101
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Fang Q, Liu Z, Zhang T. Human leukocyte antigen polymorphisms and Kaposi's sarcoma-associated herpesvirus infection outcomes: A call for deeper exploration. J Med Virol 2018; 91:541-548. [PMID: 30345532 DOI: 10.1002/jmv.25342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/08/2018] [Indexed: 12/13/2022]
Abstract
Host genetic background may influence the immunity to resist viral infection. As the most polymorphic loci in the entire human genome, the human leukocyte antigen (HLA) system plays an important role in innate and adaptive immune responses to many invading pathogens. Studies have shown that an association might exist between HLA polymorphisms and susceptibility to Kaposi's sarcoma-associated herpesvirus (KSHV) infection and associated diseases. However, discrepant conclusions were reached among different subjects with different detection methods. Therefore, it is now urgent to summarize current results and figure out the achievements and deficiencies of the existing research for the reference to future studies. A better understanding about the role of HLA polymorphisms in KSHV infection outcome would enable us to elucidate the pathways through which the virus evades the host defense system and improve strategies for the prevention and treatment of KSHV infection.
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Affiliation(s)
- Qiwen Fang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - Zhenqiu Liu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.,Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
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102
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Moyo N, Vogel AB, Buus S, Erbar S, Wee EG, Sahin U, Hanke T. Efficient Induction of T Cells against Conserved HIV-1 Regions by Mosaic Vaccines Delivered as Self-Amplifying mRNA. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:32-46. [PMID: 30547051 PMCID: PMC6258890 DOI: 10.1016/j.omtm.2018.10.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022]
Abstract
Focusing T cell responses on the most vulnerable parts of HIV-1, the functionally conserved regions of HIV-1 proteins, is likely a key prerequisite for vaccine success. For a T cell vaccine to efficiently control HIV-1 replication, the vaccine-elicited individual CD8+ T cells and as a population have to display a number of critical traits. If any one of these traits is suboptimal, the vaccine is likely to fail. Fine-tuning of individual protective characteristics of T cells will require iterative stepwise improvements in clinical trials. Although the second-generation tHIVconsvX immunogens direct CD8+ T cells to predominantly protective and conserved epitopes, in the present work, we have used formulated self-amplifying mRNA (saRNA) to deliver tHIVconsvX to the immune system. We demonstrated in BALB/c and outbred mice that regimens employing saRNA vaccines induced broadly specific, plurifunctional CD8+ and CD4+ T cells, which displayed structured memory subpopulations and were maintained at relatively high frequencies over at least 22 weeks post-administration. This is one of the first thorough analyses of mRNA vaccine-elicited T cell responses. The combination of tHIVconsvX immunogens and the highly versatile and easily manufacturable saRNA platform may provide a long-awaited opportunity to define and optimize induction of truly protective CD8+ T cell parameters in human volunteers.
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Affiliation(s)
- Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Annette B Vogel
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz 55131, Germany
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Stephanie Erbar
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz 55131, Germany
| | - Edmund G Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Ugur Sahin
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz 55131, Germany
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
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103
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Kosch TA, Silva CNS, Brannelly LA, Roberts AA, Lau Q, Marantelli G, Berger L, Skerratt LF. Genetic potential for disease resistance in critically endangered amphibians decimated by chytridiomycosis. Anim Conserv 2018. [DOI: 10.1111/acv.12459] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- T. A. Kosch
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
| | - C. N. S. Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville Qld Australia
| | - L. A. Brannelly
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
- Department of Biological Sciences University of Pittsburgh Pittsburgh PA USA
| | - A. A. Roberts
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
| | - Q. Lau
- Department of Evolutionary Studies of Biosystems Sokendai (The Graduate University for Advanced Studies) Hayama Japan
| | | | - L. Berger
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
| | - L. F. Skerratt
- One Health Research Group College of Public Health, Medical and Veterinary Sciences James Cook University Townsville Qld Australia
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104
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Sung JA, Patel S, Clohosey ML, Roesch L, Tripic T, Kuruc JD, Archin N, Hanley PJ, Cruz CR, Goonetilleke N, Eron JJ, Rooney CM, Gay CL, Bollard CM, Margolis DM. HIV-Specific, Ex Vivo Expanded T Cell Therapy: Feasibility, Safety, and Efficacy in ART-Suppressed HIV-Infected Individuals. Mol Ther 2018; 26:2496-2506. [PMID: 30249388 PMCID: PMC6171327 DOI: 10.1016/j.ymthe.2018.08.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/19/2018] [Accepted: 08/15/2018] [Indexed: 12/29/2022] Open
Abstract
Adoptive T cell therapy has had dramatic successes in the treatment of virus-related malignancies and infections following hematopoietic stem cell transplantation. We adapted this method to produce ex vivo expanded HIV-specific T cells (HXTCs), with the long-term goal of using HXTCs as part of strategies to clear persistent HIV infection. In this phase 1 proof-of-concept study (NCT02208167), we administered HXTCs to antiretroviral therapy (ART)-suppressed, HIV-infected participants. Participants received two infusions of 2 × 107 cells/m2 HXTCs at a 2-week interval. Leukapheresis was performed at baseline and 12 weeks post-infusion to measure the frequency of resting cell infection by the quantitative viral outgrowth assay (QVOA). Overall, participants tolerated HXTCs, with only grade 1 adverse events (AEs) related to HXTCs. Two of six participants exhibited a detectable increase in CD8 T cell-mediated antiviral activity following the two infusions in some, but not all, assays. As expected, however, in the absence of a latency reversing agent, no meaningful decline in the frequency of resting CD4 T cell infection was detected. HXTC therapy in ART-suppressed, HIV-infected individuals appears safe and well tolerated, without any clinical signs of immune activation, likely due to the low residual HIV antigen burden present during ART.
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Affiliation(s)
- Julia A Sung
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shabnum Patel
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC 20010, USA
| | - Matthew L Clohosey
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lauren Roesch
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC 20010, USA
| | - Tamara Tripic
- Section of Hematology-Oncology, Department of Pediatrics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - JoAnn D Kuruc
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nancie Archin
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick J Hanley
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC 20010, USA
| | - C Russell Cruz
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC 20010, USA
| | - Nilu Goonetilleke
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph J Eron
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clio M Rooney
- Section of Hematology-Oncology, Department of Pediatrics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cynthia L Gay
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC 20010, USA.
| | - David M Margolis
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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105
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de Groot NG, Stevens JM, Bontrop RE. Does the MHC Confer Protection against Malaria in Bonobos? Trends Immunol 2018; 39:768-771. [DOI: 10.1016/j.it.2018.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/13/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
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106
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Murakoshi H, Koyanagi M, Akahoshi T, Chikata T, Kuse N, Gatanaga H, Rowland-Jones SL, Oka S, Takiguchi M. Impact of a single HLA-A*24:02-associated escape mutation on the detrimental effect of HLA-B*35:01 in HIV-1 control. EBioMedicine 2018; 36:103-112. [PMID: 30249546 PMCID: PMC6197679 DOI: 10.1016/j.ebiom.2018.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 01/06/2023] Open
Abstract
Background HLA-B*35 is an HLA allele associated with rapid progression to AIDS. However, a mechanism underlying the detrimental effect of HLA-B*35 on disease outcome remains unknown. Recent studies demonstrated that most prevalent subtype HLA-B*35:01 is a detrimental allele in HIV-1 clade B-infected individuals. We here investigated the effect of mutations within the epitopes on HLA-B*35:01-restricted CD8+ T cells having abilities to suppress HIV-1 replication. Methods We analyzed 16 HLA-B*35:01-restricted epitope-specific T cells in 63 HIV-1 clade B-infected Japanese B*35:01+ individuals and identified HLA-B*35:01-restricted CD8+ T cells having abilities to suppress HIV-1 replication. We further analyzed the effect of HLA-associated mutations on the ability of these T cells. Findings The breadth of T cell responses to 4 epitopes was inversely associated with plasma viral load (pVL). However, the accumulation of an Y135F mutation in NefYF9 out of the 4 epitopes, which is selected by HLA-A*24:02-restricted T cells, affected the ability of YF9-specific T cells to suppress HIV-1 replication. HLA-B*35:01+ individuals harboring this mutation had much higher pVL than those without it. YF9-specific T cells failed to suppress replication of the Y135F mutant in vitro. These results indicate that this mutation impairs suppression of HIV-1 replication by YF9-specific T cells. Interpretation These findings indicate that the Y135F mutation is a key factor underlying the detrimental effect of HLA-B*35:01 on disease outcomes in HIV-1 clade B-infected individuals. Fund Grants-in-aid for AIDS Research from AMED and for scientific research from the Ministry of Education, Science, Sports, and Culture, Japan. T cells specific for 4 HLA-B*35:01-restricted epitopes have abilities to suppress HIV-1 replication in vivo. An Y135F mutation selected by HLA-A*24:02-restricted T cells affected HIV-1 control by NefYF9-specific T cells in vivo. The NefY135F mutation impaired suppression of HIV-1 replication by NefYF9-specific T cells in vitro.
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Affiliation(s)
- Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Tomohiro Akahoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Sarah L Rowland-Jones
- IRCMS, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK.
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107
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Martins MA, Tully DC, Pedreño-Lopez N, von Bredow B, Pauthner MG, Shin YC, Yuan M, Lima NS, Bean DJ, Gonzalez-Nieto L, Domingues A, Gutman MJ, Maxwell HS, Magnani DM, Ricciardi MJ, Bailey VK, Altman JD, Burton DR, Ejima K, Allison DB, Evans DT, Rakasz EG, Parks CL, Bonaldo MC, Capuano S, Lifson JD, Desrosiers RC, Allen TM, Watkins DI. Mamu-B*17+ Rhesus Macaques Vaccinated with env, vif, and nef Manifest Early Control of SIVmac239 Replication. J Virol 2018; 92:e00690-18. [PMID: 29875239 PMCID: PMC6069176 DOI: 10.1128/jvi.00690-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
Certain major histocompatibility complex class I (MHC-I) alleles are associated with spontaneous control of viral replication in human immunodeficiency virus (HIV)-infected people and simian immunodeficiency virus (SIV)-infected rhesus macaques (RMs). These cases of "elite" control of HIV/SIV replication are often immune-mediated, thereby providing a framework for studying anti-lentiviral immunity. In this study, we examined how vaccination impacts SIV replication in RMs expressing the MHC-I allele Mamu-B*17 Approximately 21% of Mamu-B*17+ and 50% of Mamu-B*08+ RMs control chronic-phase viremia after SIVmac239 infection. Because CD8+ T cells targeting Mamu-B*08-restricted SIV epitopes have been implicated in virologic suppression in Mamu-B*08+ RMs, we investigated whether this might also be true for Mamu-B*17+ RMs. Two groups of Mamu-B*17+ RMs were vaccinated with genes encoding Mamu-B*17-restricted epitopes in Vif and Nef. These genes were delivered by themselves (group 1) or together with env (group 2). Group 3 included MHC-I-matched RMs and served as the control group. Surprisingly, the group 1 vaccine regimen had little effect on viral replication compared to group 3, suggesting that unlike Mamu-B*08+ RMs, preexisting SIV-specific CD8+ T cells alone do not facilitate long-term virologic suppression in Mamu-B*17+ RMs. Remarkably, however, 5/8 group 2 vaccinees controlled viremia to <15 viral RNA copies/ml soon after infection. No serological neutralizing activity against SIVmac239 was detected in group 2, although vaccine-elicited gp140-binding antibodies correlated inversely with nadir viral loads. Collectively, these data shed new light on the unique mechanism of elite control in Mamu-B*17+ RMs and implicate vaccine-induced, nonneutralizing anti-Env antibodies in the containment of immunodeficiency virus infection.IMPORTANCE A better understanding of the immune correlates of protection against HIV might facilitate the development of a prophylactic vaccine. Therefore, we investigated simian immunodeficiency virus (SIV) infection outcomes in rhesus macaques expressing the major histocompatibility complex class I allele Mamu-B*17 Approximately 21% of Mamu-B*17+ macaques spontaneously controlled chronic phase viremia after SIV infection, an effect that may involve CD8+ T cells targeting Mamu-B*17-restricted SIV epitopes. We vaccinated Mamu-B*17+ macaques with genes encoding immunodominant epitopes in Vif and Nef alone (group 1) or together with env (group 2). Although neither vaccine regimen prevented SIV infection, 5/8 group 2 vaccinees controlled viremia to below detection limits shortly after infection. This outcome, which was not observed in group 1, was associated with vaccine-induced, nonneutralizing Env-binding antibodies. Together, these findings suggest a limited contribution of Vif- and Nef-specific CD8+ T cells for virologic control in Mamu-B*17+ macaques and implicate anti-Env antibodies in containment of SIV infection.
