1
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Welbourn S, Chakraborty S, Yang JE, Gleinich AS, Gangadhara S, Khan S, Ferrebee C, Yagnik B, Burton S, Charles T, Smith SA, Williams D, Mopuri R, Upadhyay AA, Thompson J, Price MA, Wang S, Qin Z, Shen X, Williams LD, Eisel N, Peters T, Zhang L, Kilembe W, Karita E, Tomaras GD, Bosinger SE, Amara RR, Azadi P, Wright ER, Gnanakaran S, Derdeyn CA. A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence. PLoS Pathog 2022; 18:e1010488. [PMID: 35503780 PMCID: PMC9106183 DOI: 10.1371/journal.ppat.1010488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/13/2022] [Accepted: 04/01/2022] [Indexed: 11/21/2022] Open
Abstract
Transmitted/founder (T/F) HIV-1 envelope proteins (Envs) from infected individuals that developed neutralization breadth are likely to possess inherent features desirable for vaccine immunogen design. To explore this premise, we conducted an immunization study in rhesus macaques (RM) using T/F Env sequences from two human subjects, one of whom developed potent and broad neutralizing antibodies (Z1800M) while the other developed little to no neutralizing antibody responses (R66M) during HIV-1 infection. Using a DNA/MVA/protein immunization protocol, 10 RM were immunized with each T/F Env. Within each T/F Env group, the protein boosts were administered as either monomeric gp120 or stabilized trimeric gp140 protein. All vaccination regimens elicited high titers of antigen-specific IgG, and two animals that received monomeric Z1800M Env gp120 developed autologous neutralizing activity. Using early Env escape variants isolated from subject Z1800M as guides, the serum neutralizing activity of the two immunized RM was found to be dependent on the gp120 V5 region. Interestingly, the exact same residues of V5 were also targeted by a neutralizing monoclonal antibody (nmAb) isolated from the subject Z1800M early in infection. Glycan profiling and computational modeling of the Z1800M Env gp120 immunogen provided further evidence that the V5 loop is exposed in this T/F Env and was a dominant feature that drove neutralizing antibody targeting during infection and immunization. An expanded B cell clonotype was isolated from one of the neutralization-positive RM and nmAbs corresponding to this group demonstrated V5-dependent neutralization similar to both the RM serum and the human Z1800M nmAb. The results demonstrate that neutralizing antibody responses elicited by the Z1800M T/F Env in RM converged with those in the HIV-1 infected human subject, illustrating the potential of using immunogens based on this or other T/F Envs with well-defined immunogenicity as a starting point to drive breadth.
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Affiliation(s)
- Sarah Welbourn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anne S. Gleinich
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Sailaja Gangadhara
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Salar Khan
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Courtney Ferrebee
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Bhrugu Yagnik
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - S. Abigail Smith
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Danielle Williams
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Rohini Mopuri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Amit A. Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Justin Thompson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Matt A. Price
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- International AIDS Vaccine Initiative, New York city, New York, United States of America
| | - Shiyu Wang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Xiaoying Shen
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - LaTonya D. Williams
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Nathan Eisel
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Tiffany Peters
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Lu Zhang
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - William Kilembe
- Center for Family Health Research in Zambia (CFHRZ), Lusaka, Zambia
| | | | - Georgia D. Tomaras
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Steven E. Bosinger
- 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
| | - Rama R. Amara
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cynthia A. Derdeyn
- 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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2
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Jecs E, Tahirovic YA, Wilson RJ, Miller EJ, Kim M, Truax V, Nguyen HH, Akins NS, Saindane M, Wang T, Sum CS, Cvijic ME, Schroeder GM, Burton SL, Derdeyn CA, Xu L, Jiang Y, Wilson LJ, Liotta DC. Synthesis and Evaluation of Novel Tetrahydronaphthyridine CXCR4 Antagonists with Improved Drug-like Profiles. J Med Chem 2022; 65:4058-4084. [PMID: 35179893 DOI: 10.1021/acs.jmedchem.1c01564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our first-generation CXCR4 antagonist TIQ15 was rationally modified to improve drug-like properties. Introducing a nitrogen atom into the aromatic portion of the tetrahydroisoquinoline ring led to several heterocyclic variants including the 5,6,7,8-tetrahydro-1,6-naphthyridine series, greatly reducing the inhibition of the CYP 2D6 enzyme. Compound 12a demonstrated the best overall properties after profiling a series of isomeric tetrahydronaphthyridine analogues in a battery of biochemical assays including CXCR4 antagonism, CYP 2D6 inhibition, metabolic stability, and permeability. The butyl amine side chain of 12a was substituted with various lipophilic groups to improve the permeability. These efforts culminated in the discovery of compound 30 as a potent CXCR4 antagonist (IC50 = 24 nM) with diminished CYP 2D6 activity, improved PAMPA permeability (309 nm/s), potent inhibition of human immunodeficiency virus entry (IC50 = 7 nM), a cleaner off-target in vitro safety profile, lower human ether a-go-go-related gene channel activity, and higher oral bioavailability in mice (% FPO = 27) compared to AMD11070 and TIQ15.
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Affiliation(s)
- Edgars Jecs
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Yesim A Tahirovic
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Robert J Wilson
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Eric J Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Michelle Kim
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Valarie Truax
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Huy H Nguyen
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Nicholas S Akins
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Manohar Saindane
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Tao Wang
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Chi S Sum
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Mary E Cvijic
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Gretchen M Schroeder
- Bristol-Myers Squibb Research & Development, Princeton, New Jersey 08543, United States
| | - Samantha L Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, United States
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30322, United States
| | - Cynthia A Derdeyn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, United States
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30322, United States
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Lingjie Xu
- Hangzhou Junrui Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Yi Jiang
- Hangzhou Junrui Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Lawrence J Wilson
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Dennis C Liotta
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
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3
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Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
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Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
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4
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Silva de Castro I, Gorini G, Mason R, Gorman J, Bissa M, Rahman MA, Arakelyan A, Kalisz I, Whitney S, Becerra-Flores M, Ni E, Peachman K, Trinh HV, Read M, Liu MH, Van Ryk D, Paquin-Proulx D, Shubin Z, Tuyishime M, Peele J, Ahmadi MS, Verardi R, Hill J, Beddall M, Nguyen R, Stamos JD, Fujikawa D, Min S, Schifanella L, Vaccari M, Galli V, Doster MN, Liyanage NP, Sarkis S, Caccuri F, LaBranche C, Montefiori DC, Tomaras GD, Shen X, Rosati M, Felber BK, Pavlakis GN, Venzon DJ, Magnanelli W, Breed M, Kramer J, Keele BF, Eller MA, Cicala C, Arthos J, Ferrari G, Margolis L, Robert-Guroff M, Kwong PD, Roederer M, Rao M, Cardozo TJ, Franchini G. Anti-V2 antibodies virus vulnerability revealed by envelope V1 deletion in HIV vaccine candidates. iScience 2021; 24:102047. [PMID: 33554060 PMCID: PMC7847973 DOI: 10.1016/j.isci.2021.102047] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/23/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
The efficacy of ALVAC-based HIV and SIV vaccines in humans and macaques correlates with antibodies to envelope variable region 2 (V2). We show here that vaccine-induced antibodies to SIV variable region 1 (V1) inhibit anti-V2 antibody-mediated cytotoxicity and reverse their ability to block V2 peptide interaction with the α4β7 integrin. SIV vaccines engineered to delete V1 and favor an α helix, rather than a β sheet V2 conformation, induced V2-specific ADCC correlating with decreased risk of SIV acquisition. Removal of V1 from the HIV-1 clade A/E A244 envelope resulted in decreased binding to antibodies recognizing V2 in the β sheet conformation. Thus, deletion of V1 in HIV envelope immunogens may improve antibody responses to V2 virus vulnerability sites and increase the efficacy of HIV vaccine candidates.
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Affiliation(s)
- Isabela Silva de Castro
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Giacomo Gorini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rosemarie Mason
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mohammad A. Rahman
- Immune Biology of Retroviral Infection Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Anush Arakelyan
- Section on Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irene Kalisz
- Advanced Bioscience Laboratories, Rockville, MD 20850, USA
| | | | | | - Eric Ni
- New York University School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Kristina Peachman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Hung V. Trinh
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Michael Read
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Mei-Hue Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donald Van Ryk
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Zhanna Shubin
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Marina Tuyishime
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Jennifer Peele
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Mohammed S. Ahmadi
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juliane Hill
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Beddall
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Nguyen
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James D. Stamos
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dai Fujikawa
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Susie Min
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luca Schifanella
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Monica Vaccari
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Veronica Galli
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Melvin N. Doster
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Namal P.M. Liyanage
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sarkis Sarkis
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Francesca Caccuri
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Celia LaBranche
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - David C. Montefiori
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | | | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University, Durham, NC 27701, USA
| | - Margherita Rosati
- Human Retrovirus Section, National Cancer Institute, Frederick, MD 21702, USA
| | - Barbara K. Felber
- Human Retrovirus Pathogenesis Section, National Cancer Institute, Frederick, MD 21702, USA
| | - George N. Pavlakis
- Human Retrovirus Section, National Cancer Institute, Frederick, MD 21702, USA
| | - David J. Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - William Magnanelli
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Matthew Breed
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Josh Kramer
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21704, USA
| | - Michael A. Eller
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guido Ferrari
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC 27701, USA
| | - Leonid Margolis
- Section on Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marjorie Robert-Guroff
- Immune Biology of Retroviral Infection Section, National Cancer Institute, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Structural Biology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Timothy J. Cardozo
- New York University School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892, USA
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5
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Charles TP, Burton SL, Arunachalam PS, Cottrell CA, Sewall LM, Bollimpelli VS, Gangadhara S, Dey AK, Ward AB, Shaw GM, Hunter E, Amara RR, Pulendran B, van Gils MJ, Derdeyn CA. The C3/465 glycan hole cluster in BG505 HIV-1 envelope is the major neutralizing target involved in preventing mucosal SHIV infection. PLoS Pathog 2021; 17:e1009257. [PMID: 33556148 PMCID: PMC7895394 DOI: 10.1371/journal.ppat.1009257] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/19/2021] [Accepted: 12/23/2020] [Indexed: 01/08/2023] Open
Abstract
Stabilized HIV-1 envelope (Env) trimers elicit tier 2 autologous neutralizing antibody (nAb) responses in immunized animals. We previously demonstrated that BG505 SOSIP.664.T332N gp140 (BG505 SOSIP) immunization of rhesus macaques (RM) provided robust protection against autologous intra-vaginal simian-human immunodeficiency virus (SHIV) challenge that was predicted by high serum nAb titers. Here, we show that nAb in these protected RM targeted a glycan hole proximal to residue 465 in gp120 in all cases. nAb also targeted another glycan hole at residues 241/289 and an epitope in V1 at varying frequencies. Non-neutralizing antibodies directed at N611-shielded epitopes in gp41 were also present but were more prevalent in RM with low nAb titers. Longitudinal analysis demonstrated that nAb broadened in some RM during sequential immunization but remained focused in others, the latter being associated with increases in nAb titer. Thirty-eight monoclonal antibodies (mAbs) isolated from a protected RM with an exceptionally high serum neutralization titer bound to the trimer in ELISA, and four of the mAbs potently neutralized the BG505 Env pseudovirus (PV) and SHIV. The four neutralizing mAbs were clonally related and targeted the 465 glycan hole to varying degrees, mimicking the serum. The data demonstrate that the C3/465 glycan hole cluster was the dominant neutralization target in high titer protected RM, despite other co-circulating neutralizing and non-neutralizing specificities. The isolation of a neutralizing mAb family argues that clonotype expansion occurred during BG505 SOSIP immunization, leading to high titer, protective nAb and setting a desirable benchmark for HIV vaccines.
