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Fernandez N, Hayes P, Makinde J, Hare J, King D, Xu R, Rehawi O, Mezzell AT, Kato L, Mugaba S, Serwanga J, Chemweno J, Nduati E, Price MA, Osier F, Ochsenbauer C, Yue L, Hunter E, Gilmour J. Assessment of a diverse panel of transmitted/founder HIV-1 infectious molecular clones in a luciferase based CD8 T-cell mediated viral inhibition assay. Front Immunol 2022; 13:1029029. [PMID: 36532063 PMCID: PMC9751811 DOI: 10.3389/fimmu.2022.1029029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction Immunological protection against human immunodeficiency virus-1 (HIV-1) infection is likely to require both humoral and cell-mediated immune responses, the latter involving cytotoxic CD8 T-cells. Characterisation of CD8 T-cell mediated direct anti-viral activity would provide understanding of potential correlates of immune protection and identification of critical epitopes associated with HIV-1 control. Methods The present report describes a functional viral inhibition assay (VIA) to assess CD8 T-cell-mediated inhibition of replication of a large and diverse panel of 45 HIV-1 infectious molecular clones (IMC) engineered with a Renilla reniformis luciferase reporter gene (LucR), referred to as IMC-LucR. HIV-1 IMC replication in CD4 T-cells and CD8 T-cell mediated inhibition was characterised in both ART naive subjects living with HIV-1 covering a broad human leukocyte antigen (HLA) distribution and compared with uninfected subjects. Results & discussion CD4 and CD8 T-cell lines were established from subjects vaccinated with a candidate HIV-1 vaccine and provided standard positive controls for both assay quality control and facilitating training and technology transfer. The assay was successfully established across 3 clinical research centres in Kenya, Uganda and the United Kingdom and shown to be reproducible. This IMC-LucR VIA enables characterisation of functional CD8 T-cell responses providing a tool for rational T-cell immunogen design of HIV-1 vaccine candidates and evaluation of vaccine-induced T-cell responses in HIV-1 clinical trials.
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Affiliation(s)
- Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,*Correspondence: Natalia Fernandez, ; Peter Hayes,
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,*Correspondence: Natalia Fernandez, ; Peter Hayes,
| | - Julia Makinde
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,IAVI, New York, NY, United States
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Ola Rehawi
- University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Laban Kato
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Susan Mugaba
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Jennifer Serwanga
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - James Chemweno
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Eunice Nduati
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matt A. Price
- IAVI, New York, NY, United States,Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States
| | - Faith Osier
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Jill Gilmour
- Department of Infectious Diseases, Imperial College, London, United Kingdom
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Nkone P, Loubser S, Quinn TC, Redd AD, Ismail A, Tiemessen CT, Mayaphi SH. Deep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages. Virol J 2022; 19:56. [PMID: 35346259 PMCID: PMC8959563 DOI: 10.1186/s12985-022-01772-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/07/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Despite multiple attempts, there is still no effective HIV-1 vaccine available. The HIV-1 polymerase (pol) gene is highly conserved and encodes cytotoxic T-lymphocyte (CTL) epitopes. The aim of the study was to characterise HIV-1 Pol CTL epitopes in mostly sample pairs obtained during early and chronic stages of infection. METHODS Illumina deep sequencing was performed for all samples while Sanger sequencing was only performed on baseline samples. Codons under immune selection pressure were assessed by computing nonsynonymous to synonymous mutation ratios using MEGA. Minority CTL epitope variants occurring at [Formula: see text] 5% were detected using low-frequency variant tool in CLC Genomics. Los Alamos HIV database was used for mapping mutations to known HIV-1 CTL epitopes. RESULTS Fifty-two participants were enrolled in the study. Their median age was 28 years (interquartile range: 24-32 years) and majority of participants (92.3%) were female. Illumina minority variant analysis identified a significantly higher number of CTL epitopes (n = 65) compared to epitopes (n = 8) identified through Sanger sequencing. Most of the identified epitopes mapped to reverse transcriptase (RT) and integrase (IN) regardless of sequencing method. There was a significantly higher proportion of minority variant epitopes in RT (n = 39, 60.0%) compared to IN (n = 17, 26.2%) and PR (n = 9, 13.8%), p = 0.002 and < 0.0001, respectively. However, no significant difference was observed between the proportion of minority variant epitopes in IN versus PR, p = 0.06. Some epitopes were detected in either early or chronic HIV-1 infection whereas others were detected in both stages. Different distribution patterns of minority variant epitopes were observed in sample pairs; with some increasing or decreasing over time, while others remained constant. Some of the identified epitopes have not been previously reported for HIV-1 subtype C. There were also variants that could not be mapped to reported CTL epitopes in the Los Alamos HIV database. CONCLUSION Deep sequencing revealed many Pol CTL epitopes, including some not previously reported for HIV-1 subtype C. The findings of this study support the inclusion of RT and IN epitopes in HIV-1 vaccine candidates as these proteins harbour many CTL epitopes.
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Affiliation(s)
- Paballo Nkone
- Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
| | - Shayne Loubser
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Arshad Ismail
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simnikiwe H Mayaphi
- Department of Medical Virology, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa. .,National Health Laboratory Service-Tshwane Academic Division (NHLS-TAD), Tshwane, South Africa.
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3
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Wee EG, Moyo N, Hannoun Z, Giorgi EE, Korber B, Hanke T. Effect of epitope variant co-delivery on the depth of CD8 T cell responses induced by HIV-1 conserved mosaic vaccines. Mol Ther Methods Clin Dev 2021; 21:741-753. [PMID: 34169114 PMCID: PMC8187930 DOI: 10.1016/j.omtm.2021.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/29/2021] [Indexed: 11/27/2022]
Abstract
To stop the HIV-1 pandemic, vaccines must induce responses capable of controlling vast HIV-1 variants circulating in the population as well as those evolved in each individual following transmission. Numerous strategies have been proposed, of which the most promising include focusing responses on the vulnerable sites of HIV-1 displaying the least entropy among global isolates and using algorithms that maximize vaccine match to circulating HIV-1 variants by vaccine cocktails of optimized complementing sequences. In this study, we investigated CD8 T cell responses induced by a bi-valent mosaic of highly conserved HIVconsvX regions delivered by a combination of simian adenovirus ChAdOx1 and poxvirus MVA. We compared partially and fully mono- and bi-valent prime-boost regimens and their ability to elicit T cells recognizing natural epitope variants using an interferon-γ enzyme-linked immunospot (ELISPOT) assay. We used 11 well-defined CD8 T cell epitopes in two mouse haplotypes and, for each epitope, assessed recognition of the two vaccine forms together with the other most frequent epitope variants in the HIV-1 database. We conclude that for the magnitude and depth of epitope recognition, CD8 T cell responses benefitted in most comparisons from the combined bi-valent mosaic and envisage the main advantage of the bi-valent vaccine during its deployment to diverse populations.
