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Moezpoor MR, Stevenson M. Help or Hinder: Protein Host Factors That Impact HIV-1 Replication. Viruses 2024; 16:1281. [PMID: 39205255 PMCID: PMC11360189 DOI: 10.3390/v16081281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Interactions between human immunodeficiency virus type 1 (HIV-1) and the host factors or restriction factors of its target cells determine the cell's susceptibility to, and outcome of, infection. Factors intrinsic to the cell are involved at every step of the HIV-1 replication cycle, contributing to productive infection and replication, or severely attenuating the chances of success. Furthermore, factors unique to certain cell types contribute to the differences in infection between these cell types. Understanding the involvement of these factors in HIV-1 infection is a key requirement for the development of anti-HIV-1 therapies. As the list of factors grows, and the dynamic interactions between these factors and the virus are elucidated, comprehensive and up-to-date summaries that recount the knowledge gathered after decades of research are beneficial to the field, displaying what is known so that researchers can build off the groundwork of others to investigate what is unknown. Herein, we aim to provide a review focusing on protein host factors, both well-known and relatively new, that impact HIV-1 replication in a positive or negative manner at each stage of the replication cycle, highlighting factors unique to the various HIV-1 target cell types where appropriate.
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Affiliation(s)
- Michael Rameen Moezpoor
- Department of Microbiology and Immunology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Stevenson
- Raymond F. Schinazi and Family Endowed Chair in Biomedicine; Professor of Medicine; Director, Institute of AIDS and Emerging Infectious Diseases; Department of Microbiology and Immunology, University of Miami Leonard M. Miller School of Medicine, Life Science Technology Park, 1951 NW 7th Avenue, Room 2331B, Suite 200, Miami, FL 33136, USA;
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2
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Rao M, Peachman KK, Alving CR. Liposome Formulations as Adjuvants for Vaccines. Curr Top Microbiol Immunol 2021; 433:1-28. [PMID: 33165871 DOI: 10.1007/82_2020_227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of liposome-based formulations as vaccine adjuvants has been intimately associated with, and dependent on, and informed by, a fundamental understanding of biochemical and biophysical properties of liposomes themselves. The Walter Reed Army Institute of Research (WRAIR) has a fifty-year history of experience of basic research on liposomes; and development of liposomes as drug carriers; and development of liposomes as adjuvant formulations for vaccines. Uptake of liposomes by phagocytic cells in vitro has served as an excellent model for studying the intracellular trafficking patterns of liposomal antigen. Differential fluorescent labeling of proteins and liposomal lipids, together with the use of inhibitors, has enabled the visualization of physical locations of antigens, peptides, and lipids to elucidate mechanisms underlying the MHC class I and class II pathways in phagocytic APCs. Army Liposome Formulation (ALF) family of vaccine adjuvants, which have been developed and improved since 1986, and which range from nanosize to microsize, are currently being employed in phase 1 studies with different types of candidate vaccines.
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Affiliation(s)
- Mangala Rao
- Chief, Laboratory of Adjuvant & Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA.
| | - Kristina K Peachman
- Laboratory of Adjuvant & Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Carl R Alving
- Laboratory of Adjuvant & Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
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3
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Boucau J, Le Gall S. Antigen processing and presentation in HIV infection. Mol Immunol 2019; 113:67-74. [PMID: 29636181 PMCID: PMC6174111 DOI: 10.1016/j.molimm.2018.03.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/09/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022]
Abstract
The presentation of virus-derived peptides by MHC molecules constitutes the earliest signals for immune recognition by T cells. In HIV infection, immune responses elicited during infection do not enable to clear infection and correlates of immune protection are not well defined. Here we review features of antigen processing and presentation specific to HIV, analyze how HIV has adapted to the antigen processing machinery and discuss how advances in biochemical and computational protein degradation analyses and in immunopeptidome definition may help identify targets for efficient immune clearance and vaccine immunogen design.
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Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, United States
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, United States.
