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Cottrell CA, Hu X, Lee JH, Skog P, Luo S, Flynn CT, McKenney KR, Hurtado J, Kalyuzhniy O, Liguori A, Willis JR, Landais E, Raemisch S, Chen X, Baboo S, Himansu S, Diedrich JK, Duan H, Cheng C, Schiffner T, Bader DLV, Kulp DW, Tingle R, Georgeson E, Eskandarzadeh S, Alavi N, Lu D, Sincomb T, Kubitz M, Mullen TM, Yates JR, Paulson JC, Mascola JR, Alt FW, Briney B, Sok D, Schief WR. Heterologous prime-boost vaccination drives early maturation of HIV broadly neutralizing antibody precursors in humanized mice. Sci Transl Med 2024; 16:eadn0223. [PMID: 38753806 PMCID: PMC11233128 DOI: 10.1126/scitranslmed.adn0223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
A protective HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). Vaccination with the germline-targeting immunogen eOD-GT8 60mer adjuvanted with AS01B was found to induce VRC01-class bnAb precursors in 97% of vaccine recipients in the IAVI G001 phase 1 clinical trial; however, heterologous boost immunizations with antigens more similar to the native glycoprotein will be required to induce bnAbs. Therefore, we designed core-g28v2 60mer, a nanoparticle immunogen to be used as a first boost after eOD-GT8 60mer priming. We found, using a humanized mouse model approximating human conditions of VRC01-class precursor B cell diversity, affinity, and frequency, that both protein- and mRNA-based heterologous prime-boost regimens induced VRC01-class antibodies that gained key mutations and bound to near-native HIV envelope trimers lacking the N276 glycan. We further showed that VRC01-class antibodies induced by mRNA-based regimens could neutralize pseudoviruses lacking the N276 glycan. These results demonstrated that heterologous boosting can drive maturation toward VRC01-class bnAb development and supported the initiation of the IAVI G002 phase 1 trial testing mRNA-encoded nanoparticle prime-boost regimens.
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Affiliation(s)
- Christopher A Cottrell
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Therapeutics, Cambridge, MA 02139, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick Skog
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sai Luo
- HHMI, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia T Flynn
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katherine R McKenney
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sebastian Raemisch
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabyasachi Baboo
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongying Duan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Torben Schiffner
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel L V Bader
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Tingle
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nushin Alavi
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Danny Lu
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Troy Sincomb
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tina-Marie Mullen
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frederick W Alt
- HHMI, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Therapeutics, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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Joshi VR, Claiborne DT, Pack ML, Power KA, Newman RM, Batorsky R, Bean DJ, Goroff MS, Lingwood D, Seaman MS, Rosenberg E, Allen TM. A VRC13-like bNAb response is associated with complex escape pathways in HIV-1 envelope. J Virol 2024; 98:e0172023. [PMID: 38412036 PMCID: PMC10949433 DOI: 10.1128/jvi.01720-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
The rational design of HIV-1 immunogens to trigger the development of broadly neutralizing antibodies (bNAbs) requires understanding the viral evolutionary pathways influencing this process. An acute HIV-1-infected individual exhibiting >50% plasma neutralization breadth developed neutralizing antibody specificities against the CD4-binding site (CD4bs) and V1V2 regions of Env gp120. Comparison of pseudoviruses derived from early and late autologous env sequences demonstrated the development of >2 log resistance to VRC13 but not to other CD4bs-specific bNAbs. Mapping studies indicated that the V3 and CD4-binding loops of Env gp120 contributed significantly to developing resistance to the autologous neutralizing response and that the CD4-binding loop (CD4BL) specifically was responsible for the developing resistance to VRC13. Tracking viral evolution during the development of this cross-neutralizing CD4bs response identified amino acid substitutions arising at only 4 of 11 known VRC13 contact sites (K282, T283, K421, and V471). However, each of these mutations was external to the V3 and CD4BL regions conferring resistance to VRC13 and was transient in nature. Rather, complete resistance to VRC13 was achieved through the cooperative expression of a cluster of single amino acid changes within and immediately adjacent to the CD4BL, including a T359I substitution, exchange of a potential N-linked glycosylation (PNLG) site to residue S362 from N363, and a P369L substitution. Collectively, our data characterize complex HIV-1 env evolution in an individual developing resistance to a VRC13-like neutralizing antibody response and identify novel VRC13-associated escape mutations that may be important to inducing VRC13-like bNAbs for lineage-based immunogens.IMPORTANCEThe pursuit of eliciting broadly neutralizing antibodies (bNAbs) through vaccination and their use as therapeutics remains a significant focus in the effort to eradicate HIV-1. Key to our understanding of this approach is a more extensive understanding of bNAb contact sites and susceptible escape mutations in HIV-1 envelope (env). We identified a broad neutralizer exhibiting VRC13-like responses, a non-germline restricted class of CD4-binding site antibody distinct from the well-studied VRC01-class. Through longitudinal envelope sequencing and Env-pseudotyped neutralization assays, we characterized a complex escape pathway requiring the cooperative evolution of four amino acid changes to confer complete resistance to VRC13. This suggests that VRC13-class bNAbs may be refractory to rapid escape and attractive for therapeutic applications. Furthermore, the identification of longitudinal viral changes concomitant with the development of neutralization breadth may help identify the viral intermediates needed for the maturation of VRC13-like responses and the design of lineage-based immunogens.
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Affiliation(s)
- Vinita R. Joshi
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Virology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Daniel T. Claiborne
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Melissa L. Pack
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Karen A. Power
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ruchi M. Newman
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rebecca Batorsky
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - David J. Bean
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Matthew S. Goroff
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Lingwood
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Eric Rosenberg
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Todd M. Allen
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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3
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Misra M, Jeffy J, Liao C, Pickthorn S, Wagh K, Herschhorn A. HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies. Bioinformatics 2024; 40:btae103. [PMID: 38426331 PMCID: PMC10919947 DOI: 10.1093/bioinformatics/btae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/14/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
MOTIVATION Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. RESULTS Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs. AVAILABILITY AND IMPLEMENTATION HIResist is freely available at https://hiresist.ahc.umn.edu/.
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Affiliation(s)
- Milind Misra
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jeffy Jeffy
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Charis Liao
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Stephanie Pickthorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kshitij Wagh
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
- Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455, United States
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States
- Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota, Minneapolis, MN 55455, United States
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4
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Anang S, Zhang S, Fritschi C, Chiu TJ, Yang D, Smith III AB, Madani N, Sodroski J. V3 tip determinants of susceptibility to inhibition by CD4-mimetic compounds in natural clade A human immunodeficiency virus (HIV-1) envelope glycoproteins. J Virol 2023; 97:e0117123. [PMID: 37888980 PMCID: PMC10688366 DOI: 10.1128/jvi.01171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE CD4-mimetic compounds (CD4mcs) are small-molecule inhibitors of human immunodeficiency virus (HIV-1) entry into host cells. CD4mcs target a pocket on the viral envelope glycoprotein (Env) spike that is used for binding to the receptor, CD4, and is highly conserved among HIV-1 strains. Nonetheless, naturally occurring HIV-1 strains exhibit a wide range of sensitivities to CD4mcs. Our study identifies changes distant from the binding pocket that can influence the susceptibility of natural HIV-1 strains to the antiviral effects of multiple CD4mcs. We relate the antiviral potency of the CD4mc against this panel of HIV-1 variants to the ability of the CD4mc to activate entry-related changes in Env conformation prematurely. These findings will guide efforts to improve the potency and breadth of CD4mcs against natural HIV-1 variants.
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Affiliation(s)
- Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher Fritschi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ta-Jung Chiu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Derek Yang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amos B. Smith III
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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5
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Dănăilă VR, Avram S, Buiu C. The applications of machine learning in HIV neutralizing antibodies research-A systematic review. Artif Intell Med 2022; 134:102429. [PMID: 36462896 DOI: 10.1016/j.artmed.2022.102429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 09/03/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022]
Abstract
Machine learning algorithms play an essential role in bioinformatics and allow exploring the vast and noisy biological data in unrivaled ways. This paper is a systematic review of the applications of machine learning in the study of HIV neutralizing antibodies. This significant and vast research domain can pave the way to novel treatments and to a vaccine. We selected the relevant papers by investigating the available literature from the Web of Science and PubMed databases in the last decade. The computational methods are applied in neutralization potency prediction, neutralization span prediction against multiple viral strains, antibody-virus binding sites detection, enhanced antibodies design, and the study of the antibody-induced immune response. These methods are viewed from multiple angles spanning data processing, model description, feature selection, evaluation, and sometimes paper comparisons. The algorithms are diverse and include supervised, unsupervised, and generative types. Both classical machine learning and modern deep learning were taken into account. The review ends with our ideas regarding future research directions and challenges.
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Affiliation(s)
- Vlad-Rareş Dănăilă
- Department of Automatic Control and Systems Engineering, Politehnica University of Bucharest, 313 Splaiul Independenţei, Bucharest 060042, Romania.
| | - Speranţa Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, Bucharest 050095, Romania.
| | - Cătălin Buiu
- Department of Automatic Control and Systems Engineering, Politehnica University of Bucharest, 313 Splaiul Independenţei, Bucharest 060042, Romania.
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Dănăilă VR, Buiu C. Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning. Bioinformatics 2022; 38:4278-4285. [PMID: 35876860 PMCID: PMC9477525 DOI: 10.1093/bioinformatics/btac530] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Knowing the sensitivity of a viral strain versus a monoclonal antibody is of interest for HIV vaccine development and therapy. The HIV strains vary in their resistance to antibodies, and the accurate prediction of virus-antibody sensitivity can be used to find potent antibody combinations that broadly neutralize multiple and diverse HIV strains. Sensitivity prediction can be combined with other methods such as generative algorithms to design novel antibodies in silico or with feature selection to uncover the sites of interest in the sequence. However, these tools are limited in the absence of in silico accurate prediction methods. RESULTS Our method leverages the CATNAP dataset, probably the most comprehensive collection of HIV-antibodies assays, and predicts the antibody-virus sensitivity in the form of binary classification. The methods proposed by others focus primarily on analyzing the virus sequences. However, our article demonstrates the advantages gained by modeling the antibody-virus sensitivity as a function of both virus and antibody sequences. The input is formed by the virus envelope and the antibody variable region aminoacid sequences. No structural features are required, which makes our system very practical, given that sequence data is more common than structures. We compare with two other state-of-the-art methods that leverage the same dataset and use sequence data only. Our approach, based on neuronal networks and transfer learning, measures increased predictive performance as measured on a set of 31 specific broadly neutralizing antibodies. AVAILABILITY AND IMPLEMENTATION https://github.com/vlad-danaila/deep_hiv_ab_pred/tree/fc-att-fix.