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Affiliation(s)
- Tysheena P. Charles
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha L. Burton
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Prabhu S. Arunachalam
- Departments of Pathology, and Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Venkata S. Bollimpelli
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sailaja Gangadhara
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Antu K. Dey
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- 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
| | - Rama R. Amara
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Bali Pulendran
- Departments of Pathology, and Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (MJVG); (CAD)
| | - Cynthia A. Derdeyn
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- 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: (MJVG); (CAD)
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6
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Arunachalam PS, Charles TP, Joag V, Bollimpelli VS, Scott MKD, Wimmers F, Burton SL, Labranche CC, Petitdemange C, Gangadhara S, Styles TM, Quarnstrom CF, Walter KA, Ketas TJ, Legere T, Jagadeesh Reddy PB, Kasturi SP, Tsai A, Yeung BZ, Gupta S, Tomai M, Vasilakos J, Shaw GM, Kang CY, Moore JP, Subramaniam S, Khatri P, Montefiori D, Kozlowski PA, Derdeyn CA, Hunter E, Masopust D, Amara RR, Pulendran B. T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nat Med 2020; 26:932-940. [PMID: 32393800 PMCID: PMC7303014 DOI: 10.1038/s41591-020-0858-8] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/27/2020] [Indexed: 01/05/2023]
Abstract
Recent efforts toward an HIV vaccine focus on inducing broadly neutralizing antibodies, but eliciting both neutralizing antibodies (nAbs) and cellular responses may be superior. Here, we immunized macaques with an HIV envelope trimer, either alone to induce nAbs, or together with a heterologous viral vector regimen to elicit nAbs and cellular immunity, including CD8+ tissue-resident memory T cells. After ten vaginal challenges with autologous virus, protection was observed in both vaccine groups at 53.3% and 66.7%, respectively. A nAb titer >300 was generally associated with protection but in the heterologous viral vector + nAb group, titers <300 were sufficient. In this group, protection was durable as the animals resisted six more challenges 5 months later. Antigen stimulation of T cells in ex vivo vaginal tissue cultures triggered antiviral responses in myeloid and CD4+ T cells. We propose that cellular immune responses reduce the threshold of nAbs required to confer superior and durable protection.
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MESH Headings
- Animals
- Antibodies, Neutralizing/drug effects
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/drug effects
- Antibodies, Viral/immunology
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- Female
- Gene Products, gag/genetics
- Gene Products, gag/immunology
- Genetic Vectors
- Immunity, Cellular/drug effects
- Immunity, Cellular/immunology
- Immunity, Heterologous
- Immunogenicity, Vaccine
- Immunologic Memory/immunology
- Macaca mulatta
- Mucous Membrane
- SAIDS Vaccines/pharmacology
- Simian Acquired Immunodeficiency Syndrome/prevention & control
- Simian Immunodeficiency Virus/immunology
- Vagina
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Tysheena P Charles
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Vineet Joag
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Venkata S Bollimpelli
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Samantha L Burton
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Celia C Labranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Caroline Petitdemange
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
- HIV Inflammation and Persistence Unit, Institut Pasteur, Paris, France
| | - Sailaja Gangadhara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Tiffany M Styles
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Clare F Quarnstrom
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Korey A Walter
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Traci Legere
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Pradeep Babu Jagadeesh Reddy
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
- Pfizer, Andover, MA, USA
| | - Sudhir Pai Kasturi
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | | | | | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Mark Tomai
- 3M Corporate Research and Materials Lab, Saint Paul, MN, USA
| | | | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chil-Yong Kang
- Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA.
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA.
| | - David Masopust
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA.
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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7
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Moore PL. The Neutralizing Antibody Response to the HIV-1 Env Protein. Curr HIV Res 2019; 16:21-28. [PMID: 29173180 DOI: 10.2174/1570162x15666171124122044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND A vaccine able to elicit broadly neutralizing antibodies capable of blocking infection by global viruses has not been achieved, and remains a key public health challenge. OBJECTIVE During infection, a robust strain-specific neutralizing response develops in most people, but only a subset of infected people develop broadly neutralizing antibodies. Understanding how and why these broadly neutralizing antibodies develop has been a focus of the HIV-1 vaccine field for many years, and has generated extraordinary insights into the neutralizing response to HIV-1 infection. RESULTS This review describes the features, targets and developmental pathways of early strainspecific antibodies and later broadly neutralizing antibodies, and explores the reasons such broad antibodies are not more commonly elicited during infection. CONCLUSION The insights from these studies have been harnessed for the development of pioneering new vaccine approaches that seek to drive B cell maturation towards breadth. Overall, this review describes how findings from infected donors have impacted on active and passive immunization approaches that seek to prevent HIV-1 infection.
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Affiliation(s)
- Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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8
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Clade C HIV-1 Envelope Vaccination Regimens Differ in Their Ability To Elicit Antibodies with Moderate Neutralization Breadth against Genetically Diverse Tier 2 HIV-1 Envelope Variants. J Virol 2019; 93:JVI.01846-18. [PMID: 30651354 DOI: 10.1128/jvi.01846-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/03/2019] [Indexed: 01/09/2023] Open
Abstract
The goals of preclinical HIV vaccine studies in nonhuman primates are to develop and test different approaches for their ability to generate protective immunity. Here, we compared the impact of 7 different vaccine modalities, all expressing the HIV-1 1086.C clade C envelope (Env), on (i) the magnitude and durability of antigen-specific serum antibody responses and (ii) autologous and heterologous neutralizing antibody capacity. These vaccination regimens included immunization with different combinations of DNA, modified vaccinia virus Ankara (MVA), soluble gp140 protein, and different adjuvants. Serum samples collected from 130 immunized monkeys at two key time points were analyzed using the TZM-bl cell assay: at 2 weeks after the final immunization (week 40/41) and on the day of challenge (week 58). Key initial findings were that inclusion of a gp140 protein boost had a significant impact on the magnitude and durability of Env-specific IgG antibodies, and addition of 3M-052 adjuvant was associated with better neutralizing activity against the SHIV1157ipd3N4 challenge virus and a heterologous HIV-1 CRF01 Env, CNE8. We measured neutralization against a panel of 12 tier 2 Envs using a newly described computational tool to quantify serum neutralization potency by factoring in the predetermined neutralization tier of each reference Env. This analysis revealed modest neutralization breadth, with DNA/MVA immunization followed by gp140 protein boosts in 3M-052 adjuvant producing the best scores. This study highlights that protein-containing regimens provide a solid foundation for the further development of novel adjuvants and inclusion of trimeric Env immunogens that could eventually elicit a higher level of neutralizing antibody breadth.IMPORTANCE Despite much progress, we still do not have a clear understanding of how to elicit a protective neutralizing antibody response against HIV-1 through vaccination. There have been great strides in the development of envelope immunogens that mimic the virus particle, but less is known about how different vaccination modalities and adjuvants contribute to shaping the antibody response. We compared seven different vaccines that were administered to rhesus macaques and that delivered the same envelope protein through various modalities and with different adjuvants. The results demonstrate that some vaccine components are better than others at eliciting neutralizing antibodies with breadth.
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9
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Smith SA, Burton SL, Kilembe W, Lakhi S, Karita E, Price M, Allen S, Derdeyn CA. VH1-69 Utilizing Antibodies Are Capable of Mediating Non-neutralizing Fc-Mediated Effector Functions Against the Transmitted/Founder gp120. Front Immunol 2019; 9:3163. [PMID: 30697215 PMCID: PMC6341001 DOI: 10.3389/fimmu.2018.03163] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/21/2018] [Indexed: 01/05/2023] Open
Abstract
Multiple antibody effector functions arise in HIV-1 infection that could be harnessed to protect against infection or clear the persistent reservoir. Here, we have investigated the genetic and functional memory B cell and antibody landscape present during early infection in six individuals infected with either subtype A, C, or an A/C recombinant HIV-1. These individuals demonstrated varying levels of plasma autologous neutralization (nAb) against the transmitted/founder envelope (T/F Env) pseudovirus and non-neutralizing Fc-mediated effector function (nnFc) antibody-dependent cell-mediated cytotoxicity (ADCC) against the T/F Env gp120 protein at ~7 months after infection. Genetic analysis of the immunoglobulin heavy (VH) and light (VL) chain variable domain gene segments from 352 autologous T/F Env gp120-specific single B cells recovered at this same 7-month time-point revealed an over-representation of the VH1-69 germline in five of six individuals. A defining feature of the VH1-69 utilizing gp120-specific antibodies was their significantly more hydrophobic complementarity-determining region-2 (CDRH2) regions compared to other VH CDRH2 sequences from each individual. While none of the VH1-69 antibodies possessed strong neutralizing activity against virions pseudotyped with the autologous T/F Env, almost a third were capable of mediating high ADCC activity, as assayed by intracellular granzyme B activity in CEM.NKr.CCR5 target cells coated with autologous T/F Env gp120. High ADCC mediating VH1-69 antibodies exhibited shorter complementarity-determining region-3 (CDRH3) lengths and a more neutral isoelectric point than antibodies lacking this function. In the individual that developed the highest autologous ADCC responses, the high granzyme B producing antibodies bound to surface expressed envelope in the absence of CD4 and were not enhanced by the addition of soluble CD4. Overall, VH1-69 utilizing antibodies are commonly induced against gp120 in diverse HIV-1 infections and a subset of these antibodies can mediate ADCC functions, serving as a bridge between the innate and adaptive immune response to HIV-1.
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Affiliation(s)
- S Abigail Smith
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Samantha L Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | | | - Shabir Lakhi
- Zambia Emory HIV Research Project, Lusaka, Zambia
| | | | - Matt Price
- International AIDS Vaccine Initiative, New York, NY, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Cynthia A Derdeyn
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
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10
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Bagaya BS, Tian M, Nickel GC, Vega JF, Li Y, He P, Klein K, Mann JFS, Jiang W, Arts EJ, Gao Y. An in vitro Model to Mimic Selection of Replication-Competent HIV-1 Intersubtype Recombination in Dual or Superinfected Patients. J Mol Biol 2017; 429:2246-2264. [PMID: 28472629 PMCID: PMC6202033 DOI: 10.1016/j.jmb.2017.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 11/23/2022]
Abstract
The low frequency of HIV-1 recombinants within entire viral populations in both individual patients and culture-based infection models impedes investigation of the underlying factors contributing to either the occurrence of recombinants or the survival of recombinants once they are formed. So far, most of the related studies have no consideration of recombinants' functionality. Here, we established a functional recombinant production (FRP) system to produce pure and functional HIV-1 intersubtype Env recombinants and utilized 454 pyrosequencing to investigate the distribution of over 4000 functional and non-functional recombination breakpoints from either the FRP system or dual infection cultures. The results revealed that most of the breakpoints converged in gp41 (62%) and C1 (25.3%) domains of gp120, which has strong correlation with the similarity between the two recombining sequences. Yet, the breakpoints also appeared in C2 (5.2%) and C5 (4.6%) domains not correlated with the recombining sequence similarity. Interestingly, none of the intersubtype gp120 recombinants recombined between C1 and gp41 regions either from the FRP system or from the dual infection culture, and very few from the HIV epidemic were functional. The present study suggests that the selection of functional Env recombinants is one of the reasons for the predominance of C1 and gp41 Env recombinants in the HIV epidemic, and it provides an in vitro model to mimic the selection of replication-competent HIV-1 intersubtype recombination in dual or superinfected patients.
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Affiliation(s)
- Bernard S Bagaya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, N6A 3K7, Uganda
| | - Meijuan Tian
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Gabrielle C Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - José F Vega
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Yuejin Li
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ping He
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Katja Klein
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Wei Jiang
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Eric J Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada
| | - Yong Gao
- Department of Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Microbiology and Immunology, Western University, London, Ontario N6A 5C1, Canada.
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11
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Murray JM, Maher S, Mota T, Suzuki K, Kelleher AD, Center RJ, Purcell D. Differentiating founder and chronic HIV envelope sequences. PLoS One 2017; 12:e0171572. [PMID: 28187204 PMCID: PMC5302377 DOI: 10.1371/journal.pone.0171572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/23/2017] [Indexed: 11/27/2022] Open
Abstract
Significant progress has been made in characterizing broadly neutralizing antibodies against the HIV envelope glycoprotein Env, but an effective vaccine has proven elusive. Vaccine development would be facilitated if common features of early founder virus required for transmission could be identified. Here we employ a combination of bioinformatic and operations research methods to determine the most prevalent features that distinguish 78 subtype B and 55 subtype C founder Env sequences from an equal number of chronic sequences. There were a number of equivalent optimal networks (based on the fewest covarying amino acid (AA) pairs or a measure of maximal covariance) that separated founders from chronics: 13 pairs for subtype B and 75 for subtype C. Every subtype B optimal solution contained the founder pairs 178–346 Asn-Val, 232–236 Thr-Ser, 240–340 Lys-Lys, 279–315 Asp-Lys, 291–792 Ala-Ile, 322–347 Asp-Thr, 535–620 Leu-Asp, 742–837 Arg-Phe, and 750–836 Asp-Ile; the most common optimal pairs for subtype C were 644–781 Lys-Ala (74 of 75 networks), 133–287 Ala-Gln (73/75) and 307–337 Ile-Gln (73/75). No pair was present in all optimal subtype C solutions highlighting the difficulty in targeting transmission with a single vaccine strain. Relative to the size of its domain (0.35% of Env), the α4β7 binding site occurred most frequently among optimal pairs, especially for subtype C: 4.2% of optimal pairs (1.2% for subtype B). Early sequences from 5 subtype B pre-seroconverters each exhibited at least one clone containing an optimal feature 553–624 (Ser-Asn), 724–747 (Arg-Arg), or 46–293 (Arg-Glu).
