build on the emerging paradigm of rational epitope-based vaccine design, by describing an immunoinformatics tool (Predivac-3.0) for proteome-wide T-cell epitope discovery that accounts for ethnic-level variations in immune responsiveness. Predivac-3.0 implements both CD8+ and CD4+ T-cell epitope predictions based on HLA allele frequencies retrieved from the Allele Frequency Net Database. The tool was thoroughly assessed, proving comparable performances (AUC ~0.9) against four state-of-the-art pan-specific immunoinformatics methods capable of population-level analysis (NetMHCPan-4.0, Pickpocket, PSSMHCPan and SMM), as well as a strong accuracy on proteome-wide T-cell epitope predictions for HIV-specific immune responses in the Japanese population. The utility of the method was investigated for the COVID-19 pandemic, by performing in silico T-cell epitope mapping of the SARS-CoV-2 spike glycoprotein according to the ethnic context of the countries where the ChAdOx1 vaccine is currently initiating phase III clinical trials. Potentially immunodominant CD8+ and CD4+ T-cell epitopes and population coverages were predicted for each population (the Epitope Discovery mode), along with optimized sets of broadly recognized (promiscuous) T-cell epitopes maximizing coverage in the target populations (the Epitope Optimization mode). Population-specific epitope-rich regions (T-cell epitope clusters) were further predicted in protein antigens based on combined criteria of epitope density and population coverage. Overall, we conclude that Predivac-3.0 holds potential to contribute in the understanding of ethnic-level variations of vaccine-induced immune responsiveness and to guide the development of epitope-based next-generation vaccines against emerging pathogens, whose geographic distributions and populations in need of vaccinations are often well-defined for regional epidemics.
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Affiliation(s)
- Patricio Oyarzun
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Manju Kashyap
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Victor Fica
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | | | - Faviel F Gonzalez-Galarza
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Antony McCabe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Derek Middleton
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
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6
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Michelo CM, Dalel JA, Hayes P, Fernandez N, Fiore-Gartland A, Kilembe W, Tang J, Streatfield C, Gilmour J, Hunter E. Comprehensive epitope mapping using polyclonally expanded human CD8 T cells and a two-step ELISpot assay for testing large peptide libraries. J Immunol Methods 2021; 491:112970. [PMID: 33529681 DOI: 10.1016/j.jim.2021.112970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 02/01/2023]
Abstract
The genetic diversity of circulating HIV-1 strains poses a major barrier to the design, development and evaluation of HIV-1 vaccines. The assessment of both vaccine- and natural infection-elicited T cell responses is commonly done with multivalent peptides that are designed to maximally capture the diversity of potential T cell epitopes (PTEs) observed in natural circulating sequences. However, depending on the sequence diversity of viral subtypes and number of the HIV immunogens under investigation, PTE estimates, including HLA-guided computational methods, can easily generate enormous peptide libraries. Evaluation of T cell epitope specificity using such extensive peptide libraries is usually limited by sample availability, even for high-throughput and robust epitope mapping techniques like ELISpot assays. Here we describe a novel, two-step protocol for in-vitro polyclonal expansion of CD8 T cells from a single vial of frozen PBMC, which facilitated the screening 441 HIV-1 Gag peptides for immune responses among 32 HIV-1 positive subjects and 40 HIV-1 negative subjects for peptide qualification. Using a pooled-peptide mapping strategy, epitopes were mapped in two sequential ELISpot assays; the first ELISpot screened 33 large peptide pools using CD8 T cells expanded for 7 days, while the second step tested pool-matrix peptides to identify individual peptides using CD8 T cells expanded for 10 days. This comprehensive epitope screening established the breadth and magnitude of HIV-1 Gag-specific CD8 T cells and further revealed the extent of immune responses to variable/polymorphic epitopes.
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Affiliation(s)
- Clive M Michelo
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jama A Dalel
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Natalia Fernandez
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - William Kilembe
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Claire Streatfield
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Eric Hunter
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia; Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329, USA.
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7
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Kallas EG, Grunenberg NA, Yu C, Manso B, Pantaleo G, Casapia M, Baden LR, Valencia J, Sobieszczyk M, Van Tieu H, Allen M, Hural J, Graham BS, Kublin J, Gilbert PB, Corey L, Goepfert PA, McElrath MJ, Johnson RP, Huang Y, Frahm N. Antigenic competition in CD4 + T cell responses in a randomized, multicenter, double-blind clinical HIV vaccine trial. Sci Transl Med 2020; 11:11/519/eaaw1673. [PMID: 31748227 DOI: 10.1126/scitranslmed.aaw1673] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 10/04/2019] [Indexed: 11/02/2022]
Abstract
T cell responses have been implicated in reduced risk of HIV acquisition in uninfected persons and control of viral replication in HIV-infected individuals. HIV Gag-specific T cells have been predominantly associated with post-infection control, whereas Env antigens are the target for protective antibodies; therefore, inclusion of both antigens is common in HIV vaccine design. However, inclusion of multiple antigens may provoke antigenic competition, reducing the potential effectiveness of the vaccine. HVTN 084 was a randomized, multicenter, double-blind phase 1 trial to investigate whether adding Env to a Gag/Pol vaccine decreases the magnitude or breadth of Gag/Pol-specific T cell responses. Fifty volunteers each received one intramuscular injection of 1 × 1010 particle units (PU) of rAd5 Gag/Pol and EnvA/B/C (3:1:1:1 mixture) or 5 × 109 PU of rAd5 Gag/Pol. CD4+ T cell responses to Gag/Pol measured 4 weeks after vaccination by cytokine expression were significantly higher in the group vaccinated without Env, whereas CD8+ T cell responses did not differ significantly between the two groups. Mapping of individual epitopes revealed greater breadth of the Gag/Pol-specific T cell response in the absence of Env compared to Env coimmunization. Addition of an Env component to a Gag/Pol vaccine led to reduced Gag/Pol CD4+ T cell response rate and magnitude as well as reduced epitope breadth, confirming the presence of antigenic competition. Therefore, T cell-based vaccine strategies should aim at choosing a minimalist set of antigens to reduce interference of individual vaccine components with the induction of the maximally achievable immune response.