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Affiliation(s)
- Vlad-Rareş Dănăilă
- Department of Automatic Control and Systems Engineering, Politehnica University of Bucharest, Bucharest 060042, Romania
| | - Cătălin Buiu
- Department of Automatic Control and Systems Engineering, Politehnica University of Bucharest, Bucharest 060042, Romania
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7
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Li Y, Guo Y, Cheng H, Zeng X, Zhang X, Sang P, Chen B, Yang L. Deciphering gp120 sequence variation and structural dynamics in
HIV
neutralization phenotype by molecular dynamics simulations and graph machine learning. Proteins 2022; 90:1413-1424. [DOI: 10.1002/prot.26322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/21/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Yi Li
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Yu‐Chen Guo
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Hong‐Han Cheng
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Xin Zeng
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Xiao‐Ling Zhang
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Peng Sang
- College of Agriculture and Biological Science Dali University Dali Yunnan China
| | - Ben‐Hui Chen
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Li‐Quan Yang
- College of Agriculture and Biological Science Dali University Dali Yunnan China
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8
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Chua JV, Davis C, Husson JS, Nelson A, Prado I, Flinko R, Lam KWJ, Mutumbi L, Mayer BT, Dong D, Fulp W, Mahoney C, Gerber M, Gottardo R, Gilliam BL, Greene K, Gao H, Yates N, Ferrari G, Tomaras G, Montefiori D, Schwartz JA, Fouts T, DeVico AL, Lewis GK, Gallo RC, Sajadi MM. Safety and immunogenicity of an HIV-1 gp120-CD4 chimeric subunit vaccine in a phase 1a randomized controlled trial. Vaccine 2021; 39:3879-3891. [PMID: 34099328 PMCID: PMC8224181 DOI: 10.1016/j.vaccine.2021.05.090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/14/2021] [Accepted: 05/23/2021] [Indexed: 01/14/2023]
Abstract
A major challenge for HIV vaccine development is to raise anti-envelope antibodies capable of recognizing and neutralizing diverse strains of HIV-1. Accordingly, a full length single chain (FLSC) of gp120-CD4 chimeric vaccine construct was designed to present a highly conserved CD4-induced (CD4i) HIV-1 envelope structure that elicits cross-reactive anti-envelope humoral responses and protective immunity in animal models of HIV infection. IHV01 is the FLSC formulated in aluminum phosphate adjuvant. We enrolled 65 healthy adult volunteers in this first-in-human phase 1a randomized, double-blind, placebo-controlled study with three dose-escalating cohorts (75 µg, 150 µg, and 300 µg doses). Intramuscular injections were given on weeks 0, 4, 8, and 24. Participants were followed for an additional 24 weeks after the last immunization. The overall incidence of adverse events (AEs) was not significantly different between vaccinees and controls. The majority (89%) of vaccine-related AE were mild. The most common vaccine-related adverse event was injection site pain. There were no vaccine-related serious AE, discontinuation due to AE, intercurrent HIV infection, or significant decreases in CD4 count. By the final vaccination, all vaccine recipients developed antibodies against IHV01 and demonstrated anti-CD4i epitope antibodies. The elicited antibodies reacted with CD4 non-liganded Env antigens from diverse HIV-1 strains. Antibody-dependent cell-mediated cytotoxicity against heterologous infected cells or gp120 bound to CD4+ cells was evident in all cohorts as were anti-gp120 T-cell responses. IHV01 vaccine was safe, well tolerated, and immunogenic at all doses tested. The vaccine raised broadly reactive humoral responses against conserved CD4i epitopes on gp120 that mediates antiviral functions.
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Affiliation(s)
- Joel V Chua
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Charles Davis
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jennifer S Husson
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amy Nelson
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ilia Prado
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robin Flinko
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ka Wing J Lam
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lydiah Mutumbi
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bryan T Mayer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Dong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - William Fulp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Celia Mahoney
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Monica Gerber
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce L Gilliam
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kelli Greene
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hongmei Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nicole Yates
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Georgia Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Timothy Fouts
- Advanced BioScience Laboratories, Rockville, MD, USA
| | - Anthony L DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA; Global Virus Network, Baltimore, MD, USA
| | - George K Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA; Global Virus Network, Baltimore, MD, USA
| | - Robert C Gallo
- Global Virus Network, Baltimore, MD, USA; Division of Basic Science, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mohammad M Sajadi
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA; Intralytix, Columbia, MD, USA.
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9
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Kumar A, Giorgi EE, Tu JJ, Martinez DR, Eudailey J, Mengual M, Honnayakanahalli Marichannegowda M, Van Dyke R, Gao F, Permar SR. Mutations that confer resistance to broadly-neutralizing antibodies define HIV-1 variants of transmitting mothers from that of non-transmitting mothers. PLoS Pathog 2021; 17:e1009478. [PMID: 33798244 PMCID: PMC8055002 DOI: 10.1371/journal.ppat.1009478] [Citation(s) in RCA: 1] [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: 01/05/2021] [Revised: 04/19/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023] Open
Abstract
Despite considerable reduction of mother-to-child transmission (MTCT) of HIV through use of maternal and infant antiretroviral therapy (ART), over 150,000 infants continue to become infected with HIV annually, falling far short of the World Health Organization goal of reaching <20,000 annual pediatric HIV cases worldwide by 2020. Prior to the widespread use of ART in the setting of pregnancy, over half of infants born to HIV-infected mothers were protected against HIV acquisition. Yet, the role of maternal immune factors in this protection against vertical transmission is still unclear, hampering the development of synergistic strategies to further reduce MTCT. It has been established that infant transmitted/founder (T/F) viruses are often resistant to maternal plasma, yet it is unknown if the neutralization resistance profile of circulating viruses predicts the maternal risk of transmission to her infant. In this study, we amplified HIV-1 envelope genes (env) by single genome amplification and produced representative Env variants from plasma of 19 non-transmitting mothers from the U.S. Women Infant Transmission Study (WITS), enrolled in the pre-ART era. Maternal HIV Env variants from non-transmitting mothers had similar sensitivity to autologous plasma as observed for non-transmitting variants from transmitting mothers. In contrast, infant variants were on average 30% less sensitive to paired plasma neutralization compared to non-transmitted maternal variants from both transmitting and non-transmitting mothers (p = 0.015). Importantly, a signature sequence analysis revealed that motifs enriched in env sequences from transmitting mothers were associated with broadly neutralizing antibody (bnAb) resistance. Altogether, our findings suggest that circulating maternal virus resistance to bnAb-mediated neutralization, but not autologous plasma neutralization, near the time of delivery, predicts increased MTCT risk. These results caution that enhancement of maternal plasma neutralization through passive or active vaccination during pregnancy may potentially drive the evolution of variants fit for vertical transmission. Despite widespread, effective use of ART among HIV infected pregnant women, new pediatric HIV infections increase by about 150,000 every year. Thus, alternative strategies will be required to reduce MTCT and eliminate pediatric HIV infections. Interestingly, in the absence of ART, less than half of HIV-infected pregnant women will transmit HIV, suggesting natural immune protection of infants from virus acquisition. To understand the impact of maternal plasma autologous virus neutralization responses on MTCT, we compared the plasma and bnAb neutralization sensitivity of the circulating viral population present at the time of delivery in untreated, HIV-infected transmitting and non-transmitting mothers. While there was no significant difference in the ability of transmitting and non-transmitting women to neutralize their own circulating virus strains, specific genetic motifs enriched in variants from transmitting mothers were associated with resistance to bnAbs, suggesting that acquired bnAb resistance is a common feature of vertically-transmitted variants. This work suggests that enhancement of plasma neutralization responses in HIV-infected mothers through passive or active vaccination could further drive selection of variants that could be vertically transmitted, and cautions the use of passive bnAbs for HIV-1 prophylaxis or therapy during pregnancy.
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Affiliation(s)
- Amit Kumar
- Duke Human Vaccine Institute, Duke University Medical Centre, Durham, North Carolina, United States of America
| | - Elena E. Giorgi
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Joshua J. Tu
- Duke Human Vaccine Institute, Duke University Medical Centre, Durham, North Carolina, United States of America
| | - David R. Martinez
- Duke Human Vaccine Institute, Duke University Medical Centre, Durham, North Carolina, United States of America
| | - Joshua Eudailey
- Duke Human Vaccine Institute, Duke University Medical Centre, Durham, North Carolina, United States of America
| | - Michael Mengual
- Department of Medicine, Duke University Medical Centre, Durham, North Carolina, United States of America
| | | | - Russell Van Dyke
- Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Feng Gao
- Department of Medicine, Duke University Medical Centre, Durham, North Carolina, United States of America
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University Medical Centre, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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10
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Characteristics of HIV-1 env genes from Chinese chronically infected donors with highly broad cross-neutralizing activity. Virology 2020; 551:16-25. [PMID: 33010671 DOI: 10.1016/j.virol.2020.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/17/2020] [Accepted: 08/23/2020] [Indexed: 11/24/2022]
Abstract
Knowledge about the special characteristics of HIV-1 envelope (env) glycoproteins in rare individuals developing >90% neutralization breadth in Chinese subtype B' slow progressors may provide insights for vaccine design against local viruses. We performed a cross-sectional analysis on 7 samples. We tested the neutralization breadth and geometric mean ID50 titers (GMTs) of these samples, and divided them into hBCN+ and hBCN- group according to whether their neutralization breadth >90%. We obtained env sequences in these samples through single genome amplification (SGA) assay. By comparing with hBCN-, subtype B chronically infected group (B-SP), and Chinese subtype B group (B-Database), we analyzed the characteristics of the env sequences of hBCN+ group. Longer V1 and V4 regions with more glycosylation sites were found in hBCN+ samples compared to hBCN- samples. Further analysis compared to B-SP and B-Database showed that hBCN+ group exhibited unique extra-long V1 region containing higher proportion of N-glycan sites and additional cysteines.
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11
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Abstract
PURPOSE OF REVIEW Broadly neutralizing antibodies (bnAbs) are considered a key component of an effective HIV-1 vaccine, but despite intensive efforts, induction of bnAbs by vaccination has thus far not been possible. Potent bnAb activity is rare in natural infection and a deeper understanding of factors that promote or limit bnAb evolution is critical to guide bnAb vaccine development. This review reflects on recent key discoveries on correlates of bnAb development and discusses what further insights are needed to move forward. RECENT FINDINGS An increasing number of parameters have been implicated to influence bnAb development in natural infection. Most recent findings highlight a range of immune factors linked with bnAb evolution. Novel approaches have brought exciting progress in defining signatures of the viral envelope associated with bnAb activity. SUMMARY Focused efforts of recent years have unraveled a multiply layered process of HIV-1 bnAb development. As it is understood today, bnAb evolution can be triggered and influenced by a range of factors and several different pathways may exist how bnAb induction and maturation can occur. To capitalize on the gained knowledge, future research needs to validate factors to identify independent drivers of bnAb induction to advance vaccine design.
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12
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A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PLoS Pathog 2020; 16:e1008171. [PMID: 32492061 PMCID: PMC7295245 DOI: 10.1371/journal.ppat.1008171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/15/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mutations. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from the p24 and gp41 regions of HIV-1 collected from 34 patients with long-term untreated HIV-1 infection. We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in most cases were have previously been associated with either CTL escape in p24 or neutralising antibody escape in gp41. We also identified a putative new CTL escape site (residue 286 in gag), and a region of gp41 (including residues 644, 648, 655 in env) likely to be associated with immune escape. Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity although not all sites with high between-host diversity were inferred to be under selection at the within-host level. Our identification of selection at sites associated with resistance to broadly neutralising antibodies (bNAbs) highlights the need to fully understand the role of selection in untreated individuals when designing bNAb based therapies.