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Affiliation(s)
| | - Damien C Tully
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Benjamin von Bredow
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Matthias G Pauthner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
| | - Young C Shin
- Department of Pathology, University of Miami, Miami, Florida, USA
| | - Maoli Yuan
- International AIDS Vaccine Initiative, AIDS Vaccine Design and Development Laboratory, Brooklyn, New York, USA
| | - Noemia S Lima
- Laboratório de Biologia Molecular de Flavivirus, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - David J Bean
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Aline Domingues
- Department of Pathology, University of Miami, Miami, Florida, USA
| | - Martin J Gutman
- Department of Pathology, University of Miami, Miami, Florida, USA
| | - Helen S Maxwell
- Department of Pathology, University of Miami, Miami, Florida, USA
| | - Diogo M Magnani
- Department of Pathology, University of Miami, Miami, Florida, USA
| | | | - Varian K Bailey
- Department of Pathology, University of Miami, Miami, Florida, USA
| | - John D Altman
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Dennis R Burton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, California, USA
| | - Keisuke Ejima
- School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - David B Allison
- School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Christopher L Parks
- International AIDS Vaccine Initiative, AIDS Vaccine Design and Development Laboratory, Brooklyn, New York, USA
| | - Myrna C Bonaldo
- Laboratório de Biologia Molecular de Flavivirus, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, Wisconsin, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Todd M Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - David I Watkins
- Department of Pathology, University of Miami, Miami, Florida, USA
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108
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Hu X, Lu Z, Valentin A, Rosati M, Broderick KE, Sardesai NY, Marx PA, Mullins JI, Pavlakis GN, Felber BK. Gag and env conserved element CE DNA vaccines elicit broad cytotoxic T cell responses targeting subdominant epitopes of HIV and SIV Able to recognize virus-infected cells in macaques. Hum Vaccin Immunother 2018; 14:2163-2177. [PMID: 29939820 PMCID: PMC6183272 DOI: 10.1080/21645515.2018.1489949] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
HIV sequence diversity and the propensity of eliciting immunodominant responses targeting inessential variable regions are hurdles in the development of an effective AIDS vaccine. We developed a DNA vaccine comprising conserved elements (CE) of SIV p27Gag and HIV-1 Env and found that priming vaccination with CE DNA is critical to efficiently overcome the dominance imposed by Gag and Env variable regions. Here, we show that DNA vaccinated macaques receiving the CE prime/CE+full-length DNA co-delivery booster vaccine regimens developed broad, potent and durable cytotoxic T cell responses targeting conserved protein segments of SIV Gag and HIV Env. Gag CE-specific T cells showed robust anamnestic responses upon infection with SIVmac239 which led to the identification of CE-specific cytotoxic lymphocytes able to recognize epitopes covering distinct CE on the surface of SIV infected cells in vivo. Though not controlling infection overall, we found an inverse correlation between Gag CE-specific CD8+ T cell responses and peak viremia. The T cell responses induced by the HIV Env CE immunogen were recalled in some animals upon SIV infection, leading to the identification of two cross-reactive epitopes between HIV and SIV Env based in sequence homology. These data demonstrate that a vaccine combining Gag and Env CE DNA subverted the normal immunodominance patterns, eliciting immune responses that included subdominant, highly conserved epitopes. These vaccine regimens augment cytotoxic T cell responses to highly conserved epitopes in the viral proteome and maximize response breadth. The vaccine-induced CE-specific T cells were expanded upon SIV infection, indicating that the predicted CE epitopes incorporated in the DNA vaccine are processed and exposed by infected cells in their natural context within the viral proteome.
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Affiliation(s)
- Xintao Hu
- a Human Retrovirus Pathogenesis Section, Center for Cancer Research, National Cancer Institute at Frederick , Frederick , MD , USA
| | - Zhongyan Lu
- a Human Retrovirus Pathogenesis Section, Center for Cancer Research, National Cancer Institute at Frederick , Frederick , MD , USA
| | - Antonio Valentin
- b Human Retrovirus Section, Vaccine Branch, Center for Cancer Research , National Cancer Institute at Frederick , Frederick, Frederick , MD , USA
| | - Margherita Rosati
- b Human Retrovirus Section, Vaccine Branch, Center for Cancer Research , National Cancer Institute at Frederick , Frederick, Frederick , MD , USA
| | | | | | - Preston A Marx
- d Tulane National Primate Research Center and Department of Tropical Medicine, School of Public Health and Tropical Medicine , Tulane University , New Orleans , LA , USA
| | - James I Mullins
- e Departments of Microbiology, Medicine and Laboratory Medicine , University of Washington , Seattle , WA , USA
| | - George N Pavlakis
- b Human Retrovirus Section, Vaccine Branch, Center for Cancer Research , National Cancer Institute at Frederick , Frederick, Frederick , MD , USA
| | - Barbara K Felber
- a Human Retrovirus Pathogenesis Section, Center for Cancer Research, National Cancer Institute at Frederick , Frederick , MD , USA
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Abstract
Human immunodeficiency virus (HIV) carries abundant human cell proteins, particularly human leukocyte antigen (HLA) molecules when the virus leaves host cells. Immunization in macaques with HLAs protects the animals from simian immunodeficiency virus infection. This finding offers an alternative approach to the development of HLA molecule-based HIV vaccines. Decades of studies have enhanced a great deal of our understanding of the mechanisms of allo-immune response-mediated anti-HIV immunity. These include cell-mediated immunity, innate immunity, and antibody response. These studies provided a rationale for the future design of effective HIV vaccines.
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Affiliation(s)
- Yufei Wang
- Mucosal Immunology Unit, Dental Institute, Kings College London, Guy's Campus, London Bridge, London, SE1 9RT, UK
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110
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Li W, Li C, Xia W, Li X. HLA-DQB1*06 and breadth of Nef core region-specific T-cell response are associated with slow disease progression in antiretroviral therapy-naive Chinese HIV-1 subtype B patients. Hum Vaccin Immunother 2018; 13:2341-2347. [PMID: 28771107 DOI: 10.1080/21645515.2017.1340138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Vaccines still are an important way to prevent and treat acquired immunodeficiency syndrome (AIDS). 1 For developing an effective T cell-based AIDS vaccine, it is critical to define the human leukocyte antigen (HLA) type and epitope that elicit the most potent responses. This study involved 29 antiretroviral therapy-naive and chronic human immunodeficiency virus (HIV)-1 subtype B-infected individuals. A polymerase chain reaction-sequence-specific primer was used to detect the HLA typing, and the enzyme-linked immunospot assay to quantify the T-cell immune function. The results showed that the HLA-DQB1*06-positive group had higher CD4 counts and lower viral load (VL) compared with the HLA-DQB1*06-negative group; A higher magnitude of HIV-1-specific T-cell response and breadth were observed in the HLA-DQB1*06-positive group; the T-cell response was proportional to VL (R2 = 0.488, P = 0.0368) in the HLA-DQB1*06-positive group. The total T-cell responses to HIV-1 Nef core region were quantified at the single-peptide level. Nine (90%) peptides were recognized in 18 (62.1%) individuals. The breath of Nef core region-specific T-cell response was correlated positively with CD4+ T cell count and inversely with VL, which improved disease outcomes. These data revealed that HLA-DQB1*06 had a protective effect on the course of HIV-1 and T-cell targeting of certain specific Nef epitopes, contributing to HIV-1 suppression. The results suggested the potential use of HLA-DQB1*06 and Nef core region in HIV-1 T-cell vaccine design.
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Affiliation(s)
- Weihua Li
- a YouAn Hospital , Capital Medical University , Beijing , China.,b Beijing Liver Disease Research Institute , Beijing , China
| | - Chuanyun Li
- a YouAn Hospital , Capital Medical University , Beijing , China
| | - Wei Xia
- a YouAn Hospital , Capital Medical University , Beijing , China
| | - Xiuhui Li
- a YouAn Hospital , Capital Medical University , Beijing , China
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Scutari R, Faieta M, D'Arrigo R, Fabeni L, Mussini C, Cossarizza A, Casoli C, Perno CF, Svicher V, Alteri C, Aquaro S. The degree of HIV-1 amino acid variability is strictly related to different disease progression rates. Virus Genes 2018; 54:493-501. [PMID: 29777446 DOI: 10.1007/s11262-018-1571-2] [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: 03/07/2018] [Accepted: 05/10/2018] [Indexed: 11/28/2022]
Abstract
The aim of this study is to evaluate the amino acid variability of HIV-1 Gp41, C2-V3, and Nef in a group of patients characterized by different disease progression rates. HIV-1 sequences were collected from 19 Long term non progressor patients (LTNPs), 9 slow progressors (SPs), and 11 rapid progressors (RPs). Phylogenetic trees were estimated by MEGA 6. Differences in amino acid variability among sequences belonging to the 3 groups have been evaluated by amino acid divergence, Shannon entropy analysis, and the number of amino acid mutations (defined as amino acid variations compared with HxB2). The involvement of amino acid mutations on epitope rich regions was also investigated. The population was mainly composed of males (74.3%) and HIV-1 subtype B strains (B: 92.32%, CRF_12BF, A1, C: 2.56% each). Viral load (log10 copies/mL) and CD4+T cell count (cells/mm3) were 3.9 (3.5-4.2) and 618 (504-857) in LTNPs, 3.3 (2.8-4.7) and 463 (333-627) in SPs, and 4.6 (4.3-5.3) and 201 (110-254) in RPs. Gp41 and C2-V3 amino acid divergence was lower in LTNP and SP strains compared to RPs (median value: 0.085 and 0.091 vs. 0.114, p = 0.005 and 0.042) and a trend of lower variability was observed for Nef (p = 0.198). A lower entropy value was observed at 10, 3, and 7 positions of Gp41, C2-V3, and Nef belonging to LTNPs and at 7, 3, and 1 positions of Gp41, C2-V3, and Nef belonging to SPs compared with RPs (p < 0.05). Focusing on epitope rich regions, again a higher degree of conservation was observed in Gp41 and C2-V3 sequences belonging to LTNPs and SPs compared to those belonging to RPs. This study shows that the extent of amino acid variability correlates with a different HIV-1 progression rate. This variability also involves CTL epitope rich regions, thus suggesting its involvement in the immune escape process modulation.
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Affiliation(s)
- Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | | | - Roberta D'Arrigo
- Department of Microbiology and Virology, San Camillo-Forlanini Hospital, Rome, Italy
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Claudio Casoli
- GEMIB Laboratory, Centre for Medical Research and Molecular Diagnostic, Parma, Italy
| | | | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy.
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112
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Immune Ecosystem of Virus-Infected Host Tissues. Int J Mol Sci 2018; 19:ijms19051379. [PMID: 29734779 PMCID: PMC5983771 DOI: 10.3390/ijms19051379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 12/11/2022] Open
Abstract
Virus infected host cells serve as a central immune ecological niche during viral infection and replication and stimulate the host immune response via molecular signaling. The viral infection and multiplication process involves complex intracellular molecular interactions between viral components and the host factors. Various types of host cells are also involved to modulate immune factors in delicate and dynamic equilibrium to maintain a balanced immune ecosystem in an infected host tissue. Antiviral host arsenals are equipped to combat or eliminate viral invasion. However, viruses have evolved with strategies to counter against antiviral immunity or hijack cellular machinery to survive inside host tissue for their multiplication. However, host immune systems have also evolved to neutralize the infection; which, in turn, either clears the virus from the infected host or causes immune-mediated host tissue injury. A complex relationship between viral pathogenesis and host antiviral defense could define the immune ecosystem of virus-infected host tissues. Understanding of the molecular mechanism underlying this ecosystem would uncover strategies to modulate host immune function for antiviral therapeutics. This review presents past and present updates of immune-ecological components of virus infected host tissue and explains how viruses subvert the host immune surveillances.
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113
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Partridge T, Nicastri A, Kliszczak AE, Yindom LM, Kessler BM, Ternette N, Borrow P. Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows. Front Immunol 2018; 9:912. [PMID: 29780384 PMCID: PMC5946011 DOI: 10.3389/fimmu.2018.00912] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/24/2022] Open
Abstract
Elucidation of novel peptides presented by human leukocyte antigen (HLA) class I alleles by immunopeptidomics constitutes a powerful approach that can inform the rational design of CD8+ T cell inducing vaccines to control infection with pathogens such as human immunodeficiency virus type 1 (HIV-1) or to combat tumors. Recent advances in the sensitivity of liquid chromatography tandem mass spectrometry instrumentation have facilitated the discovery of thousands of natural HLA-restricted peptides in a single measurement. However, the extent of contamination of class I-bound peptides identified using HLA immunoprecipitation (IP)-based immunopeptidomics approaches with peptides from other sources has not previously been evaluated in depth. Here, we investigated the specificity of the IP-based immunopeptidomics methodology using HLA class I- or II-deficient cell lines and membrane protein-specific antibody IPs. We demonstrate that the 721.221 B lymphoblastoid cell line, widely regarded to be HLA class Ia-deficient, actually expresses and presents peptides on HLA-C*01:02. Using this cell line and the C8166 (HLA class I- and II-expressing) cell line, we show that some HLA class II-bound peptides were co-purified non-specifically during HLA class I and membrane protein IPs. Furthermore, IPs of "irrelevant" membrane proteins from HIV-1-infected HLA class I- and/or II-expressing cells revealed that unusually long HIV-1-derived peptides previously reported by us and other immunopeptidomics studies as potentially novel CD8+ T cell epitopes were non-specifically co-isolated, and so constitute a source of contamination in HLA class I IPs. For example, a 16-mer (FLGKIWPSYKGRPGNF), which was detected in all samples studied represents the full p1 segment of the abundant intracellular or virion-associated proteolytically-processed HIV-1 Gag protein. This result is of importance, as these long co-purified HIV-1 Gag peptides may not elicit CD8+ T cell responses when incorporated into candidate vaccines. These results have wider implications for HLA epitope discovery from abundant or membrane-associated antigens by immunopeptidomics in the context of infectious diseases, cancer, and autoimmunity.
