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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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2
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Luo M, Zhou B, Reddem ER, Tang B, Chen B, Zhou R, Liu H, Liu L, Katsamba PS, Au KK, Man HO, To KKW, Yuen KY, Shapiro L, Dang S, Ho DD, Chen Z. Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Emerg Microbes Infect 2023; 12:2146538. [PMID: 36354024 PMCID: PMC9817130 DOI: 10.1080/22221751.2022.2146538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ABSTRACTIncreasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.
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Affiliation(s)
- Mengxiao Luo
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Biao Zhou
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | | | - Bingjie Tang
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Bohao Chen
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Runhong Zhou
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hang Liu
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Ka-Kit Au
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hiu-On Man
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behaviour Institute, New York, NY, USA,Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA, Zhiwei Chen AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Lawrence Shapiro Zuckerman Mind Brain Behaviour Institute, New York, NY 10027, USA, Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Shangyu Dang Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China, HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, People's Republic of China; David D. Ho Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shangyu Dang
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People’s Republic of China,HKUST-Shenzhen Research Institute, Nanshan, People’s Republic of China, Zhiwei Chen AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Lawrence Shapiro Zuckerman Mind Brain Behaviour Institute, New York, NY 10027, USA, Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Shangyu Dang Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China, HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, People's Republic of China; David D. Ho Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiwei Chen
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China, Zhiwei Chen AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Lawrence Shapiro Zuckerman Mind Brain Behaviour Institute, New York, NY 10027, USA, Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Shangyu Dang Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China, HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, People's Republic of China; David D. Ho Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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3
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Zhou B, Zhou R, Chan JFW, Zeng J, Zhang Q, Yuan S, Liu L, Robinot R, Shan S, Liu N, Ge J, Kwong HYH, Zhou D, Xu H, Chan CCS, Poon VKM, Chu H, Yue M, Kwan KY, Chan CY, Chan CCY, Chik KKH, Du Z, Au KK, Huang H, Man HO, Cao J, Li C, Wang Z, Zhou J, Song Y, Yeung ML, To KKW, Ho DD, Chakrabarti LA, Wang X, Zhang L, Yuen KY, Chen Z. SARS-CoV-2 hijacks neutralizing dimeric IgA for nasal infection and injury in Syrian hamsters 1. Emerg Microbes Infect 2023; 12:2245921. [PMID: 37542391 PMCID: PMC10444022 DOI: 10.1080/22221751.2023.2245921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023]
Abstract
Prevention of robust severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in nasal turbinate (NT) requires in vivo evaluation of IgA neutralizing antibodies. Here, we report the efficacy of receptor binding domain (RBD)-specific monomeric B8-mIgA1 and B8-mIgA2, and dimeric B8-dIgA1, B8-dIgA2 and TH335-dIgA1 against intranasal SARS-CoV-2 challenge in Syrian hamsters. These antibodies exhibited comparable neutralization potency against authentic virus by competing with human angiotensin converting enzyme-2 (ACE2) receptor for RBD binding. While reducing viral loads in lungs significantly, prophylactic intranasal B8-dIgA unexpectedly led to high amount of infectious viruses and extended damage in NT compared to controls. Mechanistically, B8-dIgA failed to inhibit SARS-CoV-2 cell-to-cell transmission, but was hijacked by the virus through dendritic cell-mediated trans-infection of NT epithelia leading to robust nasal infection. Cryo-EM further revealed B8 as a class II antibody binding trimeric RBDs in 3-up or 2-up/1-down conformation. Neutralizing dIgA, therefore, may engage an unexpected mode of SARS-CoV-2 nasal infection and injury.