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13
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Han Q, Bradley T, Williams WB, Cain DW, Montefiori DC, Saunders KO, Parks RJ, Edwards RW, Ferrari G, Mueller O, Shen X, Wiehe KJ, Reed S, Fox CB, Rountree W, Vandergrift NA, Wang Y, Sutherland LL, Santra S, Moody MA, Permar SR, Tomaras GD, Lewis MG, Van Rompay KKA, Haynes BF. Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization. Cell Rep 2020; 30:1553-1569.e6. [PMID: 32023469 PMCID: PMC7243677 DOI: 10.1016/j.celrep.2019.12.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/16/2019] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
HIV-1-infected infants develop broadly neutralizing antibodies (bnAbs) more rapidly than adults, suggesting differences in the neonatal versus adult responses to the HIV-1 envelope (Env). Here, trimeric forms of HIV-1 Env immunogens elicit increased gp120- and gp41-specific antibodies more rapidly in neonatal macaques than adult macaques. Transcriptome analyses of neonatal versus adult immune cells after Env vaccination reveal that neonatal macaques have higher levels of the apoptosis regulator BCL2 in T cells and lower levels of the immunosuppressive interleukin-10 (IL-10) receptor alpha (IL10RA) mRNA transcripts in T cells, B cells, natural killer (NK) cells, and monocytes. In addition, immunized neonatal macaques exhibit increased frequencies of activated blood T follicular helper-like (Tfh) cells compared to adults. Thus, neonatal macaques have transcriptome signatures of decreased immunosuppression and apoptosis compared with adult macaques, providing an immune landscape conducive to early-life immunization prior to sexual debut.
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Affiliation(s)
- Qifeng Han
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert J Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Regina W Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Olaf Mueller
- Center for Genomics of Microbial Systems, Duke University Medical Center, Durham, NC, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin J Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sallie R Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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14
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Broadly resistant HIV-1 against CD4-binding site neutralizing antibodies. PLoS Pathog 2019; 15:e1007819. [PMID: 31194843 PMCID: PMC6592578 DOI: 10.1371/journal.ppat.1007819] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/25/2019] [Accepted: 05/07/2019] [Indexed: 01/15/2023] Open
Abstract
Recently identified broadly neutralizing antibodies (bnAbs) show great potential for clinical interventions against HIV-1 infection. However, resistant strains may impose substantial challenges. Here, we report on the identification and characterization of a panel of HIV-1 strains with broad and potent resistance against a large number of bnAbs, particularly those targeting the CD4-binding site (CD4bs). Site-directed mutagenesis revealed that several key epitope mutations facilitate resistance and are located in the inner domain, loop D, and β23/loop V5/β24 of HIV-1 gp120. The resistance is largely correlated with binding affinity of antibodies to the envelope trimers expressed on the cell surface. Our results therefore demonstrate the existence of broadly resistant HIV-1 strains against CD4bs neutralizing antibodies. Treatment strategies based on the CD4bs bnAbs must overcome such resistance to achieve optimal clinical outcomes. Recently identified broadly neutralizing antibodies (bnAbs) show great potential for clinical interventions against HIV-1 infection. Among the bnAbs isolated to date, those targeting the CD4bs are the most abundant and thoroughly studied as they disrupt the crucial step of viral interaction with the cellular receptor molecule CD4. Despite the superior potency and breadth of these CD4bs bnAbs, each fails to neutralize a small but significant portion of pseudotyped virus panels. Here, we report on the identification and characterization of a panel of HIV-1 strains with broad and potent resistance against a large number of bnAbs, particularly those targeting the CD4bs. Resistance is largely attributed to mutated residues within the epitopes or steric hindrance imposed by the bulky side-chain or glycan shield of the mutated residues, and is largely correlated with reduced binding avidity of the antibody to the quaternary trimeric envelope protein expressed on the surface of the transfected cells. Treatment strategies based on the CD4bs bnAbs therefore must overcome such resistance to achieve optimal clinical outcomes.
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15
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Ancestral sequences from an elite neutralizer proximal to the development of neutralization resistance as a potential source of HIV vaccine immunogens. PLoS One 2019; 14:e0213409. [PMID: 30969970 PMCID: PMC6457492 DOI: 10.1371/journal.pone.0213409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/20/2019] [Indexed: 11/19/2022] Open
Abstract
A major challenge in HIV vaccine development is the identification of immunogens able to elicit broadly neutralizing antibodies (bNAbs). While remarkable progress has been made in the isolation and characterization of bNAbs, the epitopes they recognize appear to be poorly immunogenic. Thus, none of the candidate vaccines developed to date has induced satisfactory levels of neutralizing antibodies to the HIV envelope protein (Env). One approach to the problem of poor immunogenicity is to build vaccines based on envelope (env) genes retrieved from rare individuals termed elite neutralizers (ENs) who at one time possessed specific sequences that stimulated the formation of bNAbs. Env proteins selected from these individuals could possess uncommon, yet to be defined, structural features that enhance the immunogenicity of epitopes recognized by bNAbs. Here we describe the recovery of envs from an EN that developed unusually broad and potent bNAbs. As longitudinal specimens were not available, we combined plasma and provirus sequences acquired from a single time-point to infer a phylogenetic tree. Combining ancestral reconstruction data with virus neutralization data allowed us to sift through the myriad of virus quasi-species that evolved in this individual to identify envelope sequences from the nodes that appeared to define the transition from neutralization sensitive envs to the neutralization resistant envs that occur in EN plasma. Synthetic genes from these nodes were functional in infectivity assays and sensitive to neutralization by bNAbs, and may provide a novel source of immunogens for HIV vaccine development.
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16
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Magaret CA, Benkeser DC, Williamson BD, Borate BR, Carpp LN, Georgiev IS, Setliff I, Dingens AS, Simon N, Carone M, Simpkins C, Montefiori D, Alter G, Yu WH, Juraska M, Edlefsen PT, Karuna S, Mgodi NM, Edugupanti S, Gilbert PB. Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features. PLoS Comput Biol 2019; 15:e1006952. [PMID: 30933973 PMCID: PMC6459550 DOI: 10.1371/journal.pcbi.1006952] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 04/11/2019] [Accepted: 03/14/2019] [Indexed: 11/29/2022] Open
Abstract
The broadly neutralizing antibody (bnAb) VRC01 is being evaluated for its efficacy to prevent HIV-1 infection in the Antibody Mediated Prevention (AMP) trials. A secondary objective of AMP utilizes sieve analysis to investigate how VRC01 prevention efficacy (PE) varies with HIV-1 envelope (Env) amino acid (AA) sequence features. An exhaustive analysis that tests how PE depends on every AA feature with sufficient variation would have low statistical power. To design an adequately powered primary sieve analysis for AMP, we modeled VRC01 neutralization as a function of Env AA sequence features of 611 HIV-1 gp160 pseudoviruses from the CATNAP database, with objectives: (1) to develop models that best predict the neutralization readouts; and (2) to rank AA features by their predictive importance with classification and regression methods. The dataset was split in half, and machine learning algorithms were applied to each half, each analyzed separately using cross-validation and hold-out validation. We selected Super Learner, a nonparametric ensemble-based cross-validated learning method, for advancement to the primary sieve analysis. This method predicted the dichotomous resistance outcome of whether the IC50 neutralization titer of VRC01 for a given Env pseudovirus is right-censored (indicating resistance) with an average validated AUC of 0.868 across the two hold-out datasets. Quantitative log IC50 was predicted with an average validated R2 of 0.355. Features predicting neutralization sensitivity or resistance included 26 surface-accessible residues in the VRC01 and CD4 binding footprints, the length of gp120, the length of Env, the number of cysteines in gp120, the number of cysteines in Env, and 4 potential N-linked glycosylation sites; the top features will be advanced to the primary sieve analysis. This modeling framework may also inform the study of VRC01 in the treatment of HIV-infected persons.
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Affiliation(s)
- Craig A. Magaret
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David C. Benkeser
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Brian D. Williamson
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Bhavesh R. Borate
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lindsay N. Carpp
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ian Setliff
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Adam S. Dingens
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Division of Human Biology and Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, Washington, United States of America
| | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Marco Carone
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Christopher Simpkins
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David Montefiori
- Duke University School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Wen-Han Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Michal Juraska
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Paul T. Edlefsen
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Shelly Karuna
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Nyaradzo M. Mgodi
- University of Zimbabwe College of Health Sciences Clinical Trials Research Centre, Harare, Zimbabwe
| | - Srilatha Edugupanti
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
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17
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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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18
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Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B. HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design. Cell Host Microbe 2019; 25:59-72.e8. [PMID: 30629920 PMCID: PMC6331341 DOI: 10.1016/j.chom.2018.12.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/06/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022]
Abstract
Eliciting HIV-1-specific broadly neutralizing antibodies (bNAbs) remains a challenge for vaccine development, and the potential of passively delivered bNAbs for prophylaxis and therapeutics is being explored. We used neutralization data from four large virus panels to comprehensively map viral signatures associated with bNAb sensitivity, including amino acids, hypervariable region characteristics, and clade effects across four different classes of bNAbs. The bNAb signatures defined for the variable loop 2 (V2) epitope region of HIV-1 Env were then employed to inform immunogen design in a proof-of-concept exploration of signature-based epitope targeted (SET) vaccines. V2 bNAb signature-guided mutations were introduced into Env 459C to create a trivalent vaccine, and immunization of guinea pigs with V2-SET vaccines resulted in increased breadth of NAb responses compared with Env 459C alone. These data demonstrate that bNAb signatures can be utilized to engineer HIV-1 Env vaccine immunogens capable of eliciting antibody responses with greater neutralization breadth. HIV-1 bNAb sensitivity signatures from 4 large virus panels mapped across 4 Ab classes Non-contact hypervariable region characteristics are critical for bNAb sensitivity HIV-1 Env 459C used alone as a vaccine can elicit modest tier 2 NAbs in guinea pigs V2 bNAb signature-guided modifications in 459C enhanced neutralization breadth
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Affiliation(s)
- Christine A Bricault
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Edward F Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Johannes F Scheid
- Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA
| | - James M Kovacs
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Departments of Chemistry and Biochemistry, University of Colorado, Colorado Springs, CO 80918, USA
| | - Jennifer L Shields
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Fadi Ghantous
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michael Rist
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Madeleine G Bayne
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - George H Neubauer
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Coraline Chéneau
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Jennifer J Jones
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jie Zeng
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christina Ochsenbauer
- Department of Medicine and CFAR, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA
| | - Bing Chen
- Division of Molecular Medicine, Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - S Gnanakaran
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - LaTonya D Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA.
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
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19
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Subbaraman H, Schanz M, Trkola A. Broadly neutralizing antibodies: What is needed to move from a rare event in HIV-1 infection to vaccine efficacy? Retrovirology 2018; 15:52. [PMID: 30055627 PMCID: PMC6064177 DOI: 10.1186/s12977-018-0433-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/21/2018] [Indexed: 02/06/2023] Open
Abstract
The elicitation of broadly neutralizing antibodies (bnAbs) is considered crucial for an effective, preventive HIV-1 vaccine. Led by the discovery of a new generation of potent bnAbs, the field has significantly advanced over the past decade. There is a wealth of knowledge about the development of bnAbs in natural infection, their specificity, potency, breadth and function. Yet, devising immunogens and vaccination regimens that evoke bnAb responses has not been successful. Where are the roadblocks in their development? What can we learn from natural infection, where bnAb induction is possible but rare? Herein, we will reflect on key discoveries and discuss open questions that may bear crucial insights needed to move towards creating effective bnAb vaccines.