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Affiliation(s)
- Thomas Partridge
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Anna E Kliszczak
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Louis-Marie Yindom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom.,The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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114
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The influence of human leukocyte antigen-types on disease progression among HIV-2 infected patients in Guinea-Bissau. AIDS 2018; 32:721-728. [PMID: 29369163 DOI: 10.1097/qad.0000000000001758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES HIV-2 is endemic in West Africa and is characterized by lower transmissibility because of lower viral load, and HIV-2-infected persons usually have a slower progression to AIDS. The mechanisms behind the slower disease progression are unknown. The main objective was to identify specific HLA class I and II alleles that may influence the disease progression of HIV-2 infection. DESIGN Cohort follow-up study. METHODS We used high-resolution HLA typing of DNA from 437 antiretroviral naive HIV-2-infected patients from the Bissau HIV Cohort, Guinea-Bissau, to identify HLA alleles with an influence on HIV-2 disease progression. The effect of HLA-type on viral load and CD4 cell count was assessed initially by ranksum-test and t-test, followed by adjusted logistic regression and multivariable linear regression analysis, respectively. RESULTS Three alleles (HLA-B58:01, HLA-DPB110:01 and HLA-DRB111:01) were associated with lower possibility of detectable baseline plasma viral load (P = 0.002, P = 0.044 and P = 0.033, respectively), and no alleles were associated with higher possibility of detectable plasma viral load. HLA-DPB110:01 and HLA-DRB111:01 were in linkage disequilibrium (P = 0.047). Patients with heterozygous HLA types in all their HLA class I loci or in one or two loci were not more likely to have undetectable viral load compared with patients that were homozygous in all their class I loci after adjusting for sex and CD4 cell count (P = 0.93 and P = 0.88, respectively). CONCLUSION The three alleles HLA-B58:01, HLA-DPB110:01 and HLA-DRB111:01 may protect against HIV-2 disease progression towards AIDS.
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115
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Clemens EB, van de Sandt C, Wong SS, Wakim LM, Valkenburg SA. Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine. Vaccines (Basel) 2018; 6:vaccines6020018. [PMID: 29587436 PMCID: PMC6027237 DOI: 10.3390/vaccines6020018] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Next-generation vaccines that utilize T cells could potentially overcome the limitations of current influenza vaccines that rely on antibodies to provide narrow subtype-specific protection and are prone to antigenic mismatch with circulating strains. Evidence from animal models shows that T cells can provide heterosubtypic protection and are crucial for immune control of influenza virus infections. This has provided hope for the design of a universal vaccine able to prime against diverse influenza virus strains and subtypes. However, multiple hurdles exist for the realisation of a universal T cell vaccine. Overall primary concerns are: extrapolating human clinical studies, seeding durable effective T cell resident memory (Trm), population human leucocyte antigen (HLA) coverage, and the potential for T cell-mediated immune escape. Further comprehensive human clinical data is needed during natural infection to validate the protective role T cells play during infection in the absence of antibodies. Furthermore, fundamental questions still exist regarding the site, longevity and duration, quantity, and phenotype of T cells needed for optimal protection. Standardised experimental methods, and eventually simplified commercial assays, to assess peripheral influenza-specific T cell responses are needed for larger-scale clinical studies of T cells as a correlate of protection against influenza infection. The design and implementation of a T cell-inducing vaccine will require a consensus on the level of protection acceptable in the community, which may not provide sterilizing immunity but could protect the individual from severe disease, reduce the length of infection, and potentially reduce transmission in the community. Therefore, increasing the standard of care potentially offered by T cell vaccines should be considered in the context of pandemic preparedness and zoonotic infections, and in combination with improved antibody vaccine targeting methods. Current pandemic vaccine preparedness measures and ongoing clinical trials under-utilise T cell-inducing vaccines, reflecting the myriad questions that remain about how, when, where, and which T cells are needed to fight influenza virus infection. This review aims to bring together basic fundamentals of T cell biology with human clinical data, which need to be considered for the implementation of a universal vaccine against influenza that harnesses the power of T cells.
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Affiliation(s)
- E Bridie Clemens
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Carolien van de Sandt
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Sook San Wong
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Linda M Wakim
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Sophie A Valkenburg
- HKU Pasteur Research Pole, School of Public Health, University of Hong Kong, Hong Kong 999077, China.
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116
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Chikata T, Tran GV, Murakoshi H, Akahoshi T, Qi Y, Naranbhai V, Kuse N, Tamura Y, Koyanagi M, Sakai S, Nguyen DH, Nguyen DT, Nguyen HT, Nguyen TV, Oka S, Martin MP, Carrington M, Sakai K, Nguyen KV, Takiguchi M. HLA Class I-Mediated HIV-1 Control in Vietnamese Infected with HIV-1 Subtype A/E. J Virol 2018; 92:e01749-17. [PMID: 29237835 PMCID: PMC5809730 DOI: 10.1128/jvi.01749-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
HIV-1-specific cytotoxic T cells (CTLs) play an important role in the control of HIV-1 subtype B or C infection. However, the role of CTLs in HIV-1 subtype A/E infection still remains unclear. Here we investigated the association of HLA class I alleles with clinical outcomes in treatment-naive Vietnamese infected with subtype A/E virus. We found that HLA-C*12:02 was significantly associated with lower plasma viral loads (pVL) and higher CD4 counts and that the HLA-A*29:01-B*07:05-C*15:05 haplotype was significantly associated with higher pVL and lower CD4 counts than those for individuals without these respective genotypes. Nine Pol and three Nef mutations were associated with at least one HLA allele in the HLA-A*29:01-B*07:05-C*15:05 haplotype, with a strong negative correlation between the number of HLA-associated Pol mutations and CD4 count as well as a positive correlation with pVL for individuals with these HLA alleles. The results suggest that the accumulation of mutations selected by CTLs restricted by these HLA alleles affects HIV control.IMPORTANCE Most previous studies on HLA association with disease progression after HIV-1 infection have been performed on cohorts infected with HIV-1 subtypes B and C, whereas few such population-based studies have been reported for cohorts infected with the Asian subtype A/E virus. In this study, we analyzed the association of HLA class I alleles with clinical outcomes for 536 HIV-1 subtype A/E-infected Vietnamese individuals. We found that HLA-C*12:02 is protective, while the HLA haplotype HLA-A*29:01-B*07:05-C*15:05 is deleterious. The individuals with HIV-1 mutations associated with at least one of the HLA alleles in the deleterious HLA haplotype had higher plasma viral loads and lower CD4 counts than those of individuals without the mutations, suggesting that viral adaptation and escape from HLA-mediated immune control occurred. The present study identifies a protective allele and a deleterious haplotype for HIV-1 subtype A/E infection which are different from those identified for cohorts infected with HIV-1 subtypes B and C.
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Affiliation(s)
| | - Giang Van Tran
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- National Hospital of Tropical Diseases, Dong Da District, Hanoi, Vietnam
| | | | | | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Center for the AIDS Program of Research in South Africa (CAPRISA), Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Yoshiko Tamura
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Sachiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Dung Hoai Nguyen
- National Hospital of Tropical Diseases, Dong Da District, Hanoi, Vietnam
| | - Dung Thi Nguyen
- National Hospital of Tropical Diseases, Dong Da District, Hanoi, Vietnam
| | - Ha Thu Nguyen
- National Hospital of Tropical Diseases, Dong Da District, Hanoi, Vietnam
| | - Trung Vu Nguyen
- National Hospital of Tropical Diseases, Dong Da District, Hanoi, Vietnam
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Keiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Kinh Van Nguyen
- National Hospital of Tropical Diseases, Dong Da District, Hanoi, Vietnam
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Adland E, Hill M, Lavandier N, Csala A, Edwards A, Chen F, Radkowski M, Kowalska JD, Paraskevis D, Hatzakis A, Valenzuela-Ponce H, Pfafferott K, Williams I, Pellegrino P, Borrow P, Mori M, Rockstroh J, Prado JG, Mothe B, Dalmau J, Martinez-Picado J, Tudor-Williams G, Frater J, Stryhn A, Buus S, Teran GR, Mallal S, John M, Buchbinder S, Kirk G, Martin J, Michael N, Fellay J, Deeks S, Walker B, Avila-Rios S, Cole D, Brander C, Carrington M, Goulder P. Differential Immunodominance Hierarchy of CD8 + T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection. J Virol 2018; 92:e01685-17. [PMID: 29167337 PMCID: PMC5790925 DOI: 10.1128/jvi.01685-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/03/2017] [Indexed: 11/22/2022] Open
Abstract
The well-characterized association between HLA-B*27:05 and protection against HIV disease progression has been linked to immunodominant HLA-B*27:05-restricted CD8+ T-cell responses toward the conserved Gag KK10 (residues 263 to 272) and polymerase (Pol) KY9 (residues 901 to 909) epitopes. We studied the impact of the 3 amino acid differences between HLA-B*27:05 and the closely related HLA-B*27:02 on the HIV-specific CD8+ T-cell response hierarchy and on immune control of HIV. Genetic epidemiological data indicate that both HLA-B*27:02 and HLA-B*27:05 are associated with slower disease progression and lower viral loads. The effect of HLA-B*27:02 appeared to be consistently stronger than that of HLA-B*27:05. In contrast to HLA-B*27:05, the immunodominant HIV-specific HLA-B*27:02-restricted CD8+ T-cell response is to a Nef epitope (residues 142 to 150 [VW9]), with Pol KY9 subdominant and Gag KK10 further subdominant. This selection was driven by structural differences in the F pocket, mediated by a polymorphism between these two HLA alleles at position 81. Analysis of autologous virus sequences showed that in HLA-B*27:02-positive subjects, all three of these CD8+ T-cell responses impose selection pressure on the virus, whereas in HLA-B*27:05-positive subjects, there is no Nef VW9-mediated selection pressure. These studies demonstrate that HLA-B*27:02 mediates protection against HIV disease progression that is at least as strong as or stronger than that mediated by HLA-B*27:05. In combination with the protective Gag KK10 and Pol KY9 CD8+ T-cell responses that dominate HIV-specific CD8+ T-cell activity in HLA-B*27:05-positive subjects, a Nef VW9-specific response is additionally present and immunodominant in HLA-B*27:02-positive subjects, mediated through a polymorphism at residue 81 in the F pocket, that contributes to selection pressure against HIV.IMPORTANCE CD8+ T cells play a central role in successful control of HIV infection and have the potential also to mediate the eradication of viral reservoirs of infection. The principal means by which protective HLA class I molecules, such as HLA-B*27:05 and HLA-B*57:01, slow HIV disease progression is believed to be via the particular HIV-specific CD8+ T cell responses restricted by those alleles. We focus here on HLA-B*27:05, one of the best-characterized protective HLA molecules, and the closely related HLA-B*27:02, which differs by only 3 amino acids and which has not been well studied in relation to control of HIV infection. We show that HLA-B*27:02 is also protective against HIV disease progression, but the CD8+ T-cell immunodominance hierarchy of HLA-B*27:02 differs strikingly from that of HLA-B*27:05. These findings indicate that the immunodominant HLA-B*27:02-restricted Nef response adds to protection mediated by the Gag and Pol specificities that dominate anti-HIV CD8+ T-cell activity in HLA-B*27:05-positive subjects.