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Lee YJ, Yu JE, Kim P, Lee JY, Cheong YC, Lee YJ, Chang J, Seong BL. Eliciting unnatural immune responses by activating cryptic epitopes in viral antigens. FASEB J 2018; 32:4658-4669. [PMID: 29570395 PMCID: PMC6103170 DOI: 10.1096/fj.201701024rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antigenic variation in viral surface antigens is a strategy for escaping the host's adaptive immunity, whereas regions with pivotal functions for infection are less subject to antigenic variability. We hypothesized that genetically invariable and immunologically dormant regions of a viral surface antigen could be exposed to the host immune system and activated by rendering them susceptible to antigen-processing machinery in professional antigen-presenting cells (APCs). Considering the frequent antigen drift and shift in influenza viruses, we identified and used structural modeling to evaluate the conserved regions on the influenza hemagglutinin (HA) surface as potential epitopes. Mutant viruses containing the cleavage motifs of cathepsin S within HA were generated. Immunization of mice showed that the mutant, but not the wild-type virus, elicited specific antibodies against the cryptic epitope. Those antibodies were purified, and specific binding to HA was confirmed. These results suggest that an unnatural immune response can be elicited through the processing of target antigens in APCs, followed by presentation via the major histocompatibility complex, if not subjected to regulatory pathways. By harnessing the antigen-processing machinery, our study shows a proof-of-principle for designer vaccines with increased efficacy and safety by either activating cryptic, or inactivating naturally occurring, epitopes of viral antigens.-Lee, Y. J., Yu, J. E., Kim, P., Lee, J.-Y., Cheong, Y. C., Lee, Y. J., Chang, J., Seong, B. L. Eliciting unnatural immune responses by activating cryptic epitopes in viral antigens.
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Affiliation(s)
- Young Jae Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ji Eun Yu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Paul Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Jeong-Yoon Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea
| | - Yu Cheol Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Yoon Jae Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Jun Chang
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea.,Vaccine Translational Research Center (VTRC), Yonsei University, Seoul, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Translational Research Center (VTRC), Yonsei University, Seoul, South Korea
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5
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Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses. J Virol 2016; 90:8605-20. [PMID: 27440904 DOI: 10.1128/jvi.00599-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/13/2016] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Despite the critical role of epitope presentation for immune recognition, we still lack a comprehensive definition of HIV peptides presented by HIV-infected cells. Here we identified 107 major histocompatibility complex (MHC)-bound HIV peptides directly from the surface of live HIV-transfected 293T cells, HIV-infected B cells, and primary CD4 T cells expressing a variety of HLAs. The majority of peptides were 8 to 12 amino acids (aa) long and mostly derived from Gag and Pol. The analysis of the total MHC-peptidome and of HLA-A02-bound peptides identified new noncanonical HIV peptides of up to 16 aa that could not be predicted by HLA anchor scanning and revealed an heterogeneous surface peptidome. Nested sets of surface HIV peptides included optimal and extended HIV epitopes and peptides partly overlapping or distinct from known epitopes, revealing new immune responses in HIV-infected persons. Surprisingly, in all three cell types, a majority of Gag peptides derived from p15 rather than from the most immunogenic p24. The cytosolic degradation of peptide precursors in corresponding cells confirmed the generation of identified surface-nested peptides. Cytosolic degradation revealed peptides commonly produced in all cell types and displayed by various HLAs, peptides commonly produced in all cell types and selectively displayed by specific HLAs, and peptides produced in only one cell type. Importantly, we identified areas of proteins leading to common presentations of noncanonical peptides by several cell types with distinct HLAs. These peptides may benefit the design of immunogens, focusing T cell responses on relevant markers of HIV infection in the context of HLA diversity. IMPORTANCE The recognition of HIV-infected cells by immune T cells relies on the presentation of HIV-derived peptides by diverse HLA molecules at the surface of cells. The landscape of HIV peptides displayed by HIV-infected cells is not well defined. Considering the diversity of HLA molecules in the human population, it is critical for vaccine design to identify HIV peptides that may be displayed despite the HLA diversity. We identified 107 HIV peptides directly from the surface of three cell types infected with HIV. They corresponded to nested sets of HIV peptides of canonical and novel noncanonical lengths not predictable by the presence of HLA anchors. Importantly, we identified areas of HIV proteins leading to presentation of noncanonical peptides by several cell types with distinct HLAs. Including such peptides in vaccine immunogen may help to focus immune responses on common markers of HIV infection in the context of HLA diversity.