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Affiliation(s)
- Harini Subbaraman
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Merle Schanz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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20
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Julg B, Liu PT, Wagh K, Fischer WM, Abbink P, Mercado NB, Whitney JB, Nkolola JP, McMahan K, Tartaglia LJ, Borducchi EN, Khatiwada S, Kamath M, LeSuer JA, Seaman MS, Schmidt SD, Mascola JR, Burton DR, Korber BT, Barouch DH. Protection against a mixed SHIV challenge by a broadly neutralizing antibody cocktail. Sci Transl Med 2018; 9:9/408/eaao4235. [PMID: 28931655 DOI: 10.1126/scitranslmed.aao4235] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 07/27/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022]
Abstract
HIV-1 sequence diversity presents a major challenge for the clinical development of broadly neutralizing antibodies (bNAbs) for both therapy and prevention. Sequence variation in critical bNAb epitopes has been observed in most HIV-1-infected individuals and can lead to viral escape after bNAb monotherapy in humans. We show that viral sequence diversity can limit both the therapeutic and prophylactic efficacy of bNAbs in rhesus monkeys. We first demonstrate that monotherapy with the V3 glycan-dependent antibody 10-1074, but not PGT121, results in rapid selection of preexisting viral variants containing N332/S334 escape mutations and loss of therapeutic efficacy in simian-HIV (SHIV)-SF162P3-infected rhesus monkeys. We then show that the V3 glycan-dependent antibody PGT121 alone and the V2 glycan-dependent antibody PGDM1400 alone both fail to protect against a mixed challenge with SHIV-SF162P3 and SHIV-325c. In contrast, the combination of both bNAbs provides 100% protection against this mixed SHIV challenge. These data reveal that single bNAbs efficiently select resistant viruses from a diverse challenge swarm to establish infection, demonstrating the importance of bNAb cocktails for HIV-1 prevention.
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Affiliation(s)
- Boris Julg
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Po-Ting Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Peter Abbink
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - James B Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Lawrence J Tartaglia
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Erica N Borducchi
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Shreeya Khatiwada
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Megha Kamath
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jake A LeSuer
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dennis R Burton
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.,The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA. .,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
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21
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Seaton KE, Vandergrift NA, Deal AW, Rountree W, Bainbridge J, Grebe E, Anderson DA, Sawant S, Shen X, Yates NL, Denny TN, Liao HX, Haynes BF, Robb ML, Parkin N, Santos BR, Garrett N, Price MA, Naniche D, Duerr AC, Keating S, Hampton D, Facente S, Marson K, Welte A, Pilcher CD, Cohen MS, Tomaras GD. Computational analysis of antibody dynamics identifies recent HIV-1 infection. JCI Insight 2017; 2:94355. [PMID: 29263306 DOI: 10.1172/jci.insight.94355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Accurate HIV-1 incidence estimation is critical to the success of HIV-1 prevention strategies. Current assays are limited by high false recent rates (FRRs) in certain populations and a short mean duration of recent infection (MDRI). Dynamic early HIV-1 antibody response kinetics were harnessed to identify biomarkers for improved incidence assays. We conducted retrospective analyses on circulating antibodies from known recent and longstanding infections and evaluated binding and avidity measurements of Env and non-Env antigens and multiple antibody forms (i.e., IgG, IgA, IgG3, IgG4, dIgA, and IgM) in a diverse panel of 164 HIV-1-infected participants (clades A, B, C). Discriminant function analysis identified an optimal set of measurements that were subsequently evaluated in a 324-specimen blinded biomarker validation panel. These biomarkers included clade C gp140 IgG3, transmitted/founder clade C gp140 IgG4 avidity, clade B gp140 IgG4 avidity, and gp41 immunodominant region IgG avidity. MDRI was estimated at 215 day or alternatively, 267 days. FRRs in untreated and treated subjects were 5.0% and 3.6%, respectively. Thus, computational analysis of dynamic HIV-1 antibody isotype and antigen interactions during infection enabled design of a promising HIV-1 recency assay for improved cross-sectional incidence estimation.
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Affiliation(s)
- Kelly E Seaton
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Aaron W Deal
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - John Bainbridge
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Eduard Grebe
- South African Centre for Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | | | - Sheetal Sawant
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Nicole L Yates
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA.,Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Neil Parkin
- Foundation for Innovative New Diagnostics, Geneva, Switzerland; Data First Consulting, Belmont, California, USA
| | - Breno R Santos
- The Evaluation of Prevention Methods Linked to Acute and Recent Infection (AMPLIAR) Cohort Group Hospital Conceição is detailed in the Supplemental Acknowledgments
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Matthew A Price
- International AIDS Vaccine Initiative, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Denise Naniche
- ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ann C Duerr
- Vaccine and Infectious Disease and Public Health Science Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Sheila Keating
- Blood Systems Research Institute, San Francisco, California, USA
| | - Dylan Hampton
- Blood Systems Research Institute, San Francisco, California, USA
| | - Shelley Facente
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Kara Marson
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alex Welte
- South African Centre for Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | - Christopher D Pilcher
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Myron S Cohen
- University of North Carolina, Chapel Hill, North Carolina, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Department of Medicine, Durham, North Carolina, USA.,Department of Immunology, Duke University, Durham, North Carolina, USA.,Department of Surgery and Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
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22
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Bonsignori M, Kreider EF, Fera D, Meyerhoff RR, Bradley T, Wiehe K, Alam SM, Aussedat B, Walkowicz WE, Hwang KK, Saunders KO, Zhang R, Gladden MA, Monroe A, Kumar A, Xia SM, Cooper M, Louder MK, McKee K, Bailer RT, Pier BW, Jette CA, Kelsoe G, Williams WB, Morris L, Kappes J, Wagh K, Kamanga G, Cohen MS, Hraber PT, Montefiori DC, Trama A, Liao HX, Kepler TB, Moody MA, Gao F, Danishefsky SJ, Mascola JR, Shaw GM, Hahn BH, Harrison SC, Korber BT, Haynes BF. Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies. Sci Transl Med 2017; 9:9/381/eaai7514. [PMID: 28298420 DOI: 10.1126/scitranslmed.aai7514] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 08/18/2016] [Accepted: 01/31/2017] [Indexed: 12/30/2022]
Abstract
A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
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Affiliation(s)
- Mattia Bonsignori
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA. .,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Edward F Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniela Fera
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - R Ryan Meyerhoff
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Todd Bradley
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Kevin Wiehe
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Baptiste Aussedat
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - William E Walkowicz
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | - Amit Kumar
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brendan W Pier
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia A Jette
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Wilton B Williams
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - John Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Gift Kamanga
- University of North Carolina Project, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Peter T Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashley Trama
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Thomas B Kepler
- Department of Microbiology and Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Feng Gao
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Samuel J Danishefsky
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen C Harrison
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA. .,Duke Human Vaccine Institute, Durham, NC 27710, USA
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23
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Hake A, Pfeifer N. Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time. PLoS Comput Biol 2017; 13:e1005789. [PMID: 29065122 PMCID: PMC5669501 DOI: 10.1371/journal.pcbi.1005789] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 11/03/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
Treatment with broadly neutralizing antibodies (bNAbs) has proven effective against HIV-1 infections in humanized mice, non-human primates, and humans. Due to the high mutation rate of HIV-1, resistance testing of the patient’s viral strains to the bNAbs is still inevitable. So far, bNAb resistance can only be tested in expensive and time-consuming neutralization experiments. Here, we introduce well-performing computational models that predict the neutralization response of HIV-1 to bNAbs given only the envelope sequence of the virus. Using non-linear support vector machines based on a string kernel, the models learnt even the important binding sites of bNAbs with more complex epitopes, i.e., the CD4 binding site targeting bNAbs, proving thereby the biological relevance of the models. To increase the interpretability of the models, we additionally provide a new kind of motif logo for each query sequence, visualizing those residues of the test sequence that influenced the prediction outcome the most. Moreover, we predicted the neutralization sensitivity of around 34,000 HIV-1 samples from different time points to a broad range of bNAbs, enabling the first analysis of HIV resistance to bNAbs on a global scale. The analysis showed for many of the bNAbs a trend towards antibody resistance over time, which had previously only been discovered for a small non-representative subset of the global HIV-1 population. Several sequence-based approaches exist to predict the epitope of broadly neutralizing antibodies (bNAbs) against HIV based on the correlation between variation in the viral sequence and neutralization response to the antibody. Though the potential epitope sites can be used to predict the neutralization response, the methods are not optimized for the task, using additional structural information, additional preselection steps to identify the epitope sites, and assuming independence and/or only linear relationship between the potential sites and the neutralization response. To model also the neutralization response to bNAbs with more complex binding sites, including for example several non-consecutive residues or accompanying conformational changes, we used non-linear, multivariate machine learning techniques. Though we used only the viral sequence information, the models learnt the corresponding binding sites of the bNAbs. In general only few residues were learnt to be responsible for a change in neutralization response, which can additionally reduce the sequencing cost for application in clinical routine. We propose our tailored models to aid the patient selection process for current clinical trials for bNAb immunotherapy, but also as a basis to predict the best combinations of bNAbs, which will be required for routine clinical practice in the future.
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Affiliation(s)
- Anna Hake
- Department Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
- * E-mail: (AH); (NP)
| | - Nico Pfeifer
- Department Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Germany
- Medical Faculty, University of Tübingen, Tübingen, Germany
- * E-mail: (AH); (NP)
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24
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Bonsignori M, Liao HX, Gao F, Williams WB, Alam SM, Montefiori DC, Haynes BF. Antibody-virus co-evolution in HIV infection: paths for HIV vaccine development. Immunol Rev 2017; 275:145-160. [PMID: 28133802 PMCID: PMC5302796 DOI: 10.1111/imr.12509] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Induction of HIV-1 broadly neutralizing antibodies (bnAbs) to date has only been observed in the setting of HIV-1 infection, and then only years after HIV transmission. Thus, the concept has emerged that one path to induction of bnAbs is to define the viral and immunologic events that occur during HIV-1 infection, and then to mimic those events with a vaccine formulation. This concept has led to efforts to map both virus and antibody events that occur from the time of HIV-1 transmission to development of bnAbs. This work has revealed that a virus-antibody "arms race" occurs in which a HIV-1 transmitted/founder (TF) Env induces autologous neutralizing antibodies that can not only neutralize the TF virus but also can select virus escape mutants that in turn select affinity-matured neutralizing antibodies. From these studies has come a picture of bnAb development that has led to new insights in host-pathogen interactions and, as well, led to insight into immunologic mechanisms of control of bnAb development. Here, we review the progress to date in elucidating bnAb B cell lineages in HIV-1 infection, discuss new research leading to understanding the immunologic mechanisms of bnAb induction, and address issues relevant to the use of this information for the design of new HIV-1 sequential envelope vaccine candidates.