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Affiliation(s)
- Esper G Kallas
- Division of Clinical Immunology and Allergy, University of São Paulo, São Paulo 05508, Brazil
| | - Nicole A Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenchen Yu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bryce Manso
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Giuseppe Pantaleo
- Division of Immunology and Allergy, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | | | - Lindsey R Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javier Valencia
- Asociación Civil Impacta Salud Y Educación, Lima 15063, Peru
| | - Magdalena Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY 10025, USA
| | - Hong Van Tieu
- Laboratory of Infectious Disease Prevention, New York Blood Center, New York, NY 10065, USA
| | - Mary Allen
- Division of AIDS, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Paul A Goepfert
- Division of Infectious Disease and Department of Surgery, Division of Gastroenterology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Global Health, University of Washington, Seattle, WA 98195, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.,Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - R Paul Johnson
- Yerkes National Primate Research Center, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. .,Department of Global Health, University of Washington, Seattle, WA 98195, USA
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8
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Baden LR, Walsh SR, Seaman MS, Cohen YZ, Johnson JA, Licona JH, Filter RD, Kleinjan JA, Gothing JA, Jennings J, Peter L, Nkolola J, Abbink P, Borducchi EN, Kirilova M, Stephenson KE, Pegu P, Eller MA, Trinh HV, Rao M, Ake JA, Sarnecki M, Nijs S, Callewaert K, Schuitemaker H, Hendriks J, Pau MG, Tomaka F, Korber BT, Alter G, Dolin R, Earl PL, Moss B, Michael NL, Robb ML, Barouch DH. First-in-Human Randomized, Controlled Trial of Mosaic HIV-1 Immunogens Delivered via a Modified Vaccinia Ankara Vector. J Infect Dis 2019; 218:633-644. [PMID: 29669026 DOI: 10.1093/infdis/jiy212] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/10/2018] [Indexed: 01/17/2023] Open
Abstract
Background Mosaic immunogens are bioinformatically engineered human immunodeficiency virus type 1 (HIV-1) sequences designed to elicit clade-independent coverage against globally circulating HIV-1 strains. Methods This phase 1, double-blinded, randomized, placebo-controlled trial enrolled healthy HIV-uninfected adults who received 2 doses of a modified vaccinia Ankara (MVA)-vectored HIV-1 bivalent mosaic immunogen vaccine or placebo on days 0 and 84. Two groups were enrolled: those who were HIV-1 vaccine naive (n = 15) and those who had received an HIV-1 vaccine (Ad26.ENVA.01) 4-6 years earlier (n = 10). We performed prespecified blinded cellular and humoral immunogenicity analyses at days 0, 14, 28, 84, 98, 112, 168, 270, and 365. Results All 50 planned vaccinations were administered. Vaccination was safe and generally well tolerated. No vaccine-related serious adverse events occurred. Both cellular and humoral cross-clade immune responses were elicited after 1 or 2 vaccinations in all participants in the HIV-1 vaccine-naive group. Env-specific responses were induced after a single immunization in nearly all subjects who had previously received the prototype Ad26.ENVA.01 vaccine. Conclusions No safety concerns were identified, and multiclade HIV-1-specific immune responses were elicited. Clinical Trials Registration NCT02218125.
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Affiliation(s)
- Lindsey R Baden
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston.,Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Stephen R Walsh
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston.,Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Michael S Seaman
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Yehuda Z Cohen
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Jennifer A Johnson
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston.,Harvard Medical School, Beth Israel Deaconess Medical Center, Boston
| | - J Humberto Licona
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston.,Harvard Medical School, Beth Israel Deaconess Medical Center, Boston
| | - Rachel D Filter
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston
| | - Jane A Kleinjan
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston
| | - Jon A Gothing
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston
| | - Julia Jennings
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Joseph Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Peter Abbink
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Erica N Borducchi
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Marinela Kirilova
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston
| | - Kathryn E Stephenson
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Poonam Pegu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Michael A Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Hung V Trinh
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Mangala Rao
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring
| | - Julie A Ake
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring
| | | | - Steven Nijs
- Crucell Holland, Janssen, Johnson & Johnson, Leiden, the Netherlands
| | | | | | - Jenny Hendriks
- Crucell Holland, Janssen, Johnson & Johnson, Leiden, the Netherlands
| | - Maria G Pau
- Crucell Holland, Janssen, Johnson & Johnson, Leiden, the Netherlands
| | - Frank Tomaka
- Janssen Pharmaceutical Research and Development, Titusville, New Jersey
| | - Bette T Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
| | - Galit Alter
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Raphael Dolin
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Patricia L Earl
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Dan H Barouch
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
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9
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Hartnell F, Brown A, Capone S, Kopycinski J, Bliss C, Makvandi-Nejad S, Swadling L, Ghaffari E, Cicconi P, Del Sorbo M, Sbrocchi R, Esposito I, Vassilev V, Marriott P, Gardiner CM, Bannan C, Bergin C, Hoffmann M, Turner B, Nicosia A, Folgori A, Hanke T, Barnes E, Dorrell L. A Novel Vaccine Strategy Employing Serologically Different Chimpanzee Adenoviral Vectors for the Prevention of HIV-1 and HCV Coinfection. Front Immunol 2019; 9:3175. [PMID: 30713538 PMCID: PMC6346592 DOI: 10.3389/fimmu.2018.03175] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/24/2018] [Indexed: 12/21/2022] Open
Abstract
Background: Nearly 3 million people worldwide are coinfected with HIV and HCV. Affordable strategies for prevention are needed. We developed a novel vaccination regimen involving replication-defective and serologically distinct chimpanzee adenovirus (ChAd3, ChAd63) vector priming followed by modified vaccinia Ankara (MVA) boosts, for simultaneous delivery of HCV non-structural (NSmut) and HIV-1 conserved (HIVconsv) region immunogens. Methods: We conducted a phase I trial in which 33 healthy volunteers were sequentially enrolled and vaccinated via the intramuscular route as follows: 9 received ChAd3-NSmut [2.5 × 1010 vp] and MVA-NSmut [2 × 108 pfu] at weeks 0 and 8, respectively; 8 received ChAdV63.HIVconsv [5 × 1010 vp] and MVA.HIVconsv [2 × 108 pfu] at the same interval; 16 were co-primed with ChAd3-NSmut [2.5 × 1010 vp] and ChAdV63.HIVconsv [5 × 1010 vp] followed at week 8 by MVA-NSmut and MVA.HIVconsv [both 1 × 108 pfu]. Immunogenicity was assessed using peptide pools in ex vivo ELISpot and intracellular cytokine assays. Vaccine-induced whole blood transcriptome changes were assessed by microarray analysis. Results: All vaccines were well tolerated and no vaccine-related serious adverse events occurred. Co-administration of the prime-boost vaccine regimens induced high magnitude and broad T cell responses that were similar to those observed following immunization with either regimen alone. Median (interquartile range, IQR) peak responses to NSmut were 3,480 (2,728–4,464) and 3,405 (2,307–7,804) spot-forming cells (SFC)/106 PBMC for single and combined HCV vaccinations, respectively (p = 0.8). Median (IQR) peak responses to HIVconsv were 1,305 (1,095–4,967) and 1,005 (169–2,482) SFC/106 PBMC for single and combined HIV-1 vaccinations, respectively (p = 0.5). Responses were maintained above baseline to 34 weeks post-vaccination. Intracellular cytokine analysis indicated that the responding populations comprised polyfunctional CD4+ and CD8+ T cells. Canonical pathway analysis showed that in the single and combined vaccination groups, pathways associated with antiviral and innate immune responses were enriched for upregulated interferon-stimulated genes 24 h after priming and boosting vaccinations. Conclusions: Serologically distinct adenoviral vectors encoding HCV and HIV-1 immunogens can be safely co-administered without reducing the immunogenicity of either vaccine. This provides a novel strategy for targeting these viruses simultaneously and for other pathogens that affect the same populations. Clinical trial registration:https://clinicaltrials.gov, identifier: NCT02362217
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Affiliation(s)
- Felicity Hartnell
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anthony Brown
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jakub Kopycinski
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Carly Bliss
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Leo Swadling
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emma Ghaffari
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paola Cicconi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | | | - Ilaria Esposito
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Paula Marriott
- Centre for Clinical Vaccinology and Tropical Medicine, Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Clair M Gardiner
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | | | | | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Bethany Turner
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alfredo Nicosia
- Keires AG, Basel, Switzerland.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | | | - Tomáš Hanke
- Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Headington, United Kingdom
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Headington, United Kingdom
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10
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Borzooee F, Joris KD, Grant MD, Larijani M. APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome. Front Immunol 2019; 9:3032. [PMID: 30687306 PMCID: PMC6338068 DOI: 10.3389/fimmu.2018.03032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022] Open
Abstract
APOBEC3G (A3G) is a host enzyme that mutates the genomes of retroviruses like HIV. Since A3G is expressed pre-infection, it has classically been considered an agent of innate immunity. We and others previously showed that the impact of A3G-induced mutations on the HIV genome extends to adaptive immunity also, by generating cytotoxic T cell (CTL) escape mutations. Accordingly, HIV genomic sequences encoding CTL epitopes often contain A3G-mutable “hotspot” sequence motifs, presumably to channel A3G action toward CTL escape. Here, we studied the depths and consequences of this apparent viral genome co-evolution with A3G. We identified all potential CTL epitopes in Gag, Pol, Env, and Nef restricted to several HLA class I alleles. We simulated A3G-induced mutations within CTL epitope-encoding sequences, and flanking regions. From the immune recognition perspective, we analyzed how A3G-driven mutations are predicted to impact CTL-epitope generation through modulating proteasomal processing and HLA class I binding. We found that A3G mutations were most often predicted to result in diminishing/abolishing HLA-binding affinity of peptide epitopes. From the viral genome evolution perspective, we evaluated enrichment of A3G hotspots at sequences encoding CTL epitopes and included control sequences in which the HIV genome was randomly shuffled. We found that sequences encoding immunogenic epitopes exhibited a selective enrichment of A3G hotspots, which were strongly biased to translate to non-synonymous amino acid substitutions. When superimposed on the known mutational gradient across the entire length of the HIV genome, we observed a gradient of A3G hotspot enrichment, and an HLA-specific pattern of the potential of A3G hotspots to lead to CTL escape mutations. These data illuminate the depths and extent of the co-evolution of the viral genome to subvert the host mutator A3G.