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Affiliation(s)
- Biao Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Runhong Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Hainan-Medical University – The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, and Academician Workstation of Hainan Province, Hainan Medical University, Haikou, People’s Republic of China, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jianwei Zeng
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Qi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Shuofeng Yuan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Li Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Rémy Robinot
- Control of Chronic Viral Infections Group, Virus & Immunity Unit, Institute Pasteur, Paris, France; CNRS UMR, Paris, France
| | - Sisi Shan
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Na Liu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Hugo Yat-Hei Kwong
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Dongyan Zhou
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Haoran Xu
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chris Chung-Sing Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Hin Chu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Ming Yue
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ka-Yi Kwan
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chun-Yin Chan
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Chris Chun-Yiu Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Kenn Ka-Heng Chik
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Zhenglong Du
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ka-Kit Au
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Haode Huang
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Hiu-On Man
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Jianli Cao
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Cun Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jie Zhou
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Youqiang Song
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Man-Lung Yeung
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lisa A. Chakrabarti
- Control of Chronic Viral Infections Group, Virus & Immunity Unit, Institute Pasteur, Paris, France; CNRS UMR, Paris, France
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Linqi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Diseases, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Hainan-Medical University – The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, and Academician Workstation of Hainan Province, Hainan Medical University, Haikou, People’s Republic of China, and The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
| | - Zhiwei Chen
- AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region (SAR), People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
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4
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Wang R, Han Y, Zhang R, Zhu J, Nan X, Liu Y, Yang Z, Zhou B, Yu J, Lin Z, Li J, Chen P, Wang Y, Li Y, Liu D, Shi X, Wang X, Zhang Q, Yang YR, Li T, Zhang L. Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Immunity 2023; 56:2635-2649.e6. [PMID: 37924813 DOI: 10.1016/j.immuni.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
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Affiliation(s)
- Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China
| | - Rui Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yaping Liu
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziqing Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zichun Lin
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinqian Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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5
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Ju B, Fan Q, Liu C, Shen S, Wang M, Guo H, Zhou B, Ge X, Zhang Z. Omicron BQ.1.1 and XBB.1 unprecedentedly escape broadly neutralizing antibodies elicited by prototype vaccination. Cell Rep 2023; 42:112532. [PMID: 37219999 PMCID: PMC10201307 DOI: 10.1016/j.celrep.2023.112532] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/02/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants have seriously attacked the antibody barrier established by natural infection and/or vaccination, especially the recently emerged BQ.1.1 and XBB.1. However, crucial mechanisms underlying the virus escape and the broad neutralization remain elusive. Here, we present a panoramic analysis of broadly neutralizing activity and binding epitopes of 75 monoclonal antibodies isolated from prototype inactivated vaccinees. Nearly all neutralizing antibodies (nAbs) partly or totally lose their neutralization against BQ.1.1 and XBB.1. We report a broad nAb, VacBB-551, that effectively neutralizes all tested subvariants including BA.2.75, BQ.1.1, and XBB.1. We determine the cryoelectron microscopy (cryo-EM) structure of VacBB-551 complexed with the BA.2 spike and perform detailed functional verification to reveal the molecular basis of N460K and F486V/S mutations mediating the partial escape of BA.2.75, BQ.1.1, and XBB.1 from the neutralization of VacBB-551. Overall, BQ.1.1 and XBB.1 raised the alarm over SARS-CoV-2 evolution with unprecedented antibody evasion from broad nAbs elicited by prototype vaccination.
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Affiliation(s)
- Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China; Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen 518112, Guangdong Province, China; Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong Province, China.
| | - Qing Fan
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Congcong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Senlin Shen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Miao Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Huimin Guo
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Bing Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China; Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong Province, China
| | - Xiangyang Ge
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China; Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen 518112, Guangdong Province, China; Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong Province, China; Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen 518112, Guangdong Province, China.
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6
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Wang Z, Li D, Chen Y, Sun Y, Jin C, Hu C, Feng Y, Su J, Ren L, Hao Y, Wang S, Zhu M, Liu Y, Qi J, Zhu B, Shao Y. Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents. Front Immunol 2023; 14:1160283. [PMID: 37234155 PMCID: PMC10207940 DOI: 10.3389/fimmu.2023.1160283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies. Methods In this study, we isolated receptor binding domain (RBD)-specific memory B cells using single-cell sorting method from two COVID-19 convalescents and expressed the antibody to test their neutralizing activity against diverse SARS-CoV-2 variants. Then, we resolved antibody-RBD complex structures of potent RBD-specific neutralizing antibodies by X-ray diffraction method. Finally, we analyzed the whole antibody repertoires of the two donors and studied the evolutionary pathway of potent neutralizing antibodies. Results and discussion We identified three potent RBD-specific neutralizing antibodies (1D7, 3G10 and 3C11) from two COVID-19 convalescents that neutralized authentic SARS-CoV-2 WH-1 and Delta variant, and one of them, 1D7, presented broadly neutralizing activity against WH-1, Beta, Gamma, Delta and Omicron authentic viruses. The resolved antibody-RBD complex structures of two antibodies, 3G10 and 3C11, indicate that both of them interact with the external subdomain of the RBD and that they belong to the RBD-1 and RBD-4 communities, respectively. From the antibody repertoire analysis, we found that the CDR3 frequencies of the light chain, which shared high degrees of amino acid identity with these three antibodies, were higher than those of the heavy chain. This research will contribute to the development of RBD-specific antibody-based drugs and immunogens against multiple variants.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yulu Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junwei Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meiling Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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7
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Caniels TG, Medina-Ramírez M, Zhang J, Sarkar A, Kumar S, LaBranche A, Derking R, Allen JD, Snitselaar JL, Capella-Pujol J, Sánchez IDM, Yasmeen A, Diaz M, Aldon Y, Bijl TPL, Venkatayogi S, Martin Beem JS, Newman A, Jiang C, Lee WH, Pater M, Burger JA, van Breemen MJ, de Taeye SW, Rantalainen K, LaBranche C, Saunders KO, Montefiori D, Ozorowski G, Ward AB, Crispin M, Moore JP, Klasse PJ, Haynes BF, Wilson IA, Wiehe K, Verkoczy L, Sanders RW. Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions. Cell Rep Med 2023; 4:101003. [PMID: 37044090 PMCID: PMC10140475 DOI: 10.1016/j.xcrm.2023.101003] [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: 09/15/2022] [Revised: 01/23/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023]
Abstract
Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.