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Affiliation(s)
- Mattia Bonsignori
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hua-Xin Liao
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Feng Gao
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Wilton B Williams
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - S Munir Alam
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC, USA
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25
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Horwitz JA, Bar-On Y, Lu CL, Fera D, Lockhart AAK, Lorenzi JCC, Nogueira L, Golijanin J, Scheid JF, Seaman MS, Gazumyan A, Zolla-Pazner S, Nussenzweig MC. Non-neutralizing Antibodies Alter the Course of HIV-1 Infection In Vivo. Cell 2017; 170:637-648.e10. [PMID: 28757252 DOI: 10.1016/j.cell.2017.06.048] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 11/26/2022]
Abstract
Non-neutralizing antibodies (nnAbs) to HIV-1 show little measurable activity in prevention or therapy in animal models yet were the only correlate of protection in the RV144 vaccine trial. To investigate the role of nnAbs on HIV-1 infection in vivo, we devised a replication-competent HIV-1 reporter virus that expresses a heterologous HA-tag on the surface of infected cells and virions. Anti-HA antibodies bind to, but do not neutralize, the reporter virus in vitro. However, anti-HA protects against infection in humanized mice and strongly selects for nnAb-resistant viruses in an entirely Fc-dependent manner. Similar results were also obtained with tier 2 HIV-1 viruses using a human anti-gp41 nnAb, 246D. While nnAbs are demonstrably less effective than broadly neutralizing antibodies (bNAbs) against HIV-1 in vitro and in vivo, the data show that nnAbs can protect against and alter the course of HIV-1 infection in vivo. PAPERCLIP.
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Affiliation(s)
- Joshua A Horwitz
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Laboratory of Structural Cell Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA; Whelan Laboratory, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yotam Bar-On
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ching-Lan Lu
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Daniela Fera
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Ainsley A K Lockhart
- Laboratory of Mucosal Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Johannes F Scheid
- Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center/Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Susan Zolla-Pazner
- Zolla-Pazner Laboratory, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
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26
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Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike. Proc Natl Acad Sci U S A 2017; 114:4477-4482. [PMID: 28396421 DOI: 10.1073/pnas.1700634114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extraordinary genetic diversity of the HIV-1 envelope spike [Env; trimeric (gp160)3, cleaved to (gp120/gp41)3] poses challenges for vaccine development. Envs of different clinical isolates exhibit different sensitivities to antibody-mediated neutralization. Envs of difficult-to-neutralize viruses are thought to be more stable and conformationally homogeneous trimers than those of easy-to-neutralize viruses, thereby providing more effective concealment of conserved, functionally critical sites. In this study we have characterized the antigenic properties of an Env derived from one of the most neutralization-resistant HIV-1 isolates, CH120.6. Sequence variation at neutralizing epitopes does not fully account for its exceptional resistance to antibodies. The full-length, membrane-bound CH120.6 Env is indeed stable and conformationally homogeneous. Its antigenicity correlates closely with its neutralization sensitivity, and major changes in antigenicity upon CD4 engagement appear to be restricted to the coreceptor site. The CH120.6 gp140 trimer, the soluble and uncleaved ectodomain of (gp160)3, retains many antigenic properties of the intact Env, consistent with a conformation close to that of Env spikes on a virion, whereas its monomeric gp120 exposes many nonneutralizing or strain-specific epitopes. Thus, trimer organization and stability are important determinants not only for occluding many epitopes but also for conferring resistance to neutralization by all but a small set of antibodies. Env preparations derived from neutralization-resistant viruses may induce irrelevant antibody responses less frequently than do other Envs and may be excellent templates for developing soluble immunogens.
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27
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Histidine 375 Modulates CD4 Binding in HIV-1 CRF01_AE Envelope Glycoproteins. J Virol 2017; 91:JVI.02151-16. [PMID: 27928014 DOI: 10.1128/jvi.02151-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 11/29/2016] [Indexed: 01/11/2023] Open
Abstract
The envelope glycoproteins (Envs) from human immunodeficiency virus type 1 (HIV-1) mediate viral entry. The binding of the HIV-1 gp120 glycoprotein to CD4 triggers conformational changes in gp120 that allow high-affinity binding to its coreceptors. In contrast to all other Envs from the same phylogenetic group, M, which possess a serine (S) at position 375, those from CRF01_AE strains possess a histidine (H) at this location. This residue is part of the Phe43 cavity, where residue 43 of CD4 (a phenylalanine) engages with gp120. Here we evaluated the functional consequences of replacing this residue in two CRF01_AE Envs (CM244 and 92TH023) by a serine. We observed that reversion of amino acid 375 to a serine (H375S) resulted in a loss of functionality of both CRF01_AE Envs as measured by a dramatic loss in infectivity and ability to mediate cell-to-cell fusion. While no effects on processing or trimer stability of these variants were observed, decreased functionality could be linked to a major defect in CD4 binding induced by the replacement of H375 by a serine. Importantly, mutations of residues 61 (layer 1), 105 and 108 (layer 2), and 474 to 476 (layer 3) of the CRF01_AE gp120 inner domain layers to the consensus residues present in group M restored CD4 binding and wild-type levels of infectivity and cell-to-cell fusion. These results suggest a functional coevolution between the Phe43 cavity and the gp120 inner domain layers. Altogether, our observations describe the functional importance of amino acid 375H in CRF01_AE envelopes. IMPORTANCE A highly conserved serine located at position 375 in group M is replaced by a histidine in CRF01_AE Envs. Here we show that H375 is required for efficient CRF01_AE Env binding to CD4. Moreover, this work suggests that specific residues of the gp120 inner domain layers have coevolved with H375 in order to maintain its ability to mediate viral entry.
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28
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Williams LD, Ofek G, Schätzle S, McDaniel JR, Lu X, Nicely NI, Wu L, Lougheed CS, Bradley T, Louder MK, McKee K, Bailer RT, O'Dell S, Georgiev IS, Seaman MS, Parks RJ, Marshall DJ, Anasti K, Yang G, Nie X, Tumba NL, Wiehe K, Wagh K, Korber B, Kepler TB, Munir Alam S, Morris L, Kamanga G, Cohen MS, Bonsignori M, Xia SM, Montefiori DC, Kelsoe G, Gao F, Mascola JR, Moody MA, Saunders KO, Liao HX, Tomaras GD, Georgiou G, Haynes BF. Potent and broad HIV-neutralizing antibodies in memory B cells and plasma. Sci Immunol 2017; 2:2/7/eaal2200. [PMID: 28783671 DOI: 10.1126/sciimmunol.aal2200] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022]
Abstract
Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. Antibody 10E8, reactive with the distal portion of the membrane-proximal external region (MPER) of HIV-1 gp41, is broadly neutralizing. However, the ontogeny of distal MPER antibodies and the relationship of memory B cell to plasma bnAbs are poorly understood. HIV-1-specific memory B cell flow sorting and proteomic identification of anti-MPER plasma antibodies from an HIV-1-infected individual were used to isolate broadly neutralizing distal MPER bnAbs of the same B cell clonal lineage. Structural analysis demonstrated that antibodies from memory B cells and plasma recognized the envelope gp41 bnAb epitope in a distinct orientation compared with other distal MPER bnAbs. The unmutated common ancestor of this distal MPER bnAb was autoreactive, suggesting lineage immune tolerance control. Construction of chimeric antibodies of memory B cell and plasma antibodies yielded a bnAb that potently neutralized most HIV-1 strains.
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Affiliation(s)
- LaTonya D Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gilad Ofek
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Sebastian Schätzle
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan R McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Liming Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Caleb S Lougheed
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dawn J Marshall
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Guang Yang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoyan Nie
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nancy L Tumba
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella 4013, South Africa
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas B Kepler
- Departments of Microbiology and Mathematics & Statistics, Boston University School of Medicine, Boston, MA 02118, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella 4013, South Africa
| | - Gift Kamanga
- University of North Carolina Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA. .,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
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29
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de Almeida DV, Macieira KV, Grinsztejn BGJ, Veloso dos Santos VG, Guimarães ML. Cross-Neutralizing Antibodies in HIV-1 Individuals Infected by Subtypes B, F1, C or the B/Bbr Variant in Relation to the Genetics and Biochemical Characteristics of the env Gene. PLoS One 2016; 11:e0167690. [PMID: 27936047 PMCID: PMC5147934 DOI: 10.1371/journal.pone.0167690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/21/2016] [Indexed: 11/18/2022] Open
Abstract
Various HIV-1 env genetic and biochemical features impact the elicitation of cross-reactive neutralizing antibodies in natural infections. Thus, we aimed to investigate cross-neutralizing antibodies in individuals infected with HIV-1 env subtypes B, F1, C or the B/Bbr variant as well as env characteristics. Therefore, plasma samples from Brazilian chronically HIV-1 infected individuals were submitted to the TZM-bl neutralization assay. We also analyzed putative N-glycosylation sites (PNGLs) and the size of gp120 variable domains in the context of HIV-1 subtypes prevalent in Brazil. We observed a greater breadth and potency of the anti-Env neutralizing response in individuals infected with the F1 or B HIV-1 subtypes compared with the C subtype and the variant B/Bbr. We observed greater V1 B/Bbr and smaller V4 F1 than those of other subtypes (p<0.005), however neither was there a correlation verified between the variable region length and neutralization potency, nor between PNLG and HIV-1 subtypes. The enrichment of W at top of V3 loop in weak neutralizing response viruses and the P in viruses with higher neutralization susceptibility was statistically significant (p = 0.013). Some other signatures sites were associated to HIV-1 subtype-specific F1 and B/Bbr samples might influence in the distinct neutralizing response. These results indicate that a single amino acid substitution may lead to a distinct conformational exposure or load in the association domain of the trimer of gp120 and interfere with the induction power of the neutralizing response, which affects the sensitivity of the neutralizing antibody and has significant implications for vaccine design.
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Affiliation(s)
| | - Karine Venegas Macieira
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute - FIOCRUZ, Rio de Janeiro, Brazil
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30
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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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31
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Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Abdool Karim S, Abdool Karim Q, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C. Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization. PLoS Pathog 2016; 12:e1005742. [PMID: 27434311 PMCID: PMC4951126 DOI: 10.1371/journal.ppat.1005742] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022] Open
Abstract
The development of biomedical interventions to reduce acquisition of HIV-1 infection remains a global priority, however their potential effectiveness is challenged by very high HIV-1 envelope diversity. Two large prophylactic trials in high incidence, clade C epidemic regions in southern Africa are imminent; passive administration of the monoclonal antibody VRC01, and active immunization with a clade C modified RV144-like vaccines. We have created a large representative panel of C clade viruses to enable assessment of antibody responses to vaccines and natural infection in Southern Africa, and we investigated the genotypic and neutralization properties of recently transmitted clade C viruses to determine how viral diversity impacted antibody recognition. We further explore the implications of these findings for the potential effectiveness of these trials. A panel of 200 HIV-1 Envelope pseudoviruses was constructed from clade C viruses collected within the first 100 days following infection. Viruses collected pre-seroconversion were significantly more resistant to serum neutralization compared to post-seroconversion viruses (p = 0.001). Over 13 years of the study as the epidemic matured, HIV-1 diversified (p = 0.0009) and became more neutralization resistant to monoclonal antibodies VRC01, PG9 and 4E10. When tested at therapeutic levels (10ug/ml), VRC01 only neutralized 80% of viruses in the panel, although it did exhibit potent neutralization activity against sensitive viruses (IC50 titres of 0.42 μg/ml). The Gp120 amino acid similarity between the clade C panel and candidate C-clade vaccine protein boosts (Ce1086 and TV1) was 77%, which is 8% more distant than between CRF01_AE viruses and the RV144 CRF01_AE immunogen. Furthermore, two vaccine signature sites, K169 in V2 and I307 in V3, associated with reduced infection risk in RV144, occurred less frequently in clade C panel viruses than in CRF01_AE viruses from Thailand. Increased resistance of pre-seroconversion viruses and evidence of antigenic drift highlights the value of using panels of very recently transmitted viruses and suggests that interventions may need to be modified over time to track the changing epidemic. Furthermore, high divergence such as that observed in the older clade C epidemic in southern Africa may impact vaccine efficacy, although the correlates of infection risk are yet to be defined in the clade C setting. Findings from this study of acute/early clade C viruses will aid vaccine development, and enable identification of new broad and potent antibodies to combat the HIV-1 C-clade epidemic in southern Africa.