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6
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Nguyen HNP, Steede NK, Robinson JE, Landry SJ. Conformational instability governed by disulfide bonds partitions the dominant from subdominant helper T-cell responses specific for HIV-1 envelope glycoprotein gp120. Vaccine 2015; 33:2887-96. [PMID: 25944298 DOI: 10.1016/j.vaccine.2015.04.082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/30/2015] [Accepted: 04/22/2015] [Indexed: 01/07/2023]
Abstract
Most individuals infected with human immunodeficiency virus type 1 (HIV-1) generate a CD4(+) T-cell response that is dominated by a few epitopes. Immunodominance may be counterproductive because a broad CD4(+) T-cell response is associated with reduced viral load. Previous studies indicated that antigen three-dimensional structure controls antigen processing and presentation and therefore CD4(+) T-cell epitope dominance. Dominant epitopes occur adjacent to the V1-V2, V3, and V4 loops because proteolytic antigen processing in the loops promotes presentation of adjacent sequences. In this study, three gp120 (strain JR-FL) variants were constructed, in which deletions of single outer-domain disulfide bonds were expected to introduce local conformational flexibility and promote presentation of additional CD4(+) T-cell epitopes. Following mucosal immunization of C57BL/6 mice with wild-type or variant gp120 lacking the V3-flanking disulfide bond, the typical pattern of dominant epitopes was observed, suggesting that the disulfide bond posed no barrier to antigen presentation. In mice that lacked gamma interferon-inducible lysosomal thioreductase (GILT), proliferative responses to the typically dominant epitopes of gp120 were selectively depressed, and the dominance pattern was rearranged. Deletion of the V3-flanking disulfide bond or one of the V4-flanking disulfide bonds partially restored highly proliferative responses to the typically dominant epitopes. These results reveal an acute dependence of dominant CD4(+) T-cell responses on the native gp120 conformation.
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Affiliation(s)
- Hong-Nam P Nguyen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA
| | - N Kalaya Steede
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA
| | - James E Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samuel J Landry
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA.
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7
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Dinter J, Duong E, Lai NY, Berberich MJ, Kourjian G, Bracho-Sanchez E, Chu D, Su H, Zhang SC, Le Gall S. Variable processing and cross-presentation of HIV by dendritic cells and macrophages shapes CTL immunodominance and immune escape. PLoS Pathog 2015; 11:e1004725. [PMID: 25781895 PMCID: PMC4364612 DOI: 10.1371/journal.ppat.1004725] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 02/03/2015] [Indexed: 12/20/2022] Open
Abstract
Dendritic cells (DCs) and macrophages (Møs) internalize and process exogenous HIV-derived antigens for cross-presentation by MHC-I to cytotoxic CD8+ T cells (CTL). However, how degradation patterns of HIV antigens in the cross-presentation pathways affect immunodominance and immune escape is poorly defined. Here, we studied the processing and cross-presentation of dominant and subdominant HIV-1 Gag-derived epitopes and HLA-restricted mutants by monocyte-derived DCs and Møs. The cross-presentation of HIV proteins by both DCs and Møs led to higher CTL responses specific for immunodominant epitopes. The low CTL responses to subdominant epitopes were increased by pretreatment of target cells with peptidase inhibitors, suggestive of higher intracellular degradation of the corresponding peptides. Using DC and Mø cell extracts as a source of cytosolic, endosomal or lysosomal proteases to degrade long HIV peptides, we identified by mass spectrometry cell-specific and compartment-specific degradation patterns, which favored the production of peptides containing immunodominant epitopes in all compartments. The intracellular stability of optimal HIV-1 epitopes prior to loading onto MHC was highly variable and sequence-dependent in all compartments, and followed CTL hierarchy with immunodominant epitopes presenting higher stability rates. Common HLA-associated mutations in a dominant epitope appearing during acute HIV infection modified the degradation patterns of long HIV peptides, reduced intracellular stability and epitope production in cross-presentation-competent cell compartments, showing that impaired epitope production in the cross-presentation pathway contributes to immune escape. These findings highlight the contribution of degradation patterns in the cross-presentation pathway to HIV immunodominance and provide the first demonstration of immune escape affecting epitope cross-presentation. Pathogens such as HIV can enter cells by fusion at the plasma membrane for delivery in the cytosol, or by internalization in endolysosomal vesicles. Pathogens can be degraded in these various compartments into peptides (epitopes) displayed at the cell surface by MHC-I. The presentation of pathogen-derived peptides triggers the activation of T cell immune responses and the clearance of infected cells. How the diversity of compartments in which HIV traffics combined with the diversity of HIV sequences affects the degradation of HIV and the recognition of infected cells by immune cells is not understood. We compared the degradation of HIV proteins in subcellular compartments of dendritic cells and macrophages, two cell types targeted by HIV and the subsequent presentation of epitopes to T cells. We show variable degradation patterns of HIV according to compartments, and the preferential production and superior intracellular stability of immunodominant epitopes corresponding to stronger T cell responses. Frequent mutations in immunodominant epitopes during acute infection resulted in decreased production and intracellular stability of these epitopes. Together these results demonstrate the importance of protein degradation patterns in shaping immunodominant epitopes and the contribution of impaired epitope production in all cellular compartments to immune escape during HIV infection.
