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Lee M, Changela A, Gorman J, Rawi R, Bylund T, Chao CW, Lin BC, Louder MK, Olia AS, Zhang B, Doria-Rose NA, Zolla-Pazner S, Shapiro L, Chuang GY, Kwong PD. Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces. Nat Commun 2021; 12:6470. [PMID: 34753907 PMCID: PMC8578620 DOI: 10.1038/s41467-021-26579-z] [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: 02/25/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
Antibody-Framework-to-Antigen Distance (AFAD) - the distance between the body of an antibody and a protein antigen - is an important parameter governing antibody recognition. Here, we quantify AFAD for ~2,000 non-redundant antibody-protein-antigen complexes in the Protein Data Bank. AFADs showed a gaussian distribution with mean of 16.3 Å and standard deviation (σ) of 2.4 Å. Notably, antibody-antigen complexes with extended AFADs (>3σ) were exclusively human immunodeficiency virus-type 1 (HIV-1)-neutralizing antibodies. High correlation (R2 = 0.8110) was observed between AFADs and glycan coverage, as assessed by molecular dynamics simulations of the HIV-1-envelope trimer. Especially long AFADs were observed for antibodies targeting the glycosylated trimer apex, and we tested the impact of introducing an apex-glycan hole (N160K); the cryo-EM structure of the glycan hole-targeting HIV-1-neutralizing antibody 2909 in complex with an N160K-envelope trimer revealed a substantially shorter AFAD. Overall, extended AFADs exclusively recognized densely glycosylated surfaces, with the introduction of a glycan hole enabling closer recognition.
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Affiliation(s)
- Myungjin Lee
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anita Changela
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jason Gorman
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Reda Rawi
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tatsiana Bylund
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cara W Chao
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bob C Lin
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mark K Louder
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adam S Olia
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Susan Zolla-Pazner
- Department of Medicine and Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lawrence Shapiro
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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2
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Roark RS, Li H, Williams WB, Chug H, Mason RD, Gorman J, Wang S, Lee FH, Rando J, Bonsignori M, Hwang KK, Saunders KO, Wiehe K, Moody MA, Hraber PT, Wagh K, Giorgi EE, Russell RM, Bibollet-Ruche F, Liu W, Connell J, Smith AG, DeVoto J, Murphy AI, Smith J, Ding W, Zhao C, Chohan N, Okumura M, Rosario C, Ding Y, Lindemuth E, Bauer AM, Bar KJ, Ambrozak D, Chao CW, Chuang GY, Geng H, Lin BC, Louder MK, Nguyen R, Zhang B, Lewis MG, Raymond DD, Doria-Rose NA, Schramm CA, Douek DC, Roederer M, Kepler TB, Kelsoe G, Mascola JR, Kwong PD, Korber BT, Harrison SC, Haynes BF, Hahn BH, Shaw GM. Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth. Science 2021; 371:eabd2638. [PMID: 33214287 PMCID: PMC8040783 DOI: 10.1126/science.abd2638] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.