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Affiliation(s)
- John M. Murray
- School of Mathematics and Statistics, UNSW Sydney, Sydney, New South Wales, Australia
- * E-mail:
| | - Stephen Maher
- School of Mathematics and Statistics, UNSW Sydney, Sydney, New South Wales, Australia
- Zuse Institute Berlin, Berlin, Germany
| | - Talia Mota
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Kazuo Suzuki
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Rob J. Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Damian Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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12
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Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth. PLoS Pathog 2016; 12:e1005989. [PMID: 27851829 PMCID: PMC5112890 DOI: 10.1371/journal.ppat.1005989] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022] Open
Abstract
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12). Single-genome analysis of full-length T/F Env sequences revealed that all 21 individuals were infected with a highly homogeneous population of viral variants, which were categorized as subtype C (n = 12), A1 (n = 7), or recombinant AC (n = 2). An extensive amino acid sequence-based analysis of variable loop lengths and glycosylation patterns in the T/F Envs revealed that a lower ratio of NXS to NXT-encoded glycan motifs correlated with neutralization breadth. Further analysis comparing amino acid sequence changes, insertions/deletions, and glycan motif alterations between the T/F Env and autologous early Env variants revealed that extensive diversification focused in the V2, V4, and V5 regions of gp120, accompanied by contemporaneous viral escape, significantly favored the development of breadth. These results suggest that more efficient glycosylation of subtype A and C T/F Envs through fewer NXS-encoded glycan sites is more likely to elicit antibodies that can transition from autologous to heterologous neutralizing activity following exposure to gp120 diversification. This initiates an Env-antibody co-evolution cycle that increases neutralization breadth, and is further augmented over time by additional viral and host factors. These findings suggest that understanding how variation in the efficiency of site-specific glycosylation influences neutralizing antibody elicitation and targeting could advance the design of immunogens aimed at inducing antibodies that can transition from autologous to heterologous neutralizing activity.
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13
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Wibmer CK, Gorman J, Anthony CS, Mkhize NN, Druz A, York T, Schmidt SD, Labuschagne P, Louder MK, Bailer RT, Abdool Karim SS, Mascola JR, Williamson C, Moore PL, Kwong PD, Morris L. Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site. J Virol 2016; 90:10220-10235. [PMID: 27581986 PMCID: PMC5105658 DOI: 10.1128/jvi.01357-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/26/2016] [Indexed: 01/09/2023] Open
Abstract
All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. Defining the epitopes of strain-specific antibodies that overlap conserved sites of vulnerability might provide mechanistic insights into how broadly neutralizing antibodies arise. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. The cocrystal structure of CAP257-RH1 bound to RHPA gp120 revealed critical interactions with the N276 glycan, loop D, and V5, but not with aspartic acid 368, similarly to HJ16 and 179NC75. The CAP257-RH1 monoclonal antibody was derived from the immunoglobulin-variable IGHV3-33 and IGLV3-10 genes and neutralized RHPA but not the transmitted/founder virus from donor CAP257. Its narrow neutralization breadth was attributed to a binding angle that was incompatible with glycosylated V5 loops present in almost all HIV-1 strains, including the CAP257 transmitted/founder virus. Deep sequencing of autologous CAP257 viruses, however, revealed minority variants early in infection that lacked V5 glycans. These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycan-dependent CD4 binding site B-cell lineage. IMPORTANCE The conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of different antibody lineages to this site remain elusive. Studies have shown that strain-specific antibodies can evolve into broadly neutralizing antibodies or in some cases act as helper lineages. Therefore, characterizing the epitopes of strain-specific antibodies may help to inform the design of HIV-1 immunogens to elicit broadly neutralizing antibodies. In this study, we isolate a narrowly neutralizing N276 glycan-dependent antibody and use X-ray crystallography and viral deep sequencing to describe how gp120 lacking glycans in V5 might have elicited these early glycan-dependent CD4 binding site antibodies. These data highlight how glycan holes can play a role in the elicitation of B-cell lineages targeting the CD4 binding site.
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Affiliation(s)
- Constantinos Kurt Wibmer
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Colin S Anthony
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Nonhlanhla N Mkhize
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Talita York
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Phillip Labuschagne
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Columbia University, New York, New York, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
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14
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Hutzenthaler M, Taylor JE. Time reversal of some stationary jump diffusion processes from population genetics. ADV APPL PROBAB 2016. [DOI: 10.1239/aap/1293113155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We describe the processes obtained by time reversal of a class of stationary jump diffusion processes that model the dynamics of genetic variation in populations subject to repeated bottlenecks. Assuming that only one lineage survives each bottleneck, the forward process is a diffusion on [0,1] that jumps to the boundary before diffusing back into the interior. We show that the behavior of the time-reversed process depends on whether the boundaries are accessible to the diffusive motion of the forward process. If a boundary point is inaccessible to the forward diffusion then time reversal leads to a jump diffusion that jumps immediately into the interior whenever it arrives at that point. If, instead, a boundary point is accessible then the jumps off of that point are governed by a weighted local time of the time-reversed process.
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15
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Time reversal of some stationary jump diffusion processes from population genetics. ADV APPL PROBAB 2016. [DOI: 10.1017/s0001867800004560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We describe the processes obtained by time reversal of a class of stationary jump diffusion processes that model the dynamics of genetic variation in populations subject to repeated bottlenecks. Assuming that only one lineage survives each bottleneck, the forward process is a diffusion on [0,1] that jumps to the boundary before diffusing back into the interior. We show that the behavior of the time-reversed process depends on whether the boundaries are accessible to the diffusive motion of the forward process. If a boundary point is inaccessible to the forward diffusion then time reversal leads to a jump diffusion that jumps immediately into the interior whenever it arrives at that point. If, instead, a boundary point is accessible then the jumps off of that point are governed by a weighted local time of the time-reversed process.
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16
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Hait SH, Soares EA, Sprinz E, Arthos J, Machado ES, Soares MA. Worldwide Genetic Features of HIV-1 Env α4β7 Binding Motif: The Local Dissemination Impact of the LDI Tripeptide. J Acquir Immune Defic Syndr 2016; 70:463-71. [PMID: 26569174 DOI: 10.1097/qai.0000000000000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND HIV-1 gp120 binds to integrin α4β7, a homing receptor of lymphocytes to gut-associated lymphoid tissues. This interaction is mediated by the LDI/V tripeptide encoded in the V2-loop. This tripeptide mimics similar motifs in mucosal addressin cellular adhesion molecule (MAdCAM) and vascular CAM (VCAM), the natural ligands of α4β7. In this study, we explored the association of V2-loop LDI/V mimotopes with transmission routes and patterns of disease progression in HIV-infected adult and pediatric patients. HIV-1 env sequences available in the Los Alamos HIV Sequence database were included in the analyses. METHODS HIV-1 V2-loop sequences generated from infected adults and infants from South and Southeast Brazil, and also retrieved from the Los Alamos database, were assessed for α4β7 binding tripeptide composition. Chi-Square/Fisher Exact test and Mann Whitney U test were used for tripeptide comparisons. Shannon entropy was assessed for conservancy of the α4β7 tripeptide mimotope. RESULTS We observed no association between the tripeptide composition or conservation and virus transmission route or disease progression. However, LDI was linked to successful epidemic dissemination of HIV-1 subtype C in South America, and further to other expanding non-B subtypes in Europe and Asia. In Africa, subtypes showing increased LDV prevalence evidenced an ongoing process of selection toward LDI expansion, an observation also extended to subtype B in the Americas and Western Europe. CONCLUSIONS The V2-loop LDI mimotope was conserved in HIV-1C from South America and other expanding subtypes across the globe, which suggests that LDI may promote successful dissemination of HIV at local geographic levels by means of increased transmission fitness.
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Affiliation(s)
- Sabrina H Hait
- *Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; †Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; ‡Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Brazil; §Laboratory of Immune Regulation, National Institutes of Health, Bethesda, MD; and ‖Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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17
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Zhao J, Nie J, Jiao Y, Li L, Zhang T, Liu Q, Huang W, Wu H, Wang Y. Effect of the maturation of neutralizing antibodies on human immunodeficiency virus (HIV) envelope evolution in HIV-infected subjects. INFECTION GENETICS AND EVOLUTION 2015; 38:82-89. [PMID: 26706846 DOI: 10.1016/j.meegid.2015.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/02/2015] [Accepted: 12/14/2015] [Indexed: 01/11/2023]
Abstract
Delineating the course of NAb (neutralizing antibody) development in natural infection may provide clues for NAb-targeted HIV-1 vaccine design. Two subjects, A (non-neutralizer) and E (neutralizer), were chosen from 75 HIV-1 positive subjects of a MSM (men who have sex with men) cohort to investigate the key events of virus evolution in the development course of neutralizing antibodies. Pseudovirus quasispecies (at least 10 strains) were generated for each time points of the infection course. The diversity and divergence of the env quasispecies per time point for subject E were significantly higher than those for subject A (p<0.05). Compared with subject A, the gp160 derived from subject E acquired longer V1V2 region and more N-glycans during the development of neutralizing antibodies. The developing course of neutralizing antibody lagged behind the virus evolution, of which the pseudoviruses could only been neutralized by the latter time-point sera. The neutralization-driven evolution of the virus for subject E was mostly mapped to the C1-C3 region of gp160. Through site-directed mutagenesis, some key sites and region were identified to be associated with the virus escape, including: Q85P, H183P, K340E, L365S, L369I, I372V and insertions of 355N in C3 and NITDEVKIG in V1 region.
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Affiliation(s)
- Juan Zhao
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, Division of HIV/AIDS and sex-transmitted virus vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing 100050, China
| | - Jianhui Nie
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, Division of HIV/AIDS and sex-transmitted virus vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing 100050, China
| | - Yanmei Jiao
- Beijing You'an Hospital, Capital Medical University, Beijing 100069, China
| | - Lan Li
- Beijing You'an Hospital, Capital Medical University, Beijing 100069, China
| | - Tong Zhang
- Beijing You'an Hospital, Capital Medical University, Beijing 100069, China
| | - Qiang Liu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, Division of HIV/AIDS and sex-transmitted virus vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing 100050, China
| | - Weijin Huang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, Division of HIV/AIDS and sex-transmitted virus vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing 100050, China
| | - Hao Wu
- Beijing You'an Hospital, Capital Medical University, Beijing 100069, China.
| | - Youchun Wang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, Division of HIV/AIDS and sex-transmitted virus vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing 100050, China.
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18
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Breakthrough of SIV strain smE660 challenge in SIV strain mac239-vaccinated rhesus macaques despite potent autologous neutralizing antibody responses. Proc Natl Acad Sci U S A 2015; 112:10780-5. [PMID: 26261312 DOI: 10.1073/pnas.1509731112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Although the correlates of immunological protection from human immunodeficiency virus or simian immunodeficiency virus infection remain incompletely understood, it is generally believed that medium to high titers of serum neutralizing antibodies (nAbs) against the challenge virus will prevent infection. This paradigm is based on a series of studies in which passive transfer of HIV-specific nAbs protected rhesus macaques (RMs) from subsequent mucosal challenge with a chimeric human/simian immunodeficiency virus. However, it is unknown whether nAb titers define protection in the setting of active immunization. Here we determined serum nAb titers against breakthrough transmitted/founder (T/F) SIVsmE660-derived envelope glycoprotein (Env) variants from 14 RMs immunized with SIVmac239-based DNA-prime/modified vaccinia virus Ankara-boost vaccine regimens that included GM-CSF or CD40L adjuvants and conferred significant but incomplete protection against repeated low-dose intrarectal challenge. A single Env variant established infection in all RMs except one, with no identifiable genetic signature associated with vaccination breakthrough compared with T/F Envs from four unvaccinated monkeys. Breakthrough T/F Env pseudoviruses were potently neutralized in vitro by heterologous pooled serum from chronically SIVsmE660-infected monkeys at IC50 titers exceeding 1:1,000,000. Remarkably, the T/F Env pseudoviruses from 13 of 14 monkeys were also susceptible to neutralization by autologous prechallenge serum at in vitro IC50 titers ranging from 1:742-1:10,832. These titers were similar to those observed in vaccinated RMs that remained uninfected. These data suggest that the relationship between serum nAb titers and protection from mucosal SIV challenge in the setting of active immunization is more complex than previously recognized, warranting further studies into the balance between immune activation, target cell availability, and protective antibody responses.