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Affiliation(s)
- Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Max Medina-Ramírez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jinsong Zhang
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alex LaBranche
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Ronald Derking
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jonne L Snitselaar
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Iván Del Moral Sánchez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Marilyn Diaz
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom P L Bijl
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | | | | | - Amanda Newman
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Chuancang Jiang
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Maarten Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Mariëlle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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8
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Zhang YN, Paynter J, Antanasijevic A, Allen JD, Eldad M, Lee YZ, Copps J, Newby ML, He L, Chavez D, Frost P, Goodroe A, Dutton J, Lanford R, Chen C, Wilson IA, Crispin M, Ward AB, Zhu J. Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates. Nat Commun 2023; 14:1985. [PMID: 37031217 PMCID: PMC10082823 DOI: 10.1038/s41467-023-37742-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/10/2023] Open
Abstract
Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joel D Allen
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mor Eldad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Maddy L Newby
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deborah Chavez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Pat Frost
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Anna Goodroe
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - John Dutton
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Christopher Chen
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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9
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Ju B, Zhang Q, Wang Z, Aw ZQ, Chen P, Zhou B, Wang R, Ge X, Lv Q, Cheng L, Zhang R, Wong YH, Chen H, Wang H, Shan S, Liao X, Shi X, Liu L, Chu JJH, Wang X, Zhang Z, Zhang L. Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants. Nat Immunol 2023; 24:690-699. [PMID: 36914890 PMCID: PMC10063446 DOI: 10.1038/s41590-023-01449-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023]
Abstract
The omicron variants of SARS-CoV-2 have substantial ability to escape infection- and vaccine-elicited antibody immunity. Here, we investigated the extent of such escape in nine convalescent patients infected with the wild-type SARS-CoV-2 during the first wave of the pandemic. Among the total of 476 monoclonal antibodies (mAbs) isolated from peripheral memory B cells, we identified seven mAbs with broad neutralizing activity to all variants tested, including various omicron subvariants. Biochemical and structural analysis indicated the majority of these mAbs bound to the receptor-binding domain, mimicked the receptor ACE2 and were able to accommodate or inadvertently improve recognition of omicron substitutions. Passive delivery of representative antibodies protected K18-hACE2 mice from infection with omicron and beta SARS-CoV-2. A deeper understanding of how the memory B cells that produce these antibodies could be selectively boosted or recalled can augment antibody immunity against SARS-CoV-2 variants.
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Affiliation(s)
- Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.,The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Qi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Ziyi Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhen Qin Aw
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peng Chen
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Bing Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Ruoke Wang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xiangyang Ge
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Qining Lv
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Rui Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yi Hao Wong
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Huixin Chen
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Sisi Shan
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xuejiao Liao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xuanling Shi
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Lei Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.,The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Justin Jang Hann Chu
- Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Infectious Disease Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China. .,The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China. .,Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, China.
| | - Linqi Zhang
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China. .,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China. .,Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China.
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10
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Hu Y, Li D, Yuan Z, Feng Y, Ren L, Hao Y, Wang S, Hu X, Liu Y, Hong K, Shao Y, Wang Z. Characterization of a VRC01-like antibody lineage with immature V L from an HIV-1 infected Chinese donor. Mol Immunol 2023; 154:11-23. [PMID: 36577292 DOI: 10.1016/j.molimm.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 12/18/2022] [Indexed: 12/28/2022]
Abstract
Because of the broadly neutralizing activity, VRC01-class antibodies are attractive templates for HIV-1 vaccine development and suitable candidates for HIV-1 therapy. Although we previously revealed that glycans in gp120 may have a role in the uneven evolution of the VH and the VL of a VRC01-class antibody, DRVIA7, which was isolated from an elite neutralizer, it is unknown whether the immature VH or VL of VRC01-class antibodies are also present in the non-neutralizer. We identified a CD4bs-directed antibody - 263A9 - with low neutralizing activity from a donor whose plasma had a moderate neutralizing spectrum in this study. The 263A9 antibody, in particular, was a VRC01-like antibody whose VH and VL were derived from IGHV1-2 * 04 and IGKV1-33 * 01, respectively, and both had significant SHM rates. Surprisingly, we discovered that the VL of 263A9 hindered the neutralizing activity of the antibody, and that replacing its LCDR1 and LCDR3 with VRC01 increased the neutralizing breadth of the chimeric antibodies. Following that, an antibodyomics research revealed that the VL of 263A9 lineage was remote from VRC01-class antibodies. We also looked at the envelope sequence characteristics of donor CBJC263 and discovered that N276 in the D loop and N460/N463 glycans in the V5 region of gp120 potentially interact with VL of 263A9 at the structural level. This study will provide valuable information for immunogen screening and vaccine development for eliciting VRC01-class antibodies. DATA AVAILABILITY STATEMENT: The original data presented in the study are included in the article or Supplementary materials. Further inquiries can be directed to the corresponding author. HIV Env sequences in the manuscript had been deposited into the GenBank with the accession numbers from OL466822 to OL466859.