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Affiliation(s)
- Edmund G. Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Zara Hannoun
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
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Nasomsong W, Phokaphol K, Changpradub D. First-Line Antiretroviral Regimen Failure and Determinants in an Urban HIV Clinic at Phramongkutklao Hospital, Bangkok, Thailand: 20 Years Experience. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2021; 13:261-269. [PMID: 33692637 PMCID: PMC7939509 DOI: 10.2147/hiv.s295512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/26/2021] [Indexed: 11/23/2022]
Abstract
Purpose HIV treatment involves antiretroviral therapy (ART) endeavoring to suppress viral load to an undetectable level. Virologic failure occurs when ART fails to suppress and sustain an individual’s viral load to less than 200 copies/mL after 6 months of therapy. In Thailand, the data among first-line antiretroviral regimen failure and determinants remains limited, especially in urban HIV clinics. We aimed to demonstrate factors of first-line antiretroviral regimen failures in an urban HIV/AIDS clinic at Phramongkutklao Hospital. Patients and Methods A nested case control 1:4 study was conducted. Data were collected from the electronic patient database among naïve people living with HIV/AIDS (PLWHA), aged ≥18 years and receiving ART continuously for at least 2 years at Phramongkutklao Hospital from 1 January 2000 to 31 December 2019. Multiple logistic regression was used to identify the determinants of virologic failure. Adjusted HRs (AHRs) with 95% CIs were used to declare statistical significance. Results Of 200 PLWHA included in the study, 40 participants experienced HIV virologic failure. The median time after starting ART to virologic failure was 24 months (IQR 7–96.0). Univariate and multivariate analysis showed significant factors affecting first-line antiretroviral regimen failure included being female (37.5 vs 26.88%, adjusted odds ratio 5.08 [1.05–24.6, p-value 0.043], age ≤40 yr. (62.5 vs 49.6%, adjusted odds ratio 4.59 [1.47–14.37], p-value 0.009), CD4+count ≤200 cell/µL (77.5 vs 52.5%, adjusted odds ratio 4.83 [1.28–18.9], p value 0.02), tuberculosis (42.5 vs 7.5%, adjusted odds ratio 8.66 [2.37–31.56], p value <0.001) and initiation of ART at CD4+ count <350 cell/µL (72.5 vs 48.13%, adjusted odds ratio 31.36 [6.51–151.22], p value <0.001). Estimated prevalence of virologic failure in Phramongkutklao Hospital was 5.34%. Conclusion Our study revealed factors favoring virologic failure included being female, younger age, CD4+ count <200 cells/µL, tuberculosis and initiation of ART at CD4+ count <350 cell/µL. Multidisciplinary HIV comprehensive care teams should encourage patient adherence and support patients along HIV continuum of care to prevent virologic failure and drug resistance, especially among patients initiating ART at low CD4+ count and tuberculosis co-infection.
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Affiliation(s)
- Worapong Nasomsong
- Division of Infectious Diseases, Department of Internal Medicine, Phramongkutklao Hospital, Bangkok, Thailand
| | - Kwonchit Phokaphol
- Division of Infectious Diseases, Department of Internal Medicine, Phramongkutklao Hospital, Bangkok, Thailand
| | - Dhitiwat Changpradub
- Division of Infectious Diseases, Department of Internal Medicine, Phramongkutklao Hospital, Bangkok, Thailand
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5
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Shabani SH, Kardani K, Milani A, Bolhassani A. In Silico and in Vivo Analysis of HIV-1 Rev Regulatory Protein for Evaluation of a Multiepitope-based Vaccine Candidate. Immunol Invest 2021; 51:1-28. [PMID: 33416004 DOI: 10.1080/08820139.2020.1867163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In silico-designed multiepitope conserved regions of human immunodeficiency virus 1 (HIV-1) proteins would be a beneficial strategy for antigen design which induces effective anti-HIV-1 T-cell responses. The conserved multiple HLA-DR-binding epitopes of Rev protein were identified using IEDB MHC-I prediction tools and SYFPEITHI webserver to screen potential T-cell epitopes. We analyzed toxicity, allergenicity, immunogenicity, hemolytic activity, cross-reactivity, cell-penetrating peptide (CPP) potency, and molecular docking of the candidate epitopes using several immune-informatics tools. Afterward, we designed a novel multiepitope construct based on non-toxic and non-allergenic Rev, Nef, Gp160 and P24-derived cytotoxic T cell (CTL) and T-helper cell (HTL) epitopes. Next, the designed construct (Nef-Rev-Gp160-P24) was subjected to three B-cell epitope prediction webservers, ProtParam and Protein-Sol to obtain the physicochemical features. Then, the recombinant multiepitope DNA and polypeptide constructs were complexed with different CPPs for nanoparticle formation and pass them via the cell membranes. Finally, the immunogenicity of multiepitope constructs in a variety of modalities was evaluated in mice. The results demonstrated that groups immunized with heterologous DNA+ MPG or HR9 CPP prime/rNef-Rev-Gp160-P24 polypeptide + LDP-NLS CPP boost regimens could significantly produce higher levels of IFN-γ and Granzyme B, and lower amounts of IL-10 than other groups. Moreover, higher levels of IgG2a and IgG2b were observed in all heterologous prime-boost regimens than homologous DNA or polypeptide regimens. Altogether, the present findings indicated that the Nef-Rev-Gp160-P24 polypeptide meets the criteria to be potentially useful as a multiepitope-based vaccine candidate against HIV-1 infection.
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Affiliation(s)
- Samaneh H Shabani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Kimia Kardani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Alireza Milani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
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6
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Mohamed YS, Borthwick NJ, Moyo N, Murakoshi H, Akahoshi T, Siliquini F, Hannoun Z, Crook A, Hayes P, Fast PE, Mutua G, Jaoko W, Silva-Arrieta S, Llano A, Brander C, Takiguchi M, Hanke T. Specificity of CD8 + T-Cell Responses Following Vaccination with Conserved Regions of HIV-1 in Nairobi, Kenya. Vaccines (Basel) 2020; 8:E260. [PMID: 32485938 PMCID: PMC7349992 DOI: 10.3390/vaccines8020260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023] Open
Abstract
Sub-Saharan Africa carries the biggest burden of the human immunodeficiency virus type 1 (HIV-1)/AIDS epidemic and is in an urgent need of an effective vaccine. CD8+ T cells are an important component of the host immune response to HIV-1 and may need to be harnessed if a vaccine is to be effective. CD8+ T cells recognize human leukocyte antigen (HLA)-associated viral epitopes and the HLA alleles vary significantly among different ethnic groups. It follows that definition of HIV-1-derived peptides recognized by CD8+ T cells in the geographically relevant regions will critically guide vaccine development. Here, we study fine details of CD8+ T-cell responses elicited in HIV-1/2-uninfected individuals in Nairobi, Kenya, who received a candidate vaccine delivering conserved regions of HIV-1 proteins called HIVconsv. Using 10-day cell lines established by in vitro peptide restimulation of cryopreserved PBMC and stably HLA-transfected 721.221/C1R cell lines, we confirm experimentally many already defined epitopes, for a number of epitopes we define the restricting HLA molecule(s) and describe four novel HLA-epitope pairs. We also identify specific dominance patterns, a promiscuous T-cell epitope and a rescue of suboptimal T-cell epitope induction in vivo by its functional variant, which all together inform vaccine design.