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Affiliation(s)
- Jens Dinter
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Ellen Duong
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Nicole Y. Lai
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Matthew J. Berberich
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Georgio Kourjian
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Edith Bracho-Sanchez
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Duong Chu
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Hang Su
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Shao Chong Zhang
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
- * E-mail:
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8
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Ratto-Kim S, de Souza MS, Currier JR, Karasavvas N, Sidney J, Rolland M, Valencia-Micolta A, Madnote S, Sette A, Nitayaphan S, Pitisuttuthum P, Kaewkungwal J, Rerks-Ngarm S, O’Connell R, Michael N, Robb ML, Marovich M, Kim JH. Identification of immunodominant CD4-restricted epitopes co-located with antibody binding sites in individuals vaccinated with ALVAC-HIV and AIDSVAX B/E. PLoS One 2015; 10:e0115582. [PMID: 25665096 PMCID: PMC4321833 DOI: 10.1371/journal.pone.0115582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/29/2014] [Indexed: 11/18/2022] Open
Abstract
We performed fine epitope mapping of the CD4+ responses in the ALVAC-HIV-AIDSVAX B/E prime-boost regimen in the Thai Phase III trial (RV144). Non-transformed Env-specific T cell lines established from RV144 vaccinees were used to determine the fine epitope mapping of the V2 and C1 responses and the HLA class II restriction. Data showed that there are two CD4+ epitopes contained within the V2 loop: one encompassing the α4β7 integrin binding site (AA179-181) and the other nested between two previously described genetic sieve signatures (AA169, AA181). There was no correlation between the frequencies of CD4+ fine epitope responses and binding antibody.
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Affiliation(s)
- Silvia Ratto-Kim
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
- * E-mail:
| | - Mark S. de Souza
- United States Military HIV Research Program/United States Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Jeffrey R. Currier
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
| | - Nicos Karasavvas
- United States Military HIV Research Program/United States Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, United States of America
| | - Morgane Rolland
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
| | - Anais Valencia-Micolta
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
| | - Sirinan Madnote
- United States Military HIV Research Program/United States Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, United States of America
| | - Sorachai Nitayaphan
- Thai Component, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Punnee Pitisuttuthum
- Vaccine Trials Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Jaranit Kaewkungwal
- Centre of Excellence for Biomedical and Public Health Informatics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Supachai Rerks-Ngarm
- Department of Disease Control, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Robert O’Connell
- United States Military HIV Research Program/United States Army Medical Component, Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Nelson Michael
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
| | - Merlin L. Robb
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
| | - Mary Marovich
- Office of AIDS Research, National Institutes of Health, Bethesda, MD, 20892, United States of America
| | - Jerome H. Kim
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States of America
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9
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Mechanisms of HIV protein degradation into epitopes: implications for vaccine design. Viruses 2014; 6:3271-92. [PMID: 25196483 PMCID: PMC4147695 DOI: 10.3390/v6083271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/02/2022] Open
Abstract
The degradation of HIV-derived proteins into epitopes displayed by MHC-I or MHC-II are the first events leading to the priming of HIV-specific immune responses and to the recognition of infected cells. Despite a wealth of information about peptidases involved in protein degradation, our knowledge of epitope presentation during HIV infection remains limited. Here we review current data on HIV protein degradation linking epitope production and immunodominance, viral evolution and impaired epitope presentation. We propose that an in-depth understanding of HIV antigen processing and presentation in relevant primary cells could be exploited to identify signatures leading to efficient or inefficient epitope presentation in HIV proteomes, and to improve the design of immunogens eliciting immune responses efficiently recognizing all infected cells.