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Affiliation(s)
- Yuanyuan Hu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Zhenzhen Yuan
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Xintao Hu
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ying Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Kunxue Hong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China.
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11
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Yuan X, Lai Y. Bibliometric and visualized analysis of elite controllers based on CiteSpace: landscapes, hotspots, and frontiers. Front Cell Infect Microbiol 2023; 13:1147265. [PMID: 37124043 PMCID: PMC10130382 DOI: 10.3389/fcimb.2023.1147265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Background A unique subset of people living with HIV, known as elite controllers, possess spontaneous and consistent control over viral replication and disease progression in the absence of antiviral intervention. In-depth research on elite controllers is conducive to designing better treatment strategies for HIV. However, comprehensive and illuminating bibliometric reports on elite controllers are rare. Methods Articles on elite controllers were retrieved from the Web of Science Core Collection. A visualized analysis of this domain was conducted by CiteSpace software. Taking count, betweenness centrality, and burst value as criteria, we interpreted the visualization results and predicted future new directions and emerging trends. Results By December 31, 2022, 843 articles related to elite controllers had been published. The largest contributors in terms of country, institution, and author were the United States (485), Univ Calif San Francisco (87), and Walker B.D. (65), respectively. Migueles S.A. (325) and Journal of Virology (770) were the most cocited author and journal, respectively. Additionally, by summarizing the results of our CiteSpace software analysis on references and keywords, we considered that the research hotspots and frontiers on elite controllers mainly focus on three aspects: deciphering the mechanisms of durable control, delineating the implications for the development of treatments for HIV infection, and highlighting the clinical risks faced by elite controllers and coping strategies. Conclusion This study performed a bibliometric and visual analysis of elite controllers, identified the main characteristics and emerging trends, and provided insightful references for further development of this rapidly evolving and complex field.
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Affiliation(s)
- Xingyue Yuan
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu Lai
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Yu Lai,
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12
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Abstract
Self-replicating RNA viral vectors have been engineered for both prophylactic and therapeutic applications. Mainly the areas of infectious diseases and cancer have been targeted. Both positive and negative strand RNA viruses have been utilized including alphaviruses, flaviviruses, measles viruses and rhabdoviruses. The high-level of RNA amplification has provided efficient expression of viral surface proteins and tumor antigens. Immunization studies in animal models have elicit robust neutralizing antibody responses. In the context of infectious diseases, immunization with self-replicating RNA viral vectors has provided protection against challenges with lethal doses of pathogens in animal models. Similarly, immunization with vectors expressing tumor antigens has resulted in tumor regression and eradication and protection against tumor challenges in animal models. The transient nature and non-integration of viral RNA into the host genome are ideal features for vaccine development. Moreover, self-replicating RNA viral vectors show great flexibility as they can be applied as recombinant viral particles, RNA replicons or DNA replicon plasmids. Several clinical trials have been conducted especially in the area of cancer immunotherapy.
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13
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Zhou B, Zhou R, Tang B, Chan JFW, Luo M, Peng Q, Yuan S, Liu H, Mok BWY, Chen B, Wang P, Poon VKM, Chu H, Chan CCS, Tsang JOL, Chan CCY, Au KK, Man HO, Lu L, To KKW, Chen H, Yuen KY, Dang S, Chen Z. A broadly neutralizing antibody protects Syrian hamsters against SARS-CoV-2 Omicron challenge. Nat Commun 2022; 13:3589. [PMID: 35739114 PMCID: PMC9223271 DOI: 10.1038/s41467-022-31259-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
The strikingly high transmissibility and antibody evasion of SARS-CoV-2 Omicron variants have posed great challenges to the efficacy of current vaccines and antibody immunotherapy. Here, we screen 34 BNT162b2-vaccinees and isolate a public broadly neutralizing antibody ZCB11 derived from the IGHV1-58 family. ZCB11 targets viral receptor-binding domain specifically and neutralizes all SARS-CoV-2 variants of concern, especially with great potency against authentic Omicron and Delta variants. Pseudovirus-based mapping of 57 naturally occurred spike mutations or deletions reveals that S371L results in 11-fold neutralization resistance, but it is rescued by compensating mutations in Omicron variants. Cryo-EM analysis demonstrates that ZCB11 heavy chain predominantly interacts with Omicron spike trimer with receptor-binding domain in up conformation blocking ACE2 binding. In addition, prophylactic or therapeutic ZCB11 administration protects lung infection against Omicron viral challenge in golden Syrian hamsters. These results suggest that vaccine-induced ZCB11 is a promising broadly neutralizing antibody for biomedical interventions against pandemic SARS-CoV-2. SARS-CoV-2 variants of concern such as the Omicron variant pose a challenge for vaccination and antibody immunotherapy. Here, Zhou et al. isolate a broadly neutralizing antibody (bNAb), named ZCB11, that protects Golden Syrian hamsters against Omicron. Applying CryoEM the authors show that ZCB11 heavy chain predominantly interacts with RBD in up confirmation, which interferes with ACE2 receptor binding.