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Affiliation(s)
- Yehia S. Mohamed
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11823, Egypt
| | - Nicola J. Borthwick
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Nathifa Moyo
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Hayato Murakoshi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Tomohiro Akahoshi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Francesca Siliquini
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Zara Hannoun
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Alison Crook
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Peter Hayes
- International AIDS Vaccine Initiative IAVI-Human Immunology Laboratory, Imperial College London, London SW10 9NH, UK;
| | - Patricia E. Fast
- International AIDS Vaccine Initiative-New York, New York, NY 10004, USA;
| | - Gaudensia Mutua
- KAVI-Institute of Clinical Research, University of Nairobi, Nairobi 19676 00202, Kenya; (G.M.); (W.J.)
| | - Walter Jaoko
- KAVI-Institute of Clinical Research, University of Nairobi, Nairobi 19676 00202, Kenya; (G.M.); (W.J.)
| | - Sandra Silva-Arrieta
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
- Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
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Borthwick N, Silva-Arrieta S, Llano A, Takiguchi M, Brander C, Hanke T. Novel Nested Peptide Epitopes Recognized by CD4 + T Cells Induced by HIV-1 Conserved-Region Vaccines. Vaccines (Basel) 2020; 8:E28. [PMID: 31963212 PMCID: PMC7157676 DOI: 10.3390/vaccines8010028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 11/29/2022] Open
Abstract
CD4+ T-cell responses play an important role in the immune control of the human immunodeficiency virus type 1 (HIV-1) infection and as such should be efficiently induced by vaccination. It follows that definition of HIV-1-derived peptides recognized by CD4+ T cells in association with HLA class II molecules will guide vaccine development. Here, we have characterized the fine specificity of CD4+ T cells elicited in human recipients of a candidate vaccine delivering conserved regions of HIV-1 proteins designated HIVconsv. The majority of these 19 most immunogenic regions contained novel epitopes, that is, epitopes not listed in the Los Alamos National Laboratory HIV Sequence Database, which were able in vitro to stimulate vaccinees' CD4+ T cells to proliferate and produce interferon-γ and tumor necrosis factor-α. Accumulation of HLA class II epitopes will eventually accelerate development of HIV-1 prophylactic and therapeutic vaccines.
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Affiliation(s)
| | - Sandra Silva-Arrieta
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan;
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
- Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK;
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan;
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8
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Namazi F, Bolhassani A, Sadat SM, Irani S. Delivery of HIV-1 Polyepitope Constructs Using Cationic and Amphipathic Cell Penetrating Peptides into Mammalian Cells. Curr HIV Res 2020; 17:408-428. [DOI: 10.2174/1570162x17666191121114522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
Background:
An effective vaccine against human immunodeficiency virus 1 (HIV-1) is
an important global health priority. Despite many efforts in the development of the HIV-1 vaccine,
no effective vaccine has been approved yet. Recently, polyepitope vaccines including several immunogenic
and conserved epitopes of HIV-1 proteins have received special attention.
Methods:
In this study, HIV-1 Nef, Tat, Gp160 and P24 proteins were considered for selection of
immunodominant and conserved epitopes due to their critical roles in the viral life cycle and pathogenesis.
At first, the Nef60-84-Nef126-144-Tat29-49-Gp16030-53-Gp160308-323-P248-151 DNA construct was
designed using in silico studies. Then, the DNA construct was subcloned in pEGFP-N1 and pET-
24a (+) expression vectors and the rNef-Tat-Gp160-P24 polyepitope peptide was generated in E.coli
expression system for in vitro delivery using novel cell-penetrating peptides (CPPs), LDP-NLS and
CyLoP-1, in a non-covalent manner. Also, the HR9 and MPG CPPs were used to transfer the DNA
construct.
Results:
Our results showed that the recombinant polyepitope peptide generated in Rosetta strain
migrated as a clear band of ~31 kDa in SDS-PAGE. The SEM data confirmed the formation of stable
nanoparticles with a size below 250 nm. MTT assay revealed that the complexes did not represent
any considerable cytotoxic effect compared to untreated cells. The results of fluorescence microscopy,
flow cytometry and western blotting indicated that these CPPs successfully delivered polyepitope
constructs into HEK-293T cell line.
Conclusion:
These data suggested that these CPPs can be used as a promising approach for the development
of the HIV-1 vaccine.
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Affiliation(s)
- Fatemeh Namazi
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Shiva Irani
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
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del Moral-Sánchez I, Sliepen K. Strategies for inducing effective neutralizing antibody responses against HIV-1. Expert Rev Vaccines 2019; 18:1127-1143. [PMID: 31791150 PMCID: PMC6961309 DOI: 10.1080/14760584.2019.1690458] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Introduction: Despite intensive research efforts, there is still no effective prophylactic vaccine available against HIV-1. Currently, substantial efforts are devoted to the development of vaccines aimed at inducing broadly neutralizing antibodies (bNAbs), which are capable of neutralizing most HIV-1 strains. All bNAbs target the HIV-1 envelope glycoprotein (Env), but Env immunizations usually only induce neutralizing antibodies (NAbs) against the sequence-matched virus and not against other strains.Areas covered: We describe the different strategies that have been explored to improve the breadth and potency of anti-HIV-1 NAb responses. The discussed strategies include the application of engineered Env immunogens, optimization of (bNAb) epitopes, different cocktail and sequential vaccination strategies, nanoparticles and nucleic acid-based vaccines.Expert opinion: A combination of the strategies described in this review and future approaches are probably needed to develop an effective HIV-1 vaccine that can induce broad, potent and long-lasting NAb responses.
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Affiliation(s)
- Iván del Moral-Sánchez
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands,CONTACT Kwinten Sliepen Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Hanke T. Aiming for protective T-cell responses: a focus on the first generation conserved-region HIVconsv vaccines in preventive and therapeutic clinical trials. Expert Rev Vaccines 2019; 18:1029-1041. [PMID: 31613649 DOI: 10.1080/14760584.2019.1675518] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: Despite life-saving antiretroviral drugs, an effective HIV-1 vaccine is the best solution and likely a necessary component of any strategy for halting the AIDS epidemic. The currently prevailing aim is to pursue antibody-mediated vaccine protection. With ample evidence for the ability of T cells to control HIV-1 replication, their protective potential should be also harnessed by vaccination. The challenge is to elicit not just any, but protective T cells.Areas covered: This article reviews the clinical experience with the first-generation conserved-region immunogen HIVconsv delivered by combinations of plasmid DNA, simian adenovirus, and poxvirus MVA. The aim of our strategy is to induce strong and broad T cells targeting functionally important parts of HIV-1 proteins common to global variants. These vaccines were tested in eight phase 1/2 preventive and therapeutic clinical trials in Europe and Africa, and induced high frequencies of broadly specific CD8+ T cells capable of in vitro inhibition of four major HIV-1 clades A, B, C and D, and in combination with latency-reactivating agent provided a signal of drug-free virological control in early treated patients.Expert opinion: A number of critical T-cell traits have to come together at the same time to achieve control over HIV-1.
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Affiliation(s)
- Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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Perdiguero B, Sánchez-Corzo C, S Sorzano CO, Mediavilla P, Saiz L, Esteban M, Gómez CE. Induction of Broad and Polyfunctional HIV-1-Specific T Cell Responses by the Multiepitopic Protein TMEP-B Vectored by MVA Virus. Vaccines (Basel) 2019; 7:vaccines7030057. [PMID: 31261918 PMCID: PMC6789790 DOI: 10.3390/vaccines7030057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
A human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) vaccine able to induce long-lasting immunity remains a major challenge. We previously designed a T cell multiepitopic immunogen including protective conserved epitopes from HIV-1 Gag, Pol and Nef proteins (TMEP-B), that induced potent HIV-1-specific CD8 T cells when vectored by DNA and combined with the vaccine candidate modified vaccinia virus Ankara (MVA)-B. Here, we described the vectorization of TMEP-B in MVA (MVA-TMEP) and evaluated the T cell immunogenicity profile elicited in mice when administered in homologous (MVA/MVA) or heterologous (DNA/MVA) prime/boost vector regimens or using homologous or heterologous inserts. The heterologous vector regimen was superior to the homologous protocol in inducing T cell responses. DNA-TMEP-primed animals boosted with MVA-TMEP or MVA-B exhibited the highest magnitudes of HIV-1-specific CD8, CD4 and T follicular helper (Tfh) cells, with MVA-TMEP significantly expanding Gag-specific CD8 T cell responses. In the homologous vector regimen, all groups exhibited similar HIV-1-specific CD8 and CD4 T cell responses, but both MVA-B/MVA-B and MVA-TMEP/MVA-TMEP combinations elicited higher Gag-Pol-Nef (GPN)-specific CD8 T cell responses compared to MVA-TMEP/MVA-B. Our results revealed an enhanced induction of HIV-1-specific T cell responses by TMEP-B when vectored in both DNA and MVA, and supported their use in combined prime/boost strategies for HIV-1 prevention and/or therapy.