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Affiliation(s)
- Faezeh Borzooee
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Krista D Joris
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Michael D Grant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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11
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Understanding and Manipulating Viral Immunity: Antibody Immunodominance Enters Center Stage. Trends Immunol 2018; 39:549-561. [PMID: 29789196 DOI: 10.1016/j.it.2018.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Adaptive immune responses against antigenically variable viruses and cellular pathogens are efficient in many cases, but largely limited to the infecting or immunizing strain. A major factor that limits immunity is immunodominance (ID), the hierarchical focusing of adaptive immune responses on a subset of antigenic determinants. While CD8+ T cell ID has been extensively studied, studies of basic mechanisms of B cell ID are limited, despite the importance of antibodies (Abs) for durable protection against pathogens. Here, we review recent progress in understanding the basic rules and mechanisms of B cell ID, compare B and CD8+ T cell ID, and outline challenges to overcoming ID to develop Ab-based 'universal' vaccines for influenza A and other highly variable viruses.
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12
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Surenaud M, Lacabaratz C, Zurawski G, Lévy Y, Lelièvre JD. Development of an epitope-based HIV-1 vaccine strategy from HIV-1 lipopeptide to dendritic-based vaccines. Expert Rev Vaccines 2018; 16:955-972. [PMID: 28879788 DOI: 10.1080/14760584.2017.1374182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Development of a safe, effective and globally affordable Human Immunodeficiency Virus strain 1 (HIV-1) vaccine offers the best hope for future control of the HIV-1 pandemic. However, with the exception of the recent RV144 trial, which elicited a modest level of protection against infection, no vaccine candidate has shown efficacy in preventing HIV-1 infection or in controlling virus replication in humans. There is also a great need for a successful immunotherapeutic vaccine since combination antiretroviral therapy (cART) does not eliminate the reservoir of HIV-infected cells. But to date, no vaccine candidate has proven to significantly alter the natural history of an individual with HIV-1 infection. Areas covered: For over 25 years, the ANRS (France Recherche Nord&Sud Sida-HIV hépatites) has been committed to an original program combining basic science and clinical research developing an epitope-based vaccine strategy to induce a multiepitopic cellular response against HIV-1. This review describes the evolution of concepts, based on strategies using HIV-1 lipopeptides towards the use of dendritic cell (DC) manipulation. Expert commentary: Understanding the crucial role of DCs in immune responses allowed moving from the non-specific administration of HIV-1 sequences with lipopeptides to DC-based vaccines. These DC-targeting strategies should improve HIV-1 vaccine efficacy.
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Affiliation(s)
- Mathieu Surenaud
- a INSERM, U955 , Créteil , France.,b Faculté de médecine , Université Paris Est , Créteil , France.,c Vaccine Research Institute (VRI) , Créteil , France
| | - Christine Lacabaratz
- a INSERM, U955 , Créteil , France.,b Faculté de médecine , Université Paris Est , Créteil , France.,c Vaccine Research Institute (VRI) , Créteil , France
| | - Gérard Zurawski
- a INSERM, U955 , Créteil , France.,c Vaccine Research Institute (VRI) , Créteil , France.,d Baylor Institute for Immunology Research , Dallas , TX , USA
| | - Yves Lévy
- a INSERM, U955 , Créteil , France.,b Faculté de médecine , Université Paris Est , Créteil , France.,c Vaccine Research Institute (VRI) , Créteil , France.,e AP-HP, Hôpital H. Mondor - A. Chenevier, Service d'Immunologie Clinique et Maladies Infectieuses , Créteil , France
| | - Jean-Daniel Lelièvre
- a INSERM, U955 , Créteil , France.,b Faculté de médecine , Université Paris Est , Créteil , France.,c Vaccine Research Institute (VRI) , Créteil , France.,e AP-HP, Hôpital H. Mondor - A. Chenevier, Service d'Immunologie Clinique et Maladies Infectieuses , Créteil , France
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13
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Qiu Z, Wan ATK, Zhou Y, Gilbert PB. Smoothed Rank Regression for the Accelerated Failure Time Competing Risks Model with Missing Cause of Failure. Stat Sin 2018; 29:23-46. [PMID: 30740005 DOI: 10.5705/ss.202016.0231] [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: 11/06/2022]
Abstract
This paper examines the accelerated failure time competing risks model with missing cause of failure using the monotone class rank-based estimating equations approach. We handle the non-smoothness of the rank-based estimating equations using a kernel smoothed estimation method, and estimate the unknown selection probability and the conditional expectation by non-parametric techniques. Under this setup, we propose three methods for estimating the unknown regression parameters based on 1) inverse probability weighting, 2) estimating equations imputation and 3) augmented inverse probability weighting. We also obtain the associated asymptotic theories of the proposed estimators and investigate the estimators' small sample behaviour in a simulation study. A direct plug-in method is suggested for estimating the asymptotic variances of the proposed estimators. A real data application based on a HIV vaccine efficacy trial study is considered.