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Affiliation(s)
- Ryan S Roark
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hema Chug
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fang-Hua Lee
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juliette Rando
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Departments of Immunology and Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Departments of Pediatrics and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Peter T Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jesse Connell
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew G Smith
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julia DeVoto
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander I Murphy
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica Smith
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenge Ding
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chengyan Zhao
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neha Chohan
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maho Okumura
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina Rosario
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yu Ding
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Lindemuth
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anya M Bauer
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharine J Bar
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Nguyen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Donald D Raymond
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Departments of Immunology and Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bette T Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Stephen C Harrison
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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Featherstone A, Aiken C. SERINC5 Inhibits HIV-1 Infectivity by Altering the Conformation of gp120 on HIV-1 Particles. J Virol 2020; 94:e00594-20. [PMID: 32796070 PMCID: PMC7527050 DOI: 10.1128/jvi.00594-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/03/2020] [Indexed: 01/25/2023] Open
Abstract
SERINC5 is a 10-transmembrane-domain cellular protein that is incorporated into budding HIV-1 particles and reduces HIV-1 infectivity by inhibiting virus-cell fusion. HIV-1 susceptibility to SERINC5 is determined by sequences in the viral Env glycoprotein gp120, and the antiviral effect of SERINC5 is counteracted by the viral accessory protein Nef. While the precise mechanism by which SERINC5 inhibits HIV-1 infectivity is unclear, previous studies have suggested that SERINC5 affects Env conformation. To define the effects of SERINC5 on Env conformation, we quantified the binding of HIV-1 particles to immobilized Env-specific monoclonal antibodies. We observed that SERINC5 reduced the binding of HIV-1 particles bearing a SERINC5-susceptible Env to antibodies that recognize the V3 loop, a soluble CD4 (sCD4)-induced epitope, and an N-linked glycan. In contrast, SERINC5 did not alter the capture of HIV-1 particles bearing the SERINC5-resistant Env protein. Moreover, the effect of SERINC5 on antibody-dependent virus capture was abrogated by Nef expression. Our results indicate that SERINC5 inhibits HIV-1 infectivity by altering the conformation of gp120 on virions and/or physical masking of specific HIV-1 Env epitopes.IMPORTANCE SERINC5 is a host cell protein that inhibits the infectivity of HIV-1 by a novel and poorly understood mechanism. Here, we provide evidence that the SERINC5 protein alters the conformation of the HIV-1 Env proteins and that this action is correlated with SERINC5's ability to inhibit HIV-1 infectivity. Defining the specific effects of SERINC5 on the HIV-1 glycoprotein conformation may be useful for designing new antiviral strategies targeting Env.
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Affiliation(s)
- Austin Featherstone
- Vanderbilt University Medical Center, Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, USA
| | - Christopher Aiken
- Vanderbilt University Medical Center, Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, USA
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4
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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: 21] [Impact Index Per Article: 5.3] [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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5
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Zhang R, Verkoczy L, Wiehe K, Munir Alam S, Nicely NI, Santra S, Bradley T, Pemble CW, Zhang J, Gao F, Montefiori DC, Bouton-Verville H, Kelsoe G, Larimore K, Greenberg PD, Parks R, Foulger A, Peel JN, Luo K, Lu X, Trama AM, Vandergrift N, Tomaras GD, Kepler TB, Moody MA, Liao HX, Haynes BF. Initiation of immune tolerance-controlled HIV gp41 neutralizing B cell lineages. Sci Transl Med 2017; 8:336ra62. [PMID: 27122615 DOI: 10.1126/scitranslmed.aaf0618] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/28/2016] [Indexed: 01/09/2023]
Abstract
Development of an HIV vaccine is a global priority. A major roadblock to a vaccine is an inability to induce protective broadly neutralizing antibodies (bnAbs). HIV gp41 bnAbs have characteristics that predispose them to be controlled by tolerance. We used gp41 2F5 bnAb germline knock-in mice and macaques vaccinated with immunogens reactive with germline precursors to activate neutralizing antibodies. In germline knock-in mice, bnAb precursors were deleted, with remaining anergic B cells capable of being activated by germline-binding immunogens to make gp41-reactive immunoglobulin M (IgM). Immunized macaques made B cell clonal lineages targeted to the 2F5 bnAb epitope, but 2F5-like antibodies were either deleted or did not attain sufficient affinity for gp41-lipid complexes to achieve the neutralization potency of 2F5. Structural analysis of members of a vaccine-induced antibody lineage revealed that heavy chain complementarity-determining region 3 (HCDR3) hydrophobicity was important for neutralization. Thus, gp41 bnAbs are controlled by immune tolerance, requiring vaccination strategies to transiently circumvent tolerance controls.