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10
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Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T. Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial. J Virol 2014; 88:8242-55. [PMID: 24829343 PMCID: PMC4135964 DOI: 10.1128/jvi.01164-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The RV144 HIV-1 vaccine trial demonstrated partial efficacy of 31% against HIV-1 infection. Studies into possible correlates of protection found that antibodies specific to the V1 and V2 (V1/V2) region of envelope correlated inversely with infection risk and that viruses isolated from trial participants contained genetic signatures of vaccine-induced pressure in the V1/V2 region. We explored the hypothesis that the genetic signatures in V1 and V2 could be partly attributed to selection by vaccine-primed T cells. We performed a T-cell-based sieve analysis of breakthrough viruses in the RV144 trial and found evidence of predicted HLA binding escape that was greater in vaccine versus placebo recipients. The predicted escape depended on class I HLA A*02- and A*11-restricted epitopes in the MN strain rgp120 vaccine immunogen. Though we hypothesized that this was indicative of postacquisition selection pressure, we also found that vaccine efficacy (VE) was greater in A*02-positive (A*02(+)) participants than in A*02(-) participants (VE = 54% versus 3%, P = 0.05). Vaccine efficacy against viruses with a lysine residue at site 169, important to antibody binding and implicated in vaccine-induced immune pressure, was also greater in A*02(+) participants (VE = 74% versus 15%, P = 0.02). Additionally, a reanalysis of vaccine-induced immune responses that focused on those that were shown to correlate with infection risk suggested that the humoral responses may have differed in A*02(+) participants. These exploratory and hypothesis-generating analyses indicate there may be an association between a class I HLA allele and vaccine efficacy, highlighting the importance of considering HLA alleles and host immune genetics in HIV vaccine trials. IMPORTANCE The RV144 trial was the first to show efficacy against HIV-1 infection. Subsequently, much effort has been directed toward understanding the mechanisms of protection. Here, we conducted a T-cell-based sieve analysis, which compared the genetic sequences of viruses isolated from infected vaccine and placebo recipients. Though we hypothesized that the observed sieve effect indicated postacquisition T-cell selection, we also found that vaccine efficacy was greater for participants who expressed HLA A*02, an allele implicated in the sieve analysis. Though HLA alleles have been associated with disease progression and viral load in HIV-1 infection, these data are the first to suggest the association of a class I HLA allele and vaccine efficacy. While these statistical analyses do not provide mechanistic evidence of protection in RV144, they generate testable hypotheses for the HIV vaccine community and they highlight the importance of assessing the impact of host immune genetics in vaccine-induced immunity and protection. (This study has been registered at ClinicalTrials.gov under registration no. NCT00223080.).
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Affiliation(s)
- Andrew J Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sue Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John McNevin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daryl Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Paul T Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Brendan B Larsen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | | | | | - Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Philip Konopa
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Snehal Nariya
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Julia N Stoddard
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kim Wong
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Brandon S Maust
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Shana Howell
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Adam Bates
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Michelle Lazzaro
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | | | - Esther Lei
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Andrea Bradfield
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Grace Ibitamuno
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | | | | | | | | | | | - Merlin L Robb
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | | | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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11
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Steers NJ, Currier JR, Jobe O, Tovanabutra S, Ratto-Kim S, Marovich MA, Kim JH, Michael NL, Alving CR, Rao M. Designing the epitope flanking regions for optimal generation of CTL epitopes. Vaccine 2014; 32:3509-16. [DOI: 10.1016/j.vaccine.2014.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/15/2014] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
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12
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Recognition of synthetic glycopeptides by HIV-1 broadly neutralizing antibodies and their unmutated ancestors. Proc Natl Acad Sci U S A 2013; 110:18214-9. [PMID: 24145434 DOI: 10.1073/pnas.1317855110] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current HIV-1 vaccines elicit strain-specific neutralizing antibodies. Broadly neutralizing antibodies (BnAbs) are not induced by current vaccines, but are found in plasma in ∼20% of HIV-1-infected individuals after several years of infection. One strategy for induction of unfavored antibody responses is to produce homogeneous immunogens that selectively express BnAb epitopes but minimally express dominant strain-specific epitopes. Here we report that synthetic, homogeneously glycosylated peptides that bind avidly to variable loop 1/2 (V1V2) BnAbs PG9 and CH01 bind minimally to strain-specific neutralizing V2 antibodies that are targeted to the same envelope polypeptide site. Both oligomannose derivatization and conformational stabilization by disulfide-linked dimer formation of synthetic V1V2 peptides were required for strong binding of V1V2 BnAbs. An HIV-1 vaccine should target BnAb unmutated common ancestor (UCA) B-cell receptors of naïve B cells, but to date no HIV-1 envelope constructs have been found that bind to the UCA of V1V2 BnAb PG9. We demonstrate herein that V1V2 glycopeptide dimers bearing Man5GlcNAc2 glycan units bind with apparent nanomolar affinities to UCAs of V1V2 BnAbs PG9 and CH01 and with micromolar affinity to the UCA of a V2 strain-specific antibody. The higher-affinity binding of these V1V2 glycopeptides to BnAbs and their UCAs renders these glycopeptide constructs particularly attractive immunogens for targeting subdominant HIV-1 envelope V1V2-neutralizing antibody-producing B cells.