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Affiliation(s)
- Emily Adland
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Matilda Hill
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Nora Lavandier
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Anna Csala
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Anne Edwards
- Department of GU Medicine, The Churchill Hospital, Oxford University NHS Foundation Trust, Oxford, United Kingdom
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Justyna D Kowalska
- Department of Immunopathology of Infectious and Parasitic Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | - Angelos Hatzakis
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Humberto Valenzuela-Ponce
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Katja Pfafferott
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, Mortimer Market Centre, London, United Kingdom
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, Mortimer Market Centre, London, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Masahiko Mori
- Department of Paediatrics, University of Oxford, United Kingdom
| | - Jürgen Rockstroh
- Department of Medicine I, University Hospital Bonn, Bonn, Germany
| | - Julia G Prado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Beatriz Mothe
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
| | - Judith Dalmau
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Martin School, University of Oxford, Oxford, United Kingdom
| | - Anette Stryhn
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Soren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Gustavo Reyes Teran
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Simon Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mina John
- Institute of Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Susan Buchbinder
- San Francisco Department of Public Health, HIV Research Section, San Francisco, California, USA
| | - Gregory Kirk
- Department of Epidemiology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jeffrey Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Steve Deeks
- San Francisco Department of Public Health, HIV Research Section, San Francisco, California, USA
| | - Bruce Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - David Cole
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Immunocore Limited, Abingdon, Oxfordshire, United Kingdom
| | - Christian Brander
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland, USA
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, United Kingdom
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T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable. Proc Natl Acad Sci U S A 2018; 115:1877-1882. [PMID: 29437954 DOI: 10.1073/pnas.1718659115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HIV controllers (HCs) are individuals who can naturally control HIV infection, partially due to potent HIV-specific CD8+ T cell responses. Here, we examined the hypothesis that superior function of CD8+ T cells from HCs is encoded by their T cell receptors (TCRs). We compared the functional properties of immunodominant HIV-specific TCRs obtained from HLA-B*2705 HCs and chronic progressors (CPs) following expression in primary T cells. T cells transduced with TCRs from HCs and CPs showed equivalent induction of epitope-specific cytotoxicity, cytokine secretion, and antigen-binding properties. Transduced T cells comparably, albeit modestly, also suppressed HIV infection in vitro and in humanized mice. We also performed extensive molecular dynamics simulations that provided a structural basis for similarities in cytotoxicity and epitope cross-reactivity. These results demonstrate that the differential abilities of HIV-specific CD8+ T cells from HCs and CPs are not genetically encoded in the TCRs alone and must depend on additional factors.
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119
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Chowell D, Morris LGT, Grigg CM, Weber JK, Samstein RM, Makarov V, Kuo F, Kendall SM, Requena D, Riaz N, Greenbaum B, Carroll J, Garon E, Hyman DM, Zehir A, Solit D, Berger M, Zhou R, Rizvi NA, Chan TA. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 2018; 359:582-587. [PMID: 29217585 PMCID: PMC6057471 DOI: 10.1126/science.aao4572] [Citation(s) in RCA: 722] [Impact Index Per Article: 120.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
Abstract
CD8+ T cell-dependent killing of cancer cells requires efficient presentation of tumor antigens by human leukocyte antigen class I (HLA-I) molecules. However, the extent to which patient-specific HLA-I genotype influences response to anti-programmed cell death protein 1 or anti-cytotoxic T lymphocyte-associated protein 4 is currently unknown. We determined the HLA-I genotype of 1535 advanced cancer patients treated with immune checkpoint blockade (ICB). Maximal heterozygosity at HLA-I loci ("A," "B," and "C") improved overall survival after ICB compared with patients who were homozygous for at least one HLA locus. In two independent melanoma cohorts, patients with the HLA-B44 supertype had extended survival, whereas the HLA-B62 supertype (including HLA-B*15:01) or somatic loss of heterozygosity at HLA-I was associated with poor outcome. Molecular dynamics simulations of HLA-B*15:01 revealed different elements that may impair CD8+ T cell recognition of neoantigens. Our results have important implications for predicting response to ICB and for the design of neoantigen-based therapeutic vaccines.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claud M Grigg
- NewYork-Presbyterian/Columbia University Medical Center, 177 Fort Washington Avenue, New York, NY 10032, USA
| | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Robert M Samstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sviatoslav M Kendall
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Oncological Sciences, and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James Carroll
- David Geffen School of Medicine, University of California, Los Angeles, 2825 Santa Monica Boulevard, Suite 200, Santa Monica, CA 90404, USA
| | - Edward Garon
- David Geffen School of Medicine, University of California, Los Angeles, 2825 Santa Monica Boulevard, Suite 200, Santa Monica, CA 90404, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell School of Medicine, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Naiyer A Rizvi
- NewYork-Presbyterian/Columbia University Medical Center, 177 Fort Washington Avenue, New York, NY 10032, USA.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell School of Medicine, New York, NY 10065, USA
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Laumont CM, Perreault C. Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy. Cell Mol Life Sci 2018; 75:607-621. [PMID: 28823056 PMCID: PMC11105255 DOI: 10.1007/s00018-017-2628-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/03/2017] [Accepted: 08/16/2017] [Indexed: 01/11/2023]
Abstract
Cryptic MHC I-associated peptides (MAPs) are produced via two mechanisms: translation of protein-coding genes in non-canonical reading frames and translation of allegedly non-coding sequences. In general, cryptic MAPs are coded by relatively short open reading frames whose translation can be regulated at the level of initiation, elongation or termination. In contrast to conventional MAPs, the processing of cryptic MAPs is frequently proteasome independent. The existence of cryptic MAPs derived from allegedly non-coding regions enlarges the scope of CD8 T cell immunosurveillance from a mere ~2% to as much as ~75% of the human genome. Considering that 99% of cancer-specific mutations are located in those allegedly non-coding regions, cryptic MAPs could furthermore represent a particularly rich source of tumor-specific antigens. However, extensive proteogenomic analyses will be required to determine the breath as well as the temporal and spatial plasticity of the cryptic MAP repertoire in normal and neoplastic cells.
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Affiliation(s)
- Céline M Laumont
- Institute for Research in Immunology and Cancer, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada.
- Department of Medicine, Faculty of Medicine, Université de Montréal, Station Centre-Ville, PO Box 6128, Montreal, QC, H3C 3J7, Canada.
- Division of Hematology, Hôpital Maisonneuve-Rosemont, 5415 de l'Assomption Boulevard, Montreal, QC, H1T 2M4, Canada.
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121
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Kaufman J. Generalists and Specialists: A New View of How MHC Class I Molecules Fight Infectious Pathogens. Trends Immunol 2018; 39:367-379. [PMID: 29396014 PMCID: PMC5929564 DOI: 10.1016/j.it.2018.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/24/2022]
Abstract
In comparison with the major histocompatibility complexes (MHCs) of typical mammals, the chicken MHC is simple and compact with a single dominantly expressed class I molecule that can determine the immune response. In addition to providing useful information for the poultry industry and allowing insights into the evolution of the adaptive immune system, the simplicity of the chicken MHC has allowed the discovery of phenomena that are more difficult to discern in the more complicated mammalian systems. This review discusses the new concept that poorly expressed promiscuous class I alleles act as generalists to protect against a wide variety of infectious pathogens, while highly expressed fastidious class I alleles can act as specialists to protect against new and dangerous pathogens. A broad overview of classical MHC I expression and bound peptides reveals an inverse correlation between repertoire breadth and cell-surface expression in some chicken and human alleles. Several chicken class I alleles with wide peptide-binding repertoires (promiscuity) are associated with resistance to a variety of common diseases. Conversely, a narrow peptide-binding repertoire (fastidiousness) in some human HLA-B alleles is associated with resistance to HIV progression. Cell-surface expression of some classical class I alleles depends on the regulation of translocation to the cell surface rather than of transcription or translation. MHC translocation is influenced by peptide translocation in chickens and by tapasin interaction in humans.
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Affiliation(s)
- Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK.
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122
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Huang SH, Ren Y, Thomas AS, Chan D, Mueller S, Ward AR, Patel S, Bollard CM, Cruz CR, Karandish S, Truong R, Macedo AB, Bosque A, Kovacs C, Benko E, Piechocka-Trocha A, Wong H, Jeng E, Nixon DF, Ho YC, Siliciano RF, Walker BD, Jones RB. Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T cells. J Clin Invest 2018; 128:876-889. [PMID: 29355843 DOI: 10.1172/jci97555] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 02/06/2023] Open
Abstract
The presence of persistent, latent HIV reservoirs in CD4+ T cells obstructs current efforts to cure infection. The so-called kick-and-kill paradigm proposes to purge these reservoirs by combining latency-reversing agents with immune effectors such as cytotoxic T lymphocytes. Support for this approach is largely based on success in latency models, which do not fully reflect the makeup of latent reservoirs in individuals on long-term antiretroviral therapy (ART). Recent studies have shown that CD8+ T cells have the potential to recognize defective proviruses, which comprise the vast majority of all infected cells, and that the proviral landscape can be shaped over time due to in vivo clonal expansion of infected CD4+ T cells. Here, we have shown that treating CD4+ T cells from ART-treated individuals with combinations of potent latency-reversing agents and autologous CD8+ T cells consistently reduced cell-associated HIV DNA, but failed to deplete replication-competent virus. These CD8+ T cells recognized and potently eliminated CD4+ T cells that were newly infected with autologous reservoir virus, ruling out a role for both immune escape and CD8+ T cell dysfunction. Thus, our results suggest that cells harboring replication-competent HIV possess an inherent resistance to CD8+ T cells that may need to be addressed to cure infection.
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Affiliation(s)
- Szu-Han Huang
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Yanqin Ren
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Allison S Thomas
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Dora Chan
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Stefanie Mueller
- Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA
| | - Adam R Ward
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Shabnum Patel
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Children's National Health System, Washington DC, USA
| | - Catherine M Bollard
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Children's National Health System, Washington DC, USA
| | - Conrad Russell Cruz
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Children's National Health System, Washington DC, USA
| | - Sara Karandish
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Ronald Truong
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Amanda B Macedo
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Alberto Bosque
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA
| | - Hing Wong
- Altor Bioscience Corporation, Miramar, Florida, USA
| | - Emily Jeng
- Altor Bioscience Corporation, Miramar, Florida, USA
| | - Douglas F Nixon
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.,Institute for Medical Engineering and Sciences, MIT, Cambridge, Massachusetts, USA
| | - R Brad Jones
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, USA.,Ragon Institute of Massachusetts Institute of Technology (MIT), Massachusetts General Hospital (MGH), and Harvard University, Cambridge, Massachusetts, USA
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123
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Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. THE PHARMACOGENOMICS JOURNAL 2018; 19:136-146. [PMID: 29352165 PMCID: PMC6462828 DOI: 10.1038/s41397-017-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 11/06/2017] [Indexed: 12/30/2022]
Abstract
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
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124
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Brener J, Gall A, Hurst J, Batorsky R, Lavandier N, Chen F, Edwards A, Bolton C, Dsouza R, Allen T, Pybus OG, Kellam P, Matthews PC, Goulder PJR. Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient. Retrovirology 2018; 15:7. [PMID: 29338738 PMCID: PMC5771019 DOI: 10.1186/s12977-018-0390-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/05/2017] [Indexed: 12/03/2022] Open
Abstract
Background The factors determining differential HIV disease outcome among individuals expressing protective HLA alleles such as HLA-B*27:05 and HLA-B*57:01 remain unknown. We here analyse two HIV-infected subjects expressing both HLA-B*27:05 and HLA-B*57:01. One subject maintained low-to-undetectable viral loads for more than a decade of follow up. The other progressed to AIDS in < 3 years. Results The rapid progressor was the recipient within a known transmission pair, enabling virus sequences to be tracked from transmission. Progression was associated with a 12% Gag sequence change and 26% Nef sequence change at the amino acid level within 2 years. Although next generation sequencing from early timepoints indicated that multiple CD8+ cytotoxic T lymphocyte (CTL) escape mutants were being selected prior to superinfection, < 4% of the amino acid changes arising from superinfection could be ascribed to CTL escape. Analysis of an HLA-B*27:05/B*57:01 non-progressor, in contrast, demonstrated minimal virus sequence diversification (1.1% Gag amino acid sequence change over 10 years), and dominant HIV-specific CTL responses previously shown to be effective in control of viraemia were maintained. Clonal sequencing demonstrated that escape variants were generated within the non-progressor, but in many cases were not selected. In the rapid progressor, progression occurred despite substantial reductions in viral replicative capacity (VRC), and non-progression in the elite controller despite relatively high VRC. Conclusions These data are consistent with previous studies demonstrating rapid progression in association with superinfection and that rapid disease progression can occur despite the relatively the low VRC that is typically observed in the setting of multiple CTL escape mutants. Electronic supplementary material The online version of this article (10.1186/s12977-018-0390-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacqui Brener
- Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Astrid Gall
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jacob Hurst
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Nora Lavandier
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, UK
| | - Anne Edwards
- Department of GU Medicine, The Churchill Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Chrissy Bolton
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Reena Dsouza
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Todd Allen
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | | | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Division of Infection and Immunity, University College London, Gower Street, London, UK
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Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico. J Virol 2018; 92:JVI.01128-17. [PMID: 29093100 PMCID: PMC5752930 DOI: 10.1128/jvi.01128-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/27/2017] [Indexed: 01/24/2023] Open
Abstract
HIV circumvents HLA class I-restricted CD8+ T-cell responses through selection of escape mutations that leave characteristic mutational “footprints,” also known as HLA-associated polymorphisms (HAPs), on HIV sequences at the population level. While many HLA footprints are universal across HIV subtypes and human populations, others can be region specific as a result of the unique immunogenetic background of each host population. Using a published probabilistic phylogenetically informed model, we compared HAPs in HIV Gag and Pol (PR-RT) in 1,612 subtype B-infected, antiretroviral treatment-naive individuals from Mexico and 1,641 individuals from Canada/United States. A total of 252 HLA class I allele subtypes were represented, including 140 observed in both cohorts, 67 unique to Mexico, and 45 unique to Canada/United States. At the predefined statistical threshold of a q value of <0.2, 358 HAPs (201 in Gag, 157 in PR-RT) were identified in Mexico, while 905 (534 in Gag and 371 in PR-RT) were identified in Canada/United States. HAPs identified in Mexico included both canonical HLA-associated escape pathways and novel associations, in particular with HLA alleles enriched in Amerindian and mestizo populations. Remarkably, HLA footprints on HIV in Mexico were not only fewer but also, on average, significantly weaker than those in Canada/United States, although some exceptions were noted. Moreover, exploratory analyses suggested that the weaker HLA footprint on HIV in Mexico may be due, at least in part, to weaker and/or less reproducible HLA-mediated immune pressures on HIV in this population. The implications of these differences for natural and vaccine-induced anti-HIV immunity merit further investigation. IMPORTANCE HLA footprints on HIV identify viral regions under intense and consistent pressure by HLA-restricted immune responses and the common mutational pathways that HIV uses to evade them. In particular, HLA footprints can identify novel immunogenic regions and/or epitopes targeted by understudied HLA alleles; moreover, comparative analyses across immunogenetically distinct populations can illuminate the extent to which HIV immunogenic regions and escape pathways are shared versus population-specific pathways, information which can in turn inform the design of universal or geographically tailored HIV vaccines. We compared HLA-associated footprints on HIV in two immunogenetically distinct North American populations, those of Mexico and Canada/United States. We identify both shared and population-specific pathways of HIV adaptation but also make the surprising observation that HLA footprints on HIV in Mexico overall are fewer and weaker than those in Canada/United States, raising the possibility that HLA-restricted antiviral immune responses in Mexico are weaker, and/or escape pathways somewhat less consistent, than those in other populations.