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Affiliation(s)
- Ruijun Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles W Pemble
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinsong Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Larimore
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA
| | - Phillip D Greenberg
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jessica N Peel
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ashley M Trama
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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6
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Rationally Designed Immunogens Targeting HIV-1 gp120 V1V2 Induce Distinct Conformation-Specific Antibody Responses in Rabbits. J Virol 2016; 90:11007-11019. [PMID: 27707920 DOI: 10.1128/jvi.01409-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/23/2016] [Indexed: 11/20/2022] Open
Abstract
The V1V2 region of HIV-1 gp120 harbors a major vulnerable site targeted by a group of broadly neutralizing monoclonal antibodies (MAbs) such as PG9 through strand-strand recognition. However, this epitope region is structurally polymorphic as it can also form a helical conformation recognized by RV144 vaccine-induced MAb CH58. This structural polymorphism is a potential mechanism for masking the V1V2 vulnerable site. Designing immunogens that can induce conformation-specific antibody (Ab) responses may lead to vaccines targeting this vulnerable site. We designed a panel of immunogens engrafting the V1V2 domain into trimeric and pentameric scaffolds in structurally constrained conformations. We also fused V1V2 to an Fc fragment to mimic the unconstrained V1V2 conformation. We tested these V1V2-scaffold proteins for immunogenicity in rabbits and assessed the responses by enzyme-linked immunosorbent assay (ELISA) and competition assays. Our V1V2 immunogens induced distinct conformation-specific Ab responses. Abs induced by structurally unconstrained immunogens reacted preferentially with unconstrained V1V2 antigens, suggesting recognition of the helical configuration, while Abs induced by the structurally constrained immunogens reacted preferentially with constrained V1V2 antigens, suggesting recognition of the β-strand conformation. The Ab responses induced by the structurally constrained immunogens were more broadly reactive and had higher titers than those induced by the structurally unconstrained immunogens. Our results demonstrate that immunogens presenting the different structural conformations of the gp120 V1V2 vulnerable site can be designed and that these immunogens induce distinct Ab responses with epitope conformation specificity. Therefore, these structurally constrained V1V2 immunogens are vaccine prototypes targeting the V1V2 domain of the HIV-1 envelope. IMPORTANCE The correlates analysis of the RV144 HIV-1 vaccine trial suggested that the presence of antibodies to the V1V2 region of HIV-1 gp120 was responsible for the modest protection observed in the trial. In addition, V1V2 harbors one of the key vulnerable sites of HIV-1 Env recognized by a family of broadly neutralizing MAbs such as PG9. Thus, V1V2 is a key target for vaccine development. However, this vulnerable site is structurally polymorphic, and designing immunogens that present different conformations is crucial for targeting this site. We show here that such immunogens can be designed and that they induced conformation-specific antibody responses in rabbits. Our immunogens are therefore prototypes of vaccine candidates targeting the V1V2 region of HIV-1 Env.
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Abstract
A brief outline of antibody structure is followed by highlights from several recently determined crystal structures of human, antiviral Fabs. These Fabs all have novel structural features that allow them to potently and broadly neutralize their targets.
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Functional implications of the binding mode of a human conformation-dependent V2 monoclonal antibody against HIV. J Virol 2014; 88:4100-12. [PMID: 24478429 DOI: 10.1128/jvi.03153-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
UNLABELLED Data from the RV144 HIV vaccine trial indicated that gp120 V2 antibodies were associated with a lower risk of infection; thus, the mapping of V2 epitopes can contribute to the design of an effective HIV vaccine. We solved the crystal structure of human monoclonal antibody (MAb) 2158, which targets a conformational V2 epitope overlapping the α4β7 integrin binding site, and constructed a full-length model of V1V2. Comparison of computational energy stability to experimental enzyme-linked immunosorbent assay (ELISA) results identified a hydrophobic core that stabilizes the V2 region for optimal 2158 binding, as well as residues that directly mediate side chain interactions with MAb 2158. These data define the binding surface recognized by MAb 2158 and offer a structural explanation for why a mismatched mutation at position 181 (I181X) in the V2 loop was associated with a higher vaccine efficiency in the RV144 clinical vaccine trial. IMPORTANCE Correlate analysis of the RV144 HIV-1 vaccine trial suggested that the presence of antibodies to the second variable region (V2) of HIV-1 gp120 was responsible for the modest protection observed in the trial. V2 is a highly variable and immunogenic region, and structural information on its antigenic landscape will be important for rational design of an effective HIV-1 vaccine. Using X-ray crystallography, computational design tools, and mutagenesis assays, we carried out a detailed and systematic investigation of the epitope recognition of human V2 MAb 2158 and demonstrated that its epitope region overlaps the integrin binding site within V2. In addition, we propose a structure-based mechanism for mismatching of the isoleucine at position 181 and the increased vaccine efficacy seen in the RV144 vaccine trial.