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Peters PJ, Gonzalez-Perez MP, Musich T, Moore Simas TA, Lin R, Morse AN, Shattock RJ, Derdeyn CA, Clapham PR. Infection of ectocervical tissue and universal targeting of T-cells mediated by primary non-macrophage-tropic and highly macrophage-tropic HIV-1 R5 envelopes. Retrovirology 2015; 12:48. [PMID: 26055104 PMCID: PMC4459458 DOI: 10.1186/s12977-015-0176-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/19/2015] [Indexed: 12/21/2022] Open
Abstract
Background HIV-1 variants carrying non-macrophage-tropic HIV-1 R5 envelopes (Envs) are predominantly transmitted and persist in immune tissue even in AIDS patients who have highly macrophage-tropic variants in the brain. Non-macrophage-tropic R5 Envs require high levels of CD4 for infection contrasting with macrophage-tropic Envs, which can efficiently mediate infection of cells via low CD4. Here, we investigated whether non-macrophage-tropic R5 Envs from the acute stage of infection (including transmitted/founder Env) mediated more efficient infection of ectocervical explant cultures compared to non-macrophage-tropic and highly macrophage-tropic R5 Envs from late disease. Results We used Env+ pseudovirions that carried a GFP reporter gene to measure infection of the first cells targeted in ectocervical explant cultures. In straight titrations of Env+ pseudovirus supernatants, mac-tropic R5 Envs from late disease mediated slightly higher infectivities for ectocervical explants although this was not significant. Surprisingly, explant infection by several T/F/acute Envs was lower than for Envs from late disease. However, when infectivity for explants was corrected to account for differences in the overall infectivity of each Env+ pseudovirus (measured on highly permissive HeLa TZM-bl cells), non-mac-tropic early and late disease Env+ pseudoviruses mediated significantly higher infection. This observation suggests that cervical tissue preferentially supports non-mac-tropic Env+ viruses compared to mac-tropic viruses. Finally, we show that T-cells were the main targets for infection regardless of whether explants were stimulated with T-cell or monocyte/macrophage cytokines. There was no evidence of macrophage infection even for pseudovirions carrying highly mac-tropic Envs from brain tissue or for the highly mac-tropic, laboratory strain, BaL, which targeted T-cells in the explant tissue. Conclusions Our data support ectocervical tissue as a favorable environment for non-mac-tropic HIV-1 R5 variants and emphasize the role of T-cells as initial targets for infection even for highly mac-tropic variants. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0176-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul J Peters
- Program in Molecular Medicine and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605-2377, USA.
| | - Maria Paz Gonzalez-Perez
- Program in Molecular Medicine and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605-2377, USA.
| | - Thomas Musich
- Program in Molecular Medicine and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605-2377, USA.
| | - Tiffany A Moore Simas
- Department of Ob/Gyn, University of Massachusetts Memorial Health Care, 119 Belmont Street, Worcester, MA, 01605, USA.
| | - Rongheng Lin
- School of Public Health and Health Sciences, University of Massachusetts, 411 Arnold House, 715 North Pleasant Street, Amherst, MA, 01003-9304, USA.
| | - Abraham N Morse
- Department of Ob/Gyn, University of Massachusetts Memorial Health Care, 119 Belmont Street, Worcester, MA, 01605, USA.
| | - Robin J Shattock
- Department of Medicine, St Mary's Campus, Imperial College, Medical School Building, London, W21PG, UK.
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center at Yerkes National Primate Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA.
| | - Paul R Clapham
- Program in Molecular Medicine and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Biotech 2, 373 Plantation Street, Worcester, MA, 01605-2377, USA.
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20
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Characterization and Implementation of a Diverse Simian Immunodeficiency Virus SIVsm Envelope Panel in the Assessment of Neutralizing Antibody Breadth Elicited in Rhesus Macaques by Multimodal Vaccines Expressing the SIVmac239 Envelope. J Virol 2015; 89:8130-51. [PMID: 26018167 DOI: 10.1128/jvi.01221-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/03/2014] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Antibodies that can neutralize diverse viral strains are likely to be an important component of a protective human immunodeficiency virus type 1 (HIV-1) vaccine. To this end, preclinical simian immunodeficiency virus (SIV)-based nonhuman primate immunization regimens have been designed to evaluate and enhance antibody-mediated protection. However, these trials often rely on a limited selection of SIV strains with extreme neutralization phenotypes to assess vaccine-elicited antibody activity. To mirror the viral panels used to assess HIV-1 antibody breadth, we created and characterized a novel panel of 14 genetically and phenotypically diverse SIVsm envelope (Env) glycoproteins. To assess the utility of this panel, we characterized the neutralizing activity elicited by four SIVmac239 envelope-expressing DNA/modified vaccinia virus Ankara vector- and protein-based vaccination regimens that included the immunomodulatory adjuvants granulocyte-macrophage colony-stimulating factor, Toll-like receptor (TLR) ligands, and CD40 ligand. The SIVsm Env panel exhibited a spectrum of neutralization sensitivity to SIV-infected plasma pools and monoclonal antibodies, allowing categorization into three tiers. Pooled sera from 91 rhesus macaques immunized in the four trials consistently neutralized only the highly sensitive tier 1a SIVsm Envs, regardless of the immunization regimen. The inability of vaccine-mediated antibodies to neutralize the moderately resistant tier 1b and tier 2 SIVsm Envs defined here suggests that those antibodies were directed toward epitopes that are not accessible on most SIVsm Envs. To achieve a broader and more effective neutralization profile in preclinical vaccine studies that is relevant to known features of HIV-1 neutralization, more emphasis should be placed on optimizing the Env immunogen, as the neutralization profile achieved by the addition of adjuvants does not appear to supersede the neutralizing antibody profile determined by the immunogen. IMPORTANCE Many in the HIV/AIDS vaccine field believe that the ability to elicit broadly neutralizing antibodies capable of blocking genetically diverse HIV-1 variants is a critical component of a protective vaccine. Various SIV-based nonhuman primate vaccine studies have investigated ways to improve antibody-mediated protection against a heterologous SIV challenge, including administering adjuvants that might stimulate a greater neutralization breadth. Using a novel SIV neutralization panel and samples from four rhesus macaque vaccine trials designed for cross comparison, we show that different regimens expressing the same SIV envelope immunogen consistently elicit antibodies that neutralize only the very sensitive tier 1a SIV variants. The results argue that the neutralizing antibody profile elicited by a vaccine is primarily determined by the envelope immunogen and is not substantially broadened by including adjuvants, resulting in the conclusion that the envelope immunogen itself should be the primary consideration in efforts to elicit antibodies with greater neutralization breadth.
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Khan L, Makhdoomi MA, Kumar S, Nair A, Andrabi R, Clark BE, Auyeung K, Bhattacharya J, Vajpayee M, Wig N, Pantophlet R, Luthra K. Identification of CD4-Binding Site Dependent Plasma Neutralizing Antibodies in an HIV-1 Infected Indian Individual. PLoS One 2015; 10:e0125575. [PMID: 25962059 PMCID: PMC4427266 DOI: 10.1371/journal.pone.0125575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/24/2015] [Indexed: 12/02/2022] Open
Abstract
Dissecting antibody specificities in the plasma of HIV-1 infected individuals that develop broadly neutralizing antibodies (bNAbs) is likely to provide useful information for refining target epitopes for vaccine design. Several studies have reported CD4-binding site (CD4bs) antibodies as neutralization determinants in the plasma of subtype B-infected individuals; however there is little information on the prevalence of CD4bs specificities in HIV-infected individuals in India. Here, we report on the presence of CD4bs antibodies and their contribution to virus neutralization in the plasma from a cohort of HIV-1 infected Indian individuals. Plasma from 11 of the 140 HIV-1 infected individuals (7.9%) studied here exhibited cross-neutralization activity against a panel of subtype B and C viruses. Analyses of these 11 plasma samples for the presence of CD4bs antibodies using two CD4bs-selective probes (antigenically resurfaced HXB2gp120 core protein RSC3 and hyperglycosylated JRFLgp120 mutant ΔN2mCHO) revealed that five (AIIMS 617, 619, 627, 642, 660) contained RSC3-reactive plasma antibodies and only one (AIIMS 660) contained ΔN2mCHO-reactive antibodies. Plasma antibody depletion and competition experiments confirmed that the neutralizing activity in the AIIMS 660 plasma was dependent on CD4bs antibodies. To the best of our knowledge, this is the first study to report specifically on the presence of CD4bs antibodies in the plasma of a cohort of HIV-1 infected Indian donors. The identification of CD4bs dependent neutralizing antibodies in an HIV-1 infected Indian donor is a salient finding of this study and is supportive of ongoing efforts to induce similar antibodies by immunization.
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Affiliation(s)
- Lubina Khan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Sanjeev Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Ambili Nair
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Raiees Andrabi
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Brenda E. Clark
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kate Auyeung
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Gurgaon, Haryana, India
| | - Madhu Vajpayee
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- * E-mail:
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Raska M, Czernekova L, Moldoveanu Z, Zachova K, Elliott MC, Novak Z, Hall S, Hoelscher M, Maboko L, Brown R, Smith PD, Mestecky J, Novak J. Differential glycosylation of envelope gp120 is associated with differential recognition of HIV-1 by virus-specific antibodies and cell infection. AIDS Res Ther 2014; 11:23. [PMID: 25120578 PMCID: PMC4130436 DOI: 10.1186/1742-6405-11-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/26/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND HIV-1 entry into host cells is mediated by interactions between the virus envelope glycoprotein (gp120/gp41) and host-cell receptors. N-glycans represent approximately 50% of the molecular mass of gp120 and serve as potential antigenic determinants and/or as a shield against immune recognition. We previously reported that N-glycosylation of recombinant gp120 varied, depending on the producer cells, and the glycosylation variability affected gp120 recognition by serum antibodies from persons infected with HIV-1 subtype B. However, the impact of gp120 differential glycosylation on recognition by broadly neutralizing monoclonal antibodies or by polyclonal antibodies of individuals infected with other HIV-1 subtypes is unknown. METHODS Recombinant multimerizing gp120 antigens were expressed in different cells, HEK 293T, T-cell, rhabdomyosarcoma, hepatocellular carcinoma, and Chinese hamster ovary cell lines. Binding of broadly neutralizing monoclonal antibodies and polyclonal antibodies from sera of subtype A/C HIV-1-infected subjects with individual gp120 glycoforms was assessed by ELISA. In addition, immunodetection was performed using Western and dot blot assays. Recombinant gp120 glycoforms were tested for inhibition of infection of reporter cells by SF162 and YU.2 Env-pseudotyped R5 viruses. RESULTS We demonstrated, using ELISA, that gp120 glycans sterically adjacent to the V3 loop only moderately contribute to differential recognition of a short apex motif GPGRA and GPGR by monoclonal antibodies F425 B4e8 and 447-52D, respectively. The binding of antibodies recognizing longer peptide motifs overlapping with GPGR epitope (268 D4, 257 D4, 19b) was significantly altered. Recognition of gp120 glycoforms by monoclonal antibodies specific for other than V3-loop epitopes was significantly affected by cell types used for gp120 expression. These epitopes included CD4-binding site (VRC03, VRC01, b12), discontinuous epitope involving V1/V2 loop with the associated glycans (PG9, PG16), and an epitope including V3-base-, N332 oligomannose-, and surrounding glycans-containing epitope (PGT 121). Moreover, the different gp120 glycoforms variably inhibited HIV-1 infection of reporter cells. CONCLUSION Our data support the hypothesis that the glycosylation machinery of different cells shapes gp120 glycosylation and, consequently, impacts envelope recognition by specific antibodies as well as the interaction of HIV-1 gp120 with cellular receptors. These findings underscore the importance of selection of appropriately glycosylated HIV-1 envelope as a vaccine antigen.