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Zhang W, Ambikan AT, Sperk M, van Domselaar R, Nowak P, Noyan K, Russom A, Sönnerborg A, Neogi U. Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers. EBioMedicine 2018; 27:40-50. [PMID: 29269040 PMCID: PMC5828548 DOI: 10.1016/j.ebiom.2017.11.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022] Open
Abstract
A small subset of HIV-1 infected individuals, the "Elite Controllers" (EC), can control viral replication and restrain progression to immunodeficiency without antiretroviral therapy (ART). In this study, a cross-sectional transcriptomics and targeted proteomics analysis were performed in a well-defined Swedish cohort of untreated EC (n=19), treatment naïve patients with viremia (VP, n=32) and HIV-1-negative healthy controls (HC, n=23). The blood transcriptome identified 151 protein-coding genes that were differentially expressed (DE) in VP compared to EC. Genes like CXCR6 and SIGLEC1 were downregulated in EC compared to VP. A definite distinction in gene expression between males and females among all patient-groups were observed. The gene expression profile between female EC and the healthy females was similar but did differ between male EC and healthy males. At targeted proteomics analysis, 90% (29/32) of VPs clustered together while EC and HC clustered separately from VP. Among the soluble factors, 33 were distinctive to be statistically significant (False discovery rate=0.02). Cell surface receptor signaling pathway, programmed cell death, response to cytokine and cytokine-mediated signaling seem to synergistically play an essential role in HIV-1 control in EC.
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Affiliation(s)
- Wang Zhang
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Stockholm, Sweden
| | - Anoop T Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maike Sperk
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Faculty of Medicine, University of Tuebingen, Tuebingen, Germany
| | - Robert van Domselaar
- Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Piotr Nowak
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kajsa Noyan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aman Russom
- Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Medicine Huddinge, Unit of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Solna, Stockholm, Sweden.
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Fleury H, Tumiotto C, Bellecave P, Recordon-Pinson P. Therapeutic Vaccine Against HIV, Viral Variability, Cytotoxic T Lymphocyte Epitopes, and Genetics of Patients. AIDS Res Hum Retroviruses 2018; 34:27-30. [PMID: 28899104 DOI: 10.1089/aid.2017.0175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The scientific and medical community is seeking to cure HIV. Several pathways have been or are being explored including therapeutic vaccination. Viroimmunological studies on primary infection as well as on elite controllers have demonstrated the importance of the cytotoxic CD8 response and have mainly oriented research on vaccine constructs toward this type of response. The results of these trials are clearly not commensurate with the hope placed in them. Might there be one or more uncontrolled variables? The genetics of patients need to be taken into consideration, especially their human lymphocyte antigen (HLA) alleles. There is a need to find a balance between the conservation of cytotoxic T lymphocyte (CTL) epitopes and presentation by HLA alleles. The pathway is a narrow one between adaptation of the virus to HLA I restriction and the definition of conserved proviral CTL epitopes presentable by HLA I alleles. It is likely that the genetics of patients will need to be considered for HIV-1 vaccine studies and that multidisciplinary collaboration will be essential in this field of infectious diseases.
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Affiliation(s)
- Herve Fleury
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Camille Tumiotto
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Patricia Recordon-Pinson
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
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Gay CL, DeBenedette MA, Tcherepanova IY, Gamble A, Lewis WE, Cope AB, Kuruc JD, McGee KS, Kearney MF, Coffin JM, Archin NM, Hicks CB, Eron JJ, Nicolette CA, Margolis DM. Immunogenicity of AGS-004 Dendritic Cell Therapy in Patients Treated During Acute HIV Infection. AIDS Res Hum Retroviruses 2018. [PMID: 28636433 DOI: 10.1089/aid.2017.0071] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
AGS-004 consists of matured autologous dendritic cells co-electroporated with in vitro transcribed RNA encoding autologous HIV antigens. In an open-label, single arm sub-study of AGS-004-003, AGS-004 was administered monthly to suppressed participants who started antiretroviral therapy (ART) during acute HIV infection. HIV-1 specific T cell responses were measured by multicolor flow cytometry after 3-4 doses. The frequency of resting CD4+ T-cell infection (RCI) was measured by quantitative viral outgrowth assay. Participants demonstrating increased immune response postvaccination were eligible for analytic treatment interruption (ATI). AGS-004 induced a positive immune response defined as ≥2-fold increase from baseline in the number of multifunctional HIV-1 specific CD28+/CD45RA- CD8+ effector/memory cytoxic T-lymphocytes (CTLs) in all six participants. All participants underwent ATI with rebound viremia at a median of 29 days. Immune correlates between time to viral rebound and the induction of effector CTLs were determined. Baseline RCI was low in most participants (0.043-0.767 IUPM). One participant had a >2-fold decrease (0.179-0.067 infectious units per million [IUPM]) in RCI at week 10. One participant with the lowest RCI had the longest ATI. AGS-004 dendritic cell administration increased multifunctional HIV-specific CD28+/CD45RA- CD8+ memory T cell responses in all participants, but did not permit sustained ART interruption. However, greater expansion of CD28-/CCR7-/CD45RA- CD8+ effector T cell responses correlated with a longer time to viral rebound. AGS-004 may be a useful tool to augment immune responses in the setting of latency reversal and eradication strategies.
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Affiliation(s)
- Cynthia L. Gay
- University of North Carolina HIV Cure Center, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | | | | | | | | | - Anna B. Cope
- Department of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
- Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - JoAnn D. Kuruc
- University of North Carolina HIV Cure Center, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | | | | | | | - Nancie M. Archin
- University of North Carolina HIV Cure Center, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | | | - Joseph J. Eron
- University of North Carolina HIV Cure Center, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | | | - David M. Margolis
- University of North Carolina HIV Cure Center, Chapel Hill, North Carolina
- Department of Medicine, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
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Abstract
Research over the past decade has resulted in a much-improved understanding of how and where HIV persists in patients on otherwise suppressive antiretroviral therapy (ART). It has become clear that the establishment of a latent infection in long-lived cells is the key barrier to curing HIV or allowing for sustained ART-free remission. Informed by in vitro and ex vivo studies, several therapeutic approaches aimed at depleting the pool of latently infected cells have been tested in small-scale experimental clinical trials including studies of ART intensification, genome editing, ART during acute/early infection and latency reversal. Many studies have focused on the use of latency-reversing agents (LRAs) to induce immune- or virus-mediated elimination of virus-producing cells. These trials have been instrumental in establishing safety and have shown that it is possible to impact the state HIV latency in patients on suppressive ART. However, administration of LRAs alone has thus far not demonstrated an effect on the frequency of latently infected cells or the time to virus rebound during analytical interruption of ART. More recently, there has been an enhanced focus on immune-based therapies in the onwards search for an HIV cure including therapeutic vaccines, toll-like receptor agonists, broadly neutralising antibodies, immune checkpoint inhibitors, interferon-α and interleukin therapy. In ongoing studies immunotherapy interventions are also tested in combination with latency reversal. In this chapter, the overall results of these clinical interventions ultimately aimed at a cure for HIV are presented and discussed.
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130
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Wiener HW, Shrestha S, Lu H, Karita E, Kilembe W, Allen S, Hunter E, Goepfert PA, Tang J. Immunogenetic factors in early immune control of human immunodeficiency virus type 1 (HIV-1) infection: Evaluation of HLA class I amino acid variants in two African populations. Hum Immunol 2017; 79:166-171. [PMID: 29289742 DOI: 10.1016/j.humimm.2017.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 01/07/2023]
Abstract
Immune control of HIV-1 infection depends heavily on cytotoxic T-lymphocyte responses restricted by diverse HLA class I molecules. Recent work has uncovered specific amino acid residues (AARs) that seem to dictate the extent of immune control in African Americans, which prompted us to test these emerging hypotheses in seroconverters (SCs) from southern and eastern Africa. Based on data from 196 Zambians and 76 Rwandans with fully resolved HLA alleles and pre-therapy HIV-1 viral loads (VL) in the first 3- to 36-month of infection (>2300 person-visits), four AARs of primary interest (positions 63, 97, 116 and 245 in the mature HLA-B protein) were found to explain 8.1% and 15.8% of variance in set-point VL for these cohorts (P = .024 and 7.5 × 10-6, respectively). Two AARs not reported previously (167S in HLA-B and 116F in HLA-C) also showed relatively consistent associations with VL (adjusted P = .009-.069), while many population-specific associations were also noted (false discovery rate <0.05). Extensive and often strong linkage disequilibrium among neighboring AAR variants called for more extensive analyses of AAR haplotypes in diverse cohorts before the structural basis of antigen presentation can be fully comprehended.
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Affiliation(s)
- Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hailin Lu
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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131
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Chikata T, Murakoshi H, Koyanagi M, Honda K, Gatanaga H, Oka S, Takiguchi M. Control of HIV-1 by an HLA-B*52:01-C*12:02 Protective Haplotype. J Infect Dis 2017; 216:1415-1424. [PMID: 28968792 DOI: 10.1093/infdis/jix483] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/11/2017] [Indexed: 11/14/2022] Open
Abstract
HLA-B*52:01-C*12:02, which is found in approximately 20% of all Japanese persons, is well known to be associated with ulcerative colitis and Takayasu arteritis. This haplotype is also known to be protective in individuals infected with human immunodeficiency virus (HIV) type 1. Recent studies showed that HLA-B*52:01-restricted HIV-1-specific T cells suppress HIV-1 and that HLA-C*12:02 together with KIR2DL2 play an important role in natural killer cell-mediated control of HIV-1. However, the role of HLA-C*12:02-restricted cytotoxic T lymphocytes (CTLs) in suppressing HIV-1 replication remains unknown. In the present study, we demonstrated that HLA-C*12:02-restricted CTLs specific for 2 immunodominant epitopes, Pol IY11 and Nef MY9, contributed to the suppression of HIV-1 replication in HIV-1-infected individuals. Further analysis demonstrated that these 2 HLA-C*12:02-restricted CTLs together with 4 HLA-B*52:01-restricted ones effectively suppressed HIV-1 in individuals with the HLA-B*52:01-C*12:02 haplotype. Thus, both HLA-C*12:02 and HLA-B*52:01 alleles contribute to HIV-1 suppression via both HIV-1-specific CTLs and natural killer cells in individuals with this haplotype.