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Rabbit anti-HIV-1 monoclonal antibodies raised by immunization can mimic the antigen-binding modes of antibodies derived from HIV-1-infected humans. J Virol 2013; 87:10221-31. [PMID: 23864637 PMCID: PMC3754018 DOI: 10.1128/jvi.00843-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The rabbit is a commonly used animal model in studying antibody responses in HIV/AIDS vaccine development. However, no rabbit monoclonal antibodies (MAbs) have been developed previously to study the epitope-specific antibody responses against HIV-1 envelope (Env) glycoproteins, and little is known about how the rabbit immune system can mimic the human immune system in eliciting such antibodies. Here we present structural analyses of two rabbit MAbs, R56 and R20, against the third variable region (V3) of HIV-1 gp120. R56 recognizes the well-studied immunogenic region in the V3 crown, while R20 targets a less-studied region at the C terminus of V3. By comparison of the Fab/epitope complex structures of these two antibodies raised by immunization with that of the corresponding human antibodies derived from patients chronically infected with HIV-1, we found that rabbit antibodies can recognize immunogenic regions of gp120 and mimic the binding modes of human antibodies. This result can provide new insight into the use of the rabbit as an animal model in AIDS vaccine development.
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Possible future monoclonal antibody (mAb)-based therapy against arbovirus infections. BIOMED RESEARCH INTERNATIONAL 2013; 2013:838491. [PMID: 24058915 PMCID: PMC3766601 DOI: 10.1155/2013/838491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/05/2013] [Accepted: 07/11/2013] [Indexed: 11/17/2022]
Abstract
More than 150 arboviruses belonging to different families are known to infect humans, causing endemic infections as well as epidemic outbreaks. Effective vaccines to limit the occurrence of some of these infections have been licensed, while for the others several new immunogens are under development mostly for their improvements concerning safety and effectiveness profiles. On the other hand, specific and effective antiviral drugs are not yet available, posing an urgent medical need in particular for emergency cases. Neutralizing monoclonal antibodies (mAbs) have been demonstrated to be effective in the treatment of several infectious diseases as well as in preliminary in vitro and in vivo models of arbovirus-related infections. Given their specific antiviral activity as well-tolerated molecules with limited side effects, mAbs could represent a new therapeutic approach for the development of an effective treatment, as well as useful tools in the study of the host-virus interplay and in the development of more effective immunogens. However, before their use as candidate therapeutics, possible hurdles (e.g., Ab-dependent enhancement of infection, occurrence of viral escape variants) must be carefully evaluated. In this review are described the main arboviruses infecting humans and candidate mAbs to be possibly used in a future passive immunotherapy.