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Cenci A, D'Avenio G, Tavoschi L, Chiappi M, Becattini S, Narino MDP, Picconi O, Bernasconi D, Fanales-Belasio E, Vardas E, Sukati H, Lo Presti A, Ciccozzi M, Monini P, Ensoli B, Grigioni M, Buttò S. Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms. PLoS One 2014; 9:e95183. [PMID: 24788065 PMCID: PMC4005737 DOI: 10.1371/journal.pone.0095183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/24/2014] [Indexed: 11/17/2022] Open
Abstract
The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of “shifting” putative N-glycosylation sites (PNGSs) in the α2 helix (in C3) and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response.
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Affiliation(s)
| | - Giuseppe D'Avenio
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Lara Tavoschi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Michele Chiappi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Orietta Picconi
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | | | | | - Eftyhia Vardas
- Stellenbosch University, Division of Medical Virology, Stellenbosch, South Africa; Lancet Laboratories, Johannesburg, South Africa
| | - Hosea Sukati
- National Center Public Health Laboratory, Manzini, Swaziland
| | - Alessandra Lo Presti
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy
| | - Massimo Ciccozzi
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immunomediated Diseases, Rome, Italy; University of Biomedical Campus, Rome, Italy
| | - Paolo Monini
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Barbara Ensoli
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
| | - Mauro Grigioni
- Istituto Superiore di Sanità, Department of Technology and Health, Rome, Italy
| | - Stefano Buttò
- Istituto Superiore di Sanità, National AIDS Center, Rome, Italy
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McLinden RJ, LaBranche CC, Chenine AL, Polonis VR, Eller MA, Wieczorek L, Ochsenbauer C, Kappes JC, Perfetto S, Montefiori DC, Michael NL, Kim JH. Detection of HIV-1 neutralizing antibodies in a human CD4⁺/CXCR4⁺/CCR5⁺ T-lymphoblastoid cell assay system. PLoS One 2013; 8:e77756. [PMID: 24312168 PMCID: PMC3842913 DOI: 10.1371/journal.pone.0077756] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 09/09/2013] [Indexed: 11/18/2022] Open
Abstract
Sensitive assays are needed to meaningfully assess low levels of neutralizing antibodies (NAbs) that may be important for protection against the acquisition of HIV-1 infection in vaccine recipients. The current assay of choice uses a non-lymphoid cell line (TZM-bl) that may lack sensitivity owing to over expression of CD4 and CCR5. We used transfection of a human CD4+/CXCR4+/α4β7+ T-lymphoblastoid cell line (A3.01) with a CMV IE promoter-driven CCR5neo vector to stably express CCR5. The resulting line, designated A3R5, is permissive to a wide range of CCR5-tropic circulating strains of HIV-1, including HIV-1 molecular clones containing a Tat-inducible Renilla luciferase reporter gene and expressing multiple Env subtypes. Flow cytometric analysis found CCR5 surface expression on A3R5 cells to be markedly less than TZM-bl but similar to CD3.8 stimulated PBMC. More importantly, neutralization mediated by a diverse panel of monoclonal antibodies, HIV-1 positive polyclonal sera and sCD4 was consistently greater in A3R5 compared to TZM-bl cells. The A3R5 cell line provides a novel approach to guide the development and qualification of promising new HIV-1 vaccine immunogens.
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Affiliation(s)
- Robert J. McLinden
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Celia C. LaBranche
- Department of Surgery, Duke U. Medical Center, Durham, North Carolina, United States of America
| | - Agnès-Laurence Chenine
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
| | - Victoria R. Polonis
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
| | - Michael A. Eller
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
| | - Lindsay Wieczorek
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, Alabama, United States of America
| | - Stephen Perfetto
- Vaccine Research Center, NIH, Bethesda, Maryland, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke U. Medical Center, Durham, North Carolina, United States of America
| | - Nelson L. Michael
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
| | - Jerome H. Kim
- Military HIV- Research Program, WRAIR, Silver Spring, Maryland, United States of America
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25
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Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques. PLoS One 2013; 8:e70814. [PMID: 23967111 PMCID: PMC3743870 DOI: 10.1371/journal.pone.0070814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/24/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding the genetic, antigenic and structural changes that occur during HIV-1 infection in response to pre-existing immunity will facilitate current efforts to develop an HIV-1 vaccine. Much is known about HIV-1 variation at the population level but little with regard to specific changes occurring in the envelope glycoprotein within a host in response to immune pressure elicited by antibodies. The aim of this study was to track and map specific early genetic changes occurring in the viral envelope gene following vaccination using a highly controlled viral challenge setting in the SHIV macaque model. We generated 449 full-length env sequences from vaccinees, and 63 from the virus inoculum. Analysis revealed a different pattern in the distribution and frequency of mutations in the regions of the envelope gene targeted by the vaccine as well as different patterns of diversification between animals in the naïve control group and vaccinees. Given the high stringency of the model it is remarkable that we were able to identify genetic changes associated with the vaccination. This work provides insight into the characterization of breakthrough viral populations in less than fully efficacious vaccines and illustrates the value of HIV-1 Env SHIV challenge model in macaques to unravel the mechanisms driving HIV-1 envelope genetic diversity in the presence of vaccine induced-responses.
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26
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Yuan T, Li J, Zhang MY. HIV-1 envelope glycoprotein variable loops are indispensable for envelope structural integrity and virus entry. PLoS One 2013; 8:e69789. [PMID: 23936354 PMCID: PMC3731308 DOI: 10.1371/journal.pone.0069789] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022] Open
Abstract
HIV-1 envelope (Env) glycoprotein is a trimer of heterodimer of gp120 and gp41, and derives from a trimeric glycoprotein precursor, gp160. Gp120 contains five conserved regions that are interspersed with 5 variable loop regions (V1-V5). Env variations in variable loop length and amino acid composition may associate with virus pathogenesis, virus sensitivity to neutralizing antibodies (nAbs) and disease progression. To investigate the role of each variable loop in Env function, we generated a panel of JRFL gp160 loop deletion mutants and examined the effects of each loop deletion on Env expression, Env cell surface display and Env-mediated virus entry into permissive cells. We found that deletion of V1 and V2 (ΔV1V2), or loop D (ΔlpD) abolished virus entry, the same effect as deletion of V3 (ΔV3), while deletion of V3 crown (ΔV3C) significantly enhanced virus assembly and entry. We further found that deletion of V4 (ΔV4) or V5 (ΔV5), or replacement of V4 or V5 with flexible linkers of the same lengths knocked out the receptor and coreceptor binding sites in gp120, but significantly enhanced the exposure of the N-trimer structure and the membrane proximal external region (MPER) in gp41. Although deletion of V4 or V5 did not affect Env expression, they negatively affected Env cell surface display, leading to the failure in virus assembly and subsequent entry. Taken together, we found that Env variable loops were indispensable for Env structural integrity and virus entry. Our findings may have implications for development of HIV-1 vaccine immunogens and therapeutics.
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Affiliation(s)
- Tingting Yuan
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jingjing Li
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Mei-Yun Zhang
- AIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail:
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27
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Ping LH, Joseph SB, Anderson JA, Abrahams MR, Salazar-Gonzalez JF, Kincer LP, Treurnicht FK, Arney L, Ojeda S, Zhang M, Keys J, Potter EL, Chu H, Moore P, Salazar MG, Iyer S, Jabara C, Kirchherr J, Mapanje C, Ngandu N, Seoighe C, Hoffman I, Gao F, Tang Y, Labranche C, Lee B, Saville A, Vermeulen M, Fiscus S, Morris L, Karim SA, Haynes BF, Shaw GM, Korber BT, Hahn BH, Cohen MS, Montefiori D, Williamson C, Swanstrom R. Comparison of viral Env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design. J Virol 2013; 87:7218-33. [PMID: 23616655 PMCID: PMC3700278 DOI: 10.1128/jvi.03577-12] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 04/15/2013] [Indexed: 12/18/2022] Open
Abstract
Understanding human immunodeficiency virus type 1 (HIV-1) transmission is central to developing effective prevention strategies, including a vaccine. We compared phenotypic and genetic variation in HIV-1 env genes from subjects in acute/early infection and subjects with chronic infections in the context of subtype C heterosexual transmission. We found that the transmitted viruses all used CCR5 and required high levels of CD4 to infect target cells, suggesting selection for replication in T cells and not macrophages after transmission. In addition, the transmitted viruses were more likely to use a maraviroc-sensitive conformation of CCR5, perhaps identifying a feature of the target T cell. We confirmed an earlier observation that the transmitted viruses were, on average, modestly underglycosylated relative to the viruses from chronically infected subjects. This difference was most pronounced in comparing the viruses in acutely infected men to those in chronically infected women. These features of the transmitted virus point to selective pressures during the transmission event. We did not observe a consistent difference either in heterologous neutralization sensitivity or in sensitivity to soluble CD4 between the two groups, suggesting similar conformations between viruses from acute and chronic infection. However, the presence or absence of glycosylation sites had differential effects on neutralization sensitivity for different antibodies. We suggest that the occasional absence of glycosylation sites encoded in the conserved regions of env, further reduced in transmitted viruses, could expose specific surface structures on the protein as antibody targets.
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Affiliation(s)
- Li-Hua Ping
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah B. Joseph
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffrey A. Anderson
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Melissa-Rose Abrahams
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | | | - Laura P. Kincer
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Florette K. Treurnicht
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | - Leslie Arney
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Suany Ojeda
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, USA
| | - Jessica Keys
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Lake Potter
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haitao Chu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Penny Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maria G. Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shilpa Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cassandra Jabara
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- Duke Human Vaccine Institute, Department of Medicine, Duke University, Durham, North Carolina, USA
| | | | - Nobubelo Ngandu
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | | | - Irving Hoffman
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Yuyang Tang
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Celia Labranche
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Benhur Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, USA
| | - Andrew Saville
- South African National Blood Service, Weltevreden Park, South Africa
| | - Marion Vermeulen
- South African National Blood Service, Weltevreden Park, South Africa
| | - Susan Fiscus
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Salim Abdool Karim
- Center for AIDS Program Research in South Africa, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bette T. Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Myron S. Cohen
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Montefiori
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | - Ronald Swanstrom
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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28
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A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein. PLoS Comput Biol 2013; 9:e1003046. [PMID: 23696718 PMCID: PMC3656115 DOI: 10.1371/journal.pcbi.1003046] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 03/15/2013] [Indexed: 11/19/2022] Open
Abstract
The HIV-1 envelope (Env) spike, which consists of a compact, heterodimeric trimer of the glycoproteins gp120 and gp41, is the target of neutralizing antibodies. However, the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms. Mutations that are distant from the antibody binding site can lead to escape, probably by changing the conformation or dynamics of Env; however, these changes are difficult to identify and define mechanistically. Here we describe a network analysis-based approach to identify potential allosteric immune evasion mechanisms using three known HIV-1 Env gp120 protein structures from two different clades, B and C. First, correlation and principal component analyses of molecular dynamics (MD) simulations identified a high degree of long-distance coupled motions that exist between functionally distant regions within the intrinsic dynamics of the gp120 core, supporting the presence of long-distance communication in the protein. Then, by integrating MD simulations with network theory, we identified the optimal and suboptimal communication pathways and modules within the gp120 core. The results unveil both strain-dependent and -independent characteristics of the communication pathways in gp120. We show that within the context of three structurally homologous gp120 cores, the optimal pathway for communication is sequence sensitive, i.e. a suboptimal pathway in one strain becomes the optimal pathway in another strain. Yet the identification of conserved elements within these communication pathways, termed inter-modular hotspots, could present a new opportunity for immunogen design, as this could be an additional mechanism that HIV-1 uses to shield vulnerable antibody targets in Env that induce neutralizing antibody breadth.
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29
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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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30
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Araújo LAL, Almeida SEM. HIV-1 diversity in the envelope glycoproteins: implications for viral entry inhibition. Viruses 2013; 5:595-604. [PMID: 23389465 PMCID: PMC3640516 DOI: 10.3390/v5020595] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/24/2013] [Accepted: 01/31/2013] [Indexed: 11/16/2022] Open
Abstract
Entry of HIV-1 into a host cell is a multi-step process, with the viral envelope gp120 and gp41 acting sequentially to mediate the viral attachment, CD4 binding, coreceptor binding, and fusion of the viral and host membranes. The emerging class of antiretroviral agents, collectively known as entry inhibitors, interfere in some of these steps. However, viral diversity has implications for possible differential responses to entry inhibitors, since envelope is the most variable of all HIV genes. Different HIV genetic forms carry in their genomes genetic signatures and polymorphisms that could alter the structure of viral proteins which are targeted by drugs, thus impairing antiretroviral binding and efficacy. This review will examine current research that describes subtype differences in envelope at the genetic level and the effects of mutations on the efficacy of current entry inhibitors.