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Affiliation(s)
| | | | | | - Kazutaka Honda
- Center for AIDS Research, Kumamoto University, Tokyo, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Tokyo, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Tokyo, Japan.,AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
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132
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Muenchhoff M, Adland E, Karimanzira O, Crowther C, Pace M, Csala A, Leitman E, Moonsamy A, McGregor C, Hurst J, Groll A, Mori M, Sinmyee S, Thobakgale C, Tudor-Williams G, Prendergast AJ, Kloverpris H, Roider J, Leslie A, Shingadia D, Brits T, Daniels S, Frater J, Willberg CB, Walker BD, Ndung'u T, Jooste P, Moore PL, Morris L, Goulder P. Nonprogressing HIV-infected children share fundamental immunological features of nonpathogenic SIV infection. Sci Transl Med 2017; 8:358ra125. [PMID: 27683550 DOI: 10.1126/scitranslmed.aag1048] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
Abstract
Disease-free infection in HIV-infected adults is associated with human leukocyte antigen-mediated suppression of viremia, whereas in the sooty mangabey and other healthy natural hosts of simian immunodeficiency virus (SIV), viral replication continues unabated. To better understand factors preventing HIV disease, we investigated pediatric infection, where AIDS typically develops more rapidly than in adults. Among 170 nonprogressing antiretroviral therapy-naïve children aged >5 years maintaining normal-for-age CD4 T cell counts, immune activation levels were low despite high viremia (median, 26,000 copies/ml). Potent, broadly neutralizing antibody responses in most of the subjects and strong virus-specific T cell activity were present but did not drive pediatric nonprogression. However, reduced CCR5 expression and low HIV infection in long-lived central memory CD4 T cells were observed in pediatric nonprogressors. These children therefore express two cardinal immunological features of nonpathogenic SIV infection in sooty mangabeys-low immune activation despite high viremia and low CCR5 expression on long-lived central memory CD4 T cells-suggesting closer similarities with nonpathogenetic mechanisms evolved over thousands of years in natural SIV hosts than those operating in HIV-infected adults.
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Affiliation(s)
- Maximilian Muenchhoff
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa. Max von Pettenkofer-Institute, Department of Virology, Ludwig-Maximilians-University Munich, Munich, Germany. German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Emily Adland
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K
| | - Owen Karimanzira
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Carol Crowther
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Matthew Pace
- Institute for Emerging Infections, Oxford Martin School, University of Oxford, Oxford, U.K. Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, U.K. Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, U.K
| | - Anna Csala
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K
| | - Ellen Leitman
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K
| | - Angeline Moonsamy
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K
| | - Callum McGregor
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Jacob Hurst
- Institute of Cancer Research, Old Brompton Road, London SW7 3RP, U.K
| | - Andreas Groll
- Department of Mathematics, Ludwig-Maximilians-University Munich, Theresienstrasse 39, 80333 Munich, Germany
| | - Masahiko Mori
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K
| | - Smruti Sinmyee
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K
| | - Christina Thobakgale
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | | | | | - Henrik Kloverpris
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), University of KwaZulu-Natal (UKZN), 4001 Durban, South Africa. Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Julia Roider
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), University of KwaZulu-Natal (UKZN), 4001 Durban, South Africa
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), University of KwaZulu-Natal (UKZN), 4001 Durban, South Africa
| | - Delane Shingadia
- Department of Paediatric Infectious Diseases, Great Ormond Street Hospital for Children, London, U.K
| | - Thea Brits
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Samantha Daniels
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - John Frater
- Institute for Emerging Infections, Oxford Martin School, University of Oxford, Oxford, U.K. Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, U.K. Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, U.K
| | - Christian B Willberg
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, U.K. Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, U.K
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-4307, USA
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), University of KwaZulu-Natal (UKZN), 4001 Durban, South Africa. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139-4307, USA. Max Planck Institute for Infection Biology, Berlin, Germany
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Center for the AIDS Programme of Research in South Africa (CAPRISA), 4001 Durban, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Center for the AIDS Programme of Research in South Africa (CAPRISA), 4001 Durban, South Africa
| | - Philip Goulder
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford OX1 3SY, U.K. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa. Department of Paediatric Infectious Diseases, Great Ormond Street Hospital for Children, London, U.K.
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133
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Leitman EM, Willberg CB, Tsai MH, Chen H, Buus S, Chen F, Riddell L, Haas D, Fellay J, Goedert JJ, Piechocka-Trocha A, Walker BD, Martin J, Deeks S, Wolinsky SM, Martinson J, Martin M, Qi Y, Sáez-Cirión A, Yang OO, Matthews PC, Carrington M, Goulder PJR. HLA-B*14:02-Restricted Env-Specific CD8 + T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection. J Virol 2017; 91:e00544-17. [PMID: 28878089 PMCID: PMC5660483 DOI: 10.1128/jvi.00544-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
Immune control of human immunodeficiency virus type 1 (HIV) infection is typically associated with effective Gag-specific CD8+ T-cell responses. We here focus on HLA-B*14, which protects against HIV disease progression, but the immunodominant HLA-B*14-restricted anti-HIV response is Env specific (ERYLKDQQL, HLA-B*14-EL9). A subdominant HLA-B*14-restricted response targets Gag (DRYFKTLRA, HLA-B*14-DA9). Using HLA-B*14/peptide-saporin-conjugated tetramers, we show that HLA-B*14-EL9 is substantially more potent at inhibiting viral replication than HLA-B*14-DA9. HLA-B*14-EL9 also has significantly higher functional avidity (P < 0.0001) and drives stronger selection pressure on the virus than HLA-B*14-DA9. However, these differences were HLA-B*14 subtype specific, applying only to HLA-B*14:02 and not to HLA-B*14:01. Furthermore, the HLA-B*14-associated protection against HIV disease progression is significantly greater for HLA-B*14:02 than for HLA-B*14:01, consistent with the superior antiviral efficacy of the HLA-B*14-EL9 response. Thus, although Gag-specific CD8+ T-cell responses may usually have greater anti-HIV efficacy, factors independent of protein specificity, including functional avidity of individual responses, are also critically important to immune control of HIV.IMPORTANCE In HIV infection, although cytotoxic T lymphocytes (CTL) play a potentially critical role in eradication of viral reservoirs, the features that constitute an effective response remain poorly defined. We focus on HLA-B*14, unique among HLAs associated with control of HIV in that the dominant CTL response is Env specific, not Gag specific. We demonstrate that Env-specific HLA-B*14-restricted activity is substantially more efficacious than the subdominant HLA-B*14-restricted Gag response. Env immunodominance over Gag and strong Env-mediated selection pressure on HIV are observed only in subjects expressing HLA-B*14:02, and not HLA-B*14:01. This reflects the increased functional avidity of the Env response over Gag, substantially more marked for HLA-B*14:02. Finally, we show that HLA-B*14:02 is significantly more strongly associated with viremic control than HLA-B*14:01. These findings indicate that, although Gag-specific CTL may usually have greater anti-HIV efficacy than Env responses, factors independent of protein specificity, including functional avidity, may carry greater weight in mediating effective control of HIV.
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Affiliation(s)
- Ellen M Leitman
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Harvard Medical School, Boston, Massachusetts, USA
| | | | - Ming-Han Tsai
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Huabiao Chen
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Lynn Riddell
- Integrated Sexual Health Services, Northamptonshire Healthcare NHS Trust, Northampton, United Kingdom
| | - David Haas
- Departments of Medicine, Pharmacology, Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jeffrey Martin
- Department of Medicine, University of California San Francisco Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Steven Deeks
- Department of Medicine, University of California, San Francisco, California, USA
| | - Steven M Wolinsky
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Maureen Martin
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV, Inflammation et Persistance, Paris, France
| | - Otto O Yang
- Department of Medicine, Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- AIDS Healthcare Foundation, Los Angeles, California, USA
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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134
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de Groot NG, Heijmans CMC, de Ru AH, Janssen GMC, Drijfhout JW, Otting N, Vangenot C, Doxiadis GGM, Koning F, van Veelen PA, Bontrop RE. A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics. THE JOURNAL OF IMMUNOLOGY 2017; 199:3679-3690. [PMID: 29021373 DOI: 10.4049/jimmunol.1700502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022]
Abstract
In different macaque species, the MHC A2*05 gene is present in abundance, and its gene products are characterized by low cell-surface expression and a highly conserved peptide-binding cleft. We have characterized the peptide-binding motif of Mamu-A2*05:01, and elucidated the binding capacity for virus-derived peptides. The macaque A2*05 allotype prefers the basic amino acid arginine at the second position of the peptide, and hydrophobic and polar amino acids at the C-terminal end. These preferences are shared with HLA-B*27 and Mamu-B*008, molecules shown to be involved in elite control in human HIV type 1 and macaque SIV infections, respectively. In contrast, however, Mamu-A2*05 preferentially binds 8-mer peptides. Retention in the endoplasmic reticulum seems to be the cause of the lower cell-surface expression. Subsequent peptide-binding studies have illustrated that Mamu-A2*05:01 is able to bind SIV-epitopes known to evoke a strong CD8+ T cell response in the context of the Mamu-B*008 allotype in SIV-infected rhesus macaques. Thus, the macaque A2*05 gene encodes a specialized MHC class I molecule, and is most likely transported to the cell surface only when suitable peptides become available.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Christelle Vangenot
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; and
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
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135
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Pathogenesis of infections in HIV-infected individuals: insights from primary immunodeficiencies. Curr Opin Immunol 2017; 48:122-133. [PMID: 28992464 PMCID: PMC5682227 DOI: 10.1016/j.coi.2017.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/14/2017] [Accepted: 09/17/2017] [Indexed: 12/12/2022]
Abstract
Following infection with almost any given microorganism other than an emerging pathogen, only a minority of individuals develop life-threatening clinical disease, implying that these individuals have some form of immunodeficiency. A growing number of inherited and acquired immunodeficiencies have been deciphered over the last 50 years. HIV infection is probably the best-known acquired immunodeficiency. It emerged about 40 years ago and precipitates various severe infections, the occurrence of which is associated with a fall in circulating CD4+ T cells. However, despite the strength of this correlation, infection rates differ between patients with similar levels and durations of CD4+ T lymphopenia in the presence or absence of antiretroviral treatment. Moreover, a few infections seem to be less dependent on total CD4+ T-cell levels. The fine detail of the mechanisms underlying these infections is unknown. We discuss here how studies of the human genetics and immunology of some of these infections in patients with primary immunodeficiencies (PIDs) have provided unique insights into their molecular and cellular basis. Defects of specific CD4+ Th-cell subsets account for some of these infections, as best exemplified by Th1* for mycobacteriosis and Th17 for candidiasis. PIDs are individually rare, but collectively much more common than initially thought, with new disorders being discovered at an ever-increasing pace and a global prevalence worldwide approaching that of HIV infection. Studies of known and new PIDs should make it possible to dissect the pathogenesis of most human infections at an unprecedented level of molecular and cellular precision. The predictive, preventive, and therapeutic implications of studies of immunity to infection in PIDs may extend to HIV-infected patients and patients with infectious diseases in other settings.
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136
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Leitman EM, Thobakgale CF, Adland E, Ansari MA, Raghwani J, Prendergast AJ, Tudor-Williams G, Kiepiela P, Hemelaar J, Brener J, Tsai MH, Mori M, Riddell L, Luzzi G, Jooste P, Ndung'u T, Walker BD, Pybus OG, Kellam P, Naranbhai V, Matthews PC, Gall A, Goulder PJR. Role of HIV-specific CD8 + T cells in pediatric HIV cure strategies after widespread early viral escape. J Exp Med 2017; 214:3239-3261. [PMID: 28983013 PMCID: PMC5679167 DOI: 10.1084/jem.20162123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 06/22/2017] [Accepted: 08/30/2017] [Indexed: 11/04/2022] Open
Abstract
Recent studies have suggested greater HIV cure potential among infected children than adults. A major obstacle to HIV eradication in adults is that the viral reservoir is largely comprised of HIV-specific cytotoxic T lymphocyte (CTL) escape variants. We here evaluate the potential for CTL in HIV-infected slow-progressor children to play an effective role in "shock-and-kill" cure strategies. Two distinct subgroups of children were identified on the basis of viral load. Unexpectedly, in both groups, as in adults, HIV-specific CTL drove the selection of escape variants across a range of epitopes within the first weeks of infection. However, in HIV-infected children, but not adults, de novo autologous variant-specific CTL responses were generated, enabling the pediatric immune system to "corner" the virus. Thus, even when escape variants are selected in early infection, the capacity in children to generate variant-specific anti-HIV CTL responses maintains the potential for CTL to contribute to effective shock-and-kill cure strategies in pediatric HIV infection.