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Affiliation(s)
- Biao Zhou
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Runhong Zhou
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Bingjie Tang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Mengxiao Luo
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Qiaoli Peng
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,National Clinical Research Center for Infectious Diseases, HKU-AIDS Institute Shenzhen Research laboratory, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, People's Republic of China
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hang Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China
| | - Bobo Wing-Yee Mok
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Bohao Chen
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Pui Wang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hin Chu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Chris Chung-Sing Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jessica Oi-Ling Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Chris Chun-Yiu Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ka-Kit Au
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hiu-On Man
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Lu Lu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Honglin Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Academician Workstation of Hainan Province and Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China. .,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China.
| | - Zhiwei Chen
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China. .,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China. .,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region, People's Republic of China. .,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China.
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14
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Complementary Roles of Antibody Heavy and Light Chain Somatic Hypermutation in Conferring Breadth and Potency to the HIV-1-Specific CAP256-VRC26 bNAb Lineage. J Virol 2022; 96:e0027022. [PMID: 35510865 DOI: 10.1128/jvi.00270-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some HIV-infected people develop broadly neutralizing antibodies (bNAbs) that block many diverse, unrelated strains of HIV from infecting target cells and, through passive immunization, protect animals and humans from infection. Therefore, understanding the development of bNAbs and their neutralization can inform the design of an HIV vaccine. Here, we extend our previous studies of the ontogeny of the CAP256-VRC26 V2-targeting bNAb lineage by defining the mutations that confer neutralization to the unmutated common ancestor (CAP256.UCA). Analysis of the sequence of the CAP256.UCA showed that many improbable mutations were located in the third complementarity-determining region of the heavy chain (CDRH3) and the heavy chain framework 3 (FR3). Transferring the CDRH3 from bNAb CAP256.25 (63% breadth and 0.003 μg/mL potency) into the CAP256.UCA introduced breadth and the ability to neutralize emerging viral variants. In addition, we showed that the framework and light chain contributed to potency and that the second CDR of the light chain forms part of the paratope of CAP256.25. Notably, a minimally mutated CAP256 antibody, with 41% of the mutations compared to bNAb CAP256.25, was broader (64% breadth) and more potent (0.39 μg/mL geometric potency) than many unrelated bNAbs. Together, we have identified key regions and mutations that confer breadth and potency in a V2-specific bNAb lineage. These data indicate that immunogens that target affinity maturation to key sites in CAP256-VRC26-like precursors, including the CDRHs and light chain, could rapidly elicit breadth through vaccination. IMPORTANCE A major focus in the search for an HIV vaccine is elucidating the ontogeny of broadly neutralizing antibodies (bNAbs), which prevent HIV infection in vitro and in vivo. The unmutated common ancestors (UCAs) of bNAbs are generally strain specific and acquire breadth through extensive, and sometimes redundant, somatic hypermutation during affinity maturation. We investigated which mutations in the CAP256-VRC26 bNAb lineage conferred neutralization capacity to the UCA. We found that mutations in the antibody heavy and light chains had complementary roles in neutralization breadth and potency, respectively. The heavy chain, particularly the third complementarity-determining region, was responsible for conferring breadth. In addition, previously uninvestigated mutations in the framework also contributed to breadth. Together, approximately half of the mutations in CAP256.25 were necessary for broader and more potent neutralization than many unrelated neutralizing antibodies. Vaccine approaches that promote affinity maturation at key sites could therefore more rapidly produce antibodies with neutralization breadth.