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Affiliation(s)
- Leonardo Augusto Luvison Araújo
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Porto Alegre, 90610-000, Brazil.
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31
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Baan E, van der Sluis RM, Bakker ME, Bekker V, Pajkrt D, Jurriaans S, Kuijpers TW, Berkhout B, Wolthers KC, Paxton WA, Pollakis G. Human immunodeficiency virus type 1 gp120 envelope characteristics associated with disease progression differ in family members infected with genetically similar viruses. J Gen Virol 2012; 94:20-29. [PMID: 23015744 DOI: 10.1099/vir.0.046185-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) envelope protein provides the primary contact between the virus and host, and is the main target of the adaptive humoral immune response. The length of gp120 variable loops and the number of N-linked glycosylation events are key determinants for virus infectivity and immune escape, while the V3 loop overall positive charge is known to affect co-receptor tropism. We selected two families in which both parents and two children had been infected with HIV-1 for nearly 10 years, but who demonstrated variable parameters of disease progression. We analysed the gp120 envelope sequence and compared individuals that progressed to those that did not in order to decipher evolutionary alterations that are associated with disease progression when individuals are infected with genetically related virus strains. The analysis of the V3-positive charge demonstrated an association between higher V3-positive charges with disease progression. The ratio between the amino acid length and the number of potential N-linked glycosylation sites was also shown to be associated with disease progression with the healthier family members having a lower ratio. In conclusion in individuals initially infected with genetically linked virus strains the V3-positive charges and N-linked glycosylation are associated with HIV-1 disease progression and follow varied evolutionary paths for individuals with varied disease progression.
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Affiliation(s)
- Elly Baan
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Renée M van der Sluis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Margreet E Bakker
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Vincent Bekker
- Emma Children's Hospital, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Emma Children's Hospital, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Suzanne Jurriaans
- Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Taco W Kuijpers
- Emma Children's Hospital, Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Katja C Wolthers
- Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - William A Paxton
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology (LEV), Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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32
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Baan E, de Ronde A, Luchters S, Vyankandondera J, Lange JM, Pollakis G, Paxton WA. HIV type 1 mother-to-child transmission facilitated by distinctive glycosylation sites in the gp120 envelope glycoprotein. AIDS Res Hum Retroviruses 2012; 28:715-24. [PMID: 21916748 DOI: 10.1089/aid.2011.0023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) characteristics associated with mother-to-child transmission (MTCT) are still poorly understood. We studied a cohort of 30 mothers from Rwanda infected with HIV-1 subtype A or C viruses of whom seven infected their children either during gestation or soon after birth. CD4 counts and viral load did not significantly differ between nontransmitting mother (NTM) versus transmitting mother (TM) groups. In contrast to earlier studies we not only analyzed and compared the genotypic characteristics of the V1-V5 region of the gp120 envelope of viruses found in TM and their infected children, but also included data from the NTM. No differences were found with respect to length and number of potential N-glycosylation sites (PNGS) in the V1-V2 and the V1-V5 region. We identified that viruses with a PNGS on positions AA234 and AA339 were preferably transmitted and that viruses with PNGS-N295 showed a disadvantage in transmission. We also showed that the frequency of PNGS-N339 in the viruses of TM and infected children was significantly higher than the frequency in NTM in our cohort and in viruses undergoing sexual transmission while the frequency of PNGS-N295 in children was significantly lower than the frequency in TM and acute horizontal infections. Collectively, our results provide evidence that the presence of the PNGS-N339 site and absence of the PNGS-N295 site in the gp120 envelope confers an advantage to HIV-1 when considering MTCT.
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Affiliation(s)
- Elly Baan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
| | - Anthony de Ronde
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Luchters
- IATEC, International Antiviral Therapy Evaluation Center, Amsterdam, the Netherlands
| | - Joseph Vyankandondera
- CHUK, Centre Hospitalier Universitaire de Kigali and Belgian Technical Cooperation, Kigali, Rwanda
| | - Joep M. Lange
- IATEC, International Antiviral Therapy Evaluation Center, Amsterdam, the Netherlands
| | - Georgios Pollakis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
| | - William A. Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre of the University of Amsterdam, Amsterdam, the Netherlands
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Boonchawalit S, Jullaksorn D, Uttiyoung J, Yowang A, Krathong N, Chautrakul S, Yamashita A, Ikuta K, Roobsoong A, Kanitvittaya S, Sawanpanyalert P, Kameoka M. Molecular evolution of HIV-1 CRF01_AE Env in Thai patients. PLoS One 2011; 6:e27098. [PMID: 22073263 PMCID: PMC3206936 DOI: 10.1371/journal.pone.0027098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/10/2011] [Indexed: 12/03/2022] Open
Abstract
Background The envelope glycoproteins (Env), gp120 and gp41, are the most variable proteins of human immunodeficiency virus type 1 (HIV-1), and are the major targets of humoral immune responses against HIV-1. A circulating recombinant form of HIV-1, CRF01_AE, is prevalent throughout Southeast Asia; however, only limited information regarding the immunological characteristics of CRF01_AE Env is currently available. In this study, we attempted to examine the evolutionary pattern of CRF01_AE Env under the selection pressure of host immune responses. Methodology/Principal Findings Peripheral blood samples were collected periodically over 3 years from 15 HIV-1-infected individuals residing in northern Thailand, and amplified env genes from the samples were subjected to computational analysis. The V5 region of gp120 showed highest variability in several samples over 3 years, whereas the V1/V2 and/or V4 regions of gp120 also showed high variability in many samples. In addition, the N-terminal part of the C3 region of gp120 showed highest amino acid diversity among the conserved regions of gp120. Chronological changes in the numbers of amino acid residues in gp120 variable regions and potential N-linked glycosylation (PNLG) sites are involved in increasing the variability of Env gp120. Furthermore, the C3 region contained several amino acid residues potentially under positive selection, and APOBEC3 family protein-mediated G to A mutations were frequently detected in such residues. Conclusions/Significance Several factors, including amino acid substitutions particularly in gp120 C3 and V5 regions as well as changes in the number of PNLG sites and in the length of gp120 variable regions, were revealed to be involved in the molecular evolution of CRF01_AE Env. In addition, a similar tendency was observed between CRF01_AE and subtype C Env with regard to the amino acid variation of gp120 V3 and C3 regions. These results may provide important information for understanding the immunological characteristics of CRF01_AE Env.
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Affiliation(s)
- Samatchaya Boonchawalit
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Nonthaburi, Thailand
| | - Duangrat Jullaksorn
- National Institute of Health, Department of Medical Sciences (DMSc), Ministry of Public Health (MOPH), Nonthaburi, Thailand
| | - Jiraporn Uttiyoung
- Regional Medical Science Center Chiangrai, DMSc, MOPH, Chiangrai, Thailand
| | - Amara Yowang
- Regional Medical Science Center Chiangrai, DMSc, MOPH, Chiangrai, Thailand
| | | | | | | | - Kazuyoshi Ikuta
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | | | - Pathom Sawanpanyalert
- National Institute of Health, Department of Medical Sciences (DMSc), Ministry of Public Health (MOPH), Nonthaburi, Thailand
| | - Masanori Kameoka
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Nonthaburi, Thailand
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- * E-mail:
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34
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Tomaras GD, Binley JM, Gray ES, Crooks ET, Osawa K, Moore PL, Tumba N, Tong T, Shen X, Yates NL, Decker J, Wibmer CK, Gao F, Alam SM, Easterbrook P, Abdool Karim S, Kamanga G, Crump JA, Cohen M, Shaw GM, Mascola JR, Haynes BF, Montefiori DC, Morris L. Polyclonal B cell responses to conserved neutralization epitopes in a subset of HIV-1-infected individuals. J Virol 2011; 85:11502-19. [PMID: 21849452 PMCID: PMC3194956 DOI: 10.1128/jvi.05363-11] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 08/08/2011] [Indexed: 12/23/2022] Open
Abstract
A small proportion of HIV-infected individuals generate a neutralizing antibody (NAb) response of exceptional magnitude and breadth. A detailed analysis of the critical epitopes targeted by broadly neutralizing antibodies should help to define optimal targets for vaccine design. HIV-1-infected subjects with potent cross-reactive serum neutralizing antibodies were identified by assaying sera from 308 subjects against a multiclade panel of 12 "tier 2" viruses (4 each of subtypes A, B, and C). Various neutralizing epitope specificities were determined for the top 9 neutralizers, including clade A-, clade B-, clade C-, and clade A/C-infected donors, by using a comprehensive set of assays. In some subjects, neutralization breadth was mediated by two or more antibody specificities. Although antibodies to the gp41 membrane-proximal external region (MPER) were identified in some subjects, the subjects with the greatest neutralization breadth targeted gp120 epitopes, including the CD4 binding site, a glycan-containing quaternary epitope formed by the V2 and V3 loops, or an outer domain epitope containing a glycan at residue N332. The broadly reactive HIV-1 neutralization observed in some subjects is mediated by antibodies targeting several conserved regions on the HIV-1 envelope glycoprotein.
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Affiliation(s)
- Georgia D Tomaras
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Box 2926, Durham, NC 27710, USA.
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35
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Hosie MJ, Pajek D, Samman A, Willett BJ. Feline immunodeficiency virus (FIV) neutralization: a review. Viruses 2011; 3:1870-90. [PMID: 22069520 PMCID: PMC3205386 DOI: 10.3390/v3101870] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/28/2011] [Accepted: 09/29/2011] [Indexed: 11/16/2022] Open
Abstract
One of the major obstacles that must be overcome in the design of effective lentiviral vaccines is the ability of lentiviruses to evolve in order to escape from neutralizing antibodies. The primary target for neutralizing antibodies is the highly variable viral envelope glycoprotein (Env), a glycoprotein that is essential for viral entry and comprises both variable and conserved regions. As a result of the complex trimeric nature of Env, there is steric hindrance of conserved epitopes required for receptor binding so that these are not accessible to antibodies. Instead, the humoral response is targeted towards decoy immunodominant epitopes on variable domains such as the third hypervariable loop (V3) of Env. For feline immunodeficiency virus (FIV), as well as the related human immunodeficiency virus-1 (HIV-1), little is known about the factors that lead to the development of broadly neutralizing antibodies. In cats infected with FIV and patients infected with HIV-1, only rarely are plasma samples found that contain antibodies capable of neutralizing isolates from other clades. In this review we examine the neutralizing response to FIV, comparing and contrasting with the response to HIV. We ask whether broadly neutralizing antibodies are induced by FIV infection and discuss the comparative value of studies of neutralizing antibodies in FIV infection for the development of more effective vaccine strategies against lentiviral infections in general, including HIV-1.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Cat Diseases/immunology
- Cat Diseases/prevention & control
- Cat Diseases/virology
- Cats
- Gene Products, env/genetics
- Gene Products, env/immunology
- Gene Products, env/metabolism
- Humans
- Immune Evasion
- Immunity, Humoral
- Immunodeficiency Virus, Feline/genetics
- Immunodeficiency Virus, Feline/immunology
- Immunodominant Epitopes/immunology
- Lentivirus Infections/immunology
- Lentivirus Infections/prevention & control
- Lentivirus Infections/veterinary
- Lentivirus Infections/virology
- Molecular Sequence Data
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Affiliation(s)
- Margaret J Hosie
- Medical Research Council, University of Glasgow Centre for Virus Research, Henry Wellcome Building for Comparative Medical Sciences, 464 Bearsden Road, Glasgow G61 1QH, UK.
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36
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He X, Mokili JL, Hong K, Chen J, Wei J, Xin R, Song YH, Feng Y, Jia M, Xing H, Shao Y. Conservancy of the α4β7 integrin mimotope in the V2 domain of HIV type 1 CRF07_BC compared to subtype B' strains in China. AIDS Res Hum Retroviruses 2011; 27:1127-33. [PMID: 21417760 DOI: 10.1089/aid.2011.0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 is capable of mimicking the ligand of integrin α(4)β(7) by displaying a tripeptide mimotope on the V2 region. Through this mimicry HIV can bind the α(4)β(7) integrin and get carried through the lymphocyte proliferation signaling pathway, cell-to-cell adhesion and can migrate to gut-associated lymphoid tissues. The same tripeptide motif was suggested to be the epicenter of neutralization in laboratory strains of HIV-1. In this study, we compared the α(4)β(7) binding sites of two HIV-1 subtypes prevalent in China and found that the tripeptide binding domain of α(4)β(7) was more diverse in subtype B' strains than in CRF07_BC.