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Affiliation(s)
- Zhiping Qiu
- School of Mathematical Sciences, Huaqiao University, Quanzhou 362021, China.,Research Center for Applied Statistics and Big Data, Huaqiao University, Xiamen 361021, China
| | - Alan T K Wan
- City University of Hong Kong, Kowloon, Hong Kong
| | - Yong Zhou
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China.,Institute of Applied Mathematics, Chinese Academy of Science, Beijing 100190, China
| | - Peter B Gilbert
- Department of Biostatistics, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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14
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Preferential Targeting of Conserved Gag Regions after Vaccination with a Heterologous DNA Prime-Modified Vaccinia Virus Ankara Boost HIV-1 Vaccine Regimen. J Virol 2017; 91:JVI.00730-17. [PMID: 28701395 DOI: 10.1128/jvi.00730-17] [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] [Received: 05/18/2017] [Accepted: 06/14/2017] [Indexed: 11/20/2022] Open
Abstract
Prime-boost vaccination strategies against HIV-1 often include multiple variants for a given immunogen for better coverage of the extensive viral diversity. To study the immunologic effects of this approach, we characterized breadth, phenotype, function, and specificity of Gag-specific T cells induced by a DNA-prime modified vaccinia virus Ankara (MVA)-boost vaccination strategy, which uses mismatched Gag immunogens in the TamoVac 01 phase IIa trial. Healthy Tanzanian volunteers received three injections of the DNA-SMI vaccine encoding a subtype B and AB-recombinant Gagp37 and two vaccinations with MVA-CMDR encoding subtype A Gagp55 Gag-specific T-cell responses were studied in 42 vaccinees using fresh peripheral blood mononuclear cells. After the first MVA-CMDR boost, vaccine-induced gamma interferon-positive (IFN-γ+) Gag-specific T-cell responses were dominated by CD4+ T cells (P < 0.001 compared to CD8+ T cells) that coexpressed interleukin-2 (IL-2) (66.4%) and/or tumor necrosis factor alpha (TNF-α) (63.7%). A median of 3 antigenic regions were targeted with a higher-magnitude median response to Gagp24 regions, more conserved between prime and boost, compared to those of regions within Gagp15 (not primed) and Gagp17 (less conserved; P < 0.0001 for both). Four regions within Gagp24 each were targeted by 45% to 74% of vaccinees upon restimulation with DNA-SMI-Gag matched peptides. The response rate to individual antigenic regions correlated with the sequence homology between the MVA- and DNA Gag-encoded immunogens (P = 0.04, r2 = 0.47). In summary, after the first MVA-CMDR boost, the sequence-mismatched DNA-prime MVA-boost vaccine strategy induced a Gag-specific T-cell response that was dominated by polyfunctional CD4+ T cells and that targeted multiple antigenic regions within the conserved Gagp24 protein.IMPORTANCE Genetic diversity is a major challenge for the design of vaccines against variable viruses. While including multiple variants for a given immunogen in prime-boost vaccination strategies is one approach that aims to improve coverage for global virus variants, the immunologic consequences of this strategy have been poorly defined so far. It is unclear whether inclusion of multiple variants in prime-boost vaccination strategies improves recognition of variant viruses by T cells and by which mechanisms this would be achieved, either by improved cross-recognition of multiple variants for a given antigenic region or through preferential targeting of antigenic regions more conserved between prime and boost. Engineering vaccines to induce adaptive immune responses that preferentially target conserved antigenic regions of viral vulnerability might facilitate better immune control after preventive and therapeutic vaccination for HIV and for other variable viruses.
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15
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Tomaras GD, Plotkin SA. Complex immune correlates of protection in HIV-1 vaccine efficacy trials. Immunol Rev 2017; 275:245-261. [PMID: 28133811 DOI: 10.1111/imr.12514] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Development of an efficacious HIV-1 vaccine is a major priority for improving human health worldwide. Vaccine-mediated protection against human pathogens can be achieved through elicitation of protective innate, humoral, and cellular responses. Identification of specific immune responses responsible for pathogen protection enables vaccine development and provides insights into host defenses against pathogens and the immunological mechanisms that most effectively fight infection. Defining immunological correlates of transmission risk in preclinical and clinical HIV-1 vaccine trials has moved the HIV-1 vaccine development field forward and directed new candidate vaccine development. Immune correlate studies are providing novel hypotheses about immunological mechanisms that may be responsible for preventing HIV-1 acquisition. Recent results from HIV-1 immune correlates work has demonstrated that there are multiple types of immune responses that together, comprise an immune correlate-thus implicating polyfunctional immune control of HIV-1 transmission. An in depth understanding of these complex immunological mechanisms of protection against HIV-1 will accelerate the development of an efficacious HIV-1 vaccine.
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Affiliation(s)
- Georgia D Tomaras
- Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Duke Human Vaccine Institute, Durham, NC, USA
| | - Stanley A Plotkin
- Vaxconsult, Doylestown, PA, USA.,University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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Ford T, Wenden C, Mbekeani A, Dally L, Cox JH, Morin M, Winstone N, Hill AVS, Gilmour J, Ewer KJ. Cryopreservation-related loss of antigen-specific IFNγ producing CD4 + T-cells can skew immunogenicity data in vaccine trials: Lessons from a malaria vaccine trial substudy. Vaccine 2017; 35:1898-1906. [PMID: 28285985 PMCID: PMC5387668 DOI: 10.1016/j.vaccine.2017.02.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/31/2017] [Accepted: 02/18/2017] [Indexed: 12/19/2022]
Abstract
Ex vivo functional immunoassays such as ELISpot and intracellular cytokine staining (ICS) by flow cytometry are crucial tools in vaccine development both in the identification of novel immunogenic targets and in the immunological assessment of samples from clinical trials. Cryopreservation and subsequent thawing of PBMCs via validated processes has become a mainstay of clinical trials due to processing restrictions inherent in the disparate location and capacity of trial centres, and also in the need to standardize biological assays at central testing facilities. Logistical and financial requirement to batch process samples from multiple study timepoints are also key. We used ELISpot and ICS assays to assess antigen-specific immunogenicity in blood samples taken from subjects enrolled in a phase II malaria heterologous prime-boost vaccine trial and showed that the freeze thaw process can result in a 3–5-fold reduction of malaria antigen-specific IFNγ-producing CD3+CD4+ effector populations from PBMC samples taken post vaccination. We have also demonstrated that peptide responsive CD8+ T cells are relatively unaffected, as well as CD4+ T cell populations that do not produce IFNγ. These findings contribute to a growing body of data that could be consolidated and synthesised as guidelines for clinical trials with the aim of increasing the efficiency of vaccine development pipelines.
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Affiliation(s)
- Tom Ford
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK.
| | - Claire Wenden
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Alison Mbekeani
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Len Dally
- EMMES Corporation, Rockville, MD, USA
| | - Josephine H Cox
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK
| | | | - Nicola Winstone
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Adrian V S Hill
- Centre for Clinical Vaccinology and Tropical Medicine and the Jenner Institute Laboratories, University of Oxford, UK
| | - Jill Gilmour
- IAVI-HIL, Human Immunology Laboratory, International AIDS Vaccine Initiative, London, UK; Department of Medicine, Imperial College, London, UK
| | - Katie J Ewer
- Centre for Clinical Vaccinology and Tropical Medicine and the Jenner Institute Laboratories, University of Oxford, UK
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Hsu DC, Ananworanich J. Immune Interventions to Eliminate the HIV Reservoir. Curr Top Microbiol Immunol 2017; 417:181-210. [PMID: 29071472 DOI: 10.1007/82_2017_70] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inducing HIV remission is a monumental challenge. A potential strategy is the "kick and kill" approach where latently infected cells are first activated to express viral proteins and then eliminated through cytopathic effects of HIV or immune-mediated killing. However, pre-existing immune responses to HIV cannot eradicate HIV infection due to the presence of escape variants, inadequate magnitude, and breadth of responses as well as immune exhaustion. The two major approaches to boost immune-mediated elimination of infected cells include enhancing cytotoxic T lymphocyte mediated killing and harnessing antibodies to eliminate HIV. Specific strategies include increasing the magnitude and breadth of T cell responses through therapeutic vaccinations, reversing the effects of T cell exhaustion using immune checkpoint inhibition, employing bispecific T cell targeting immunomodulatory proteins or dual-affinity re-targeting molecules to direct cytotoxic T lymphocytes to virus-expressing cells and broadly neutralizing antibody infusions. Methods to steer immune responses to tissue sites where latently infected cells are located need to be further explored. Ultimately, strategies to induce HIV remission must be tolerable, safe, and scalable in order to make a global impact.
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Affiliation(s)
- Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. .,US Military HIV Research Program (MHRP), 6720-A Rockledge Drive, Suite 400, Bethesda, MD, 20817, USA.