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15
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Zhang D, Liu Z, Wang W, Chen MX, Hou JL, Zhang Z, Ren WH, Ren L, Hao YL. Viral resistance to VRC01-like antibodies with mutations in loop D and V5 from an HIV-1 B′ subtype infected individual with broadly neutralization activity. Mol Immunol 2022; 145:50-58. [DOI: 10.1016/j.molimm.2022.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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16
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Lee JH, Nakao C, Appel M, Le A, Landais E, Kalyuzhniy O, Hu X, Liguori A, Mullen TM, Groschel B, Abbott RK, Sok D, Schief WR, Crotty S. Highly mutated antibodies capable of neutralizing N276 glycan-deficient HIV after a single immunization with an Env trimer. Cell Rep 2022; 38:110485. [PMID: 35263576 PMCID: PMC8924373 DOI: 10.1016/j.celrep.2022.110485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/10/2021] [Accepted: 02/14/2022] [Indexed: 11/08/2022] Open
Abstract
Elicitation of HIV broadly neutralizing antibodies (bnAbs) is challenging because unmutated bnAb precursors are rare and seldom bind HIV envelope glycoprotein (Env) trimers. One strategy to initiate bnAb responses is to use germline-targeting (GT) immunogens with high affinity to bnAb-class precursor B cells and then shepherd affinity maturation with booster immunogens that successively look more like native Env. In a mouse model where the frequency of VRC01-precursor (VRC01gHL) B cells mimics that of humans, we show that following a GT HIV Env trimer protein prime, VRC01-class B cells in the germinal center (GC) acquire high-affinity VRC01-class B cell somatic hypermutations (SHMs). Many GC-derived VRC01gHL antibodies robustly bind N276 glycan-deficient Env trimers and neutralize several N276 glycan-deficient tier 2 HIV strains. These results are encouraging for GT Env trimer vaccine designs and demonstrate accumulation of substantial SHMs, including deletions, uncommon point mutations, and functional bnAb features, after a single immunization.
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Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Michael Appel
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amber Le
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Oleksandr Kalyuzhniy
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Xiaozhen Hu
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Alessia Liguori
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Tina-Marie Mullen
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Bettina Groschel
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Robert K Abbott
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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17
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Wang Z, Tang Q, Liu B, Zhang W, Chen Y, Ji N, Peng Y, Yang X, Cui D, Kong W, Tang X, Yang T, Zhang M, Chang X, Zhu J, Huang M, Feng Z. A SARS-CoV-2 neutralizing antibody discovery by single cell sequencing and molecular modeling. J Biomed Res 2022; 37:166-178. [PMID: 36992606 DOI: 10.7555/jbr.36.20220221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although vaccines have been developed, mutations of SARS-CoV-2, especially the dominant B.1.617.2 (delta) and B.1.529 (omicron) strains with more than 30 mutations on their spike protein, have caused a significant decline in prophylaxis, calling for the need for drug improvement. Antibodies are drugs preferentially used in infectious diseases and are easy to get from immunized organisms. The current study combined molecular modeling and single memory B cell sequencing to assess candidate sequences before experiments, providing a strategy for the fabrication of SARS-CoV-2 neutralizing antibodies. A total of 128 sequences were obtained after sequencing 196 memory B cells, and 42 sequences were left after merging extremely similar ones and discarding incomplete ones, followed by homology modeling of the antibody variable region. Thirteen candidate sequences were expressed, of which three were tested positive for receptor binding domain recognition but only one was confirmed as having broad neutralization against several SARS-CoV-2 variants. The current study successfully obtained a SARS-CoV-2 antibody with broad neutralizing abilities and provided a strategy for antibody development in emerging infectious diseases using single memory B cell BCR sequencing and computer assistance in antibody fabrication.
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Affiliation(s)
- Zheyue Wang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qi Tang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Bende Liu
- Department of Cardiology, the First People's Hospital of Jiangxia District, Wuhan, Hubei 430299, China
| | - Wenqing Zhang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yufeng Chen
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ningfei Ji
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yan Peng
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaohui Yang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Daixun Cui
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Weiyu Kong
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaojun Tang
- Department of Rheumatology and Immunology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Tingting Yang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mingshun Zhang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xinxia Chang
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jin Zhu
- Huadong Medical Institute of Biotechniques, Nanjing, Jiangsu 210028, China
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Zhenqing Feng
- National Health Commission Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Pathology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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18
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Cottrell CA, Manne K, Kong R, Wang S, Zhou T, Chuang GY, Edwards RJ, Henderson R, Janowska K, Kopp M, Lin BC, Louder MK, Olia AS, Rawi R, Shen CH, Taft JD, Torres JL, Wu NR, Zhang B, Doria-Rose NA, Cohen MS, Haynes BF, Shapiro L, Ward AB, Acharya P, Mascola JR, Kwong PD. Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cell Rep 2021; 37:109922. [PMID: 34731616 PMCID: PMC9058982 DOI: 10.1016/j.celrep.2021.109922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
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Affiliation(s)
- Christopher A Cottrell
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kartik Manne
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert J Edwards
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Rory Henderson
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Katarzyna Janowska
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Megan Kopp
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin D Taft
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan L Torres
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nelson R Wu
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, and Microbiology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barton F Haynes
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Priyamvada Acharya
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA; 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.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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19
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Shipley MM, Mangala Prasad V, Doepker LE, Dingens A, Ralph DK, Harkins E, Dhar A, Arenz D, Chohan V, Weight H, Mandaliya K, Bloom JD, Matsen FA, Lee KK, Overbaugh JM. Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. eLife 2021; 10:68110. [PMID: 34263727 PMCID: PMC8376252 DOI: 10.7554/elife.68110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.