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Murphy MK, Yue L, Pan R, Boliar S, Sethi A, Tian J, Pfafferot K, Karita E, Allen SA, Cormier E, Goepfert PA, Borrow P, Robinson JE, Gnanakaran S, Hunter E, Kong XP, Derdeyn CA. Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth. PLoS Pathog 2013; 9:e1003173. [PMID: 23468623 PMCID: PMC3585129 DOI: 10.1371/journal.ppat.1003173] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 12/19/2012] [Indexed: 01/07/2023] Open
Abstract
Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here we characterized the earliest nAb responses in a subtype A HIV-1 infected Rwandan seroconverter who later developed moderate cross-clade nAb breadth, using (i) envelope (Env) glycoproteins from the transmitted/founder virus and twenty longitudinal nAb escape variants, (ii) longitudinal autologous plasma, and (iii) autologous monoclonal antibodies (mAbs). Initially, nAbs targeted a single region of gp120, which flanked the V3 domain and involved the alpha2 helix. A single amino acid change at one of three positions in this region conferred early escape. One immunoglobulin heavy chain and two light chains recovered from autologous B cells comprised two mAbs, 19.3H-L1 and 19.3H-L3, which neutralized the founder Env along with one or three of the early escape variants carrying these mutations, respectively. Neither mAb neutralized later nAb escape or heterologous Envs. Crystal structures of the antigen-binding fragments (Fabs) revealed flat epitope contact surfaces, where minimal light chain mutation in 19.3H-L3 allowed for additional antigenic interactions. Resistance to mAb neutralization arose in later Envs through alteration of two glycans spatially adjacent to the initial escape signatures. The cross-neutralizing nAbs that ultimately developed failed to target any of the defined V3-proximal changes generated during the first year of infection in this subject. Our data demonstrate that this subject's first recognized nAb epitope elicited strain-specific mAbs, which incrementally acquired autologous breadth, and directed later B cell responses to target distinct portions of Env. This immune re-focusing could have triggered the evolution of cross-clade antibodies and suggests that exposure to a specific sequence of immune escape variants might promote broad humoral responses during HIV-1 infection.
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Affiliation(s)
- Megan K. Murphy
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Saikat Boliar
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Anurag Sethi
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Katja Pfafferot
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Susan A. Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- Departments of Epidemiology and Global Health, Emory University, Atlanta, Georgia, United States of America
| | - Emmanuel Cormier
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - James E. Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Cynthia A. Derdeyn
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Antigenicity and immunogenicity of transmitted/founder, consensus, and chronic envelope glycoproteins of human immunodeficiency virus type 1. J Virol 2013; 87:4185-201. [PMID: 23365441 DOI: 10.1128/jvi.02297-12] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) vaccine development requires selection of appropriate envelope (Env) immunogens. Twenty HIV-1 Env glycoproteins were examined for their ability to bind human anti-HIV-1 monoclonal antibodies (MAbs) and then used as immunogens in guinea pigs to identify promising immunogens. These included five Envs derived from chronically infected individuals, each representing one of five common clades and eight consensus Envs based on these five clades, as well as the consensus of the entire HIV-1 M group, and seven transmitted/founder (T/F) Envs from clades B and C. Sera from immunized guinea pigs were tested for neutralizing activity using 36 HIV-1 Env-pseudotyped viruses. All Envs bound to CD4 binding site, membrane-proximal, and V1/V2 MAbs with similar apparent affinities, although the T/F Envs bound with higher affinity to the MAb 17b, a CCR5 coreceptor binding site antibody. However, the various Envs differed in their ability to induce neutralizing antibodies. Consensus Envs elicited the most potent responses, but neutralized only a subset of viruses, including mostly easy-to-neutralize tier 1 and some more-difficult-to-neutralize tier 2 viruses. T/F Envs elicited fewer potent neutralizing antibodies but exhibited greater breadth than chronic or consensus Envs. Finally, chronic Envs elicited the lowest level and most limited breadth of neutralizing antibodies overall. Thus, each group of Env immunogens elicited a different antibody response profile. The complementary benefits of consensus and T/F Env immunogens raise the possibility that vaccines utilizing a combination of consensus and T/F Envs may be able to induce neutralizing responses with greater breadth and potency than single Env immunogens.
