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Jain S, Uritskiy G, Mahalingam M, Batra H, Chand S, Trinh HV, Beck C, Shin WH, Alsalmi W, Kijak G, Eller LA, Kim J, Kihara D, Tovanabutra S, Ferrari G, Robb ML, Rao M, Rao VB. A remarkable genetic shift in a transmitted/founder virus broadens antibody responses against HIV-1. eLife 2024; 13:RP92379. [PMID: 38619110 PMCID: PMC11018346 DOI: 10.7554/elife.92379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
A productive HIV-1 infection in humans is often established by transmission and propagation of a single transmitted/founder (T/F) virus, which then evolves into a complex mixture of variants during the lifetime of infection. An effective HIV-1 vaccine should elicit broad immune responses in order to block the entry of diverse T/F viruses. Currently, no such vaccine exists. An in-depth study of escape variants emerging under host immune pressure during very early stages of infection might provide insights into such a HIV-1 vaccine design. Here, in a rare longitudinal study involving HIV-1 infected individuals just days after infection in the absence of antiretroviral therapy, we discovered a remarkable genetic shift that resulted in near complete disappearance of the original T/F virus and appearance of a variant with H173Y mutation in the variable V2 domain of the HIV-1 envelope protein. This coincided with the disappearance of the first wave of strictly H173-specific antibodies and emergence of a second wave of Y173-specific antibodies with increased breadth. Structural analyses indicated conformational dynamism of the envelope protein which likely allowed selection of escape variants with a conformational switch in the V2 domain from an α-helix (H173) to a β-strand (Y173) and induction of broadly reactive antibody responses. This differential breadth due to a single mutational change was also recapitulated in a mouse model. Rationally designed combinatorial libraries containing 54 conformational variants of V2 domain around position 173 further demonstrated increased breadth of antibody responses elicited to diverse HIV-1 envelope proteins. These results offer new insights into designing broadly effective HIV-1 vaccines.
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Affiliation(s)
- Swati Jain
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Gherman Uritskiy
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Marthandan Mahalingam
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Himanshu Batra
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Subhash Chand
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Charles Beck
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Woong-Hee Shin
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
- Department of Chemistry Education, Sunchon National UniversitySuncheonRepublic of Korea
- Department of Advanced Components and Materials Engineering, Sunchon National UniversitySuncheonRepublic of Korea
| | - Wadad Alsalmi
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Gustavo Kijak
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Leigh A Eller
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
| | - Jerome Kim
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
- Department of Computer Science, Purdue UniversityWest LafayetteUnited States
| | - Sodsai Tovanabutra
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Guido Ferrari
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Merlin L Robb
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
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2
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Delgado KN, Montezuma-Rusca JM, Orbe IC, Caimano MJ, La Vake CJ, Luthra A, Hennelly CM, Nindo FN, Meyer JW, Jones LD, Parr JB, Salazar JC, Moody MA, Radolf JD, Hawley KL. Extracellular Loops of the Treponema pallidum FadL Orthologs TP0856 and TP0858 Elicit IgG Antibodies and IgG +-Specific B-Cells in the Rabbit Model of Experimental Syphilis. mBio 2022; 13:e0163922. [PMID: 35862766 PMCID: PMC9426418 DOI: 10.1128/mbio.01639-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
The resurgence of syphilis in the new millennium has called attention to the importance of a vaccine for global containment strategies. Studies with immune rabbit serum (IRS) indicate that a syphilis vaccine should elicit antibodies (Abs) that promote opsonophagocytosis of treponemes by activated macrophages. The availability of three-dimensional models for Treponema pallidum's (Tp) repertoire of outer membrane proteins (OMPs) provides an architectural framework for identification of candidate vaccinogens with extracellular loops (ECLs) as the targets for protective Abs. Herein, we used Pyrococcus furiosus thioredoxin (PfTrx) as a scaffold to display Tp OMP ECLs to interrogate sera and peripheral blood mononuclear cells (PBMCs) from immune rabbits for ECL-specific Abs and B cells. We validated this approach using a PfTrx scaffold presenting ECL4 from BamA, a known opsonic target. Using scaffolds displaying ECLs of the FadL orthologs TP0856 and TP0858, we determined that ECL2 and ECL4 of both proteins are strongly antigenic. Comparison of ELISA and immunoblot results suggested that the PfTrx scaffolds present conformational and linear epitopes. We then used the FadL ECL2 and ECL4 PfTrx constructs as "hooks" to confirm the presence of ECL-specific B cells in PBMCs from immune rabbits. Our results pinpoint immunogenic ECLs of two newly discovered OMPs, while advancing the utility of the rabbit model for circumventing bottlenecks in vaccine development associated with large-scale production of folded OMPs. They also lay the groundwork for production of rabbit monoclonal Abs (MAbs) to characterize potentially protective ECL epitopes at the atomic level. IMPORTANCE Recent identification and structural modeling of Treponema pallidum's (Tp) repertoire of outer membrane proteins (OMPs) represent a critical breakthrough in the decades long quest for a syphilis vaccine. However, little is known about the antigenic nature of these β-barrel-forming OMPs and, more specifically, their surface exposed regions, the extracellular loops (ECLs). In this study, using Pyrococcus furiosus thioredoxin (PfTrx) as a scaffold to display Tp OMP ECLs, we interrogated immune rabbit sera and peripheral blood mononuclear cells for the presence of antibodies (Abs) and circulating rare antigen-specific B cells. Our results pinpoint immunogenic ECLs of two newly discovered OMPs, while advancing the utility of the rabbit model for surveying the entire Tp OMPeome for promising OMP vaccinogens. This work represents a major advancement toward characterizing potentially protective OMP ECLs and future vaccine studies. Additionally, this strategy could be applied to OMPs of nonspirochetal bacterial pathogens.