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Affiliation(s)
- Mackenzie M Shipley
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, United States
| | - Laura E Doepker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Adam Dingens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Duncan K Ralph
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Elias Harkins
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Amrit Dhar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Dana Arenz
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Vrasha Chohan
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Haidyn Weight
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kishor Mandaliya
- Coast Provincial General Hospital, Women's Health Project, Mombasa, Kenya
| | - Jesse D Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, United States
| | - Julie M Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
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20
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Kumar S, Lin X, Ngo T, Shapero B, Sou C, Allen JD, Copps J, Zhang L, Ozorowski G, He L, Crispin M, Ward AB, Wilson IA, Zhu J. Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles. mBio 2021; 12:e0042921. [PMID: 34156262 PMCID: PMC8262854 DOI: 10.1128/mbio.00429-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-Å-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display. IMPORTANCE Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env. This study validates the gp41 stabilization strategy for HIV-1 Env vaccine design and highlights the challenge in eliciting a broad NAb response.
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Affiliation(s)
- Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Benjamin Shapero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lei Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
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21
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Simonich C, Shipley MM, Doepker L, Gobillot T, Garrett M, Cale EM, Hennessy B, Itell H, Chohan V, Doria-Rose N, Nduati R, Overbaugh J. A diverse collection of B cells responded to HIV infection in infant BG505. Cell Rep Med 2021; 2:100314. [PMID: 34195680 PMCID: PMC8233660 DOI: 10.1016/j.xcrm.2021.100314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 02/23/2021] [Accepted: 05/18/2021] [Indexed: 12/03/2022]
Abstract
Increasing evidence suggests infants develop unique neutralizing antibody (nAb) responses to HIV compared to adults. Here, we dissected the nAb response of an infant whose virus is in clinical trials as a vaccine immunogen, with a goal of characterizing the broad responses in the infant to this antigen. We isolated 73 nAbs from infant BG505 and identified a large number of clonal families. Twenty-six antibodies neutralized tier 2 viruses-in some cases, viruses from the same clade as BG505, and in others, a different clade, although none showed notable breadth. Several nAbs demonstrated antibody-dependent cellular cytotoxicity activity and targeted the V3 loop. These findings suggest an impressive polyclonal response to HIV infection in infant BG505, adding to the growing evidence that the nAb response to HIV in infants is polyclonal-a desirable vaccine response to a rapidly evolving virus like HIV.
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Affiliation(s)
- Cassandra Simonich
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Mackenzie M. Shipley
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laura Doepker
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Theodore Gobillot
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Meghan Garrett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Evan M. Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brianna Hennessy
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hannah Itell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Nduati
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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22
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Hu Y, Li D, Fu H, Hao Y, Ren L, Wang S, Hu X, Shao Y, Hong K, Wang Z. Identification of a CD4-binding site-directed antibody with ADCC activity from a chronic HIV-1B'-infected Chinese donor. Virus Res 2021; 302:198470. [PMID: 34097932 DOI: 10.1016/j.virusres.2021.198470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/19/2022]
Abstract
Antibody-dependent cell-mediated cytotoxicity (ADCC) plays an important role in controlling HIV-1 invasion and replication in vivo. Isolation and identification of monoclonal antibodies (mAbs) with ADCC activity help design effective vaccines and develop novel treatment strategies. In this study, we first identified a broad neutralizer who had been infected with an HIV-1B' strain for over 10 years. Next, through probe-specific single-B-cell sorting and PCR amplification, we obtained genes for variable regions of the heavy chain (VHs) and light chain (VLs) of six antibodies and ligated them into expression vectors. After antibody expression and ELISA screening, we obtained a CD4-binding site-directed antibody (451-B4), whose VH and VL originated from the IGHV1-24 and IGLV1-40 germlines, respectively. Although 451-B4 neutralized only the SF162 tier 1 pseudovirus and 398F1 tier 2 pseudovirus, it could mediate comparable ADCC activity to a broadly neutralizing antibody, VRC01. The 451-B4 antibody will be a useful candidate for developing an ADCC-based treatment strategy against HIV-1 replication or latent infection in vivo.
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Affiliation(s)
- Yuanyuan Hu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Hongyang Fu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Xintao Hu
- Present address: Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Kunxue Hong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China
| | - Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China; Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing 102206, China.