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Zolla-Pazner S, deCamp AC, Cardozo T, Karasavvas N, Gottardo R, Williams C, Morris DE, Tomaras G, Rao M, Billings E, Berman P, Shen X, Andrews C, O'Connell RJ, Ngauy V, Nitayaphan S, de Souza M, Korber B, Koup R, Bailer RT, Mascola JR, Pinter A, Montefiori D, Haynes BF, Robb ML, Rerks-Ngarm S, Michael NL, Gilbert PB, Kim JH. Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial. PLoS One 2013; 8:e53629. [PMID: 23349725 PMCID: PMC3547933 DOI: 10.1371/journal.pone.0053629] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/23/2012] [Indexed: 12/18/2022] Open
Abstract
The RV144 clinical trial of a prime/boost immunizing regimen using recombinant canary pox (ALVAC-HIV) and two gp120 proteins (AIDSVAX B and E) was previously shown to have a 31.2% efficacy rate. Plasma specimens from vaccine and placebo recipients were used in an extensive set of assays to identify correlates of HIV-1 infection risk. Of six primary variables that were studied, only one displayed a significant inverse correlation with risk of infection: the antibody (Ab) response to a fusion protein containing the V1 and V2 regions of gp120 (gp70-V1V2). This finding prompted a thorough examination of the results generated with the complete panel of 13 assays measuring various V2 Abs in the stored plasma used in the initial pilot studies and those used in the subsequent case-control study. The studies revealed that the ALVAC-HIV/AIDSVAX vaccine induced V2-specific Abs that cross-react with multiple HIV-1 subgroups and recognize both conformational and linear epitopes. The conformational epitope was present on gp70-V1V2, while the predominant linear V2 epitope mapped to residues 165–178, immediately N-terminal to the putative α4β7 binding motif in the mid-loop region of V2. Odds ratios (ORs) were calculated to compare the risk of infection with data from 12 V2 assays, and in 11 of these, the ORs were ≤1, reaching statistical significance for two of the variables: Ab responses to gp70-V1V2 and to overlapping V2 linear peptides. It remains to be determined whether anti-V2 Ab responses were directly responsible for the reduced infection rate in RV144 and whether anti-V2 Abs will prove to be important with other candidate HIV vaccines that show efficacy, however, the results support continued dissection of Ab responses to the V2 region which may illuminate mechanisms of protection from HIV-1 infection and may facilitate the development of an effective HIV-1 vaccine.
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Affiliation(s)
- Susan Zolla-Pazner
- Research Service, Veterans Affairs Medical Center, New York, New York, United States of America.
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14
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Karasavvas N, Billings E, Rao M, Williams C, Zolla-Pazner S, Bailer RT, Koup RA, Madnote S, Arworn D, Shen X, Tomaras GD, Currier JR, Jiang M, Magaret C, Andrews C, Gottardo R, Gilbert P, Cardozo TJ, Rerks-Ngarm S, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Paris R, Greene K, Gao H, Gurunathan S, Tartaglia J, Sinangil F, Korber BT, Montefiori DC, Mascola JR, Robb ML, Haynes BF, Ngauy V, Michael NL, Kim JH, de Souza, for the MOPH TAVEG Collab MS. The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120. AIDS Res Hum Retroviruses 2012; 28:1444-57. [PMID: 23035746 DOI: 10.1089/aid.2012.0103] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Thai Phase III clinical trial (RV144) showed modest efficacy in preventing HIV-1 acquisition. Plasma collected from HIV-1-uninfected trial participants completing all injections with ALVAC-HIV (vCP1521) prime and AIDSVAX B/E boost were tested for antibody responses against HIV-1 gp120 envelope (Env). Peptide microarray analysis from six HIV-1 subtypes and group M consensus showed that vaccination induced antibody responses to the second variable (V2) loop of gp120 of multiple subtypes. We further evaluated V2 responses by ELISA and surface plasmon resonance using cyclic (Cyc) and linear V2 loop peptides. Thirty-one of 32 vaccine recipients tested (97%) had antibody responses against Cyc V2 at 2 weeks postimmunization with a reciprocal geometric mean titer (GMT) of 1100 (range: 200-3200). The frequency of detecting plasma V2 antibodies declined to 19% at 28 weeks post-last injection (GMT: 110, range: 100-200). Antibody responses targeted the mid-region of the V2 loop that contains conserved epitopes and has the amino acid sequence KQKVHALFYKLDIVPI (HXB2 Numbering sequence 169-184). Valine at position 172 was critical for antibody binding. The frequency of V3 responses at 2 weeks postimmunization was modest (18/32, 56%) with a GMT of 185 (range: 100-800). In contrast, naturally infected HIV-1 individuals had a lower frequency of antibody responses to V2 (10/20, 50%; p=0.003) and a higher frequency of responses to V3 (19/20, 95%), with GMTs of 400 (range: 100-3200) and 3570 (range: 200-12,800), respectively. RV144 vaccination induced antibodies that targeted a region of the V2 loop that contains conserved epitopes. Early HIV-1 transmission events involve V2 loop interactions, raising the possibility that anti-V2 antibodies in RV144 may have contributed to viral inhibition.