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Affiliation(s)
| | - Jairo M. Montezuma-Rusca
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
| | - Isabel C. Orbe
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
| | - Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Carson J. La Vake
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Christopher M. Hennelly
- Division of Infectious Diseases, Department of Medicine, and Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Fredrick N. Nindo
- Division of Infectious Diseases, Department of Medicine, and Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jacob W. Meyer
- Duke Human Vaccine Institute, Durham, North Carolina, USA
| | | | - Jonathan B. Parr
- Division of Infectious Diseases, Department of Medicine, and Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Juan C. Salazar
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Durham, North Carolina, USA
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
| | - Kelly L. Hawley
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, Connecticut, USA
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3
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Styles TM, Gangadhara S, Reddy PBJ, Sahoo A, Shiferaw A, Welbourn S, Kozlowski PA, Derdeyn CA, Velu V, Amara RR. V2 hotspot optimized MVA vaccine expressing stabilized HIV-1 Clade C envelope Gp140 delays acquisition of heterologous Clade C Tier 2 challenges in Mamu-A*01 negative Rhesus Macaques. Front Immunol 2022; 13:914969. [PMID: 35935987 PMCID: PMC9353326 DOI: 10.3389/fimmu.2022.914969] [Citation(s) in RCA: 4] [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: 04/07/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Stabilized HIV envelope (Env) trimeric protein immunogens have been shown to induce strong autologous neutralizing antibody response. However, there is limited data on the immunogenicity and efficacy of stabilized Env expressed by a viral vector-based immunogen. Here, we compared the immunogenicity and efficacy of two modified vaccinia Ankara (MVA) vaccines based on variable loop 2 hotspot (V2 HS) optimized C.1086 envelope (Env) sequences, one expressing the membrane anchored gp150 (MVA-150) and the other expressing soluble uncleaved pre-fusion optimized (UFO) gp140 trimer (MVA-UFO) in a DNA prime/MVA boost approach against heterologous tier 2 SHIV1157ipd3N4 intrarectal challenges in rhesus macaques (RMs). Both MVA vaccines also expressed SIVmac239 Gag and form virus-like particles. The DNA vaccine expressed SIVmac239 Gag, C.1086 gp160 Env and rhesus CD40L as a built-in adjuvant. Additionally, all immunizations were administered intradermally (ID) to reduce induction of vaccine-specific IFNγ+ CD4 T cell responses. Our results showed that both MVA-150 and MVA-UFO vaccines induce comparable Env specific IgG responses in serum and rectal secretions. The vaccine-induced serum antibody showed ADCC and ADCVI activities against the challenge virus. Comparison with a previous study that used similar immunogens via intramuscular route (IM) showed that ID immunizations induced markedly lower SHIV specific CD4 and CD8 T cell responses compared to IM immunizations. Following challenge, MVA-UFO vaccinated animals showed a significant delay in acquisition of SHIV1157ipd3N4 infection but only in Mamu-A*01 negative macaques with an estimated vaccine efficacy of 64% per exposure. The MVA-150 group also showed a trend (p=0.1) for delay in acquisition of SHIV infection with an estimated vaccine efficacy of 57%. The vaccine-induced IFNγ secreting CD8 T cell responses showed a direct association and CD4 T cells showed an inverse association with delay in acquisition of SHIV infection. These results demonstrated that both MVA-150 and MVA-UFO immunogens induce comparable humoral and cellular immunity and the latter provides marginally better protection against heterologous tier 2 SHIV infection. They also demonstrate that DNA/MVA vaccinations delivered by ID route induce better antibody and lower CD4 and CD8 T cell responses compared to IM.