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Affiliation(s)
- Cecilia Rademeyer
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Bette Korber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Elena E. Giorgi
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Ruwayhida Thebus
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Alexander Robles
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Daniel J. Sheward
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Kshitij Wagh
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Jetta Garrity
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Brittany R. Carey
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kelli M. Greene
- 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
| | - Gama P. Bandawe
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Jinny C. Marais
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | | | - Peter Hraber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Nancy Tumba
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases (NICD), NHLS & 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
| | - Glenda E. Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and South African Medical Research Council, Cape Town, South Africa
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marion Vermeulen
- South African National Blood Service, Weltevreden Park, South Africa
| | - Keren Middelkoop
- Desmond Tutu HIV Centre, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT), Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT), Cape Town, South Africa
| | - Michael Hoelscher
- Department for Infectious Diseases & Tropical Medicine, Klinikum University of Munich, LMU and German Center for Infection Research (DZIF) partner site Munich, Munich, Germany
| | | | - Joseph Makhema
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- International Vaccine Institute, Seoul, Republic of Korea
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Feng Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lynn Morris
- National Institute for Communicable Diseases (NICD), NHLS & 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
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carolyn Williamson
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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Detection of Broadly Neutralizing Activity within the First Months of HIV-1 Infection. J Virol 2016; 90:5231-5245. [PMID: 26984721 DOI: 10.1128/jvi.00049-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/08/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A fraction of HIV-1 patients are able to generate broadly neutralizing antibodies (bNAbs) after 2 to 4 years of infection. In rare occasions such antibodies are observed close to the first year of HIV-1 infection but never within the first 6 months. In this study, we analyzed the neutralization breadth of sera from 157 antiretroviral-naive individuals who were infected for less than 1 year. A range of neutralizing activities was observed with a previously described panel of six recombinant viruses from five different subtypes (M. Medina-Ramirez et al., J Virol 85:5804-5813, 2011, http://dx.doi.org/10.1128/JVI.02482-10). Some sera were broadly reactive, predominantly targeting envelope epitopes within the V2 glycan-dependent region. The neutralization breadth was positively associated with time postinfection (P = 0.0001), but contrary to what has been reported for chronic infections, no association with the viral load was observed. Notably, five individuals within the first 6 months of infection (two as early as 77 and 96 days postinfection) showed substantial cross-neutralization. This was confirmed with an extended panel of 20 Env pseudoviruses from four different subtypes (two in tier 3, 14 in tier 2, and four in tier 1). Sera from these individuals were capable of neutralizing viruses from four different subtypes with a geometric mean 50% infective dose (ID50) between 100 and 800. These results indicate that induction of cross-neutralizing responses, albeit rare, is achievable even within 6 months of HIV-1 infection. These observations encourage the search for immunogens able to elicit this kind of response in preventive HIV-1 vaccine approaches. IMPORTANCE There are very few individuals able to mount broadly neutralizing activity (bNA) close to the first year postinfection. It is not known how early in the infection cross-neutralizing responses can be induced. In the present study, we show that bNAbs, despite being rare, can be induced much earlier than previously thought. The identification of HIV-1-infected patients with these activities within the first months of infection and characterization of these responses will help in defining new immunogen designs and neutralization targets for vaccine-mediated induction of bNAbs.
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Yoon H, Macke J, West AP, Foley B, Bjorkman PJ, Korber B, Yusim K. CATNAP: a tool to compile, analyze and tally neutralizing antibody panels. Nucleic Acids Res 2015; 43:W213-9. [PMID: 26044712 PMCID: PMC4489231 DOI: 10.1093/nar/gkv404] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/15/2015] [Indexed: 02/01/2023] Open
Abstract
CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody. Website name: CATNAP (Compile, Analyze and Tally NAb Panels). Website address: http://hiv.lanl.gov/catnap.
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Affiliation(s)
- Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | - Brian Foley
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM, USA
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Moore PL, Williamson C, Morris L. Virological features associated with the development of broadly neutralizing antibodies to HIV-1. Trends Microbiol 2015; 23:204-11. [PMID: 25572881 PMCID: PMC4380704 DOI: 10.1016/j.tim.2014.12.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/02/2014] [Accepted: 12/10/2014] [Indexed: 12/12/2022]
Abstract
The development of a preventative HIV-1 vaccine remains a global public health priority. This will likely require the elicitation of broadly neutralizing antibodies (bNAbs) able to block infection by diverse viral strains from across the world. Understanding the pathway to neutralization breadth in HIV-1 infected humans will provide insights into how bNAb lineages arise, a process that probably involves a combination of host and viral factors. Here, we focus on the role of viral characteristics and evolution in shaping bNAbs during HIV-1 infection, and describe how these findings may be translated into novel vaccine strategies.
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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; 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.
| | - Carolyn Williamson
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa; Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town & National Health Laboratory Services, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; 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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35
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Cross-neutralizing antibody profile of Chinese HIV-1-infected individuals and the viral envelope features from elite neutralizers. J Acquir Immune Defic Syndr 2015; 67:472-80. [PMID: 25202919 DOI: 10.1097/qai.0000000000000345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Knowledge about the profile of neutralization responses and the viral envelope features of HIV-1-infected individuals in China may provide new insights for vaccine design against local viruses. METHODS Eight hundred sixty plasma samples from antiretroviral treatment-naive HIV-1-infected individuals in Xinjiang province (611) and Guangxi province (249), who had acquired infection over 3 years through intravenous drug use or sexual contact, were examined for their ability to neutralize diverse envelope-pseudoviruses of 5 subtypes. The sequence features of the envelopes from elite neutralizers were analyzed. RESULTS From Xinjiang and Guangxi, 29.1% and 5.2% of plasmas displayed intrasubtype cross neutralization against subtype B and subtype C, respectively. From Xinjiang, 10.6% of the plasmas displayed broad neutralization against the 3 subtypes, B, C, and CRF01_AE; whereas only 2.4% from Guangxi displayed broad neutralization. Envelopes from 6 elite neutralizers were obtained by single-genome amplification. The variations of their envelopes including the lengths, glycans, and net charges in V1, V2, and V4 regions were compared with those from CRF07_BC env sequences from the HIV Sequence Database. The Envs from 3 elite neutralizers displayed the sensitivities to the monoclonal broadly neutralizing antibodies such as PG9, PG16, and 4E10. Some unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers were found. CONCLUSIONS The neutralization profile of HIV-1-infected individuals in the 2 regions of China, where the HIV-1 subtypes are the representative in China, and the unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers provide useful information for viral infection prevention and an insight for vaccine design against locally epidemic viruses.
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36
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Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Arroyo MA, O’Connell RJ, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T, Georgiev IS, Kwong PD, Scheffler K, Pond SLK, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB. Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol 2015; 11:e1003973. [PMID: 25646817 PMCID: PMC4315437 DOI: 10.1371/journal.pcbi.1003973] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/08/2014] [Indexed: 01/25/2023] Open
Abstract
The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.
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Affiliation(s)
- Paul T. Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Morgane Rolland
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- The Shraga Segal Dept. of Microbiology, Immunology and Genetics, Faculty of Health Sciences, and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Andrew J. Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Allan C. deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Craig A. Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Connor McCoy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Brendan B. Larsen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Eric Sanders-Buell
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Chris Carrico
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sergey Menis
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
| | - Meera Bose
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | | | | | | | | | | | | | | | - Merlin L. Robb
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tatsiana Kirys
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Ivelin S. Georgiev
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Konrad Scheffler
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan M. Carlson
- eSience Research Group, Microsoft Research, Redmond, Washington, United States of America
| | - Nelson L. Michael
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- IAVI Neutralizing Antibody Center and Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jerome H. Kim
- US Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Ramirez Valdez KP, Kuwata T, Maruta Y, Tanaka K, Alam M, Yoshimura K, Matsushita S. Complementary and synergistic activities of anti-V3, CD4bs and CD4i antibodies derived from a single individual can cover a wide range of HIV-1 strains. Virology 2014; 475:187-203. [PMID: 25486586 DOI: 10.1016/j.virol.2014.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/17/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
Antibodies with modest neutralizing activity and narrow breadth are commonly elicited in HIV-1. Here, we evaluated the complementary and synergistic activities of a set of monoclonal antibodies (MAb) isolated from a single patient, directed to V3, CD4 binding site (CD4bs), and CD4 induced (CD4i) epitopes. Despite low somatic hypermutation percentages in the variable regions, these MAbs covered viral strains from subtypes B, C, A and CRF01_AE and transmitted/founder viruses in terms of binding, neutralizing and antibody-dependent cell-mediated cytotoxicity (ADCC) activities. In addition, a combination of the anti-V3 and CD4bs MAbs showed a synergistic effect over the neutralization of HIV-1JR-FL. A humoral response from a single patient covered a wide range of viruses by complementary and synergistic activities of antibodies with different specificities. Inducing a set of narrow neutralizing antibodies, easier to induce than the broadly neutralizing antibodies, could be a strategy for developing an effective vaccine against HIV-1.
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Affiliation(s)
| | - Takeo Kuwata
- Matsushita Project Laboratory, Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Yasuhiro Maruta
- Matsushita Project Laboratory, Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Kazuki Tanaka
- Matsushita Project Laboratory, Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Muntasir Alam
- Matsushita Project Laboratory, Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Kazuhisa Yoshimura
- Matsushita Project Laboratory, Center for AIDS Research, Kumamoto University, Kumamoto, Japan; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shuzo Matsushita
- Matsushita Project Laboratory, Center for AIDS Research, Kumamoto University, Kumamoto, Japan.
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Wiehe K, Easterhoff D, Luo K, Nicely NI, Bradley T, Jaeger FH, Dennison SM, Zhang R, Lloyd KE, Stolarchuk C, Parks R, Sutherland LL, Scearce RM, Morris L, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Sinangil F, Phogat S, Michael NL, Kim JH, Kelsoe G, Montefiori DC, Tomaras GD, Bonsignori M, Santra S, Kepler TB, Alam SM, Moody MA, Liao HX, Haynes BF. Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved. Immunity 2014; 41:909-18. [PMID: 25526306 DOI: 10.1016/j.immuni.2014.11.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/20/2014] [Indexed: 01/21/2023]
Abstract
In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognition prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. These data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.