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Affiliation(s)
- Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Cristina Sánchez-Corzo
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pilar Mediavilla
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Lidia Saiz
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
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Mothe B, Manzardo C, Sanchez-Bernabeu A, Coll P, Morón-López S, Puertas MC, Rosas-Umbert M, Cobarsi P, Escrig R, Perez-Alvarez N, Ruiz I, Rovira C, Meulbroek M, Crook A, Borthwick N, Wee EG, Yang H, Miró JM, Dorrell L, Clotet B, Martinez-Picado J, Brander C, Hanke T. Therapeutic Vaccination Refocuses T-cell Responses Towards Conserved Regions of HIV-1 in Early Treated Individuals (BCN 01 study). EClinicalMedicine 2019; 11:65-80. [PMID: 31312806 PMCID: PMC6610778 DOI: 10.1016/j.eclinm.2019.05.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Strong and broad antiviral T-cell responses targeting vulnerable sites of HIV-1 will likely be a critical component for any effective cure strategy. METHODS BCN01 trial was a phase I, open-label, non-randomized, multicenter study in HIV-1-positive individuals diagnosed and treated during early HIV-1 infection to evaluate two vaccination regimen arms, which differed in the time (8 versus 24 week) between the ChAdV63.HIVconsv prime and MVA.HIVconsv boost vaccinations. The primary outcome was safety. Secondary endpoints included frequencies of vaccine-induced IFN-γ+ CD8+ T cells, in vitro virus-inhibitory capacity, plasma HIV-1 RNA and total CD4+ T-cells associated HIV-1 DNA. (NCT01712425). FINDINGS No differences in safety, peak magnitude or durability of vaccine-induced responses were observed between long and short interval vaccination arms. Grade 1/2 local and systemic post-vaccination events occurred in 22/24 individuals and resolved within 3 days. Weak responses to conserved HIV-1 regions were detected in 50% of the individuals before cART initiation, representing median of less than 10% of their total HIV-1-specific T cells. All participants significantly elevated these subdominant T-cell responses, which after MVA.HIVconsv peaked at median (range) of 938 (73-6,805) IFN-γ SFU/106 PBMC, representing on average 58% of their total anti-HIV-1 T cells. The decay in the size of the HIV-1 reservoir was consistent with the first year of early cART initiation in both arms. INTERPRETATION Heterologous prime-boost vaccination with ChAdV63-MVA/HIVconsv was well-tolerated and refocused pre-cART T-cell responses towards more protective epitopes, in which immune escape is frequently associated with reduced HIV-1 replicative fitness and which are common to most global HIV-1 variants. FUNDING HIVACAT Catalan research program for an HIV vaccine and Fundació Gloria Soler. Vaccine manufacture was jointly funded by the Medical Research Council (MRC) UK and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreements (G0701669. RESEARCH IN CONTEXT Evidence Before this Study: T cells play an important role in the control of HIV infection and may be particularly useful for HIV-1 cure by killing cells with reactivated HIV-1. Evidence is emerging that not all T-cell responses are protective and mainly only those targeting conserved regions of HIV-1 proteins are effective, but typically immunologically subdominant, while those recognizing hypervariable, easy-to-escape immunodominant 'decoys' do not control viremia and do not protect from a loss of CD4 T cells. We pioneered a vaccine strategy focusing T-cell responses on the most conserved regions of the HIV-1 proteome using an immunogen designated HIVconsv. T cells elicited by the HIVconsv vaccines in HIV-uninfected UK and Kenyan adults inhibited in vitro replication of HIV-1 isolates from 4 major global clades A, B, C and D.Added Value of this Study: The present study demonstrated the concept that epitopes subdominant in natural infection, when taken out of the context of the whole HIV-1 proteome and presented to the immune system by a potent simian adenovirus prime-poxvirus MVA boost regimen, can induce strong responses in patients on antiretroviral treatment and efficiently refocus HIV-1-specific T-cells to the protective epitopes delivered by the vaccine.Implications of all the Available Evidence: Nearly all HIV-1 vaccine strategies currently emphasize induction of broadly neutralizing Abs. The HIVconsv vaccine is one of a very few approaches focussing exclusively on elicitation of T cells and, therefore, can complement antibody induction for better prevention and cure. Given the cross-clade reach on the HIVconsv immunogen design, if efficient, the HIVconsv vaccines could be deployed globally. Effective vaccines will likely be a necessary component in combination with other available preventive measures for halting the HIV-1/AIDS epidemic.
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Affiliation(s)
- Beatriz Mothe
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Fundació Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
- Corresponding author at: IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Crta Canyet s/n, 08916, Badalona, Barcelona, Spain.