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Affiliation(s)
- Tiffany M. Styles
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Sailaja Gangadhara
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Pradeep B. J. Reddy
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Anusmita Sahoo
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Ayalensh Shiferaw
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Sarah Welbourn
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Pamela A. Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Cynthia A. Derdeyn
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA, United States
| | - Vijayakumar Velu
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA, United States
| | - Rama Rao Amara
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, United States
- *Correspondence: Rama Rao Amara,
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4
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Sahoo A, Hodge EA, LaBranche CC, Styles TM, Shen X, Cheedarla N, Shiferaw A, Ozorowski G, Lee WH, Ward AB, Tomaras GD, Montefiori DC, Irvine DJ, Lee KK, Amara RR. Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies. Cell Rep 2022; 38:110436. [PMID: 35235790 PMCID: PMC8982139 DOI: 10.1016/j.celrep.2022.110436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/13/2021] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
HIV-1 clade C envelope immunogens that elicit both neutralizing and non-neutralizing V1V2-scaffold-specific antibodies (protective correlates from RV144 human trial) are urgently needed due to the prevalence of this clade in the most impacted regions worldwide. To achieve this, we introduce structure-guided changes followed by consensus-C-sequence-guided optimizations at the V2 region to generate UFO-v2-RQH173 trimer. This improves the abundance of well-formed trimers. Following the immunization of rabbits, the wild-type protein fails to elicit any autologous neutralizing antibodies, but UFO-v2-RQH173 elicits both autologous neutralizing and broad V1V2-scaffold antibodies. The variant with a 173Y modification in the V2 region, most prevalent among HIV-1 sequences, shows decreased ability in displaying a native-like V1V2 epitope with time in vitro and elicited antibodies with lower neutralizing and higher V1V2-scaffold activities. Our results identify a stabilized clade C trimer capable of eliciting improved neutralizing and V1V2-scaffold antibodies and reveal the importance of the V2 region in tuning this.
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Affiliation(s)
- Anusmita Sahoo
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Edgar A Hodge
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA 92121, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA 92121, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA 92121, USA
| | - Georgia D Tomaras
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical School, Duke University, Durham, NC 27710, USA
| | - Darrell J Irvine
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
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5
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Weiss S, Itri V, Pan R, Jiang X, Luo CC, Morris L, Malherbe DC, Barnette P, Alexander J, Kong XP, Haigwood NL, Hessell AJ, Duerr R, Zolla-Pazner S. Differential V2-directed antibody responses in non-human primates infected with SHIVs or immunized with diverse HIV vaccines. Nat Commun 2022; 13:903. [PMID: 35173151 PMCID: PMC8850611 DOI: 10.1038/s41467-022-28450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
V2p and V2i antibodies (Abs) that are specific for epitopes in the V1V2 region of the HIV gp120 envelope (Env) do not effectively neutralize HIV but mediate Fc-dependent anti-viral activities that have been correlated with protection from, or control of HIV, SIV and SHIV infections. Here, we describe a novel molecular toolbox that allows the discrimination of antigenically and functionally distinct polyclonal V2 Ab responses. We identify different patterns of V2 Ab induction by SHIV infection and three separate vaccine regimens that aid in fine-tuning an optimized immunization protocol for inducing V2p and V2i Abs. We observe no, or weak and sporadic V2p and V2i Abs in non-vaccinated SHIV-infected NHPs, but strong V2p and/or V2i Ab responses after immunization with a V2-targeting vaccine protocol. The V2-focused vaccination is superior to both natural infection and to immunization with whole Env constructs for inducing functional V2p- and V2i-specific responses. Strikingly, levels of V2-directed Abs correlate inversely with Abs specific for peptides of V3 and C5. These data demonstrate that a V1V2-targeting vaccine has advantages over the imprecise targeting of SIV/SHIV infections and of whole Env-based immunization regimens for inducing a more focused functional V2p- and V2i-specific Ab response. Here the authors show that an HIV vaccine in non-human primates that focuses antibodies on the V1V2 region of gp120 is superior to infection or immunization with whole envelope vaccines for inducing V1V2 antibodies with anti-viral functions that correlate with protection.
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Affiliation(s)
- Svenja Weiss
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vincenza Itri
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Xunqing Jiang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Christina C Luo
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Johannesburg, South Africa.,MRC Antibody Research Unit, University of the Witwatersrand, Johannesburg and Center for the AIDS Program of Research in South Africa, Johannesburg, South Africa
| | - Delphine C Malherbe
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA.,University of Texas Medical Branch, Department of Pathology, Galveston National Laboratory, Galveston, TX, USA
| | - Philip Barnette
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Jeff Alexander
- PaxVax Corporation, Redwood City, CA, USA.,JL Alexander Research and Development Consulting LLC, San Diego, CA, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Nancy L Haigwood
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ann J Hessell
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Microbiology, Icahn School of Medicine, New York, NY, USA.
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6
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Griffith SA, McCoy LE. To bnAb or Not to bnAb: Defining Broadly Neutralising Antibodies Against HIV-1. Front Immunol 2021; 12:708227. [PMID: 34737737 PMCID: PMC8560739 DOI: 10.3389/fimmu.2021.708227] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Since their discovery, antibodies capable of broad neutralisation have been at the forefront of HIV-1 research and are of particular interest due to in vivo passive transfer studies demonstrating their potential to provide protection. Currently an exact definition of what is required for a monoclonal antibody to be classed as a broadly neutralising antibody (bnAb) has not yet been established. This has led to hundreds of antibodies with varying neutralisation breadth being studied and has given insight into antibody maturation pathways and epitopes targeted. However, even with this knowledge, immunisation studies and vaccination trials to date have had limited success in eliciting antibodies with neutralisation breadth. For this reason there is a growing need to identify factors specifically associated with bnAb development, yet to do this a set of criteria is necessary to distinguish bnAbs from non-bnAbs. This review aims to define what it means to be a HIV-1 bnAb by comparing neutralisation breadth, genetic features and epitopes of bnAbs, and in the process highlights the challenges of comparing the array of antibodies that have been isolated over the years.