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Affiliation(s)
- Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| | - David Easterhoff
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick H Jaeger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Moses Dennison
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christina Stolarchuk
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, SA and the Centre for the AIDS Programme of Research in South Africa (CAPRISA)
| | - Jaranit Kaewkungwal
- Department of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Sorachai Nitayaphan
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | | | - Supachai Rerks-Ngarm
- Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand
| | | | - Sanjay Phogat
- Global Solutions for Infectious Diseases, South San Francisco, CA 94080, USA
| | - Nelson L Michael
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jerome H Kim
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Harvard University School of Medicine, Boston, MA 02215, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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Three amino acid residues in the envelope of human immunodeficiency virus type 1 CRF07_BC regulate viral neutralization susceptibility to the human monoclonal neutralizing antibody IgG1b12. Virol Sin 2014; 29:299-307. [PMID: 25273335 DOI: 10.1007/s12250-014-3485-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/11/2014] [Indexed: 01/11/2023] Open
Abstract
The CD4 binding site (CD4bs) of envelope glycoprotein (Env) is an important conserved target for anti-human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies. Neutralizing monoclonal antibodies IgG1 b12 (b12) could recognize conformational epitopes that overlap the CD4bs of Env. Different virus strains, even derived from the same individual, showed distinct neutralization susceptibility to b12. We examined the key amino acid residues affecting b12 neutralization susceptibility using single genome amplification and pseudovirus neutralization assay. Eleven amino acid residues were identified that affect the sensitivity of Env to b12. Through site-directed mutagenesis, an amino acid substitution at position 182 in the V2 region of Env was confirmed to play a key role in regulating the b12 neutralization susceptibility. The introduction of V182L to a resistant strain enhanced its sensitivity to b12 more than twofold. Correspondingly, the introduction of L182V to a sensitive strain reduced its sensitivity to b12 more than tenfold. Amino acid substitution at positions 267 and 346 could both enhance the sensitivity to b12 more than twofold. However, no additive effect was observed when the three site mutageneses were introduced into the same strain, and the sensitivity was equivalent to the single V182L mutation. CRF07_BC is a major circulating recombinant form of HIV-1 prevalent in China. Our data may provide important information for understanding the molecular mechanism regulating the neutralization susceptibility of CRF07_BC viruses to b12 and may be helpful for a vaccine design targeting the CD4bs epitopes.
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IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Comput Biol 2014; 10:e1003842. [PMID: 25254639 PMCID: PMC4177671 DOI: 10.1371/journal.pcbi.1003842] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/01/2014] [Indexed: 11/19/2022] Open
Abstract
Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals--a cure and a vaccine--remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.
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Envelope variants circulating as initial neutralization breadth developed in two HIV-infected subjects stimulate multiclade neutralizing antibodies in rabbits. J Virol 2014; 88:12949-67. [PMID: 25210191 DOI: 10.1128/jvi.01812-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
UNLABELLED Identifying characteristics of the human immunodeficiency virus type 1 (HIV-1) envelope that are effective in generating broad, protective antibodies remains a hurdle to HIV vaccine design. Emerging evidence of the development of broad and potent neutralizing antibodies in HIV-infected subjects suggests that founder and subsequent progeny viruses may express unique antigenic motifs that contribute to this developmental pathway. We hypothesize that over the course of natural infection, B cells are programmed to develop broad antibodies by exposure to select populations of emerging envelope quasispecies variants. To test this hypothesis, we identified two unrelated subjects whose antibodies demonstrated increasing neutralization breadth against a panel of HIV-1 isolates over time. Full-length functional env genes were cloned longitudinally from these subjects from months after infection through 2.6 to 5.8 years of infection. Motifs associated with the development of breadth in published, cross-sectional studies were found in both subjects. We compared the immunogenicity of envelope vaccines derived from time points obtained during and after broadening of neutralization activity within these subjects. Rabbits were coimmunized four times with selected multiple gp160 DNAs and gp140-trimeric envelope proteins. The affinity of the polyclonal response increased as a function of boosting. The most rapid and persistent neutralization of multiclade tier 1 viruses was elicited by envelopes that were circulating in plasma at time points prior to the development of 50% neutralization breadth in both human subjects. The breadth elicited in rabbits was not improved by exposure to later envelope variants. These data have implications for vaccine development in describing a target time point to identify optimal envelope immunogens. IMPORTANCE Vaccine protection against viral infections correlates with the presence of neutralizing antibodies; thus, vaccine components capable of generating potent neutralization are likely to be critical constituents in an effective HIV vaccine. However, vaccines tested thus far have elicited only weak antibody responses and very modest, waning protection. We hypothesized that B cells develop broad antibodies by exposure to the evolving viral envelope population and tested this concept using multiple envelopes from two subjects who developed neutralization breadth within a few years of infection. We compared different combinations of envelopes from each subject to identify the most effective immunogens and regimens. In each subject, use of HIV envelopes circulating during the early development and maturation of breadth generated more-potent antibodies that were modestly cross neutralizing. These data suggest a new approach to identifying envelope immunogens that may be more effective in generating protective antibodies in humans.
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Utachee P, Isarangkura-na-ayuthaya P, Tokunaga K, Ikuta K, Takeda N, Kameoka M. Impact of amino acid substitutions in the V2 and C2 regions of human immunodeficiency virus type 1 CRF01_AE envelope glycoprotein gp120 on viral neutralization susceptibility to broadly neutralizing antibodies specific for the CD4 binding site. Retrovirology 2014; 11:32. [PMID: 24758333 PMCID: PMC4003292 DOI: 10.1186/1742-4690-11-32] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/09/2014] [Indexed: 01/15/2023] Open
Abstract
Background The CD4 binding site (CD4bs) of envelope glycoprotein (Env) gp120 is a functionally conserved, important target of anti-human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies. Two neutralizing human monoclonal antibodies, IgG1 b12 (b12) and VRC01, are broadly reactive neutralizing antibodies which recognize conformational epitopes that overlap the CD4bs of Env gp120; however, many CRF01_AE viruses are resistant to neutralization mediated by these antibodies. We examined the mechanism underlying the b12 resistance of the viruses using CRF01_AE Env (AE-Env)-recombinant viruses in this study. Results Our results showed that an amino acid substitution at position 185 in the V2 region of gp120 played a crucial role in regulating the b12 susceptibility of AE-Env-recombinant viruses by cooperating with 2 previously reported potential N-linked glycosylation (PNLG) sites at positions 186 (N186) and 197 (N197) in the V2 and C2 regions of Env gp120. The amino acid residue at position 185 and 2 PNLG sites were responsible for the b12 resistance of 21 of 23 (>91%) AE-Env clones tested. Namely, the introduction of aspartic acid at position 185 (D185) conferred b12 susceptibility of 12 resistant AE-Env clones in the absence of N186 and/or N197, while the introduction of glycine at position 185 (G185) reduced the b12 susceptibility of 9 susceptible AE-Env clones in the absence of N186 and/or N197. In addition, these amino acid mutations altered the VRC01 susceptibility of many AE-Env clones. Conclusions We propose that the V2 and C2 regions of AE-Env gp120 contain the major determinants of viral resistance to CD4bs antibodies. CRF01_AE is a major circulating recombinant form of HIV-1 prevalent in Southeast Asia. Our data may provide important information to understand the molecular mechanism regulating the neutralization susceptibility of CRF01_AE viruses to CD4bs antibodies.
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Affiliation(s)
| | | | | | | | | | - Masanori Kameoka
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Nonthaburi, Thailand.
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Evans MC, Phung P, Paquet AC, Parikh A, Petropoulos CJ, Wrin T, Haddad M. Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method. BMC Bioinformatics 2014; 15:77. [PMID: 24646213 PMCID: PMC3999910 DOI: 10.1186/1471-2105-15-77] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/03/2014] [Indexed: 11/26/2022] Open
Abstract
Background Recent efforts in HIV-1 vaccine design have focused on immunogens that evoke potent neutralizing antibody responses to a broad spectrum of viruses circulating worldwide. However, the development of effective vaccines will depend on the identification and characterization of the neutralizing antibodies and their epitopes. We developed bioinformatics methods to predict epitope networks and antigenic determinants using structural information, as well as corresponding genotypes and phenotypes generated by a highly sensitive and reproducible neutralization assay. 282 clonal envelope sequences from a multiclade panel of HIV-1 viruses were tested in viral neutralization assays with an array of broadly neutralizing monoclonal antibodies (mAbs: b12, PG9,16, PGT121 - 128, PGT130 - 131, PGT135 - 137, PGT141 - 145, and PGV04). We correlated IC50 titers with the envelope sequences, and used this information to predict antibody epitope networks. Structural patches were defined as amino acid groups based on solvent-accessibility, radius, atomic depth, and interaction networks within 3D envelope models. We applied a boosted algorithm consisting of multiple machine-learning and statistical models to evaluate these patches as possible antibody epitope regions, evidenced by strong correlations with the neutralization response for each antibody. Results We identified patch clusters with significant correlation to IC50 titers as sites that impact neutralization sensitivity and therefore are potentially part of the antibody binding sites. Predicted epitope networks were mostly located within the variable loops of the envelope glycoprotein (gp120), particularly in V1/V2. Site-directed mutagenesis experiments involving residues identified as epitope networks across multiple mAbs confirmed association of these residues with loss or gain of neutralization sensitivity. Conclusions Computational methods were implemented to rapidly survey protein structures and predict epitope networks associated with response to individual monoclonal antibodies, which resulted in the identification and deeper understanding of immunological hotspots targeted by broadly neutralizing HIV-1 antibodies.
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Affiliation(s)
| | | | | | | | | | | | - Mojgan Haddad
- Monogram Biosciences Inc,, 345 Oyster Point Blvd,, South San Francisco, CA 94080, USA.
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Lacerda M, Moore PL, Ngandu NK, Seaman M, Gray ES, Murrell B, Krishnamoorthy M, Nonyane M, Madiga M, Wibmer CK, Sheward D, Bailer RT, Gao H, Greene KM, Karim SSA, Mascola JR, Korber BTM, Montefiori DC, Morris L, Williamson C, Seoighe C. Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models. Virol J 2013; 10:347. [PMID: 24295501 PMCID: PMC4220805 DOI: 10.1186/1743-422x-10-347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022] Open
Abstract
Background Identification of the epitopes targeted by antibodies that can neutralize diverse HIV-1 strains can provide important clues for the design of a preventative vaccine. Methods We have developed a computational approach that can identify key amino acids within the HIV-1 envelope glycoprotein that influence sensitivity to broadly cross-neutralizing antibodies. Given a sequence alignment and neutralization titers for a panel of viruses, the method works by fitting a phylogenetic model that allows the amino acid frequencies at each site to depend on neutralization sensitivities. Sites at which viral evolution influences neutralization sensitivity were identified using Bayes factors (BFs) to compare the fit of this model to that of a null model in which sequences evolved independently of antibody sensitivity. Conformational epitopes were identified with a Metropolis algorithm that searched for a cluster of sites with large Bayes factors on the tertiary structure of the viral envelope. Results We applied our method to ID50 neutralization data generated from seven HIV-1 subtype C serum samples with neutralization breadth that had been tested against a multi-clade panel of 225 pseudoviruses for which envelope sequences were also available. For each sample, between two and four sites were identified that were strongly associated with neutralization sensitivity (2ln(BF) > 6), a subset of which were experimentally confirmed using site-directed mutagenesis. Conclusions Our results provide strong support for the use of evolutionary models applied to cross-sectional viral neutralization data to identify the epitopes of serum antibodies that confer neutralization breadth.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland.