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Affiliation(s)
- Xiang He
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - John L. Mokili
- Department of Biology, San Diego State University, San Diego, California
- Global Viral Forecasting, San Francisco, California
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Jianping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Jing Wei
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Ruolei Xin
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Yan-Hui Song
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Mingming Jia
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China
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37
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Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Ban YEA, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog 2011; 7:e1002209. [PMID: 21980282 PMCID: PMC3182927 DOI: 10.1371/journal.ppat.1002209] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 06/26/2011] [Indexed: 12/15/2022] Open
Abstract
Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.
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Affiliation(s)
- S. Gnanakaran
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Marcus Daniels
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brandon F. Keele
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter T. Hraber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tongye Shen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brian Gaschen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mohan Krishnamoorthy
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jesus F. Salazar-Gonzalez
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chunlai Jiang
- National Engineering Laboratory of AIDS Vaccine School of Life Science, Jilin University, Changchun, China
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Anderson
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Li-Hua Ping
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, New York, United States of America
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joseph J. Eron
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles B. Hicks
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - William A. Blattner
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Georgia D. Tomaras
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Mohammed Asmal
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Norman L. Letvin
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Division of Viral Pathogenesis, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter B. Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Allan C. DeCamp
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Craig A. Magaret
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yih-En Andrew Ban
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Arzeda Corporation, Seattle, Washington, United States of America
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
| | - Kelly A. Soderberg
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Joseph G. Sodroski
- Dana-Farber Cancer Institute, Department of Cancer Immunology and AIDS, Boston, Massachusetts, United States of America
| | - Barton F. Haynes
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bette Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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38
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Tang H, Robinson JE, Gnanakaran S, Li M, Rosenberg ES, Perez LG, Haynes BF, Liao HX, LaBranche CC, Korber BT, Montefiori DC. epitopes immediately below the base of the V3 loop of gp120 as targets for the initial autologous neutralizing antibody response in two HIV-1 subtype B-infected individuals. J Virol 2011; 85:9286-99. [PMID: 21734041 PMCID: PMC3165744 DOI: 10.1128/jvi.02286-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 06/15/2011] [Indexed: 01/01/2023] Open
Abstract
Epitopes that drive the initial autologous neutralizing antibody response in HIV-1-infected individuals could provide insights for vaccine design. Although highly strain specific, these epitopes are immunogenic, vulnerable to antibody attack on infectious virus, and could be involved in the ontogeny of broadly neutralizing antibody responses. To delineate such epitopes, we used site-directed mutagenesis, autologous plasma samples, and autologous monoclonal antibodies to map the amino acid changes that led to escape from the initial autologous neutralizing antibody response in two HIV-1 subtype B-infected individuals. Additional mapping of the epitopes was accomplished by using alanine scanning mutagenesis. Escape in the two individuals occurred by different pathways, but the responses in both cases appeared to be directed against the same region of gp120. In total, three amino acid positions were identified that were independently associated with autologous neutralization. Positions 295 and 332 are located immediately before and after the N- and C-terminal cysteines of the V3 loop, respectively, the latter of which affected an N-linked glycan that was critical to the neutralization epitope. Position 415 affected an N-linked glycan at position 413 in the C terminus of V4 that might mask epitopes near the base of V3. All three sites lie in close proximity on a four-stranded antiparallel sheet on the outer domain of gp120. We conclude that a region just below the base of the V3 loop, near the coreceptor binding domain of gp120, can be a target for autologous neutralization.
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Affiliation(s)
| | - James E. Robinson
- Department of Pediatrics, Tulane University Medical Center, New Orleans, Louisiana
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - Eric S. Rosenberg
- Pathology Service and Infectious Disease Division, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts
| | | | - Barton F. Haynes
- Medicine, Duke University Medical Center, Durham, North Carolina
| | - Hua-Xin Liao
- Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Bette T. Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
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39
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Ringe R, Sharma D, Zolla-Pazner S, Phogat S, Risbud A, Thakar M, Paranjape R, Bhattacharya J. A single amino acid substitution in the C4 region in gp120 confers enhanced neutralization of HIV-1 by modulating CD4 binding sites and V3 loop. Virology 2011; 418:123-32. [PMID: 21851958 DOI: 10.1016/j.virol.2011.07.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 05/12/2011] [Accepted: 07/25/2011] [Indexed: 02/04/2023]
Abstract
Identification of vulnerability in the HIV-1 envelope (Env) will aid in Env-based vaccine design. We recently found an HIV-1 clade C Env clone (4-2.J45) amplified from a recently infected Indian patient showing exceptional neutralization sensitivity to autologous plasma in contrast to other autologous Envs obtained at the same time point. By constructing chimeric Envs and fine mapping between sensitive and resistant Env clones, we found that substitution of highly conserved isoleucine (I) with methionine (M) (ATA to ATG) at position 424 in the C4 domain conferred enhanced neutralization sensitivity of Env-pseudotyped viruses to autologous and heterologous plasma antibodies. When tested against monoclonal antibodies targeting different sites in gp120 and gp41, Envs expressing M424 showed significant sensitivity to anti-V3 monoclonal antibodies and modestly to sCD4 and b12. Substitution of I424M in unrelated Envs also showed similar neutralization phenotype, indicating that M424 in C4 region induces exposure of neutralizing epitopes particularly in CD4 binding sites and V3 loop.
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Affiliation(s)
- Rajesh Ringe
- Department of Molecular Virology, National AIDS Research Institute, Pune, India
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40
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Antibody-dependent cell-mediated viral inhibition emerges after simian immunodeficiency virus SIVmac251 infection of rhesus monkeys coincident with gp140-binding antibodies and is effective against neutralization-resistant viruses. J Virol 2011; 85:5465-75. [PMID: 21450829 DOI: 10.1128/jvi.00313-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibody-dependent cell-mediated viral inhibition (ADCVI) is an attractive target for vaccination because it takes advantage of both the anamnestic properties of an adaptive immune response and the rapid early response characteristics of an innate immune response. Effective utilization of ADCVI in vaccine strategies will depend on an understanding of the natural history of ADCVI during acute and chronic human immunodeficiency virus type 1 (HIV-1) infection. We used the simian immunodeficiency virus (SIV)-infected rhesus monkey as a model to study the kinetics of ADCVI in early infection, the durability of ADCVI through the course of infection, and the effectiveness of ADCVI against viruses with envelope mutations that are known to confer escape from antibody neutralization. We demonstrate the development of ADCVI, capable of inhibiting viral replication 100-fold, within 3 weeks of infection, preceding the development of a comparable-titer neutralizing antibody response by weeks to months. The emergence of ADCVI was temporally associated with the emergence of gp140-binding antibodies, and in most animals, ADCVI persisted through the course of infection. Highly evolved viral envelopes from viruses isolated at late time points following infection that were resistant to plasma neutralization remained susceptible to ADCVI, suggesting that the epitope determinants of neutralization escape are not shared by antibodies that mediate ADCVI. These findings suggest that despite the ability of SIV to mutate and adapt to multiple immunologic pressures during the course of infection, SIV envelope may not escape the binding of autologous antibodies that mediate ADCVI.
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41
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Phylogenetic characterisation of naturally occurring feline immunodeficiency virus in the United Kingdom. Vet Microbiol 2011; 150:239-47. [PMID: 21349661 PMCID: PMC3103826 DOI: 10.1016/j.vetmic.2011.01.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/20/2011] [Accepted: 01/24/2011] [Indexed: 11/23/2022]
Abstract
Feline immunodeficiency virus (FIV) is a significant pathogen of domestic and non-domestic felids worldwide. In domestic cats, FIV is classified into five distinct subtypes (A–E) with subtypes A and B distributed most widely. However, little is known about the degree of intrasubtype viral diversity and this may prove critical in determining whether monovalent vaccines are likely to protect against FIV strains within a single subtype. Here, we characterise novel env sequences from 47 FIV strains recovered from infected cats in the United Kingdom and its environs. Phylogenetic analyses revealed that all bar one sequence belonged to subtype A, the predominant subtype in Western Europe. A single sequence was identified as a likely subtype A/C recombinant, intriguing given that subtype C does not appear to exist in either the UK or North Western Europe and suggestive of a recombination event predating its introduction into the UK. Subtype A strains from the UK were not significantly differentiated from representative subtype A isolates found elsewhere suggesting multiple introductions of FIV into the country. Divergence among isolates was comparable to that observed for subtype A isolates worldwide, indicating that FIV in the UK covers the full spectrum of subtype A diversity seen globally. This study demonstrates that while subtype A is predominant in the UK, novel introductions may result in the emergence of novel subtypes or intersubtype recombinants, potentially circumventing vaccine strategies. However, the dominance of subtype A suggests that the development of a regional or subtype-specific protective vaccine for the UK could be achievable.
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Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection. PLoS One 2011; 6:e14548. [PMID: 21283793 PMCID: PMC3024314 DOI: 10.1371/journal.pone.0014548] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/10/2010] [Indexed: 11/21/2022] Open
Abstract
Background Unlike in HIV-1 infection, the majority of HIV-2 patients produce broadly reactive neutralizing antibodies, control viral replication and survive as elite controllers. The identification of the molecular, structural and evolutionary footprints underlying these very distinct immunological and clinical outcomes may lead to the development of new strategies for the prevention and treatment of HIV infection. Methodology/Principal Findings We performed a side-by-side molecular, evolutionary and structural comparison of the C2, V3 and C3 envelope regions from HIV-1 and HIV-2. These regions contain major antigenic targets and are important for receptor binding. In HIV-2, these regions also have immune modulatory properties. We found that these regions are significantly more variable in HIV-1 than in HIV-2. Within each virus, C3 is the most entropic region followed by either C2 (HIV-2) or V3 (HIV-1). The C3 region is well exposed in the HIV-2 envelope and is under strong diversifying selection suggesting that, like in HIV-1, it may harbour neutralizing epitopes. Notably, however, extreme diversification of C2 and C3 seems to be deleterious for HIV-2 and prevent its transmission. Computer modelling simulations showed that in HIV-2 the V3 loop is much less exposed than C2 and C3 and has a retractile conformation due to a physical interaction with both C2 and C3. The concealed and conserved nature of V3 in the HIV-2 is consistent with its lack of immunodominancy in vivo and with its role in preventing immune activation. In contrast, HIV-1 had an extended and accessible V3 loop that is consistent with its immunodominant and neutralizing nature. Conclusions/Significance We identify significant structural and functional constrains to the diversification and evolution of C2, V3 and C3 in the HIV-2 envelope but not in HIV-1. These studies highlight fundamental differences in the biology and infection of HIV-1 and HIV-2 and in their mode of interaction with the human immune system and may inform new vaccine and therapeutic interventions against these viruses.
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Lynch RM, Rong R, Boliar S, Sethi A, Li B, Mulenga J, Allen S, Robinson JE, Gnanakaran S, Derdeyn CA. The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconverter. J Virol 2011; 85:905-15. [PMID: 20980495 PMCID: PMC3020014 DOI: 10.1128/jvi.02006-10] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 10/21/2010] [Indexed: 12/13/2022] Open
Abstract
High-titer autologous neutralizing antibody responses have been demonstrated during early subtype C human immunodeficiency virus type 1 (HIV-1) infection. However, characterization of this response against autologous virus at the monoclonal antibody (MAb) level has only recently begun to be elucidated. Here we describe five monoclonal antibodies derived from a subtype C-infected seroconverter and their neutralizing activities against pseudoviruses that carry envelope glycoproteins from 48 days (0 month), 2 months, and 8 months after the estimated time of infection. Sequence analysis indicated that the MAbs arose from three distinct B cell clones, and their pattern of neutralization compared to that in patient plasma suggested that they circulated between 2 and 8 months after infection. Neutralization by MAbs representative of each B cell clone was mapped to two residues: position 134 in V1 and position 189 in V2. Mutational analysis revealed cooperative effects between glycans and residues at these two positions, arguing that they contribute to a single epitope. Analysis of the cognate gp120 sequence through homology modeling places this potential epitope near the interface between the V1 and V2 loops. Additionally, the escape mutation R189S in V2, which conferred resistance against all three MAbs, had no detrimental effect on virus replication in vitro. Taken together, our data demonstrate that independent B cells repeatedly targeted a single structure in V1V2 during early infection. Despite this assault, a single amino acid change was sufficient to confer complete escape with minimal impact on replication fitness.