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Affiliation(s)
- Sarah A Griffith
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Laura E McCoy
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
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7
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Sherburn R, Tolbert WD, Gottumukkala S, Hederman AP, Beaudoin-Bussières G, Stanfield-Oakley S, Tuyishime M, Ferrari G, Finzi A, Ackerman ME, Pazgier M. Incorporating the Cluster A and V1V2 Targets into a Minimal Structural Unit of the HIV-1 Envelope to Elicit a Cross-Clade Response with Potent Fc-Effector Functions. Vaccines (Basel) 2021; 9:vaccines9090975. [PMID: 34579212 PMCID: PMC8472903 DOI: 10.3390/vaccines9090975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 12/01/2022] Open
Abstract
The generation of a potent vaccine for the prevention and/or control of HIV-1 has been unsuccessful to date, despite decades of research. Existing evidence from both infected individuals and clinical trials support a role for non-neutralizing or weakly neutralizing antibodies with potent Fc-effector functions in the prevention and control of HIV-1 infection. Vaccination strategies that induce such antibodies have proven partially successful in preventing HIV-1 infection. This is largely thought to be due to the polyclonal response that is induced in a vaccine setting, as opposed to the infusion of a single therapeutic antibody, which is capable of diverse Fc-effector functions and targets multiple but highly conserved epitopes. Here, we build on the success of our inner domain antigen, ID2, which incorporates conformational CD4-inducible (CD4i) epitopes of constant region 1 and 2 (C1C2 or Cluster A), in the absence of neutralizing antibody epitopes, into a minimal structural unit of gp120. ID2 has been shown to induce Cluster A-specific antibodies in a BALB/c mouse model with Fc-effector functions against CD4i targets. In order to generate an immunogen that incorporates both epitope targets implicated in the protective Fc-effector functions of antibodies from the only partially successful human vaccine trial, RV144, we incorporated the V1V2 domain into our ID2 antigen generating ID2-V1V2, which we used to immunize in combination with ID2. Immunized BALB/c mice generated both Cluster A- and V1V2-specific antibodies, which synergized to significantly improve the Fc-mediated effector functions compared to mice immunized with ID2 alone. The sera were able to mediate both antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). We therefore conclude that ID2-V1V2 + ID2 represents a promising vaccine immunogen candidate for the induction of antibodies with optimal Fc-mediated effector functions against HIV-1.
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Affiliation(s)
- Rebekah Sherburn
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, MD 20814, USA; (R.S.); (W.D.T.); (S.G.)
| | - William D. Tolbert
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, MD 20814, USA; (R.S.); (W.D.T.); (S.G.)
| | - Suneetha Gottumukkala
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, MD 20814, USA; (R.S.); (W.D.T.); (S.G.)
| | - Andrew P. Hederman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; (A.P.H.); (M.E.A.)
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X0A9, Canada; (G.B.-B.); (A.F.)
| | - Sherry Stanfield-Oakley
- Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA; (S.S.-O.); (M.T.); (G.F.)
| | - Marina Tuyishime
- Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA; (S.S.-O.); (M.T.); (G.F.)
| | - Guido Ferrari
- Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA; (S.S.-O.); (M.T.); (G.F.)
| | - Andrés Finzi
- Centre de Recherche du CHUM, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X0A9, Canada; (G.B.-B.); (A.F.)
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; (A.P.H.); (M.E.A.)
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, MD 20814, USA; (R.S.); (W.D.T.); (S.G.)
- Correspondence:
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8
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Abstract
PURPOSE OF REVIEW Recent work defining Fc-mediated effector functions for both viral control and protection against infection is summarized and considered along with new strategies to drive robust Fc-mediated responses. RECENT FINDINGS In new human and nonhuman primate (NHP) vaccine trials as well as studies of natural infection, Fc-mediated effector responses have sometimes been observed to correlate with decreased risk of infection or with better clinical outcomes, suggesting a potential role for these responses in HIV-1 prevention and therapy. Recent highlights include use of antibody-dependent cellular cytotoxicity-sensitizing CD4-induced mimetic compounds, novel V1V2 immunogens, passive transfer studies, and vaccine regimens that successfully elicited Fc-mediated responses and were reported to decrease risk of infection in challenge studies in NHPs. Lastly, detailed studies of IgG3 forms of HIV-specific antibodies have reported that both neutralizing and Fc-mediated responses can be increased relative to the more prevalent IgG1 subclass. SUMMARY Successful harmonization of neutralizing and Fc-mediated responses may make key contributions to the goal of reducing HIV-1 infection via active and passive vaccination. New studies continue to highlight the importance of Fc-mediated antibody responses as correlates of decreased risk of infection and suggest enhanced phagocytosis is a potential mechanism of reduced risk of infection associated with human IgG3 responses. Results from recent studies may help guide the rational design of therapies and vaccines that aim to specifically leverage antibody effector function.