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Mutua G, Farah B, Langat R, Indangasi J, Ogola S, Onsembe B, Kopycinski JT, Hayes P, Borthwick NJ, Ashraf A, Dally L, Barin B, Tillander A, Gilmour J, De Bont J, Crook A, Hannaman D, Cox JH, Anzala O, Fast PE, Reilly M, Chinyenze K, Jaoko W, Hanke T, HIV-CORE 004 study group T. Broad HIV-1 inhibition in vitro by vaccine-elicited CD8(+) T cells in African adults. Mol Ther Methods Clin Dev 2016; 3:16061. [PMID: 27617268 PMCID: PMC5006719 DOI: 10.1038/mtm.2016.61] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023]
Abstract
We are developing a pan-clade HIV-1 T-cell vaccine HIVconsv, which could complement Env vaccines for prophylaxis and be a key to HIV cure. Our strategy focuses vaccine-elicited effector T-cells on functionally and structurally conserved regions (not full-length proteins and not only epitopes) of the HIV-1 proteome, which are common to most global variants and which, if mutated, cause a replicative fitness loss. Our first clinical trial in low risk HIV-1-negative adults in Oxford demonstrated the principle that naturally mostly subdominant epitopes, when taken out of the context of full-length proteins/virus and delivered by potent regimens involving combinations of simian adenovirus and poxvirus modified vaccinia virus Ankara, can induce robust CD8(+) T cells of broad specificities and functions capable of inhibiting in vitro HIV-1 replication. Here and for the first time, we tested this strategy in low risk HIV-1-negative adults in Africa. We showed that the vaccines were well tolerated and induced high frequencies of broadly HIVconsv-specific plurifunctional T cells, which inhibited in vitro viruses from four major clades A, B, C, and D. Because sub-Saharan Africa is globally the region most affected by HIV-1/AIDS, trial HIV-CORE 004 represents an important stage in the path toward efficacy evaluation of this highly rational and promising vaccine strategy.
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Affiliation(s)
- Gaudensia Mutua
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Bashir Farah
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Robert Langat
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | | | - Simon Ogola
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Brian Onsembe
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Jakub T Kopycinski
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | | | - Ambreen Ashraf
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Len Dally
- Emmes Corporation, Rockville, Maryland, USA
| | - Burc Barin
- Emmes Corporation, Rockville, Maryland, USA
| | | | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Jan De Bont
- International AIDS Vaccine Initiative-New York, New York, New York, USA
| | - Alison Crook
- Jenner Institute, University of Oxford, Oxford, UK
| | - Drew Hannaman
- ICHOR Medical Systems, Inc., San Diego, California, USA
| | - Josephine H Cox
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Omu Anzala
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Patricia E Fast
- International AIDS Vaccine Initiative-New York, New York, New York, USA
| | | | - Kundai Chinyenze
- International AIDS Vaccine Initiative-New York, New York, New York, USA
| | - Walter Jaoko
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Tomáš Hanke
- Jenner Institute, University of Oxford, Oxford, UK
- International Research Center for Medical Sciences, Kumamoto University, Japan
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Adenovirus-based HIV-1 vaccine candidates tested in efficacy trials elicit CD8+ T cells with limited breadth of HIV-1 inhibition. AIDS 2016; 30:1703-12. [PMID: 27088318 DOI: 10.1097/qad.0000000000001122] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVES The ability of HIV-1 vaccine candidates MRKAd5, VRC DNA/Ad5 and ALVAC/AIDSVAX to elicit CD8 T cells with direct antiviral function was assessed and compared with HIV-1-infected volunteers. DESIGN Adenovirus serotype 5 (Ad5)-based regimens MRKAd5 and VRC DNA/Ad5, designed to elicit HIV-1-specific T cells, are immunogenic but failed to prevent infection or impact on viral loads in volunteers infected subsequently. Failure may be due in part to a lack of CD8 T cells with effective antiviral functions. METHODS An in-vitro viral inhibition assay tested the ability of bispecific antibody expanded CD8 T cells from peripheral blood mononuclear cells to inhibit replication of a multiclade panel of HIV-1 isolates in autologous CD4 T cells. HIV-1 proteins recognized by CD8 T cells were assessed by IFNγ enzyme-linked immunospot assay. RESULTS Ad5-based regimens elicited CD8 T cells that inhibited replication of HIV-1 IIIB isolate with more limited inhibition of other isolates. IIIB isolate Gag and Pol genes have high sequence identities (>96%) to vector HIV-1 gene inserts, and these were the predominant HIV-1 proteins recognized by CD8 T cells. Virus inhibition breadth was greater in antiretroviral naïve HIV-1-infected volunteers naturally controlling viremia (plasma viral load < 10 000/ml). HIV-1-inhibitory CD8 T cells were not elicited by the ALVAC/AIDSVAX regimen. CONCLUSION The Ad5-based regimens, although immunogenic, elicited CD8 T cells with limited HIV-1-inhibition breadth. Effective T-cell-based vaccines should presumably elicit broader HIV-1-inhibition profiles. The viral inhibition assay can be used in vaccine design and to prioritize promising candidates with greater inhibition breadth for further clinical trials.
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Balance between activation and regulation of HIV-specific CD8+ T-cell response after modified vaccinia Ankara B therapeutic vaccination. AIDS 2016; 30:553-62. [PMID: 26558724 DOI: 10.1097/qad.0000000000000966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The causes of HIV-vaccines failure are poorly understood. Therapeutic vaccination with modified vaccinia Ankara (MVA)-B in HIV-1-infected individuals did not control the virus upon analytical treatment interruption (ATI). We investigated whether the functional characteristics of HIV-specific CD8 T-cell responses stimulated by this vaccine, and the level of exhaustion of these cells might explain these results. METHODS Twenty-one HIV-1 chronically infected patients on combination antiretroviral therapy, included in the therapeutic vaccine trial RISVAC03, were studied: 13 immunized and eight controls. Functional characteristics, cytotoxic potential and exhaustion of HIV-specific CD8 T cells, were evaluated by polychromatic flow cytometry. Differences between groups were tested using nonparametric tests. RESULTS MVA-B vaccine induced an increase in HIV-specific CD8 T-cell response, but also increased their levels of exhaustion. At week 18 (following three immunizations) the level of response increased with respect to baseline (P = 0.02). A significant increase at weeks 18 and 24 (ATI) in granzyme B content was also observed. Interestingly, an increase in expression of exhaustion markers was found at weeks 18 (P = 0.006) and 24 (P = 0.01). However, there was no significant change in the functional profile of vaccine-induced CD8 cells. At week 36, in parallel to the rebound of plasma viremia after 12 weeks ATI, a significant increase in the level of CD8 response, in granzyme B content and in exhaustion markers expression, was observed in both groups. CONCLUSION We show that therapeutic vaccination with MVA-B tilts the balance between activation and regulation of the response of HIV-specific CD8 T cells towards regulation, which impacts on the viral rebound after ATI.