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Affiliation(s)
- Nicos Karasavvas
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Erik Billings
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Mangala Rao
- USMHRP, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Constance Williams
- Department of Pathology and Pharmacology, NYU School of Medicine, New York, New York
| | - Susan Zolla-Pazner
- Department of Pathology and Pharmacology, NYU School of Medicine, New York, New York
- Veterans Affairs Harbor Healthcare System, New York, New York
| | - Robert T. Bailer
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Richard A. Koup
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sirinan Madnote
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Duangnapa Arworn
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - Jeffrey R. Currier
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Mike Jiang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Craig Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Charla Andrews
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Timothy J. Cardozo
- Department of Pathology and Pharmacology, NYU School of Medicine, New York, New York
| | | | - Sorachai Nitayaphan
- Royal Thai Army Component, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok Thailand
| | - Punnee Pitisuttithum
- Vaccine Trial Center and Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jaranit Kaewkungwal
- Center of Excellence for Biomedical and Public Health Informatics (BIOPHICS), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Robert Paris
- USMHRP, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Kelli Greene
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | | | | | - Faruk Sinangil
- Global Solutions for Infectious Diseases, South San Francisco, California
| | - Bette T. Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - John R. Mascola
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Merlin L. Robb
- U.S. Military HIV Research Program (MHRP), Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - Viseth Ngauy
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Nelson L. Michael
- USMHRP, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jerome H. Kim
- USMHRP, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes. PLoS One 2012; 7:e36750. [PMID: 22590602 PMCID: PMC3348910 DOI: 10.1371/journal.pone.0036750] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/07/2012] [Indexed: 12/27/2022] Open
Abstract
A number of antibodies that efficiently neutralize microbial targets contain long heavy chain complementarity determining region 3 (HCDR3) loops. For HIV, several of the most broad and potently neutralizing antibodies have exceptionally long HCDR3s. Two broad potently neutralizing HIV-specific antibodies, PG9 and PG16, exhibit secondary structure. Two other long HCDR3 antibodies, 2F5 and 4E10, protect against mucosal challenge with SHIV. Induction of such long HCDR3 antibodies may be critical to the design of an effective vaccine strategy for HIV and other pathogens, however it is unclear at present how to induce such antibodies. Here, we present genetic evidence that human peripheral blood antibodies containing long HCDR3s are not primarily generated by insertions introduced during the somatic hypermutation process. Instead, they are typically formed by processes occurring as part of the original recombination event. Thus, the response of B cells encoding antibodies with long HCDR3s results from selection of unusual clones from the naïve repertoire rather than through accumulation of insertions. These antibodies typically use a small subset of D and J gene segments that are particularly suited to encoding long HCDR3s, resulting in the incorporation of highly conserved genetic elements in the majority of antibody sequences encoding long HCDR3s.