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Affiliation(s)
- Rebecca M Lynch
- Emory Vaccine Center, Emory University, 954 Gatewood Rd., Atlanta, GA 30329, USA
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Archary D, Gordon ML, Green TN, Coovadia HM, Goulder PJR, Ndung'u T. HIV-1 subtype C envelope characteristics associated with divergent rates of chronic disease progression. Retrovirology 2010; 7:92. [PMID: 21050445 PMCID: PMC2992043 DOI: 10.1186/1742-4690-7-92] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/04/2010] [Indexed: 11/10/2022] Open
Abstract
Background HIV-1 envelope diversity remains a significant challenge for the development of an efficacious vaccine. The evolutionary forces that shape the diversity of envelope are incompletely understood. HIV-1 subtype C envelope in particular shows significant differences and unique characteristics compared to its subtype B counterpart. Here we applied the single genome sequencing strategy of plasma derived virus from a cohort of therapy naïve chronically infected individuals in order to study diversity, divergence patterns and envelope characteristics across the entire HIV-1 subtype C gp160 in 4 slow progressors and 4 progressors over an average of 19.5 months. Results Sequence analysis indicated that intra-patient nucleotide diversity within the entire envelope was higher in slow progressors, but did not reach statistical significance (p = 0.07). However, intra-patient nucleotide diversity was significantly higher in slow progressors compared to progressors in the C2 (p = 0.0006), V3 (p = 0.01) and C3 (p = 0.005) regions. Increased amino acid length and fewer potential N-linked glycosylation sites (PNGs) were observed in the V1-V4 in slow progressors compared to progressors (p = 0.009 and p = 0.02 respectively). Similarly, gp41 in the progressors was significantly longer and had fewer PNGs compared to slow progressors (p = 0.02 and p = 0.02 respectively). Positive selection hotspots mapped mainly to V1, C3, V4, C4 and gp41 in slow progressors, whereas hotspots mapped mainly to gp41 in progressors. Signature consensus sequence differences between the groups occurred mainly in gp41. Conclusions These data suggest that separate regions of envelope are under differential selective forces, and that envelope evolution differs based on disease course. Differences between slow progressors and progressors may reflect differences in immunological pressure and immune evasion mechanisms. These data also indicate that the pattern of envelope evolution is an important correlate of disease progression in chronic HIV-1 subtype C infection.
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Affiliation(s)
- Derseree Archary
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R, Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Kirchherr JL, Hamilton J, Lu X, Gnanakaran S, Muldoon M, Daniels M, Kasongo W, Chalwe V, Mulenga C, Mwananyanda L, Musonda RM, Yuan X, Montefiori DC, Korber BT, Haynes BF, Gao F. Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology 2010; 409:163-74. [PMID: 21036380 DOI: 10.1016/j.virol.2010.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/22/2010] [Accepted: 09/27/2010] [Indexed: 10/18/2022]
Abstract
Neutralizing antibodies (Nabs) are thought to play an important role in prevention and control of HIV-1 infection and should be targeted by an AIDS vaccine. It is critical to understand how HIV-1 induces Nabs by analyzing viral sequences in both tested viruses and sera. Neutralization susceptibility to antibodies in autologous and heterologous plasma was determined for multiple Envs (3-6) from each of 15 subtype-C-infected individuals. Heterologous neutralization was divided into two distinct groups: plasma with strong, cross-reactive neutralization (n=9) and plasma with weak neutralization (n=6). Plasma with cross-reactive heterologous Nabs also more potently neutralized contemporaneous autologous viruses. Analysis of Env sequences in plasma from both groups revealed a three-amino-acid substitution pattern in the V4 region that was associated with greater neutralization potency and breadth. Identification of such potential neutralization signatures may have important implications for the development of HIV-1 vaccines capable of inducing Nabs to subtype C HIV-1.
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Affiliation(s)
- Jennifer L Kirchherr
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
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Gnanakaran S, Daniels MG, Bhattacharya T, Lapedes AS, Sethi A, Li M, Tang H, Greene K, Gao H, Haynes BF, Cohen MS, Shaw GM, Seaman MS, Kumar A, Gao F, Montefiori DC, Korber B. Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. PLoS Comput Biol 2010; 6:e1000955. [PMID: 20949103 PMCID: PMC2951345 DOI: 10.1371/journal.pcbi.1000955] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 09/10/2010] [Indexed: 11/27/2022] Open
Abstract
A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1.
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Affiliation(s)
- S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marcus G. Daniels
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anurag Sethi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ming Li
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Haili Tang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kelli Greene
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - George M. Shaw
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Amit Kumar
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Feng Gao
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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Ringe R, Thakar M, Bhattacharya J. Variations in autologous neutralization and CD4 dependence of b12 resistant HIV-1 clade C env clones obtained at different time points from antiretroviral naïve Indian patients with recent infection. Retrovirology 2010; 7:76. [PMID: 20860805 PMCID: PMC2955667 DOI: 10.1186/1742-4690-7-76] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Limited information is available on HIV-1 Indian clade C sensitivities to autologous antibodies during the course of natural infection. In the present study, a total of 37 complete envelope clones (Env) were amplified at different time points predominantly from the plasma of five Indian patients with recent HIV-1 infection and envelope-pseudotyped viruses were examined for their magnitude of sensitivity to autologous plasma antibodies during natural course of infection. Results Variable low levels of neutralization were consistently detected with contemporaneous autologous plasma. In contrast to clade B and African clade C HIV-1 envelopes, Env clones obtained from four patients were found to be resistant to IgG1b12. The majority of the Env clones were resistant to 2G12 and 2F5 due to the absence of the minimal motifs required for antibody recognition, but were sensitive to 4E10. Nonetheless, Env clones from one patient were found to be sensitive to 2G12, atypical for clade C, and one Env clone exhibited unusual sensitivity to 17b, suggesting spontaneous exposure of CD4i epitopes. Phylogenetic analysis revealed that Env clones were closely clustered within patients. Variation in the potential N-linked glycosylation pattern also appeared to be different in patients over the course of infection. Interestingly, we found that the sensitivity of Envs to contemporaneous autologous NAbs correlated positively with increased sensitivity to soluble CD4 and inversely with anti-CD4 antibody and Envs with increased NAb sensitivity were able to efficiently infect HeLa cells expressing low CD4. Conclusion Our data showed considerable variations in autologous neutralization of these early HIV-1 clade C Envs in each of these patients and indicate greater exposure to CD4 of Envs that showed increased autologous neutralization. Interestingly, Env clones obtained from a single patient at different time points were found to retain sensitivity to b12 antibody that binds to CD4 binding site in Env in contrast to Envs obtained from other patients. However, we did not find any association between increased b12 sensitivity of Envs obtained from this particular patient with their degree of exposure to CD4.
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Affiliation(s)
- Rajesh Ringe
- Department of Molecular Virology, National AIDS Research Institute, Indian Council of Medical Research, G-73 MIDC, Bhosari, Pune, India
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Raska M, Takahashi K, Czernekova L, Zachova K, Hall S, Moldoveanu Z, Elliott MC, Wilson L, Brown R, Jancova D, Barnes S, Vrbkova J, Tomana M, Smith PD, Mestecky J, Renfrow MB, Novak J. Glycosylation patterns of HIV-1 gp120 depend on the type of expressing cells and affect antibody recognition. J Biol Chem 2010; 285:20860-9. [PMID: 20439465 PMCID: PMC2898351 DOI: 10.1074/jbc.m109.085472] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 04/28/2010] [Indexed: 01/18/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) entry is mediated by the interaction between a variably glycosylated envelope glycoprotein (gp120) and host-cell receptors. Approximately half of the molecular mass of gp120 is contributed by N-glycans, which serve as potential epitopes and may shield gp120 from immune recognition. The role of gp120 glycans in the host immune response to HIV-1 has not been comprehensively studied at the molecular level. We developed a new approach to characterize cell-specific gp120 glycosylation, the regulation of glycosylation, and the effect of variable glycosylation on antibody reactivity. A model oligomeric gp120 was expressed in different cell types, including cell lines that represent host-infected cells or cells used to produce gp120 for vaccination purposes. N-Glycosylation of gp120 varied, depending on the cell type used for its expression and the metabolic manipulation during expression. The resultant glycosylation included changes in the ratio of high-mannose to complex N-glycans, terminal decoration, and branching. Differential glycosylation of gp120 affected envelope recognition by polyclonal antibodies from the sera of HIV-1-infected subjects. These results indicate that gp120 glycans contribute to antibody reactivity and should be considered in HIV-1 vaccine design.
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Affiliation(s)
- Milan Raska
- From the Departments of Immunology and
- the Departments of Microbiology
| | | | | | | | | | | | | | | | | | | | | | - Jana Vrbkova
- Mathematical Analysis and Applications of Mathematics, Palacky University in Olomouc, Olomouc 77100, Czech Republic
| | | | - Phillip D. Smith
- Medicine, and
- the Veterans Affairs Medical Center, Birmingham, Alabama 35205, and
| | - Jiri Mestecky
- the Departments of Microbiology
- Medicine, and
- the Institute of Microbiology and Immunology, First Faculty of Medicine, Charles University, Prague, Czech Republic 12108
| | - Matthew B. Renfrow
- Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Barton HD, Gregory AJ, Davis R, Hanlon CA, Wisely SM. Contrasting landscape epidemiology of two sympatric rabies virus strains. Mol Ecol 2010; 19:2725-38. [PMID: 20546130 DOI: 10.1111/j.1365-294x.2010.04668.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Viral strain evolution and disease emergence are influenced by anthropogenic change to the environment. We investigated viral characteristics, host ecology, and landscape features in the rabies-striped skunk disease system of the central Great Plains to determine how these factors interact to influence disease emergence. We amplified portions of the N and G genes of rabies viral RNA from 269 samples extracted from striped skunk brains throughout the distribution of two different rabies strains for which striped skunks were the reservoir. Because the distribution of these two strains overlapped on the landscape and were present in the same host population, we could evaluate how viral properties influenced epidemiological patterns in the area of sympatry. We found that South Central Skunk rabies (SCSK) exhibited intense purifying selection and high infectivity, which are both characteristics of an epizootic virus. Conversely, North Central Skunk rabies (NCSK) exhibited relaxed purifying selection and comparatively lower infectivity, suggesting the presence of an enzootic virus. The host population in the area of sympatry was highly admixed, and skunks among allopatric and sympatric areas had similar effective population sizes. Spatial analysis indicated that landscape features had minimal influence on NCSK movement across the landscape, but those same features were partial barriers to the spread of SCSK. We conclude that NCSK and SCSK have different epidemiological properties that interact differently with both host and landscape features to influence rabies spread in the central Great Plains. We suggest a holistic approach for future studies of emerging infectious diseases that includes studies of viral properties, host characteristics, and spatial features.
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Affiliation(s)
- Heather D Barton
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
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50
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Lynch RM, Rong R, Li B, Shen T, Honnen W, Mulenga J, Allen S, Pinter A, Gnanakaran S, Derdeyn CA. Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection. Virology 2010; 404:59-70. [PMID: 20494390 DOI: 10.1016/j.virol.2010.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 03/17/2010] [Accepted: 04/10/2010] [Indexed: 11/19/2022]
Abstract
The V3 region of the HIV-1 envelope (Env) glycoprotein gp120 is a key functional domain yet it exhibits distinct mutational patterns across subtypes. Here an invariant residue (Ile 309) was replaced with Leu in 7 subtype C patient-derived Envs from recent infection and 4 related neutralizing antibody escape variants that emerged later. For these 11 Envs, I309L did not alter replication in primary CD4 T cells; however, replication in monocyte-derived macrophages was enhanced. Infection of cell lines with low CD4 or CCR5 revealed that I309L enhanced utilization of CD4 but did not affect the ability to use CCR5. This CD4-enhanced phenotype tracked with sensitivity to sCD4, indicating increased exposure of the CD4 binding site. The results suggest that Ile 309 preserves a V3-mediated masking function that occludes the CD4 binding site. The findings point to an immune evasion strategy in subtype C Env to protect this vulnerable immune target.
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Affiliation(s)
- Rebecca M Lynch
- Immunology and Molecular Pathogenesis Program, Emory University, Atlanta, GA 30329, USA
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