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9
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Immune Complex Vaccine Strategies to Combat HIV-1 and Other Infectious Diseases. Vaccines (Basel) 2021; 9:vaccines9020112. [PMID: 33540685 PMCID: PMC7913084 DOI: 10.3390/vaccines9020112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 01/16/2023] Open
Abstract
Immune complexes (ICs) made of antibody-bound antigens exhibit immunomodulatory activities exploitable in a vaccination strategy to optimize vaccine efficacy. The modulatory effects of ICs are typically attributed to the Fc fragments of the antibody components, which engage Fc receptors, complement and complement receptors on various immune cells. These Fc-mediated functions facilitate the critical interplay between innate and adaptive immune systems to impact the quality and quantity of the elicited adaptive responses. In addition to the Fc contribution, the Fab fragment also plays an immunoregulation role. The antigen-binding domains of the Fab fragment can bind their specific epitopes at high affinity to sterically occlude these antigenic sites from recognition by other antibodies. Moreover, the Fab-mediated binding has been demonstrated to induce allosteric alterations at nearby or distant antigenic sites. In this review article, we survey published studies to illuminate how the immunomodulatory functions of ICs have been investigated or utilized in a vaccination strategy to fight against an array of infectious pathogens, culminating with IC vaccine designs aimed at preventing HIV-1 infection. In particular, we highlight IC vaccine candidates that exploit Fab-mediated steric and allosteric effects to direct antibody responses away or toward the V1V2 domain, the V3 loop, and other antigenic sites on the HIV-1 envelope gp120 glycoprotein. Like other HIV-1 vaccine approaches, the path for IC-based vaccines to reach the clinic faces major hurdles yet to be overcome; however, investigations into this vaccine strategy have provided insights into the multifaceted activities of antibodies beyond their conventional roles in the host defense against HIV-1 and other microbial pathogens.
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10
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Signal peptide of HIV-1 envelope modulates glycosylation impacting exposure of V1V2 and other epitopes. PLoS Pathog 2020; 16:e1009185. [PMID: 33370382 PMCID: PMC7793277 DOI: 10.1371/journal.ppat.1009185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/08/2021] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
HIV-1 envelope (Env) is a trimer of gp120-gp41 heterodimers, synthesized from a precursor gp160 that contains an ER-targeting signal peptide (SP) at its amino-terminus. Each trimer is swathed by ~90 N-linked glycans, comprising complex-type and oligomannose-type glycans, which play an important role in determining virus sensitivity to neutralizing antibodies. We previously examined the effects of single point SP mutations on Env properties and functions. Here, we aimed to understand the impact of the SP diversity on glycosylation of virus-derived Env and virus neutralization by swapping SPs. Analyses of site-specific glycans revealed that SP swapping altered Env glycan content and occupancy on multiple N-linked glycosites, including conserved N156 and N160 glycans in the V1V2 region at the Env trimer apex and N88 at the trimer base. Virus neutralization was also affected, especially by antibodies against V1V2, V3, and gp41. Likewise, SP swaps affected the recognition of soluble and cell-associated Env by antibodies targeting distinct V1V2 configurations, V3 crown, and gp41 epitopes. These data highlight the contribution of SP sequence diversity in shaping the Env glycan content and its impact on the configuration and accessibility of V1V2 and other Env epitopes. HIV-1 Env glycoprotein is produced by a precursor gp160 that has a signal peptide at its N-terminus. The SP is highly diverse among the HIV-1 isolates. This study presents site-specific analyses of N-linked glycosylation on HIV-1 envelope glycoproteins from infectious viruses produced with different envelope signal peptides. We show that signal peptide swapping alters the envelope glycan shield, including the conserved N156 and N160 glycans located in the V1V2 region on the trimer apex, to impact Env recognition and virus neutralization by antibodies. The data offer crucial insights into the role of signal peptide in the interplay between HIV-1 and antibodies and its potential utility to control Env glycosylation in the development of Env-based HIV-1 vaccine.
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11
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The V2 loop of HIV gp120 delivers costimulatory signals to CD4 + T cells through Integrin α 4β 7 and promotes cellular activation and infection. Proc Natl Acad Sci U S A 2020; 117:32566-32573. [PMID: 33288704 DOI: 10.1073/pnas.2011501117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Acute HIV infection is characterized by rapid viral seeding of immunologic inductive sites in the gut followed by the severe depletion of gut CD4+ T cells. Trafficking of α4β7-expressing lymphocytes to the gut is mediated by MAdCAM, the natural ligand of α4β7 that is expressed on gut endothelial cells. MAdCAM signaling through α4β7 costimulates CD4+ T cells and promotes HIV replication. Similar to MAdCAM, the V2 domain of the gp120 HIV envelope protein binds to α4β7 In this study, we report that gp120 V2 shares with MAdCAM the capacity to signal through α4β7 resulting in CD4+ T cell activation and proliferation. As with MAdCAM-mediated costimulation, cellular activation induced by gp120 V2 is inhibited by anti-α4β7 monoclonal antibodies (mAbs). It is also inhibited by anti-V2 domain antibodies including nonneutralizing mAbs that recognize an epitope in V2 that has been linked to reduced risk of acquisition in the RV144 vaccine trial. The capacity of the V2 domain of gp120 to mediate signaling through α4β7 likely impacts early events in HIV infection. The capacity of nonneutralizing V2 antibodies to block this activity reveals a previously unrecognized mechanism whereby such antibodies might impact HIV transmission and pathogenesis.