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16
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Identification of human neutralizing antibodies that bind to complex epitopes on dengue virions. Proc Natl Acad Sci U S A 2012; 109:7439-44. [PMID: 22499787 DOI: 10.1073/pnas.1200566109] [Citation(s) in RCA: 320] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Dengue is a mosquito-borne flavivirus that is spreading at an unprecedented rate and has developed into a major health and economic burden in over 50 countries. Even though infected individuals develop potent and long-lasting serotype-specific neutralizing antibodies (Abs), the epitopes engaged by human neutralizing Abs have not been identified. Here, we demonstrate that the dengue virus (DENV)-specific serum Ab response in humans consists of a large fraction of cross-reactive, poorly neutralizing Abs and a small fraction of serotype-specific, potently inhibitory Abs. Although many mouse-generated, strongly neutralizing monoclonal antibodies (mAbs) recognize epitopes that are present on recombinant DENV envelope (E) proteins, unexpectedly, the majority of neutralizing Abs in human immune sera bound to intact virions but not to the ectodomain of purified soluble E proteins. These conclusions with polyclonal Abs were confirmed with newly generated human mAbs derived from DENV-immune individuals. Two of three strongly neutralizing human mAbs bound to E protein epitopes that were preserved on the virion but not on recombinant E (rE) protein. We propose that humans produce Abs that neutralize DENV infection by binding a complex, quaternary structure epitope that is expressed only when E proteins are assembled on a virus particle. Mapping studies indicate that this epitope has a footprint that spans adjacent E protein dimers and includes residues at the hinge between domains I and II of E protein. These results have significant implications for the DENV Ab and vaccine field.
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Gorny MK, Pan R, Williams C, Wang XH, Volsky B, O'Neal T, Spurrier B, Sampson JM, Li L, Seaman MS, Kong XP, Zolla-Pazner S. Functional and immunochemical cross-reactivity of V2-specific monoclonal antibodies from HIV-1-infected individuals. Virology 2012; 427:198-207. [PMID: 22402248 DOI: 10.1016/j.virol.2012.02.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 01/20/2012] [Accepted: 02/03/2012] [Indexed: 01/19/2023]
Abstract
The recent analysis of the first successful RV144 vaccine trial revealed that a high titer of plasma anti-V2 antibodies (Abs) correlated with a decreased risk of HIV-1 infection in vaccine recipients. To understand the mechanism of immune correlates, we studied seven anti-V2 monoclonal Abs (mAbs) developed from HIV-1 infected individuals. The V2 mAbs target conserved epitopes, including the binding site for α4β7 integrin, and are broadly cross-reactive with various gp120 proteins. Preferential usage of the VH1-69 gene by V2 mAbs may depend on selection by the same antigenic structure. Six of seven V2 mAbs weakly neutralized four to eight of the 41 pseudoviruses tested and resistance to neutralization was correlated with longer V2 domains. The data suggest the presence of shared, conserved structural elements in the V2 loop, and these can be used in the design of vaccine immunogens inducing broadly reactive Abs with anti-viral activities.
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Affiliation(s)
- Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
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McLellan JS, Pancera M, Carrico C, Gorman J, Julien JP, Khayat R, Louder R, Pejchal R, Sastry M, Dai K, O'Dell S, Patel N, Shahzad-ul-Hussan S, Yang Y, Zhang B, Zhou T, Zhu J, Boyington JC, Chuang GY, Diwanji D, Georgiev I, Kwon YD, Lee D, Louder MK, Moquin S, Schmidt SD, Yang ZY, Bonsignori M, Crump JA, Kapiga SH, Sam NE, Haynes BF, Burton DR, Koff WC, Walker LM, Phogat S, Wyatt R, Orwenyo J, Wang LX, Arthos J, Bewley CA, Mascola JR, Nabel GJ, Schief WR, Ward AB, Wilson IA, Kwong PD. Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature 2011; 480:336-43. [PMID: 22113616 PMCID: PMC3406929 DOI: 10.1038/nature10696] [Citation(s) in RCA: 703] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/04/2011] [Indexed: 01/26/2023]
Abstract
Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.
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Affiliation(s)
- Jason S McLellan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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