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Walsh SR, Moodie Z, Fiore-Gartland AJ, Morgan C, Wilck MB, Hammer SM, Buchbinder SP, Kalams SA, Goepfert PA, Mulligan MJ, Keefer MC, Baden LR, Swann EM, Grant S, Ahmed H, Li F, Hertz T, Self SG, Friedrich D, Frahm N, Liao HX, Montefiori DC, Tomaras GD, McElrath MJ, Hural J, Graham BS, Jin X. Vaccination With Heterologous HIV-1 Envelope Sequences and Heterologous Adenovirus Vectors Increases T-Cell Responses to Conserved Regions: HVTN 083. J Infect Dis 2015; 213:541-50. [PMID: 26475930 DOI: 10.1093/infdis/jiv496] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/09/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Increasing the breadth of human immunodeficiency virus type 1 (HIV-1) vaccine-elicited immune responses or targeting conserved regions may improve coverage of circulating strains. HIV Vaccine Trials Network 083 tested whether cellular immune responses with these features are induced by prime-boost strategies, using heterologous vectors, heterologous inserts, or a combination of both. METHODS A total of 180 participants were randomly assigned to receive combinations of adenovirus vectors (Ad5 or Ad35) and HIV-1 envelope (Env) gene inserts (clade A or B) in a prime-boost regimen. RESULTS T-cell responses to heterologous and homologous insert regimens targeted a similar number of epitopes (ratio of means, 1.0; 95% confidence interval [CI], .6-1.6; P = .91), but heterologous insert regimens induced significantly more epitopes that were shared between EnvA and EnvB than homologous insert regimens (ratio of means, 2.7; 95% CI, 1.2-5.7; P = .01). Participants in the heterologous versus homologous insert groups had T-cell responses that targeted epitopes with greater evolutionary conservation (mean entropy [±SD], 0.32 ± 0.1 bits; P = .003), and epitopes recognized by responders provided higher coverage (49%; P = .035). Heterologous vector regimens had higher numbers of total, EnvA, and EnvB epitopes than homologous vector regimens (P = .02, .044, and .045, respectively). CONCLUSIONS These data demonstrate that vaccination with heterologous insert prime boosting increased T-cell responses to shared epitopes, while heterologous vector prime boosting increased the number of T-cell epitopes recognized. CLINICAL TRIALS REGISTRATION NCT01095224.
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Affiliation(s)
- Stephen R Walsh
- Division of Infectious Diseases, Brigham and Women's Hospital Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center Harvard Medical School, Boston, Massachusetts
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | | | - Cecilia Morgan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Marissa B Wilck
- Division of Infectious Diseases, Brigham and Women's Hospital Harvard Medical School, Boston, Massachusetts
| | | | | | - Spyros A Kalams
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | - Lindsey R Baden
- Division of Infectious Diseases, Brigham and Women's Hospital Harvard Medical School, Boston, Massachusetts
| | | | - Shannon Grant
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Fusheng Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Steven G Self
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - David Friedrich
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Global Health, University of Washington, Seattle
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina
| | | | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Global Health, University of Washington, Seattle Departments of Medicine and Laboratory Medicine, University of Washington, Seattle
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Barney S Graham
- Dale and Betty Bumpers Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Xia Jin
- University of Rochester, New York
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Tomaras GD, Haynes BF. Advancing Toward HIV-1 Vaccine Efficacy through the Intersections of Immune Correlates. Vaccines (Basel) 2015; 2:15-35. [PMID: 24932411 PMCID: PMC4053939 DOI: 10.3390/vaccines2010015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interrogating immune correlates of infection risk for efficacious and non-efficacious HIV-1 vaccine clinical trials have provided hypotheses regarding the mechanisms of induction of protective immunity to HIV-1. To date, there have been six HIV-1 vaccine efficacy trials (VAX003, Vaxgen, Inc., San Francisco, CA, USA), VAX004 (Vaxgen, Inc.), HIV-1 Vaccine Trials Network (HVTN) 502 (Step), HVTN 503 (Phambili), RV144 (sponsored by the U.S. Military HIV Research Program, MHRP) and HVTN 505). Cellular, humoral, host genetic and virus sieve analyses of these human clinical trials each can provide information that may point to potentially protective mechanisms for vaccine-induced immunity. Critical to staying on the path toward development of an efficacious vaccine is utilizing information from previous human and non-human primate studies in concert with new discoveries of basic HIV-1 host-virus interactions. One way that past discoveries from correlate analyses can lead to novel inventions or new pathways toward vaccine efficacy is to examine the intersections where different components of the correlate analyses overlap (e.g., virus sieve analysis combined with humoral correlates) that can point to mechanistic hypotheses. Additionally, differences in durability among vaccine-induced T- and B-cell responses indicate that time post-vaccination is an important variable. Thus, understanding the nature of protective responses, the degree to which such responses have, or have not, as yet, been induced by previous vaccine trials and the design of strategies to induce durable T- and B-cell responses are critical to the development of a protective HIV-1 vaccine.
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Affiliation(s)
- Georgia D. Tomaras
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-919-681-5598; Fax: +1-919-684-5230
| | - Barton F. Haynes
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-919-681-5598; Fax: +1-919-684-5230
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Zhao Z, Sun HQ, Wei SS, Li B, Feng Q, Zhu J, Zeng H, Zou QM, Wu C. Multiple B-cell epitope vaccine induces a Staphylococcus enterotoxin B-specific IgG1 protective response against MRSA infection. Sci Rep 2015. [PMID: 26201558 PMCID: PMC4511869 DOI: 10.1038/srep12371] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
No vaccine against methicillin-resistant Staphylococcus aureus (MRSA) has been currently approved for use in humans. Staphylococcus enterotoxin B (SEB) is one of the most potent MRSA exotoxins. In the present study, we evaluated the efficacy and immunologic mechanisms of an SEB multiple B-cell epitope vaccine against MRSA infection. Synthetic overlapping peptide ELISA identified three novel B-cell immunodominant SEB epitopes (in addition to those previously known): SEB31–48, SEB133–150, and SEB193–210. Six B-cell immunodominant epitopes (amino acid residues 31–48, 97–114, 133–150, 193–210, 205–222, and 247–261) were sufficient to induce robust IgG1/IgG2b-specific protective responses against MRSA infection. Therefore, we constructed a recombinant MRSA SEB-specific multiple B-cell epitope vaccine Polypeptides by combining the six SEB immunodominant epitopes and demonstrated its ability to induce a robust SEB-specific IgG1 response to MRSA, as well as a Th2-directing isotype response. Moreover, Polypeptides-induced antisera stimulated synergetic opsonophagocytosis killing of MRSA. Most importantly, Polypeptides was more effective at clearing the bacteria in MRSA-infected mice than the whole SEB antigen, and was able to successfully protect mice from infection by various clinical MRSA isolates. Altogether, these results support further evaluation of the SEB multiple B-cell epitope-vaccine to address MRSA infection in humans.
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Affiliation(s)
- Zhuo Zhao
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - He-Qiang Sun
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Shan-Shan Wei
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Bin Li
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Qiang Feng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Jiang Zhu
- Department of Pathology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Hao Zeng
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Quan-Ming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
| | - Chao Wu
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing 400038, PR China
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Cellular immune correlates analysis of an HIV-1 preexposure prophylaxis trial. Proc Natl Acad Sci U S A 2015; 112:8379-84. [PMID: 26100867 DOI: 10.1073/pnas.1501443112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
HIV-1-specific T-cell responses in exposed seronegative subjects suggest that a viral breach of the exposure site is more common than current transmission rates would suggest and that host immunity can extinguish subsequent infection foci. The Preexposure Prophylaxis Initiative (iPrEx) chemoprophylaxis trial provided an opportunity to rigorously investigate these responses in a case-control immunology study; 84 preinfection peripheral blood mononuclear cell samples from individuals enrolled in the iPrEx trial who later seroconverted were matched with 480 samples from enrolled subjects who remained seronegative from both the placebo and active treatment arms. T-cell responses to HIV-1 Gag, Protease, Integrase, Reverse Transcriptase, Vif, and Nef antigens were quantified for all subjects in an IFN-γ enzyme-linked immunospot (ELISpot) assay. IFN-γ responses varied in magnitude and frequency across subjects. A positive response was more prevalent in those who remained persistently HIV-1-negative for Gag (P = 0.007), Integrase (P < 0.001), Vif (P < 0.001), and Nef (P < 0.001). When correlated with outcomes in the iPrEx trial, Vif- and Integrase-specific T-cell responses were associated with reduced HIV-1 infection risk [hazard ratio (HR) = 0.36, 95% confidence interval (95% CI) = 0.19-0.66 and HR = 0.52, 95% CI = 0.28-0.96, respectively]. Antigen-specific responses were independent of emtricitabine/tenofovir disoproxil fumarate use. IFN-γ secretion in the ELISpot was confirmed using multiparametric flow cytometry and largely attributed to effector memory CD4+ or CD8+ T cells. Our results show that HIV-1-specific T-cell immunity can be detected in exposed but uninfected individuals and that these T-cell responses can differentiate individuals according to infection outcomes.