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12
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Hessell AJ, Powell R, Jiang X, Luo C, Weiss S, Dussupt V, Itri V, Fox A, Shapiro MB, Pandey S, Cheever T, Fuller DH, Park B, Krebs SJ, Totrov M, Haigwood NL, Kong XP, Zolla-Pazner S. Multimeric Epitope-Scaffold HIV Vaccines Target V1V2 and Differentially Tune Polyfunctional Antibody Responses. Cell Rep 2020; 28:877-895.e6. [PMID: 31340151 DOI: 10.1016/j.celrep.2019.06.074] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/12/2019] [Accepted: 06/21/2019] [Indexed: 11/24/2022] Open
Abstract
The V1V2 region of the HIV-1 envelope is the target of several broadly neutralizing antibodies (bNAbs). Antibodies to V1V2 elicited in the RV144 clinical trial correlated with a reduced risk of HIV infection, but these antibodies were without broad neutralizing activity. Antibodies targeting V1V2 also correlated with a reduced viral load in immunized macaques challenged with simian immunodeficiency virus (SIV) or simian/human immunodeficiency virus (SHIV). To focus immune responses on V1V2, we engrafted the native, glycosylated V1V2 domain onto five different multimeric scaffold proteins and conducted comparative immunogenicity studies in macaques. Vaccinated macaques developed high titers of plasma and mucosal antibodies that targeted structurally distinct V1V2 epitopes. Plasma antibodies displayed limited neutralizing activity but were functionally active for ADCC and phagocytosis, which was detectable 1-2 years after immunizations ended. This study demonstrates that multivalent, glycosylated V1V2-scaffold protein immunogens focus the antibody response on V1V2 and are differentially effective at inducing polyfunctional antibodies with characteristics associated with protection.
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Affiliation(s)
- Ann J Hessell
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
| | - Rebecca Powell
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xunqing Jiang
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Christina Luo
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Svenja Weiss
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Vincenza Itri
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alisa Fox
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mariya B Shapiro
- Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, OR 97239
| | - Shilpi Pandey
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Tracy Cheever
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Deborah H Fuller
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Washington National Primate Research Center, Seattle, WA 98195, USA
| | - Byung Park
- Primate Genetics Program, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | | | - Nancy L Haigwood
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, OR 97239.
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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13
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Abstract
PURPOSE OF REVIEW Although the goal of preventive HIV vaccine design is primarily the induction of broadly neutralizing antibodies (bNAbs), recent evidence suggests that a protective response will also benefit from Fc effector functions. Here, we provide an update on the antibody response to HIV infection, including both Fab and Fc-mediated antibody responses. We also highlight recent studies showing the interplay between these functions, focusing primarily on studies published in the last year. RECENT FINDINGS Identification and characterization of bNAb donors continues to provide insights into viral factors that are potentially translatable to vaccine design. Improved and more diverse measures of Fc effector function, and modulators thereof, are enabling a deeper understanding of their role in infection. New data providing mechanistic links between the innate and adaptive humoral immune responses are creating exciting opportunities for vaccine strategies, with the aim of eliciting a polyfunctional protective response. SUMMARY New insights into the overall humoral response to HIV infection are defining diverse and synergistic mechanisms required for antibody protection from HIV through vaccination.
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14
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Lai JI, Eszterhas SK, Brooks SA, Guo C, Zolla-Pazner S, Seaman MS, Bailey-Kellogg C, Griswold KE, Ackerman ME. Induction of cross-reactive HIV-1 specific antibody responses by engineered V1V2 immunogens with reduced conformational plasticity. Vaccine 2020; 38:3436-3446. [PMID: 32192810 PMCID: PMC7132531 DOI: 10.1016/j.vaccine.2020.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 01/13/2023]
Abstract
Antibodies against the HIV-1 V1V2 loops were the only correlate of reduced infection risk in the RV144 vaccine trial, highlighting the V1V2 loops as promising targets for vaccine design. The V1V2 loops are structurally plastic, exhibiting either an α-helix-coil or β-strand conformation. V1V2-specific antibodies may thus recognize distinct conformations, and an antibody's conformational specificity can be an important determinant of breadth and function. Restricting V1V2 conformational plasticity in an immunogen may thus provide control over the conformational specificity and quality of a vaccine-elicited antibody response. Previously, we identified a V1V2 sequence variant (K155M) that results in enhanced recognition by cross-reactive antibodies recognizing the β-strand conformation. Here, we relate V1V2 antigenicity to immunogenicity by comparing the immunogenicity profiles of wildtype and K155M immunogens in two mouse models. In one model, immunization with gp70 V1V2 K155M but not wildtype elicited antibody responses that were cross-reactive to a panel of heterologous gp120 and gp140 antigens. In a second model, we compared the effect of K155M on immunogenicity in the context of gp70 V1V2, gD V1V2 and gp120, examining the effects of scaffold, epitope-focusing and immunization regimen. K155M variants, especially in the context of a gp120 immunogen, resulted in more robust, durable and cross-reactive antibody responses than wildtype immunogens. Restriction of the β-stranded V1V2 conformation in K155M immunogens may thus be associated with the induction of cross-reactive antibody responses thought to be required of a protective HIV-1 vaccine.