| | | | | | - Pep Coll
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Fundació Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | | | - Miriam Rosas-Umbert
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Patricia Cobarsi
- Fundació Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Roser Escrig
- Fundació Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Núria Perez-Alvarez
- Fundació Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Technical University of Catalonia, Barcelona, Spain
| | - Irene Ruiz
- Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Cristina Rovira
- Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | | | - Alison Crook
- The Jenner Institute, University of Oxford, Oxford, UK
| | | | - Edmund G. Wee
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Hongbing Yang
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Jose M. Miró
- Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Lucy Dorrell
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Fundació Lluita contra la Sida, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
- Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
- ICREA, Pg. Luis Companys 23, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Badalona, Spain
- Universitat de Vic - Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
- ICREA, Pg. Luis Companys 23, Barcelona, Spain
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, UK
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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Thema N, Tshilwane S, Pretorius A, Son L, Smith R, Steyn H, Liebenberg J, van Kleef M. Identification and characterisation of conserved epitopes of E. ruminantium that activate Th1 CD4+ T cells: Towards the development of a multi-epitope vaccine. Mol Immunol 2019; 107:106-114. [DOI: 10.1016/j.molimm.2018.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/06/2018] [Accepted: 12/09/2018] [Indexed: 01/21/2023]
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Thema N, Tshilwane S, Son L, Smith R, Faber F, Steyn H, van Kleef M, Liebenberg J, Pretorius A. Ehrlichia ruminantium antigens and peptides induce cytotoxic T cell responses in vitro. Vet Immunol Immunopathol 2019; 207:1-9. [DOI: 10.1016/j.vetimm.2018.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/25/2018] [Accepted: 11/18/2018] [Indexed: 01/31/2023]
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CD8+ T cells: mechanistic target of rapamycin and eukaryotic initiation factor 2 in elite HIV-1 control. AIDS 2018; 32:2835-2838. [PMID: 30407253 DOI: 10.1097/qad.0000000000002008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection. J Virol 2018; 92:JVI.00811-18. [PMID: 29997209 DOI: 10.1128/jvi.00811-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/20/2018] [Indexed: 01/31/2023] Open
Abstract
CD8+ T cell-mediated escape mutations in Gag can reduce HIV-1 replication capacity (RC) and alter disease progression, but less is known about immune-mediated attenuation in other HIV-1 proteins. We generated 487 recombinant viruses encoding RT-integrase from individuals with chronic (n = 406) and recent (n = 81) HIV-1 subtype C infection and measured their in vitro RC using a green fluorescent protein (GFP) reporter T cell assay. In recently infected individuals, reverse transcriptase (RT)-integrase-driven RC correlated significantly with viral load set point (r = 0.25; P = 0.03) and CD4+ T cell decline (P = 0.013). Moreover, significant associations between RT integrase-driven RC and viral load (r = 0.28; P < 0.0001) and CD4+ T cell count (r = -0.29; P < 0.0001) remained in chronic infection. In early HIV infection, host expression of the protective HLA-B*81 allele was associated with lower RC (P = 0.05), as was expression of HLA-B*07 (P = 0.02), suggesting early immune-driven attenuation of RT-integrase by these alleles. In chronic infection, HLA-A*30:09 (in linkage disequilibrium with HLA-B*81) was significantly associated with lower RC (P = 0.05), and all 6 HLA-B alleles with the lowest RC measurements represented protective alleles, consistent with long-term effects of host immune pressures on lowering RT-integrase RC. The polymorphisms V241I, I257V, P272K, and E297K in reverse transcriptase and I201V in integrase, all relatively uncommon polymorphisms occurring in or adjacent to optimally described HLA-restricted cytotoxic T-lymphocyte epitopes, were associated with reduced RC. Together, our data suggest that RT-integrase-driven RC is clinically relevant and provide evidence that immune-driven selection of mutations in RT-integrase can compromise RC.IMPORTANCE Identification of viral mutations that compromise HIV's ability to replicate may aid rational vaccine design. However, while certain escape mutations in Gag have been shown to reduce HIV replication and influence clinical progression, less is known about the consequences of mutations that naturally arise in other HIV proteins. Pol is a highly conserved protein, but the impact of Pol function on HIV disease progression is not well defined. Here, we generated recombinant viruses using the RT-integrase region of Pol derived from HIV-1C-infected individuals with recent and chronic infection and measured their ability to replicate in vitro We demonstrate that RT-integrase-driven replication ability significantly impacts HIV disease progression. We further show evidence of immune-mediated attenuation in RT-integrase and identify specific polymorphisms in RT-integrase that significantly decrease HIV-1 replication ability, suggesting which Pol epitopes could be explored in vaccine development.
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Perdiguero B, Raman SC, Sánchez-Corzo C, Sorzano COS, Valverde JR, Esteban M, Gómez CE. Potent HIV-1-Specific CD8 T Cell Responses Induced in Mice after Priming with a Multiepitopic DNA-TMEP and Boosting with the HIV Vaccine MVA-B. Viruses 2018; 10:v10080424. [PMID: 30104537 PMCID: PMC6116222 DOI: 10.3390/v10080424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 11/16/2022] Open
Abstract
An effective vaccine against Human Immunodeficiency Virus (HIV) still remains the best solution to provide a sustainable control and/or eradication of the virus. We have previously generated the HIV-1 vaccine modified vaccinia virus Ankara (MVA)-B, which exhibited good immunogenicity profile in phase I prophylactic and therapeutic clinical trials, but was unable to prevent viral rebound after antiretroviral (ART) removal. To potentiate the immunogenicity of MVA-B, here we described the design and immune responses elicited in mice by a new T cell multi-epitopic B (TMEP-B) immunogen, vectored by DNA, when administered in homologous or heterologous prime/boost regimens in combination with MVA-B. The TMEP-B protein contained conserved regions from Gag, Pol, and Nef proteins including multiple CD4 and CD8 T cell epitopes functionally associated with HIV control. Heterologous DNA-TMEP/MVA-B regimen induced higher HIV-1-specific CD8 T cell responses with broader epitope recognition and higher polyfunctional profile than the homologous DNA-TMEP/DNA-TMEP or the heterologous DNA-GPN/MVA-B combinations. Moreover, higher HIV-1-specific CD4 and Tfh immune responses were also detected using this regimen. After MVA-B boost, the magnitude of the anti-VACV CD8 T cell response was significantly compromised in DNA-TMEP-primed animals. Our results revealed the immunological potential of DNA-TMEP prime/MVA-B boost regimen and supported the application of these combined vectors in HIV-1 prevention and/or therapy.
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Affiliation(s)
- Beatriz Perdiguero
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Suresh C Raman
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Cristina Sánchez-Corzo
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - José Ramón Valverde
- Scientific Computing Service, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Carmen Elena Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
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Codon optimization and improved delivery/immunization regimen enhance the immune response against wild-type and drug-resistant HIV-1 reverse transcriptase, preserving its Th2-polarity. Sci Rep 2018; 8:8078. [PMID: 29799015 PMCID: PMC5967322 DOI: 10.1038/s41598-018-26281-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
DNA vaccines require a considerable enhancement of immunogenicity. Here, we optimized a prototype DNA vaccine against drug-resistant HIV-1 based on a weak Th2-immunogen, HIV-1 reverse transcriptase (RT). We designed expression-optimized genes encoding inactivated wild-type and drug-resistant RTs (RT-DNAs) and introduced them into mice by intradermal injections followed by electroporation. RT-DNAs were administered as single or double primes with or without cyclic-di-GMP, or as a prime followed by boost with RT-DNA mixed with a luciferase-encoding plasmid (“surrogate challenge”). Repeated primes improved cellular responses and broadened epitope specificity. Addition of cyclic-di-GMP induced a transient increase in IFN-γ production. The strongest anti-RT immune response was achieved in a prime-boost protocol with electroporation by short 100V pulses done using penetrating electrodes. The RT-specific response, dominated by CD4+ T-cells, targeted epitopes at aa 199–220 and aa 528–543. Drug-resistance mutations disrupted the epitope at aa 205–220, while the CTL epitope at aa 202–210 was not affected. Overall, multiparametric optimization of RT strengthened its Th2- performance. A rapid loss of RT/luciferase-expressing cells in the surrogate challenge experiment revealed a lytic potential of anti-RT response. Such lytic CD4+ response would be beneficial for an HIV vaccine due to its comparative insensitivity to immune escape.
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Damilano GD, Sued O, Ruiz MJ, Ghiglione Y, Canitano F, Pando M, Turk G, Cahn P, Salomón H, Dilernia D. Computational comparison of availability in CTL/gag epitopes among patients with acute and chronic HIV-1 infection. Vaccine 2018; 36:4142-4151. [PMID: 29802001 DOI: 10.1016/j.vaccine.2018.04.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Recent studies indicate that there is selection bias for transmission of viral polymorphisms associated with higher viral fitness. Furthermore, after transmission and before a specific immune response is mounted in the recipient, the virus undergoes a number of reversions which allow an increase in their replicative capacity. These aspects, and others, affect the viral population characteristic of early acute infection. METHODS 160 singlegag-gene amplifications were obtained by limiting-dilution RT-PCR from plasma samples of 8 ARV-naïve patients with early acute infection (<30 days, 22 days average) and 8 ARV-naive patients with approximately a year of infection (10 amplicons per patient). Sanger sequencing and NGS SMRT technology (Pacific Biosciences) were implemented to sequence the amplicons. Phylogenetic analysis was performed by using MEGA 6.06. HLA-I (A and B) typing was performed by SSOP-PCR method. The chromatograms were analyzed with Sequencher 4.10. Epitopes and immune-proteosomal cleavages prediction was performed with CBS prediction server for the 30 HLA-A and -B alleles most prevalent in our population with peptide lengths from 8 to 14 mer. Cytotoxic response prediction was performed by using IEDB Analysis Resource. RESULTS After implementing epitope prediction analysis, we identified a total number of 325 possible viral epitopes present in two or more acute or chronic patients. 60.3% (n = 196) of them were present only in acute infection (prevalent acute epitopes) while 39.7% (n = 129) were present only in chronic infection (prevalent chronic epitopes). Within p24, the difference was equally dramatic with 59.4% (79/133) being acute epitopes (p < 0.05). This is consistent with progressive viral adaptation to immune response in time and further supported by the fact that cytotoxic responses prediction showed that acute epitopes are more likely to generate immune response than chronic epitopes. Interestingly, only 27.5% of acute epitopes match the population-level consensus sequence of the virus. CONCLUSIONS Our results indicate that certain non-consensus viral residues might be transmitted more frequently than consensus-residues when located in immunological relevant positions (epitopes). This observation might be relevant to the rationale behind development of an effective vaccineto reduce viral reservoir and induce functional cure of HIV infection based in prevalent acute epitopes.