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Hancock G, Yang H, Yorke E, Wainwright E, Bourne V, Frisbee A, Payne TL, Berrong M, Ferrari G, Chopera D, Hanke T, Mothe B, Brander C, McElrath MJ, McMichael A, Goonetilleke N, Tomaras GD, Frahm N, Dorrell L. Identification of effective subdominant anti-HIV-1 CD8+ T cells within entire post-infection and post-vaccination immune responses. PLoS Pathog 2015; 11:e1004658. [PMID: 25723536 PMCID: PMC4344337 DOI: 10.1371/journal.ppat.1004658] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 01/05/2015] [Indexed: 01/01/2023] Open
Abstract
Defining the components of an HIV immunogen that could induce effective CD8+ T cell responses is critical to vaccine development. We addressed this question by investigating the viral targets of CD8+ T cells that potently inhibit HIV replication in vitro, as this is highly predictive of virus control in vivo. We observed broad and potent ex vivo CD8+ T cell-mediated viral inhibitory activity against a panel of HIV isolates among viremic controllers (VC, viral loads <5000 copies/ml), in contrast to unselected HIV-infected HIV Vaccine trials Network (HVTN) participants. Viral inhibition of clade-matched HIV isolates was strongly correlated with the frequency of CD8+ T cells targeting vulnerable regions within Gag, Pol, Nef and Vif that had been identified in an independent study of nearly 1000 chronically infected individuals. These vulnerable and so-called “beneficial” regions were of low entropy overall, yet several were not predicted by stringent conservation algorithms. Consistent with this, stronger inhibition of clade-matched than mismatched viruses was observed in the majority of subjects, indicating better targeting of clade-specific than conserved epitopes. The magnitude of CD8+ T cell responses to beneficial regions, together with viral entropy and HLA class I genotype, explained up to 59% of the variation in viral inhibitory activity, with magnitude of the T cell response making the strongest unique contribution. However, beneficial regions were infrequently targeted by CD8+ T cells elicited by vaccines encoding full-length HIV proteins, when the latter were administered to healthy volunteers and HIV-positive ART-treated subjects, suggesting that immunodominance hierarchies undermine effective anti-HIV CD8+ T cell responses. Taken together, our data support HIV immunogen design that is based on systematic selection of empirically defined vulnerable regions within the viral proteome, with exclusion of immunodominant decoy epitopes that are irrelevant for HIV control. Attempts to develop an HIV vaccine that elicits potent cell-mediated immunity have so far been unsuccessful. This is due in part to the use of immunogens that appear to recapitulate responses induced naturally by HIV that are, at best, partially effective. We previously showed that the capacity of CD8+ T cells from patients to block HIV replication in culture is strongly correlated with HIV control in vivo, therefore, we investigated the virological determinants of potent CD8+ T cell inhibitory activity. We observed that CD8+ T cells from patients with naturally low plasma viral loads (viremic controllers) were better able to inhibit the replication of diverse HIV strains in vitro than CD8+ T cells from HIV-noncontroller patients. Importantly, we also found that the potency of the antiviral activity in the latter group was strongly correlated with recognition of selected regions across the viral proteome that are critical to viral fitness. Vaccines that encode full-length viral proteins rarely elicited responses to these vulnerable regions. Taken together, our results provide insight into the characteristics of effective cell-mediated immune responses against HIV and how these may inform the design of better immunogens.
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Affiliation(s)
- Gemma Hancock
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Hongbing Yang
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Emma Wainwright
- Department of Sexual Health, Royal Berkshire NHS Foundation Trust, Reading, United Kingdom
| | - Victoria Bourne
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alyse Frisbee
- Departments of Molecular Genetics and Microbiology, Surgery, Immunology, and Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Tamika L. Payne
- Departments of Molecular Genetics and Microbiology, Surgery, Immunology, and Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Mark Berrong
- Departments of Molecular Genetics and Microbiology, Surgery, Immunology, and Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Departments of Molecular Genetics and Microbiology, Surgery, Immunology, and Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Denis Chopera
- Institute of Infectious Diseases and Molecular Medicine & Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Tomas Hanke
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Beatriz Mothe
- Irsicaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Christian Brander
- Irsicaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M. Juliana McElrath
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrew McMichael
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Georgia D. Tomaras
- Departments of Molecular Genetics and Microbiology, Surgery, Immunology, and Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Nicole Frahm
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- * E-mail:
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26
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Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol 2015; 23:212-24. [PMID: 25613992 DOI: 10.1016/j.tim.2014.12.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
HIV-1 develops specific mutations within its genome that allow it to escape detection by human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8(+) cytotoxic T lymphocytes (CTL). HLA thus represents a major force driving the evolution and diversification of HIV-1 within individuals and at the population level. Importantly, the study of HIV-1 adaptation to HLA also represents an opportunity to identify what qualities constitute an effective immune response, how the virus in turn adapts to these pressures, and how we may harness this information to design HIV-1 vaccines that stimulate effective cellular immunity.
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Affiliation(s)
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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27
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Tongo M, Burgers WA. Challenges in the design of a T cell vaccine in the context of HIV-1 diversity. Viruses 2014; 6:3968-90. [PMID: 25341662 PMCID: PMC4213573 DOI: 10.3390/v6103968] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/15/2014] [Accepted: 10/18/2014] [Indexed: 12/27/2022] Open
Abstract
The extraordinary variability of HIV-1 poses a major obstacle to vaccine development. The effectiveness of a vaccine is likely to vary dramatically in different populations infected with different HIV-1 subtypes, unless innovative vaccine immunogens are developed to protect against the range of HIV-1 diversity. Immunogen design for stimulating neutralizing antibody responses focuses on “breadth” – the targeting of a handful of highly conserved neutralizing determinants on the HIV-1 Envelope protein that can recognize the majority of viruses across all HIV-1 subtypes. An effective vaccine will likely require the generation of both broadly cross-neutralizing antibodies and non-neutralizing antibodies, as well as broadly cross-reactive T cells. Several approaches have been taken to design such broadly-reactive and cross-protective T cell immunogens. Artificial sequences have been designed that reduce the genetic distance between a vaccine strain and contemporary circulating viruses; “mosaic” immunogens extend this concept to contain multiple potential T cell epitope (PTE) variants; and further efforts attempt to focus T cell immunity on highly conserved regions of the HIV-1 genome. Thus far, a number of pre-clinical and early clinical studies have been performed assessing these new immunogens. In this review, the potential use of these new immunogens is explored.