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Affiliation(s)
- Jennifer I Lai
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | | | - Seth A Brooks
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Chengzi Guo
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Karl E Griswold
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA; Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
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15
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Mabvakure BM, Rott R, Dobrowsky L, Van Heusden P, Morris L, Scheepers C, Moore PL. Advancing HIV Vaccine Research With Low-Cost High-Performance Computing Infrastructure: An Alternative Approach for Resource-Limited Settings. Bioinform Biol Insights 2019; 13:1177932219882347. [PMID: 35173421 PMCID: PMC8842485 DOI: 10.1177/1177932219882347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/21/2019] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized biological research by generating genomic data that were once unaffordable by traditional first-generation sequencing technologies. These sequencing methodologies provide an opportunity for in-depth analyses of host and pathogen genomes as they are able to sequence millions of templates at a time. However, these large datasets can only be efficiently explored using bioinformatics analyses requiring huge data storage and computational resources adapted for high-performance processing. High-performance computing allows for efficient handling of large data and tasks that may require multi-threading and prolonged computational times, which is not feasible with ordinary computers. However, high-performance computing resources are costly and therefore not always readily available in low-income settings. We describe the establishment of an affordable high-performance computing bioinformatics cluster consisting of 3 nodes, constructed using ordinary desktop computers and open-source software including Linux Fedora, SLURM Workload Manager, and the Conda package manager. For the analysis of large antibody sequence datasets and for complex viral phylodynamic analyses, the cluster out-performed desktop computers. This has demonstrated that it is possible to construct high-performance computing capacity capable of analyzing large NGS data from relatively low-cost hardware and entirely free (open-source) software, even in resource-limited settings. Such a cluster design has broad utility beyond bioinformatics to other studies that require high-performance computing.
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Affiliation(s)
- Batsirai M Mabvakure
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Peter Van Heusden
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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16
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Duerr R, Gorny MK. V2-Specific Antibodies in HIV-1 Vaccine Research and Natural Infection: Controllers or Surrogate Markers. Vaccines (Basel) 2019; 7:vaccines7030082. [PMID: 31390725 PMCID: PMC6789775 DOI: 10.3390/vaccines7030082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/20/2022] Open
Abstract
Most human immunodeficiency virus (HIV) vaccine trials have lacked efficacy and empirical vaccine lead targets are scarce. Thus far, the only independent correlate of reduced risk of HIV-1 acquisition in humans is elevated levels of V2-specific antibodies identified in the modestly protective RV144 vaccine trial. Ten years after RV144, human and non-human primate vaccine studies have reassessed the potential contribution of V2-specific antibodies to vaccine efficacy. In addition, studies of natural HIV-1 infection in humans have provided insight into the development of V1V2-directed antibody responses and their impact on clinical parameters and disease progression. Functionally diverse anti-V2 monoclonal antibodies were isolated and their structurally distinct V2 epitope regions characterized. After RV144, a plethora of research studies were performed using different model systems, immunogens, protocols, and challenge viruses. These diverse studies failed to provide a clear picture regarding the contribution of V2 antibodies to vaccine efficacy. Here, we summarize the biological functions and clinical findings associated with V2-specific antibodies and discuss their impact on HIV vaccine research.
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Affiliation(s)
- Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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17
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Fabrizio C, Bavaro DF, Scudeller L, Lepore L, Balena F, Lagioia A, Angarano G, Monno L, Saracino A. Variability OF HIV-1 V2 env domain for integrin binding: Clinical correlates. Virology 2019; 535:266-271. [PMID: 31357165 DOI: 10.1016/j.virol.2019.07.019] [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] [Received: 05/20/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 11/27/2022]
Abstract
The HIV V2179-181 (HXB2 numbering) tripeptide mediates binding to α4β7 integrin, which is responsible for GALT homing. Our study aimed to assess V2 variability in naive HIV-1 infected patients and its association with clinical and viro-immunological features. Gp120 sequences were obtained from 322 subjects; length, potential N-linked glycosylation sites (PNGs), net-charge (NC) and 179-181tripeptide α4β7-binding-motif of V2 were evaluated. At multivariate analysis, lower V2 length and higher NC correlated with low CD4 cells; no association was found with PNGs. A greater variability pertained positions 162-163, 164-167, 169, 175-179, 187, 194 and 195 in B sequences, and 163 and 177 in X4 tropic viruses. LDV was the most common tripeptide. Asp180 was highly conserved; Leu179 was more frequently observed in non-B and in recent infections compared to others, while Val181 was found in recent infections and in MSM. Further studies to deeply explore the clinical significance of these associations are warranted.