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13
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Bergmann-Leitner ES, Chaudhury S, Steers NJ, Sabato M, Delvecchio V, Wallqvist AS, Ockenhouse CF, Angov E. Computational and experimental validation of B and T-cell epitopes of the in vivo immune response to a novel malarial antigen. PLoS One 2013; 8:e71610. [PMID: 23977087 PMCID: PMC3745447 DOI: 10.1371/journal.pone.0071610] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/01/2013] [Indexed: 11/26/2022] Open
Abstract
Vaccine development efforts will be guided by algorithms that predict immunogenic epitopes. Such prediction methods rely on classification-based algorithms that are trained against curated data sets of known B and T cell epitopes. It is unclear whether this empirical approach can be applied prospectively to predict epitopes associated with protective immunity for novel antigens. We present a comprehensive comparison of in silico B and T cell epitope predictions with in vivo validation using an previously uncharacterized malaria antigen, CelTOS. CelTOS has no known conserved structural elements with any known proteins, and thus is not represented in any epitope databases used to train prediction algorithms. This analysis represents a blind assessment of this approach in the context of a novel, immunologically relevant antigen. The limited accuracy of the tested algorithms to predict the in vivo immune responses emphasizes the need to improve their predictive capabilities for use as tools in vaccine design.
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Affiliation(s)
- Elke S. Bergmann-Leitner
- Malaria Vaccine Branch, U.S. Military Malaria Vaccine Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sidhartha Chaudhury
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Nicholas J. Steers
- U.S. Military HIV Research Program, Division of Retrovirology, Silver Spring, Maryland, United States of America
| | - Mark Sabato
- Vital Probes, Inc., Mayfield, Pennsylvania, United States of America
| | - Vito Delvecchio
- Vital Probes, Inc., Mayfield, Pennsylvania, United States of America
| | - Anders S. Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Christian F. Ockenhouse
- Malaria Vaccine Branch, U.S. Military Malaria Vaccine Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Evelina Angov
- Malaria Vaccine Branch, U.S. Military Malaria Vaccine Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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14
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Vaithilingam A, Lai NY, Duong E, Boucau J, Xu Y, Shimada M, Gandhi M, Le Gall S. A simple methodology to assess endolysosomal protease activity involved in antigen processing in human primary cells. BMC Cell Biol 2013; 14:35. [PMID: 23937268 PMCID: PMC3751085 DOI: 10.1186/1471-2121-14-35] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Endolysosomes play a key role in maintaining the homeostasis of the cell. They are made of a complex set of proteins that degrade lipids, proteins and sugars. Studies involving endolysosome contribution to cellular functions such as MHC class I and II epitope production have used recombinant endolysosomal proteins, knockout mice that lack one of the enzymes or purified organelles from human tissue. Each of these approaches has some caveats in analyzing endolysosomal enzyme functions. RESULTS In this study, we have developed a simple methodology to assess endolysosomal protease activity. By varying the pH in crude lysate from human peripheral blood mononuclear cells (PBMCs), we documented increased endolysosomal cathepsin activity in acidic conditions. Using this new method, we showed that the degradation of HIV peptides in low pH extracts analyzed by mass spectrometry followed similar kinetics and degradation patterns as those performed with purified endolysosomes. CONCLUSION By using crude lysate in the place of purified organelles this method will be a quick and useful tool to assess endolysosomal protease activities in primary cells of limited availability. This quick method will especially be useful to screen peptide susceptibility to degradation in endolysosomal compartments for antigen processing studies, following which detailed analysis using purified organelles may be used to study specific peptides.
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Affiliation(s)
- Archana Vaithilingam
- Ragon Institute of MGH, MIT and Harvard, 400 Technology Square, Cambridge, MA 02139, USA
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