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Affiliation(s)
- Gabriel Dario Damilano
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Omar Sued
- Fundación Huésped, Buenos Aires, Argentina.
| | - Maria Julia Ruiz
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Yanina Ghiglione
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Flavia Canitano
- Instituto de Investigaciones Médicas Alfredo Lanari, Buenos Aires, Argentina.
| | - Maria Pando
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Gabriela Turk
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Pedro Cahn
- Fundación Huésped, Buenos Aires, Argentina.
| | - Horacio Salomón
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Dario Dilernia
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina; Emory University, Atlanta, USA.
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Borthwick NJ, Lane T, Moyo N, Crook A, Shim JM, Baines I, Wee EG, Hawkins PN, Gillmore JD, Hanke T, Pepys MB. Randomized phase I trial HIV-CORE 003: Depletion of serum amyloid P component and immunogenicity of DNA vaccination against HIV-1. PLoS One 2018; 13:e0197299. [PMID: 29772028 PMCID: PMC5957335 DOI: 10.1371/journal.pone.0197299] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/27/2018] [Indexed: 11/22/2022] Open
Abstract
Background The failure of DNA vaccination in humans, in contrast to its efficacy in some species, is unexplained. Observational and interventional experimental evidence suggests that DNA immunogenicity may be prevented by binding of human serum amyloid P component (SAP). SAP is the single normal DNA binding protein in human plasma. The drug (R)-1-[6-[(R)-2-carboxypyrrolidin-1-yl]-6-oxo-hexanoyl]pyrrolidine-2-carboxylic acid (CPHPC, miridesap), developed for treatment of systemic amyloidosis and Alzheimer’s disease, depletes circulating SAP by 95–99%. The proof-of-concept HIV-CORE 003 clinical trial tested whether SAP depletion by CPHPC would enhance the immune response in human volunteers to DNA vaccination delivering the HIVconsv immunogen derived from conserved sub-protein regions of HIV-1. Methods Human volunteers received 3 intramuscular immunizations with an experimental DNA vaccine (DDD) expressing HIV-1-derived immunogen HIVconsv, with or without prior depletion of SAP by CPHPC. All subjects were subsequently boosted by simian (chimpanzee) adenovirus (C)- and poxvirus MVA (M)-vectored vaccines delivering the same immunogen. After administration of each vaccine modality, the peak total magnitudes, kinetics, functionality and memory subsets of the T-cell responses to HIVconsv were thoroughly characterized. Results No differences were observed between the CPHPC treated and control groups in any of the multiple quantitative and qualitative parameters of the T-cell responses to HIVconsv, except that after SAP depletion, there was a statistically significantly greater breadth of T-cell specificities, that is the number of recognized epitopes, following the DDDC vaccination. Conclusions The protocol used here for SAP depletion by CPHPC prior to DNA vaccination produced only a very modest suggestion of enhanced immunogenicity. Further studies will be required to determine whether SAP depletion might have a practical value in DNA vaccination for other plasmid backbones and/or immunogens. Trial registration Clinicaltrials.gov NCT02425241
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Affiliation(s)
- Nicola J. Borthwick
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Thirusha Lane
- Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alison Crook
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jung Min Shim
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ian Baines
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Edmund G. Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Philip N. Hawkins
- Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Julian D. Gillmore
- Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- * E-mail:
| | - Mark B. Pepys
- Centre for Amyloidosis and Acute Phase Proteins, University College London, London, United Kingdom
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, UCL, London, United Kingdom
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21
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Moyo N, Borthwick NJ, Wee EG, Capucci S, Crook A, Dorrell L, Hanke T. Long-term follow up of human T-cell responses to conserved HIV-1 regions elicited by DNA/simian adenovirus/MVA vaccine regimens. PLoS One 2017; 12:e0181382. [PMID: 28719652 PMCID: PMC5515449 DOI: 10.1371/journal.pone.0181382] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Durability of vaccine-elicited immune responses is one of the key determinants for vaccine success. Our aim is to develop a vaccination strategy against the human immunodeficiency virus type 1 (HIV-1), which induces protective and durable CD8+ T-cell responses. The central theorem of our approach is to focus T cells on highly conserved regions of the HIV-1 proteome and this is achieved through the use of the first-generation conserved vaccine immunogen HIVconsv. This immunogen vectored by plasmid DNA, simian adenovirus and poxvirus MVA was tested in healthy, HIV-1-negative adults in UK and induced high magnitudes of HIVconsv-specific plurifunctional CD8+ T cells capable of in vitro HIV-1 inhibition. Here, we assessed the durability of these responses. METHODS Vaccine recipients in trial HIV-CORE 002 were invited to provide a blood sample at 1 and 2 years after vaccination. Their PBMCs were tested in IFN-γ ELISPOT, 25-analyte Luminex, CFSE proliferation and intracellular cytokine staining assays, the last enhanced by HLA-peptide dextramer analysis. RESULTS 12/12 (1 year) and 8/8 (2 years) returning subjects had median (range) of 990 (150-2495) and 763 (70-1745) IFN-γ SFU/106 PBMC specific for HIVconsv, respectively, and recognized 5 (1-6) out of 6 peptide pools at 2 years. Over one-half of the HIVconsv-specific cells expressed at least 3 functions IFN-γ, TNF-α and CD107a, and were capable of proliferation. Among dextramer-reactive cells, naïve, transitional, effector and terminally differentiated memory subsets were similarly represented. CONCLUSIONS First generation HIVconsv vaccine induced human T cells, which were plurifunctional and persisted for at least 2 years. TRIAL REGISTRATION ClinicalTrials.gov NCT01151319.