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Affiliation(s)
- Ellen M Leitman
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - Christina F Thobakgale
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - M Azim Ansari
- Oxford Martin School, University of Oxford, Oxford, England, UK
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, England, UK
| | - Andrew J Prendergast
- Blizard Institute, Queen Mary University of London, London, England, UK.,Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Gareth Tudor-Williams
- Division of Medicine, Department of Paediatrics, Imperial College London, London, England, UK
| | - Photini Kiepiela
- Medical Research Council, Durban, South Africa.,Witwatersrand Health Consortium, Johannesburg, South Africa
| | - Joris Hemelaar
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, England, UK.,Linacre Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Jacqui Brener
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - Ming-Han Tsai
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - Masahiko Mori
- Department of Paediatrics, University of Oxford, Oxford, England, UK.,Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Lynn Riddell
- Northampton Healthcare NHS Foundation Trust, Cliftonville, England, UK
| | - Graz Luzzi
- Buckinghampshire Healthcare NHS Foundation Trust, High Wycombe, England, UK
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, England, UK
| | - Paul Kellam
- Kymab Ltd., Babraham Research Campus, Babraham, England, UK.,Department of Medicine, Division of Infectious Diseases, Imperial College Faculty of Medicine, London, England, UK
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA.,Centre for the AIDS Programme of Research in South Africa, University of KwaZulu Natal, Durban, South Africa
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, England, UK
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Hinxton, England, UK
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, Oxford, England, UK .,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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137
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Rosás-Umbert M, Mothe B, Noguera-Julian M, Bellido R, Puertas MC, Carrillo J, Rodriguez C, Perez-Alvarez N, Cobarsí P, Gomez CE, Esteban M, Jímenez JL, García F, Blanco J, Martinez-Picado J, Paredes R, Brander C. Virological and immunological outcome of treatment interruption in HIV-1-infected subjects vaccinated with MVA-B. PLoS One 2017; 12:e0184929. [PMID: 28953921 PMCID: PMC5617163 DOI: 10.1371/journal.pone.0184929] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/13/2017] [Indexed: 01/02/2023] Open
Abstract
The most relevant endpoint in therapeutic HIV vaccination is the assessment of time to viral rebound or duration of sustained control of low-level viremia upon cART treatment cessation. Structured treatment interruptions (STI) are however not without risk to the patient and reliable predictors of viral rebound/control after therapeutic HIV-1 vaccination are urgently needed to ensure patient safety and guide therapeutic vaccine development. Here, we integrated immunological and virological parameters together with viral rebound dynamics after STI in a phase I therapeutic vaccine trial of a polyvalent MVA-B vaccine candidate to define predictors of viral control. Clinical parameters, proviral DNA, host HLA genetics and measures of humoral and cellular immunity were evaluated. A sieve effect analysis was conducted comparing pre-treatment viral sequences to breakthrough viruses after STI. Our results show that a reduced proviral HIV-1 DNA at study entry was independently associated with two virological parameters, delayed HIV-1 RNA rebound (p = 0.029) and lower peak viremia after treatment cessation (p = 0.019). Reduced peak viremia was also positively correlated with a decreased number of HLA class I allele associated polymorphisms in Gag sequences in the rebounding virus population (p = 0.012). Our findings suggest that proviral DNA levels and the number of HLA-associated Gag polymorphisms may have an impact on the clinical outcome of STI. Incorporation of these parameters in future therapeutic vaccine trials may guide refined immunogen design and help conduct safer STI approaches.
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Affiliation(s)
- Miriam Rosás-Umbert
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
| | - Rocío Bellido
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Maria C. Puertas
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - C. Rodriguez
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Núria Perez-Alvarez
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Patricia Cobarsí
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
| | | | | | | | - Felipe García
- Hospital Clinic–HIVACAT, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
- Health Sciences Research Institute Germans Trias i Pujol, IGTP, Badalona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- “Lluita contra la SIDA” Foundation, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute—HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
- University of VIC and Central Catalonia, Vic, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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138
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Memory responses of natural killer cells. Semin Immunol 2017; 31:11-19. [PMID: 28863960 DOI: 10.1016/j.smim.2017.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 12/20/2022]
Abstract
Natural killer (NK) cells have traditionally been classified as a cellular component of the innate immune system, given their ability to rapidly produce effector cytokines and kill infected or transformed cells without prior exposure. More recently, NK cells have been shown to possess features of adaptive immunity such as clonal expansion, longevity, and robust recall responses. NK cell memory can be broadly divided into two categories: antigen-specific and antigen-independent. In the first case, exposure to certain viral or hapten stimuli endows NK cells with antigen-specific immunological memory, similar to T and B cells. In the second case, exposure of NK cells to specific cytokine milieus can imprint long-lasting changes on effector functions, resulting in antigen-independent memory-like NK cells. In this review, we discuss the various conditions that promote generation of these two categories of memory NK cells, and the mechanistic requirements underlying these processes.
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139
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Abstract
Despite major advances in antiretroviral therapy against HIV-1, an effective HIV vaccine is urgently required to reduce the number of new cases of HIV infections in the world. Vaccines are the ultimate tool in the medical arsenal to control and prevent the spread of infectious diseases such as HIV/AIDS. Several failed phase-IIb to –III clinical vaccine trials against HIV-1 in the past generated a plethora of information that could be used for better designing of an effective HIV vaccine in the future. Most of the tested vaccine candidates produced strong humoral responses against the HIV proteins; however, failed to protect due to: 1) the low levels and the narrow breadth of the HIV-1 neutralizing antibodies and the HIV-specific antibody-dependent Fc-mediated effector activities, 2) the low levels and the poor quality of the anti-HIV T-cell responses, and 3) the excessive responses to immunodominant non-protective HIV epitopes, which in some cases blocked the protective immunity and/or enhanced HIV infection. The B-cell epitopes on HIV for producing broadly neutralizing antibodies (bNAbs) against HIV have been extensively characterized, and the next step is to develop bNAb epitope immunogen for HIV vaccine. The bNAb epitopes are often conformational epitopes and therefore more difficult to construct as vaccine immunogen and likely to include immunodominant non-protective HIV epitopes. In comparison, T-cell epitopes are short linear peptides which are easier to construct into vaccine immunogen free of immunodominant non-protective epitopes. However, its difficulty lies in identifying the T-cell epitopes conserved among HIV subtypes and induce long-lasting, potent polyfunctional T-cell and cytotoxic T lymphocyte (CTL) activities against HIV. In addition, these protective T-cell epitopes must be recognized by the HLA prevalent in the country(s) targeted for the vaccine trial. In conclusion, extending from the findings from previous vaccine trials, future vaccines should combine both T- and B-cell epitopes as vaccine immunogen to induce multitude of broad and potent immune effector activities required for sterilizing protection against global HIV subtypes.
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Affiliation(s)
- Bikash Sahay
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL 32611-0880, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL 32611-0880, USA
| | - Janet K Yamamoto
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL 32611-0880, USA
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140
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Preferential Targeting of Conserved Gag Regions after Vaccination with a Heterologous DNA Prime-Modified Vaccinia Virus Ankara Boost HIV-1 Vaccine Regimen. J Virol 2017; 91:JVI.00730-17. [PMID: 28701395 DOI: 10.1128/jvi.00730-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/14/2017] [Indexed: 11/20/2022] Open
Abstract
Prime-boost vaccination strategies against HIV-1 often include multiple variants for a given immunogen for better coverage of the extensive viral diversity. To study the immunologic effects of this approach, we characterized breadth, phenotype, function, and specificity of Gag-specific T cells induced by a DNA-prime modified vaccinia virus Ankara (MVA)-boost vaccination strategy, which uses mismatched Gag immunogens in the TamoVac 01 phase IIa trial. Healthy Tanzanian volunteers received three injections of the DNA-SMI vaccine encoding a subtype B and AB-recombinant Gagp37 and two vaccinations with MVA-CMDR encoding subtype A Gagp55 Gag-specific T-cell responses were studied in 42 vaccinees using fresh peripheral blood mononuclear cells. After the first MVA-CMDR boost, vaccine-induced gamma interferon-positive (IFN-γ+) Gag-specific T-cell responses were dominated by CD4+ T cells (P < 0.001 compared to CD8+ T cells) that coexpressed interleukin-2 (IL-2) (66.4%) and/or tumor necrosis factor alpha (TNF-α) (63.7%). A median of 3 antigenic regions were targeted with a higher-magnitude median response to Gagp24 regions, more conserved between prime and boost, compared to those of regions within Gagp15 (not primed) and Gagp17 (less conserved; P < 0.0001 for both). Four regions within Gagp24 each were targeted by 45% to 74% of vaccinees upon restimulation with DNA-SMI-Gag matched peptides. The response rate to individual antigenic regions correlated with the sequence homology between the MVA- and DNA Gag-encoded immunogens (P = 0.04, r2 = 0.47). In summary, after the first MVA-CMDR boost, the sequence-mismatched DNA-prime MVA-boost vaccine strategy induced a Gag-specific T-cell response that was dominated by polyfunctional CD4+ T cells and that targeted multiple antigenic regions within the conserved Gagp24 protein.IMPORTANCE Genetic diversity is a major challenge for the design of vaccines against variable viruses. While including multiple variants for a given immunogen in prime-boost vaccination strategies is one approach that aims to improve coverage for global virus variants, the immunologic consequences of this strategy have been poorly defined so far. It is unclear whether inclusion of multiple variants in prime-boost vaccination strategies improves recognition of variant viruses by T cells and by which mechanisms this would be achieved, either by improved cross-recognition of multiple variants for a given antigenic region or through preferential targeting of antigenic regions more conserved between prime and boost. Engineering vaccines to induce adaptive immune responses that preferentially target conserved antigenic regions of viral vulnerability might facilitate better immune control after preventive and therapeutic vaccination for HIV and for other variable viruses.
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141
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Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell 2017; 62:157-168. [PMID: 27105112 DOI: 10.1016/j.molcel.2016.03.019] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 12/29/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022]
Abstract
HIV-infected individuals are living longer on antiretroviral therapy, but many patients display signs that in some ways resemble premature aging. To investigate and quantify the impact of chronic HIV infection on aging, we report a global analysis of the whole-blood DNA methylomes of 137 HIV+ individuals under sustained therapy along with 44 matched HIV- individuals. First, we develop and validate epigenetic models of aging that are independent of blood cell composition. Using these models, we find that both chronic and recent HIV infection lead to an average aging advancement of 4.9 years, increasing expected mortality risk by 19%. In addition, sustained infection results in global deregulation of the methylome across >80,000 CpGs and specific hypomethylation of the region encoding the human leukocyte antigen locus (HLA). We find that decreased HLA methylation is predictive of lower CD4 / CD8 T cell ratio, linking molecular aging, epigenetic regulation, and disease progression.
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Affiliation(s)
- Andrew M Gross
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Philipp A Jaeger
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristen L Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mahdieh Khosroheidari
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brenda M Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Susan Swindells
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Cherie T Ng
- aTyr Pharmaceuticals, San Diego, CA 92121, USA
| | - Ken Flagg
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Guangzhou Kang Rui Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, China
| | - Daniel Chen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kang Zhang
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Veterans Administration Healthcare System, San Diego, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Trey Ideker
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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142
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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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143
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Almeida CA, van Miert P, O'Driscoll K, Zoet YM, Chopra A, Watson M, de Santis D, Witt C, John M, Claas FHJ, D'Orsogna LJ. Stimulation of HIV-specific T cell clonotypes using allogeneic HLA. Cell Immunol 2017; 316:32-40. [PMID: 28372798 DOI: 10.1016/j.cellimm.2017.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/15/2017] [Accepted: 03/25/2017] [Indexed: 01/26/2023]
Abstract
We hypothesized that HIV-specific CD8 T cell clonotypes can be stimulated by allogeneic HLA molecules. Multiple HIV-specific CD8 T cell clones were derived from 12 individuals with chronic HIV infection, specific for 13 different HIV Gag antigens and restricted to 7 different HLA molecules. The generated T cell clones were assayed for alloreactivity against a panel of single HLA class I expressing cell lines (SALs). HIV-specific T cells recognising at least one allogeneic HLA molecule could be identified from 7 of 12 patients tested. Allorecognition was associated with IFNγ cytokine production, CD137 upregulation and cytotoxicity, suggesting high avidity allo-stimulation. Allo-HLA recognition by HIV-specific T cells was specific to the HIV target peptide/HLA restriction and TCR TRBV usage of the T cells. HIV-specific T cells do crossreact against allogeneic HLA molecules in an epitope and TRBV specific manner. Therefore allo-HLA stimulation could be exploited to induce or augment HIV-specific T cell responses.