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Affiliation(s)
- Marcel Tongo
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
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28
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Ensoli B, Cafaro A, Monini P, Marcotullio S, Ensoli F. Challenges in HIV Vaccine Research for Treatment and Prevention. Front Immunol 2014; 5:417. [PMID: 25250026 PMCID: PMC4157563 DOI: 10.3389/fimmu.2014.00417] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/18/2014] [Indexed: 12/17/2022] Open
Abstract
Many attempts have been made or are ongoing for HIV prevention and HIV cure. Many successes are in the list, particularly for HIV drugs, recently proposed also for prevention. However, no eradication of infection has been achieved so far with any drug. Further, a residual immune dysregulation associated to chronic immune activation and incomplete restoration of B and T cell subsets, together with HIV DNA persistence in reservoirs, are still unmet needs of the highly active antiretroviral therapy, causing novel “non-AIDS related” diseases that account for a higher risk of death even in virologically suppressed patients. These “ART unmet needs” represent a problem, which is expected to increase by ART roll out. Further, in countries such as South Africa, where six millions of individuals are infected, ART appears unable to contain the epidemics. Regretfully, all the attempts at developing a preventative vaccine have been largely disappointing. However, recent therapeutic immunization strategies have opened new avenues for HIV treatment, which might be exploitable also for preventative vaccine approaches. For example, immunization strategies aimed at targeting key viral products responsible of virus transmission, activation, and maintenance of virus reservoirs may intensify drug efficacy and lead to a functional cure providing new perspectives also for prevention and future virus eradication strategies. However, this approach imposes new challenges to the scientific community, vaccine developers, and regulatory bodies, such as the identification of novel immunological and virological biomarkers to assess efficacy end-points, taking advantage from the natural history of infection and exploiting lessons from former trials. This review will focus first on recent advancement of therapeutic strategies, then on the progresses made in preventative approaches, discussing concepts, and problems for the way ahead for the development of vaccines for HIV treatment and prevention.
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Affiliation(s)
- Barbara Ensoli
- National AIDS Center, Istituto Superiore di Sanità , Rome , Italy
| | - Aurelio Cafaro
- National AIDS Center, Istituto Superiore di Sanità , Rome , Italy
| | - Paolo Monini
- National AIDS Center, Istituto Superiore di Sanità , Rome , Italy
| | | | - Fabrizio Ensoli
- Pathology and Microbiology, San Gallicano Institute, "Istituti Fisioterapici Ospitalieri" , Rome , Italy
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29
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Mechanisms of HIV protein degradation into epitopes: implications for vaccine design. Viruses 2014; 6:3271-92. [PMID: 25196483 PMCID: PMC4147695 DOI: 10.3390/v6083271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/02/2022] Open
Abstract
The degradation of HIV-derived proteins into epitopes displayed by MHC-I or MHC-II are the first events leading to the priming of HIV-specific immune responses and to the recognition of infected cells. Despite a wealth of information about peptidases involved in protein degradation, our knowledge of epitope presentation during HIV infection remains limited. Here we review current data on HIV protein degradation linking epitope production and immunodominance, viral evolution and impaired epitope presentation. We propose that an in-depth understanding of HIV antigen processing and presentation in relevant primary cells could be exploited to identify signatures leading to efficient or inefficient epitope presentation in HIV proteomes, and to improve the design of immunogens eliciting immune responses efficiently recognizing all infected cells.
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30
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Kramer VG, Byrareddy SN. The value of HIV protective epitope research for informed vaccine design against diverse viral pathogens. Expert Rev Vaccines 2014; 13:935-7. [PMID: 24964950 DOI: 10.1586/14760584.2014.928597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The success of vaccine regimens against viral pathogens hinges on the elicitation of protective responses. Hypervariable pathogens such as HIV avoid neutralization by masking protective epitopes with more immunogenic decoys. The identification of protective, conserved epitopes is crucial for future vaccine candidate design. The strategies employed for identification of HIV protective epitopes will also aid towards rational vaccine design for other viral pathogens.
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Affiliation(s)
- Victor G Kramer
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
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31
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Kulkarni V, Valentin A, Rosati M, Alicea C, Singh AK, Jalah R, Broderick KE, Sardesai NY, Le Gall S, Mothe B, Brander C, Rolland M, Mullins JI, Pavlakis GN, Felber BK. Altered response hierarchy and increased T-cell breadth upon HIV-1 conserved element DNA vaccination in macaques. PLoS One 2014; 9:e86254. [PMID: 24465991 PMCID: PMC3900501 DOI: 10.1371/journal.pone.0086254] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/09/2013] [Indexed: 11/23/2022] Open
Abstract
HIV sequence diversity and potential decoy epitopes are hurdles in the development of an effective AIDS vaccine. A DNA vaccine candidate comprising of highly conserved p24gag elements (CE) induced robust immunity in all 10 vaccinated macaques, whereas full-length gag DNA vaccination elicited responses to these conserved elements in only 5 of 11 animals, targeting fewer CE per animal. Importantly, boosting CE-primed macaques with DNA expressing full-length p55gag increased both magnitude of CE responses and breadth of Gag immunity, demonstrating alteration of the hierarchy of epitope recognition in the presence of pre-existing CE-specific responses. Inclusion of a conserved element immunogen provides a novel and effective strategy to broaden responses against highly diverse pathogens by avoiding decoy epitopes, while focusing responses to critical viral elements for which few escape pathways exist.
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Affiliation(s)
- Viraj Kulkarni
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Antonio Valentin
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Margherita Rosati
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Candido Alicea
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ashish K. Singh
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Rashmi Jalah
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Kate E. Broderick
- Inovio Pharmaceuticals, Inc., Blue Bell, Pennsylvania, United States of America
| | | | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute-HIVACAT, Autonomous University of Barcelona, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Autonomous University of Barcelona, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
| | - 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
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - George N. Pavlakis
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail: (GNP); (BKF)
| | - Barbara K. Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail: (GNP); (BKF)
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32
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Lukashevich IS, Shirwan H. Adenovirus-Based Vectors for the Development of Prophylactic and Therapeutic Vaccines. NOVEL TECHNOLOGIES FOR VACCINE DEVELOPMENT 2014. [PMCID: PMC7121347 DOI: 10.1007/978-3-7091-1818-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Emerging and reemerging infectious diseases as well as cancer pose great global health impacts on the society. Vaccines have emerged as effective treatments to prevent or reduce the burdens of already developed diseases. This is achieved by means of activating various components of the immune system to generate systemic inflammatory reactions targeting infectious agents or diseased cells for control/elimination. DNA virus-based genetic vaccines gained significant attention in the past decades owing to the development of DNA manipulation technologies, which allowed engineering of recombinant viral vectors encoding sequences for foreign antigens or their immunogenic epitopes as well as various immunomodulatory molecules. Despite tremendous progress in the past 50 years, many hurdles still remain for achieving the full clinical potential of viral-vectored vaccines. This chapter will present the evolution of vaccines from “live” or “attenuated” first-generation agents to recombinant DNA and viral-vectored vaccines. Particular emphasis will be given to human adenovirus (Ad) for the development of prophylactic and therapeutic vaccines. Ad biological properties related to vaccine development will be highlighted along with their advantages and potential hurdles to be overcome. In particular, we will discuss (1) genetic modifications in the Ad capsid protein to reduce the intrinsic viral immunogenicity, (2) antigen capsid incorporation for effective presentation of foreign antigens to the immune system, (3) modification of the hexon and fiber capsid proteins for Ad liver de-targeting and selective retargeting to cancer cells, (4) Ad-based vaccines carrying “arming” transgenes with immunostimulatory functions as immune adjuvants, and (5) oncolytic Ad vectors as a new therapeutic approach against cancer. Finally, the combination of adenoviral vectors with other non-adenoviral vector systems, the prime/boost strategy of immunization, clinical trials involving Ad-based vaccines, and the perspectives for the field development will be discussed.
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Affiliation(s)
- Igor S Lukashevich
- Department of Pharmacology and Toxicolog Department of Microbiology and Immunolog, University of Louisville, Louisville, Kentucky USA
| | - Haval Shirwan
- Department of Microbiology and Immunolog, University of Louisville, Louisville, Kentucky USA
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