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Affiliation(s)
- Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola J Borthwick
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Edmund G Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Capucci
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alison Crook
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lucy Dorrell
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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22
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Fusion to Flaviviral Leader Peptide Targets HIV-1 Reverse Transcriptase for Secretion and Reduces Its Enzymatic Activity and Ability to Induce Oxidative Stress but Has No Major Effects on Its Immunogenic Performance in DNA-Immunized Mice. J Immunol Res 2017; 2017:7407136. [PMID: 28717654 PMCID: PMC5498913 DOI: 10.1155/2017/7407136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/13/2017] [Indexed: 01/10/2023] Open
Abstract
Reverse transcriptase (RT) is a key enzyme in viral replication and susceptibility to ART and a crucial target of immunotherapy against drug-resistant HIV-1. RT induces oxidative stress which undermines the attempts to make it immunogenic. We hypothesized that artificial secretion may reduce the stress and make RT more immunogenic. Inactivated multidrug-resistant RT (RT1.14opt-in) was N-terminally fused to the signal providing secretion of NS1 protein of TBEV (Ld) generating optimized inactivated Ld-carrying enzyme RT1.14oil. Promotion of secretion prohibited proteasomal degradation increasing the half-life and content of RT1.14oil in cells and cell culture medium, drastically reduced the residual polymerase activity, and downmodulated oxidative stress. BALB/c mice were DNA-immunized with RT1.14opt-in or parental RT1.14oil by intradermal injections with electroporation. Fluorospot and ELISA tests revealed that RT1.14opt-in and RT1.14oil induced IFN-γ/IL-2, RT1.14opt-in induced granzyme B, and RT1.14oil induced perforin production. Perforin secretion correlated with coproduction of IFN-γ and IL-2 (R = 0,97). Both DNA immunogens induced strong anti-RT antibody response. Ld peptide was not immunogenic. Thus, Ld-driven secretion inferred little change to RT performance in DNA immunization. Positive outcome was the abrogation of polymerase activity increasing safety of RT-based DNA vaccines. Identification of the molecular determinants of low cellular immunogenicity of RT requires further studies.
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23
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Wee EG, Ondondo B, Berglund P, Archer J, McMichael AJ, Baltimore D, Ter Meulen JH, Hanke T. HIV-1 Conserved Mosaics Delivered by Regimens with Integration-Deficient DC-Targeting Lentiviral Vector Induce Robust T Cells. Mol Ther 2017; 25:494-503. [PMID: 28153096 PMCID: PMC5368423 DOI: 10.1016/j.ymthe.2016.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
To be effective against HIV type 1 (HIV-1), vaccine-induced T cells must selectively target epitopes, which are functionally conserved (present in the majority of currently circulating and reactivated HIV-1 strains) and, at the same time, beneficial (responses to which are associated with better clinical status and control of HIV-1 replication), and rapidly reach protective frequencies upon exposure to the virus. Heterologous prime-boost regimens using virally vectored vaccines are currently the most promising vaccine strategies; nevertheless, induction of robust long-term memory remains challenging. To this end, lentiviral vectors induce high frequencies of memory cells due to their low-inflammatory nature, while typically inducing only low anti-vector immune responses. Here, we describe construction of novel candidate vaccines ZVex.tHIVconsv1 and ZVex.tHIVconsv2, which are based on an integration-deficient lentiviral vector platform with preferential transduction of human dendritic cells and express a bivalent mosaic of conserved-region T cell immunogens with a high global HIV-1 match. Each of the two mosaic vaccines was individually immunogenic. When administered together in heterologous prime-boost regimens with chimpanzee adenovirus and/or poxvirus modified vaccinia virus Ankara (MVA) vaccines to BALB/c and outbred CD1-Swiss mice, they induced a median frequency of over 6,000 T cells/106 splenocytes, which were plurifunctional, broadly specific, and cross-reactive. These results support further development of this vaccine concept.
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Affiliation(s)
- Edmund G Wee
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | | | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-8555, Japan.
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24
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Novel, in-natural-infection subdominant HIV-1 CD8+ T-cell epitopes revealed in human recipients of conserved-region T-cell vaccines. PLoS One 2017; 12:e0176418. [PMID: 28448594 PMCID: PMC5407754 DOI: 10.1371/journal.pone.0176418] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/10/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Fine definition of targeted CD8+ T-cell epitopes and their human leucocyte antigen (HLA) class I restriction informs iterative improvements of HIV-1 T-cell vaccine designs and may predict early vaccine success or failure. Here, lymphocytes from volunteers, who had received candidate HIVconsv vaccines expressing conserved sub-protein regions of HIV-1, were used to define the optimum-length target epitopes and their HLA restriction. In HIV-1-positive patients, CD8+ T-cell responses predominantly recognize immunodominant, but hypervariable and therefore less protective epitopes. The less variable, more protective epitopes in conserved regions are typically subdominant. Therefore, induction of strong responses to conserved regions by vaccination provides an opportunity to discover novel important epitopes. METHODS Cryopreserved lymphocytes from vaccine recipients were expanded by stimulation with 15-mer responder peptides for 10 days to establish short term-cell-line (STCL) effector cells. These were subjected to intracellular cytokine staining using serially truncated peptides and peptide-pulsed 721.221 cells expressing individual HLA class I alleles to define minimal epitope length and HLA restriction by stimulation of IFN-γ and TNF-α production and surface expression of CD107a. RESULTS Using lymphocyte samples of 12 vaccine recipients, we defined 14 previously unreported optimal CD8+ T-cell HIV-1 epitopes and their four-digit HLA allele restriction (6 HLA-A, 7 HLA-B and 1 HLA-C alleles). Further 13 novel targets with incomplete information were revealed. CONCLUSIONS The high rate of discovery of novel CD8+ T-cell effector epitopes warrants further epitope mining in recipients of the conserved-region vaccines in other populations and informs development of HIV-1/AIDS vaccines. TRIAL REGISTRATION ClinicalTrials.gov NCT01151319.
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25
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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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26
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Delagrèverie HM, Delaugerre C, Lewin SR, Deeks SG, Li JZ. Ongoing Clinical Trials of Human Immunodeficiency Virus Latency-Reversing and Immunomodulatory Agents. Open Forum Infect Dis 2016; 3:ofw189. [PMID: 27757411 PMCID: PMC5066458 DOI: 10.1093/ofid/ofw189] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
In chronic human immunodeficiency virus (HIV)-1 infection, long-lived latently infected cells are the major barrier to virus eradication and functional cure. Several therapeutic strategies to perturb, eliminate, and/or control this reservoir are now being pursued in the clinic. These strategies include latency reversal agents (LRAs) designed to reactivate HIV-1 ribonucleic acid transcription and virus production and a variety of immune-modifying drugs designed to reverse latency, block homeostatic proliferation, and replenish the viral reservoir, eliminate virus-producing cells, and/or control HIV replication after cessation of antiretroviral therapy. This review provides a summary of ongoing clinical trials of HIV LRAs and immunomodulatory molecules, and it highlights challenges in the comparison and interpretation of the expected trial results.
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Affiliation(s)
- Héloïse M Delagrèverie
- INSERM U941, Université Paris Diderot, Laboratoire de Virologie, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris , France
| | - Constance Delaugerre
- INSERM U941, Université Paris Diderot, Laboratoire de Virologie, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris , France
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Australia; Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Victoria, Australia
| | - Steven G Deeks
- HIV/AIDS Division, Department of Medicine , San Francisco General Hospital, University of California
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts
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27
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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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28
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Ström P, Støer N, Borthwick N, Dong T, Hanke T, Reilly M. A statistical approach to determining responses to individual peptides from pooled-peptide ELISpot data. J Immunol Methods 2016; 435:43-9. [PMID: 27196788 DOI: 10.1016/j.jim.2016.05.006] [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] [Received: 02/20/2016] [Revised: 04/27/2016] [Accepted: 05/04/2016] [Indexed: 11/24/2022]
Abstract
To investigate in detail the effect of infection or vaccination on the human immune system, ELISpot assays are used to simultaneously test the immune response to a large number of peptides of interest. Scientists commonly use "peptide pools", where, instead of an individual peptide, a test well contains a group of peptides. Since the response from a well may be due to any or many of the peptides in the pool, pooled assays usually need to be followed by confirmatory assays of a number of individual peptides. We present a statistical method that enables estimation of individual peptide responses from pool responses using the Expectation Maximization (EM) algorithm for "incomplete data". We demonstrate the accuracy and precision of these estimates in simulation studies of ELISpot plates with 90 pools of 6 or 7 peptides arranged in three dimensions and three Mock wells for the estimation of background. In analysis of real pooled data from 6 subjects in a HIV-1 vaccine trial, where 199 peptides were arranged in 80 pools if size 9 or 10, our estimates were in very good agreement with the results from individual-peptide confirmatory assays. Compared to the classical approach, we could identify almost all the same peptides with high or moderate response, with less than half the number of confirmatory tests. Our method facilitates efficient use of the information available in pooled ELISpot data to avoid or reduce the need for confirmatory testing. We provide an easy-to-use free online application for implementing the method, where on uploading two spreadsheets with the pool design and pool responses, the user obtains the estimates of the individual peptide responses.