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Joshi A, Lee RTC, Mohl J, Sedano M, Khong WX, Ng OT, Maurer-Stroh S, Garg H. Genetic signatures of HIV-1 envelope-mediated bystander apoptosis. J Biol Chem 2013; 289:2497-514. [PMID: 24265318 DOI: 10.1074/jbc.m113.514018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The envelope (Env) glycoprotein of HIV is an important determinant of viral pathogenesis. Several lines of evidence support the role of HIV-1 Env in inducing bystander apoptosis that may be a contributing factor in CD4(+) T cell loss. However, most of the studies testing this phenomenon have been conducted with laboratory-adapted HIV-1 isolates. This raises the question of whether primary Envs derived from HIV-infected patients are capable of inducing bystander apoptosis and whether specific Env signatures are associated with this phenomenon. We developed a high throughput assay to determine the bystander apoptosis inducing activity of a panel of primary Envs. We tested 38 different Envs for bystander apoptosis, virion infectivity, neutralizing antibody sensitivity, and putative N-linked glycosylation sites along with a comprehensive sequence analysis to determine if specific sequence signatures within the viral Env are associated with bystander apoptosis. Our studies show that primary Envs vary considerably in their bystander apoptosis-inducing potential, a phenomenon that correlates inversely with putative N-linked glycosylation sites and positively with virion infectivity. By use of a novel phylogenetic analysis that avoids subtype bias coupled with structural considerations, we found specific residues like Arg-476 and Asn-425 that were associated with differences in bystander apoptosis induction. A specific role of these residues was also confirmed experimentally. These data demonstrate for the first time the potential of primary R5 Envs to mediate bystander apoptosis in CD4(+) T cells. Furthermore, we identify specific genetic signatures within the Env that may be associated with the bystander apoptosis-inducing phenotype.
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Affiliation(s)
- Anjali Joshi
- From the Center of Excellence for Infectious Diseases, Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, Texas 79905
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Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial. PLoS One 2013; 8:e75665. [PMID: 24086607 PMCID: PMC3784573 DOI: 10.1371/journal.pone.0075665] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/19/2013] [Indexed: 11/26/2022] Open
Abstract
Neutralizing and non-neutralizing antibodies to linear epitopes on HIV-1 envelope glycoproteins have potential to mediate antiviral effector functions that could be beneficial to vaccine-induced protection. Here, plasma IgG responses were assessed in three HIV-1 gp120 vaccine efficacy trials (RV144, Vax003, Vax004) and in HIV-1-infected individuals by using arrays of overlapping peptides spanning the entire consensus gp160 of all major genetic subtypes and circulating recombinant forms (CRFs) of the virus. In RV144, where 31.2% efficacy against HIV-1 infection was seen, dominant responses targeted the C1, V2, V3 and C5 regions of gp120. An analysis of RV144 case-control samples showed that IgG to V2 CRF01_AE significantly inversely correlated with infection risk (OR= 0.54, p=0.0042), as did the response to other V2 subtypes (OR=0.60-0.63, p=0.016-0.025). The response to V3 CRF01_AE also inversely correlated with infection risk but only in vaccine recipients who had lower levels of other antibodies, especially Env-specific plasma IgA (OR=0.49, p=0.007) and neutralizing antibodies (OR=0.5, p=0.008). Responses to C1 and C5 showed no significant correlation with infection risk. In Vax003 and Vax004, where no significant protection was seen, serum IgG responses targeted the same epitopes as in RV144 with the exception of an additional C1 reactivity in Vax003 and infrequent V2 reactivity in Vax004. In HIV-1 infected subjects, dominant responses targeted the V3 and C5 regions of gp120, as well as the immunodominant domain, heptad repeat 1 (HR-1) and membrane proximal external region (MPER) of gp41. These results highlight the presence of several dominant linear B cell epitopes on the HIV-1 envelope glycoproteins. They also generate the hypothesis that IgG to linear epitopes in the V2 and V3 regions of gp120 are part of a complex interplay of immune responses that contributed to protection in RV144.
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47
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van den Kerkhof TLGM, Feenstra KA, Euler Z, van Gils MJ, Rijsdijk LWE, Boeser-Nunnink BD, Heringa J, Schuitemaker H, Sanders RW. HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity. Retrovirology 2013; 10:102. [PMID: 24059682 PMCID: PMC3849187 DOI: 10.1186/1742-4690-10-102] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/12/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Current HIV-1 envelope glycoprotein (Env) vaccines are unable to induce cross-reactive neutralizing antibodies. However, such antibodies are elicited in 10-30% of HIV-1 infected individuals, but it is unknown why these antibodies are induced in some individuals and not in others. We hypothesized that the Envs of early HIV-1 variants in individuals who develop cross-reactive neutralizing activity (CrNA) might have unique characteristics that support the induction of CrNA. RESULTS We retrospectively generated and analyzed env sequences of early HIV-1 clonal variants from 31 individuals with diverse levels of CrNA 2-4 years post-seroconversion. These sequences revealed a number of Env signatures that coincided with CrNA development. These included a statistically shorter variable region 1 and a lower probability of glycosylation as implied by a high ratio of NXS versus NXT glycosylation motifs. Furthermore, lower probability of glycosylation at position 332, which is involved in the epitopes of many broadly reactive neutralizing antibodies, was associated with the induction of CrNA. Finally, Sequence Harmony identified a number of amino acid changes associated with the development of CrNA. These residues mapped to various Env subdomains, but in particular to the first and fourth variable region as well as the underlying α2 helix of the third constant region. CONCLUSIONS These findings imply that the development of CrNA might depend on specific characteristics of early Env. Env signatures that correlate with the induction of CrNA might be relevant for the design of effective HIV-1 vaccines.
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Affiliation(s)
- Tom L G M van den Kerkhof
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - K Anton Feenstra
- Center for Integrative Bioinformatics VU (IBIVU) and Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
- Netherlands Bioinformatics Center (NBIC), 6525 GA Nijmegen, the Netherlands
| | - Zelda Euler
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Marit J van Gils
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Linda W E Rijsdijk
- Center for Integrative Bioinformatics VU (IBIVU) and Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Brigitte D Boeser-Nunnink
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jaap Heringa
- Center for Integrative Bioinformatics VU (IBIVU) and Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
- Netherlands Bioinformatics Center (NBIC), 6525 GA Nijmegen, the Netherlands
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- Crucell Holland BV, 2333 CN Leiden, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY 10065 USA
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HIV-1 envelope glycoprotein resistance to monoclonal antibody 2G12 is subject-specific and context-dependent in macaques and humans. PLoS One 2013; 8:e75277. [PMID: 24040404 PMCID: PMC3767832 DOI: 10.1371/journal.pone.0075277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/15/2013] [Indexed: 11/19/2022] Open
Abstract
HIV-1 Envelope (Env) protein is the sole target of neutralizing antibodies (NAbs) that arise during infection to neutralize autologous variants. Under this immune pressure, HIV escape variants are continuously selected and over the course of infection Env becomes more neutralization resistant. Many common alterations are known to affect sensitivity to NAbs, including residues encoding potential N-linked glycosylation sites (PNGS). Knowledge of Env motifs associated with neutralization resistance is valuable for the design of an effective Env-based vaccine so we characterized Envs isolated longitudinally from a SHIV(SF162P4) infected macaque for sensitivity to neutralizing monoclonal antibodies (MAbs) B12, 2G12, 4E10 and 2F5. The early Env, isolated from plasma at day 56 after infection, was the most sensitive and the late Env, from day 670, was the most resistant to MAbs. We identified four PNGS in these Envs that accumulated over time at positions 130, 139, 160 and 397. We determined that removal of these PNGS significantly increased neutralization sensitivity to 2G12, and conversely, we identified mutations by in silico analyses that contributed resistance to 2G12 neutralization. In order to expand our understanding of these PNGS, we analyzed Envs from clade B HIV-infected human subjects and identified additional glycan and amino acid changes that could affect neutralization by 2G12 in a context-dependent manner. Taken together, these in vitro and in silico analyses of clade B Envs revealed that 2G12 resistance is achieved by previously unrecognized PNGS substitutions in a context-dependent manner and by subject-specific pathways.
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Residue-level prediction of HIV-1 antibody epitopes based on neutralization of diverse viral strains. J Virol 2013; 87:10047-58. [PMID: 23843642 DOI: 10.1128/jvi.00984-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Delineation of antibody epitopes at the residue level is key to understanding antigen resistance mutations, designing epitope-specific probes for antibody isolation, and developing epitope-based vaccines. Ideally, epitope residues are determined in the context of the atomic-level structure of the antibody-antigen complex, though structure determination may in many cases be impractical. Here we describe an efficient computational method to predict antibody-specific HIV-1 envelope (Env) epitopes at the residue level, based on neutralization panels of diverse viral strains. The method primarily utilizes neutralization potency data over a set of diverse viral strains representing the antigen, and enhanced accuracy could be achieved by incorporating information from the unbound structure of the antigen. The method was evaluated on 19 HIV-1 Env antibodies with neutralization panels comprising 181 diverse viral strains and with available antibody-antigen complex structures. Prediction accuracy was shown to improve significantly over random selection, with an average of greater-than-8-fold enrichment of true positives at the 0.05 false-positive rate level. The method was used to prospectively predict epitope residues for two HIV-1 antibodies, 8ANC131 and 8ANC195, for which we experimentally validated the predictions. The method is inherently applicable to antigens that exhibit sequence diversity, and its accuracy was found to correlate inversely with sequence conservation of the epitope. Together the results show how knowledge inherent to a neutralization panel and unbound antigen structure can be utilized for residue-level prediction of antibody epitopes.
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50
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Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues. Proc Natl Acad Sci U S A 2013; 110:10598-603. [PMID: 23754383 DOI: 10.1073/pnas.1309215110] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Advances in single-cell antibody cloning methods have led to the identification of a variety of broadly neutralizing anti-HIV-1 antibodies. We developed a computational tool (Antibody Database) to help identify critical residues on the HIV-1 envelope protein whose natural variation affects antibody activity. Our simplifying assumption was that, for a given antibody, a significant portion of the dispersion of neutralization activity across a panel of HIV-1 strains is due to the amino acid identity or glycosylation state at a small number of specific sites, each acting independently. A model of an antibody's neutralization IC50 was developed in which each site contributes a term to the logarithm of the modeled IC50. The analysis program attempts to determine the set of rules that minimizes the sum of the residuals between observed and modeled IC50 values. The predictive quality of the identified rules may be assessed in part by whether there is support for rules within individual viral clades. As a test case, we analyzed antibody 8ANC195, an anti-glycoprotein gp120 antibody of unknown specificity. The model for this antibody indicated that several glycosylation sites were critical for neutralization. We evaluated this prediction by measuring neutralization potencies of 8ANC195 against HIV-1 in vitro and in an antibody therapy experiment in humanized mice. These experiments confirmed that 8ANC195 represents a distinct class of glycan-dependent anti-HIV-1 antibody and validated the utility of computational analysis of neutralization panel data.
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