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Affiliation(s)
- Coral-Ann Almeida
- Department of Clinical Immunology, Fiona Stanley Hospital, Perth, Australia; Pathwest Laboratory Medicine, Perth, Australia; Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Paula van Miert
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kane O'Driscoll
- Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | - Yvonne M Zoet
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Mark Watson
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Dianne de Santis
- Department of Clinical Immunology, Fiona Stanley Hospital, Perth, Australia; Pathwest Laboratory Medicine, Perth, Australia
| | - Campbell Witt
- Pathwest Laboratory Medicine, Perth, Australia; Department of Clinical Immunology, Royal Perth Hospital, Perth, Australia
| | - Mina John
- Pathwest Laboratory Medicine, Perth, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia; Department of Clinical Immunology, Royal Perth Hospital, Perth, Australia
| | - Frans H J Claas
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lloyd J D'Orsogna
- Department of Clinical Immunology, Fiona Stanley Hospital, Perth, Australia; Pathwest Laboratory Medicine, Perth, Australia; Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia.
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144
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Chakraborty AK, Barton JP. Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:032601. [PMID: 28059778 DOI: 10.1088/1361-6633/aa574a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Vaccination has saved more lives than any other medical procedure. Pathogens have now evolved that have not succumbed to vaccination using the empirical paradigms pioneered by Pasteur and Jenner. Vaccine design strategies that are based on a mechanistic understanding of the pertinent immunology and virology are required to confront and eliminate these scourges. In this perspective, we describe just a few examples of work aimed to achieve this goal by bringing together approaches from statistical physics with biology and clinical research.
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Affiliation(s)
- Arup K Chakraborty
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Departments of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Departments of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Ragon Institute of MIT, MGH, & Harvard, Cambridge, MA 02139, United States of America
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145
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Abstract
Supplemental Digital Content is available in the text Objective(s): An HIV cure will impose aviraemia that is sustained following the withdrawal of antiretroviral therapy (ART). Understanding the efficacy of novel interventions aimed at curing HIV requires characterization of both natural viral control and the effect of ART on viral control after treatment interruption. Design: Analysis of transient viral control in recent seroconverters in the Short Pulse AntiRetroviral Therapy at Acute Seroconversion trial. Methods: We compared untreated and treated HIV seroconverters (n = 292) and identified periods of control (plasma HIV RNA < 400 copies/ml for ≥16 weeks off therapy) in 7.9% of ART-naive participants, and in 12.0% overall. HIV DNA was measured by qPCR, and HIV-specific CD8+ responses were measured by enzyme-linked immunosorbent spot assay (ELISpot). T-cell activation and exhaustion were measured by flow cytometry. Results: At baseline, future controllers had lower HIV DNA, lower plasma HIV RNA, higher CD4+ : CD8+ ratios (all P < 0.001) and higher CD4+ cell counts (P < 0.05) than noncontrollers. Among controllers, the only difference between the untreated and those who received ART was higher baseline HIV RNA in the latter (P = 0.003), supporting an added ART effect. Conclusion: Consideration of spontaneous remission in untreated individuals will be critical to avoid overestimating the effect size of new interventions used in HIV cure studies.
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146
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Malnati MS, Ugolotti E, Monti MC, Battista DD, Vanni I, Bordo D, Sironi F, Larghero P, Marco ED, Biswas P, Poli G, Vicenzi E, Riva A, Tarkowski M, Tambussi G, Nozza S, Tripodi G, Marras F, Maria AD, Pistorio A, Biassoni R. Activating Killer Immunoglobulin Receptors and HLA-C: a successful combination providing HIV-1 control. Sci Rep 2017; 7:42470. [PMID: 28211903 PMCID: PMC5304173 DOI: 10.1038/srep42470] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 01/11/2017] [Indexed: 11/29/2022] Open
Abstract
Several studies demonstrated a relevant role of polymorphisms located within the HLA-B and -C loci and the Killer Immunoglobulin Receptors (KIRs) 3DL1 and 3DS1 in controlling HIV-1 replication. KIRs are regulatory receptors expressed at the surface of NK and CD8+ T-cells that specifically bind HLA-A and -B alleles belonging to the Bw4 supratype and all the -C alleles expressing the C1 or C2 supratype. We here disclose a novel signature associated with the Elite Controller but not with the long-term nonprogressor status concerning 2DS activating KIRs and HLA-C2 alleles insensitive to miRNA148a regulation. Overall, our findings support a crucial role of NK cells in the control of HIV-1 viremia.
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Affiliation(s)
- Mauro S. Malnati
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Maria Cristina Monti
- Department of Public Health Unit of biostatistics and clinical epidemiology University of Pavia, Pavia Italy
| | - Davide De Battista
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Francesca Sironi
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Priscilla Biswas
- Unit of Human Virology, Division of Immunology, transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | - Guido Poli
- Vita-Salute San Raffaele University, School of Medicine, Milan, Italy
| | - Elisa Vicenzi
- Unit of Viral Pathogens and Biosafety, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Agostino Riva
- Department of Clinical Sciences Chair of Infectious Diseases and Tropical Medicine University of Milan,“L. Sacco” Hospital, Milan, Italy
| | - Maciej Tarkowski
- Department of Clinical Sciences Chair of Infectious Diseases and Tropical Medicine University of Milan,“L. Sacco” Hospital, Milan, Italy
| | - Giuseppe Tambussi
- Department of Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Silvia Nozza
- Department of Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | - Andrea De Maria
- IRCCS AOU San Martino-IST, Genoa, Italy
- Department of Health Science, DISSAL and Center for excellence in Biomedical Research CEBR University of Genoa, Genoa, Italy
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147
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John M, Gaudieri S, Mallal S. Immunogenetics and Vaccination. HUMAN VACCINES 2017. [DOI: 10.1016/b978-0-12-802302-0.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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148
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Arcia D, Acevedo-Sáenz L, Rugeles MT, Velilla PA. Role of CD8 + T Cells in the Selection of HIV-1 Immune Escape Mutations. Viral Immunol 2016; 30:3-12. [PMID: 27805477 DOI: 10.1089/vim.2016.0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) infection represents one of the biggest public health problems worldwide. The immune response, mainly the effector mechanisms mediated by CD8+ T cells, induces the selection of mutations that allows the virus to escape the immune control. These mutations are generally selected within CD8+ T cell epitopes restricted to human leukocyte antigen class I (HLA-I), leading to a decrease in the presentation and recognition of the epitope, decreasing the activation of CD8+ T cells. However, these mutations may also affect cellular processing of the peptide or recognition by the T cell receptor. Escape mutations often carry a negative impact in viral fitness that is partially or totally compensated by the selection of compensatory mutations. The selection of either escape mutations or compensatory mutations may negatively affect the course of the infection. In addition, these mutations are a major barrier for the development of new therapeutic strategies focused on the induction of specific CD8+ T cell responses.
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Affiliation(s)
- David Arcia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
| | - Paula A Velilla
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA , Medellín, Colombia
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149
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Hussain SK, Makgoeng SB, Everly MJ, Goodman MT, Martínez-Maza O, Morton LM, Clarke CA, Lynch CF, Snyder J, Israni A, Kasiske BL, Engels EA. HLA and Risk of Diffuse Large B cell Lymphoma After Solid Organ Transplantation. Transplantation 2016; 100:2453-2460. [PMID: 26636741 PMCID: PMC4893345 DOI: 10.1097/tp.0000000000001025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Solid organ transplant recipients have heightened risk for diffuse large B cell lymphoma (DLBCL). The role of donor-recipient HLA mismatch and recipient HLA type on DLBCL risk are not well established. METHODS We examined 172 231 kidney, heart, pancreas, and lung recipients transplanted in the United States between 1987 and 2010, including 902 with DLBCL. Incidence rate ratios (IRRs) were calculated using Poisson regression for DLBCL risk in relation to HLA mismatch, types, and zygosity, adjusting for sex, age, race/ethnicity, year, organ, and transplant number. RESULTS Compared with recipients who had 2 HLA-DR mismatches, those with zero or 1 mismatch had reduced DLBCL risk, (zero: IRR, 0.76, 95% confidence interval [95% CI], 0.61-0.95; one: IRR, 0.83; 95% CI, 0.69-1.00). In stratified analyses, recipients matched at either HLA-A, -B, or -DR had a significantly reduced risk of late-onset (>2 years after transplantation), but not early-onset DLBCL, and there was a trend for decreasing risk with decreasing mismatch across all 3 loci (P = 0.0003). Several individual recipient HLA-A, -B, -C, -DR, and -DQ antigens were also associated with DLBCL risk, including DR13 (IRR, 0.74; 95% CI, 0.57-0.93) and B38 (IRR, 1.48; 95% CI, 1.10-1.93), confirming prior findings that these 2 antigens are associated with risk of infection-associated cancers. CONCLUSIONS In conclusion, variation in HLA is related to susceptibility to DLBCL, perhaps reflecting intensity of immunosuppression, control of Epstein-Barr virus infection among transplant recipients or chronic immune stimulation.
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Affiliation(s)
- Shehnaz K. Hussain
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA
| | - Solomon B. Makgoeng
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA
| | | | - Marc T. Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Otoniel Martínez-Maza
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA
- Departments of Obstetrics and Gynecology and Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Christina A. Clarke
- Cancer Prevention Institute of California, Fremont, CA; Division of Epidemiology, Department of Health Research and Policy and Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Jon Snyder
- Scientific Registry of Transplant Recipients and Minneapolis Medical Research Foundation, Minneapolis, Minneapolis, MN
| | - Ajay Israni
- Scientific Registry of Transplant Recipients and Minneapolis Medical Research Foundation, Minneapolis, Minneapolis, MN
| | - Bertram L. Kasiske
- Scientific Registry of Transplant Recipients and Minneapolis Medical Research Foundation, Minneapolis, Minneapolis, MN
| | - Eric A. Engels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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150
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Jimenez-Moyano E, Ruiz A, Kløverpris HN, Rodriguez-Plata MT, Peña R, Blondeau C, Selwood DL, Izquierdo-Useros N, Moris A, Clotet B, Goulder P, Towers GJ, Prado JG. Nonhuman TRIM5 Variants Enhance Recognition of HIV-1-Infected Cells by CD8+ T Cells. J Virol 2016; 90:8552-62. [PMID: 27440884 PMCID: PMC5021395 DOI: 10.1128/jvi.00819-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Tripartite motif-containing protein 5 (TRIM5) restricts human immunodeficiency virus type 1 (HIV-1) in a species-specific manner by uncoating viral particles while activating early innate responses. Although the contribution of TRIM5 proteins to cellular immunity has not yet been studied, their interactions with the incoming viral capsid and the cellular proteasome led us to hypothesize a role for them. Here, we investigate whether the expression of two nonhuman TRIM5 orthologs, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), both of which are potent restrictors of HIV-1, could enhance immune recognition of infected cells by CD8(+) T cells. We illustrate how TRIM5 restriction improves CD8(+) T-cell-mediated HIV-1 inhibition. Moreover, when TRIM5 activity was blocked by the nonimmunosuppressive analog of cyclosporine (CsA), sarcosine-3(4-methylbenzoate)-CsA (SmBz-CsA), we found a significant reduction in CD107a/MIP-1β expression in HIV-1-specific CD8(+) T cells. This finding underscores the direct link between TRIM5 restriction and activation of CD8(+) T-cell responses. Interestingly, cells expressing RhT5 induced stronger CD8(+) T-cell responses through the specific recognition of the HIV-1 capsid by the immune system. The underlying mechanism of this process may involve TRIM5-specific capsid recruitment to cellular proteasomes and increase peptide availability for loading and presentation of HLA class I antigens. In summary, we identified a novel function for nonhuman TRIM5 variants in cellular immunity. We hypothesize that TRIM5 can couple innate viral sensing and CD8(+) T-cell activation to increase species barriers against retrovirus infection. IMPORTANCE New therapeutics to tackle HIV-1 infection should aim to combine rapid innate viral sensing and cellular immune recognition. Such strategies could prevent seeding of the viral reservoir and the immune damage that occurs during acute infection. The nonhuman TRIM5 variants, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), are attractive candidates owing to their potency in sensing HIV-1 and blocking its activity. Here, we show that expression of RhT5 and TCyp in HIV-1-infected cells improves CD8(+) T-cell-mediated inhibition through the direct activation of HIV-1-specific CD8(+) T-cell responses. We found that the potency in CD8(+) activation was stronger for RhT5 variants and capsid-specific CD8(+) T cells in a mechanism that relies on TRIM5-dependent particle recruitment to cellular proteasomes. This novel mechanism couples innate viral sensing with cellular immunity in a single protein and could be exploited to develop innovative therapeutics for control of HIV-1 infection.
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Affiliation(s)
| | - Alba Ruiz
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Henrik N Kløverpris
- KwaZulu-Natal Research Institute for TB and HIV, University of KwaZulu-Natal, Durban, South Africa
| | | | - Ruth Peña
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Caroline Blondeau
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - David L Selwood
- The Wolfson Institute for Biomedical Research, University College London, United Kingdom
| | | | - Arnaud Moris
- Sorbonne Universités, UPMC University Paris 6, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections-Paris, Paris, France
| | - Bonaventura Clotet
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Julia G Prado
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
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