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Affiliation(s)
- Peter Ström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
| | - Nathalie Støer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
| | | | - Tao Dong
- Weatherall institute of Molecular Medicine, Oxford, UK
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, UK; Weatherall institute of Molecular Medicine, Oxford, UK
| | - Marie Reilly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden.
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29
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Ondondo B, Murakoshi H, Clutton G, Abdul-Jawad S, Wee EGT, Gatanaga H, Oka S, McMichael AJ, Takiguchi M, Korber B, Hanke T. Novel Conserved-region T-cell Mosaic Vaccine With High Global HIV-1 Coverage Is Recognized by Protective Responses in Untreated Infection. Mol Ther 2016; 24:832-42. [PMID: 26743582 PMCID: PMC4886941 DOI: 10.1038/mt.2016.3] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/31/2015] [Indexed: 12/12/2022] Open
Abstract
An effective human immunodeficiency virus type 1 (HIV-1) vaccine is the best solution for halting the acquired immune deficiency syndrome epidemic. Here, we describe the design and preclinical immunogenicity of T-cell vaccine expressing novel immunogens tHIVconsvX, vectored by DNA, simian (chimpanzee) adenovirus, and poxvirus modified vaccinia virus Ankara (MVA), a combination highly immunogenic in humans. The tHIVconsvX immunogens combine the three leading strategies for elicitation of effective CD8(+) T cells: use of regions of HIV-1 proteins functionally conserved across all M group viruses (to make HIV-1 escape costly on viral fitness), inclusion of bivalent complementary mosaic immunogens (to maximize global epitope matching and breadth of responses, and block common escape paths), and inclusion of epitopes known to be associated with low viral load in infected untreated people (to induce field-proven protective responses). tHIVconsvX was highly immunogenic in two strains of mice. Furthermore, the magnitude and breadth of CD8(+) T-cell responses to tHIVconsvX-derived peptides in treatment-naive HIV-1(+) patients significantly correlated with high CD4(+) T-cell count and low viral load. Overall, the tHIVconsvX design, combining the mosaic and conserved-region approaches, provides an indisputably better coverage of global HIV-1 variants than previous T-cell vaccines. These immunogens delivered in a highly immunogenic framework of adenovirus prime and MVA boost are ready for clinical development.
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Affiliation(s)
- Beatrice Ondondo
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
| | | | - Genevieve Clutton
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
- Current address: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Edmund G-T Wee
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Bette Korber
- Los Alamo National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA
- The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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30
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Abdul-Jawad S, Ondondo B, van Hateren A, Gardner A, Elliott T, Korber B, Hanke T. Increased Valency of Conserved-mosaic Vaccines Enhances the Breadth and Depth of Epitope Recognition. Mol Ther 2016; 24:375-384. [PMID: 26581160 PMCID: PMC4817818 DOI: 10.1038/mt.2015.210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022] Open
Abstract
The biggest roadblock in development of effective vaccines against human immunodeficiency virus type 1 (HIV-1) is the virus genetic diversity. For T-cell vaccine, this can be tackled by focusing the vaccine-elicited T-cells on the highly functionally conserved regions of HIV-1 proteins, mutations in which typically cause a replicative fitness loss, and by computing multivalent mosaic proteins, which maximize the coverage of potential 9-mer T-cell epitopes of the input viral sequences. Our first conserved region vaccines HIVconsv employed clade alternating consensus sequences and showed promise in the initial clinical trials in terms of magnitude and breadth of elicited CD8(+) T-cells. Here, monitoring T-cells restricted by HLA-A*02:01 in transgenic mice, we assessed whether or not the tHIVconsv design (HIVconsv with a tissue plasminogen activator leader sequence) benefits from combining with a complementing conserved mosaic immunogen tHIVcmo, and compared the bivalent immunization to that with trivalent conserved mosaic vaccines. A hierarchy of tHIVconsv ≤ tHIVconsv+tHIVcmo < tCmo1+tCmo2+tCmo3 vaccinations for induction of CD8(+) T-cell responses was observed in terms of recognition of tested peptide variants. Thus, our HLA-A*02:01-restricted epitope data concur with previously published mouse and macaque observations and suggest that even conserved region vaccines benefit from oligovalent mosaic design.
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Affiliation(s)
| | | | - Andy van Hateren
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | | | - Tim Elliott
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | - Bette Korber
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA; The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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31
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Ternette N, Yang H, Partridge T, Llano A, Cedeño S, Fischer R, Charles PD, Dudek NL, Mothe B, Crespo M, Fischer WM, Korber BTM, Nielsen M, Borrow P, Purcell AW, Brander C, Dorrell L, Kessler BM, Hanke T. Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells. Eur J Immunol 2015; 46:60-9. [PMID: 26467324 PMCID: PMC4737398 DOI: 10.1002/eji.201545890] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/27/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022]
Abstract
Recognition and eradication of infected cells by cytotoxic T lymphocytes is a key defense mechanism against intracellular pathogens. High‐throughput definition of HLA class I‐associated immunopeptidomes by mass spectrometry is an increasingly important analytical tool to advance our understanding of the induction of T‐cell responses against pathogens such as HIV‐1. We utilized a liquid chromatography tandem mass spectrometry workflow including de novo‐assisted database searching to define the HLA class I‐associated immunopeptidome of HIV‐1‐infected human cells. We here report for the first time the identification of 75 HIV‐1‐derived peptides bound to HLA class I complexes that were purified directly from HIV‐1‐infected human primary CD4+ T cells and the C8166 human T‐cell line. Importantly, one‐third of eluted HIV‐1 peptides had not been previously known to be presented by HLA class I. Over 82% of the identified sequences originated from viral protein regions for which T‐cell responses have previously been reported but for which the precise HLA class I‐binding sequences have not yet been defined. These results validate and expand the current knowledge of virus‐specific antigenic peptide presentation during HIV‐1 infection and provide novel targets for T‐cell vaccine development.
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Affiliation(s)
- Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hongbing Yang
- NIHR Oxford Biomedical Research Centre, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Partridge
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anuska Llano
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Samandhy Cedeño
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nadine L Dudek
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Beatriz Mothe
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain.,Lluita contra la Sida' Foundation, Hospital Germans Trias i Pujol, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
| | - Manuel Crespo
- HIV Unit, Hospital de la Vall d'Hebrón, Barcelona, Spain
| | - William M Fischer
- Group T-6, Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bette T M Korber
- Group T-6, Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Morten Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Persephone Borrow
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Christian Brander
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lucy Dorrell
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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