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Affiliation(s)
- Claudia Fabrizio
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy; Malattie Infettive e Tropicali Ospedale Oncologico San Giuseppe Moscati, Taranto, Italy
| | - Davide F Bavaro
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Luigia Scudeller
- Scientific Direction, Clinical Epidemiology Unit, IRCCS San Matteo Foundation, Viale Camillo Golgi, 19, 27100, Pavia, Italy
| | - Luciana Lepore
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Flavia Balena
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Antonella Lagioia
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Gioacchino Angarano
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy
| | - Annalisa Saracino
- Clinic of Infectious Diseases, University of Bari, University Hospital Policlinico, Piazza Giulio Cesare n. 11, 70124, Bari, Italy.
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18
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Zolla-Pazner S, Alvarez R, Kong XP, Weiss S. Vaccine-induced V1V2-specific antibodies control and or protect against infection with HIV, SIV and SHIV. Curr Opin HIV AIDS 2019; 14:309-317. [PMID: 30994501 PMCID: PMC6542703 DOI: 10.1097/coh.0000000000000551] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW In humans, only one independent immunologic correlate of reduced risk of HIV infection has been identified: a robust antibody (Ab) response to the V1V2 domain of the gp120 envelope (Env) protein. In recent years, the presence and level of V1V2-specific Abs has also been correlated with protection from SIV and SHIV infections. Here, we review the multitude of studies showing the in-vivo protective effects of V1V2 Abs and review their immunologic characteristics and antiviral functions. RECENT FINDINGS Structural and immunologic studies have defined four epitope families in the V1V2 domain: one epitope family, V2q, which preferentially presents as a quaternary structure of the Env trimer, and another epitope family (V2qt) which requires the quaternary trimeric Env structure; these two epitope types are recognized by two families of monoclonal Abs (mAbs)-V2q-specific and V2qt-specific mAbs-which display broad and potent neutralizing activity. A third epitope family, V2i, is present as a discontinuous conformational structure that overlays the α4β7 integrin binding motif, and a fourth epitope family (V2p) exists on V2 peptides. Antibodies specific for V2i and V2p epitopes display only poor neutralizing activity but effectively mediate other antiviral activities and have been correlated with control of and/or protection from HIV, SIV and SHIV. Notably, V2q and V2qt Abs have not been induced by any vaccines, but V2p and V2i Abs have been readily induced with various vaccines in nonhuman primates and humans. SUMMARY The correlation of vaccine-induced V2p and V2i Abs with protection from HIV, SIV and SHIV suggests that these Ab types are extremely important to induce with prophylactic vaccines.
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Affiliation(s)
- Susan Zolla-Pazner
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai
| | - Raymond Alvarez
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Svenja Weiss
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai
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19
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van den Berg FT, Makoah NA, Ali SA, Scott TA, Mapengo RE, Mutsvunguma LZ, Mkhize NN, Lambson BE, Kgagudi PD, Crowther C, Abdool Karim SS, Balazs AB, Weinberg MS, Ely A, Arbuthnot PB, Morris L. AAV-Mediated Expression of Broadly Neutralizing and Vaccine-like Antibodies Targeting the HIV-1 Envelope V2 Region. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 14:100-112. [PMID: 31334303 PMCID: PMC6616373 DOI: 10.1016/j.omtm.2019.06.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
Abstract
HIV-1 infection continues to be a global health challenge and a vaccine is urgently needed. Broadly neutralizing antibodies (bNAbs) are considered essential as they inhibit multiple HIV-1 strains, but they are difficult to elicit by conventional immunization. In contrast, non-neutralizing antibodies that correlated with reduced risk of infection in the RV144 HIV vaccine trial are relatively easy to induce, but responses are not durable. To overcome these obstacles, adeno-associated virus (AAV) vectors were used to provide long-term expression of antibodies targeting the V2 region of the HIV-1 envelope protein, including the potent CAP256-VRC26.25 bNAb, as well as non-neutralizing CAP228 antibodies that resemble those elicited by vaccination. AAVs mediated effective antibody expression in cell culture and immunocompetent mice. Mean concentrations of human immunoglobulin G (IgG) in mouse sera increased rapidly following a single AAV injection, reaching 8–60 μg/mL for CAP256 antibodies and 44–220 μg/mL for CAP228 antibodies over 24 weeks, but antibody concentrations varied for individual mice. Secreted antibodies collected from serum retained the expected binding and neutralizing activity. The vectors generated here are, therefore, suitable for the delivery of V2-targeting HIV antibodies, and they could be used in a vectored immunoprophylaxis (VIP) approach to sustain the level of antibody expression required to prevent HIV infection.
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Affiliation(s)
- Fiona T van den Berg
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel A Makoah
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stuart A Ali
- HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tristan A Scott
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rutendo E Mapengo
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Lorraine Z Mutsvunguma
- HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonhlanhla N Mkhize
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Bronwen E Lambson
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Prudence D Kgagudi
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Carol Crowther
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,Department of Epidemiology, Columbia University, New York, NY, USA
| | | | - Marc S Weinberg
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Abdullah Ely
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick B Arbuthnot
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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