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23
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Chen F, Tzarum N, Lin X, Giang E, Velázquez-Moctezuma R, Augestad EH, Nagy K, He L, Hernandez M, Fouch ME, Grinyó A, Chavez D, Doranz BJ, Prentoe J, Stanfield RL, Lanford R, Bukh J, Wilson IA, Zhu J, Law M. Functional convergence of a germline-encoded neutralizing antibody response in rhesus macaques immunized with HCV envelope glycoproteins. Immunity 2021; 54:781-796.e4. [PMID: 33675683 PMCID: PMC8046733 DOI: 10.1016/j.immuni.2021.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/14/2020] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Human IGHV1-69-encoded broadly neutralizing antibodies (bnAbs) that target the hepatitis C virus (HCV) envelope glycoprotein (Env) E2 are important for protection against HCV infection. An IGHV1-69 ortholog gene, VH1.36, is preferentially used for bnAbs isolated from HCV Env-immunized rhesus macaques (RMs). Here, we studied the genetic, structural, and functional properties of VH1.36-encoded bnAbs generated by vaccination, in comparison to IGHV1-69-encoded bnAbs from HCV patients. Global B cell repertoire analysis confirmed the expansion of VH1.36-derived B cells in immunized animals. Most E2-specific, VH1.36-encoded antibodies cross-neutralized HCV. Crystal structures of two RM bnAbs with E2 revealed that the RM bnAbs engaged conserved E2 epitopes using similar molecular features as human bnAbs but with a different binding mode. Longitudinal analyses of the RM antibody repertoire responses during immunization indicated rapid lineage development of VH1.36-encoded bnAbs with limited somatic hypermutation. Our findings suggest functional convergence of a germline-encoded bnAb response to HCV Env with implications for vaccination in humans.
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Affiliation(s)
- Fang Chen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Netanel Tzarum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erick Giang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rodrigo Velázquez-Moctezuma
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Elias H Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Kenna Nagy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | - Deborah Chavez
- Southwest National Primate Research Center at Texas Biomedical Research Institute, San Antonio, TX 788227, USA
| | | | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert Lanford
- Southwest National Primate Research Center at Texas Biomedical Research Institute, San Antonio, TX 788227, USA
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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24
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Virus Evolution and Neutralization Sensitivity in an HIV-1 Subtype B' Infected Plasma Donor with Broadly Neutralizing Activity. Vaccines (Basel) 2021; 9:vaccines9040311. [PMID: 33805985 PMCID: PMC8064334 DOI: 10.3390/vaccines9040311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
We sought to analyze the evolutionary characteristics and neutralization sensitivity of viruses in a human immunodeficiency virus type 1 (HIV-1) subtype B′ infected plasma donor with broadly neutralizing activity, which may provide information for new broadly neutralizing antibodies (bNAbs) isolation and immunogen design. A total of 83 full-length envelope genes were obtained by single-genome amplification (SGA) from the patient’s plasma at three consecutive time points (2005, 2006, and 2008) spanning four years. In addition, 28 Env-pseudotyped viruses were constructed and their neutralization sensitivity to autologous plasma and several representative bNAbs were measured. Phylogenetic analysis showed that these env sequences formed two evolutionary clusters (Cluster I and II). Cluster I viruses vanished in 2006 and then appeared as recombinants two years later. In Cluster II viruses, the V1 length and N-glycosylation sites increased over the four years of the study period. Most viruses were sensitive to concurrent and subsequent autologous plasma, and to bNAbs, including 10E8, PGT121, VRC01, and 12A21, but all viruses were resistant to PGT135. Overall, 90% of Cluster I viruses were resistant to 2G12, while 94% of Cluster II viruses were sensitive to 2G12. We confirmed that HIV-1 continued to evolve even in the presence of bNAbs, and two virus clusters in this donor adopted different escape mechanisms under the same humoral immune pressure.
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25
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Conti S, Kaczorowski KJ, Song G, Porter K, Andrabi R, Burton DR, Chakraborty AK, Karplus M. Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site. Proc Natl Acad Sci U S A 2021; 118:e2018338118. [PMID: 33637649 PMCID: PMC7936365 DOI: 10.1073/pnas.2018338118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A vaccine which is effective against the HIV virus is considered to be the best solution to the ongoing global HIV/AIDS epidemic. In the past thirty years, numerous attempts to develop an effective vaccine have been made with little or no success, due, in large part, to the high mutability of the virus. More recent studies showed that a vaccine able to elicit broadly neutralizing antibodies (bnAbs), that is, antibodies that can neutralize a high fraction of global virus variants, has promise to protect against HIV. Such a vaccine has been proposed to involve at least three separate stages: First, activate the appropriate precursor B cells; second, shepherd affinity maturation along pathways toward bnAbs; and, third, polish the Ab response to bind with high affinity to diverse HIV envelopes (Env). This final stage may require immunization with a mixture of Envs. In this paper, we set up a framework based on theory and modeling to design optimal panels of antigens to use in such a mixture. The designed antigens are characterized experimentally and are shown to be stable and to be recognized by known HIV antibodies.
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Affiliation(s)
- Simone Conti
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Kevin J Kaczorowski
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ge Song
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Katelyn Porter
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Raiees Andrabi
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Dennis R Burton
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Arup K Chakraborty
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138;
- Laboratoire de Chimie Biophysique, Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 67000 Strasbourg, France
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26
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Vaccination induces maturation in a mouse model of diverse unmutated VRC01-class precursors to HIV-neutralizing antibodies with >50% breadth. Immunity 2021; 54:324-339.e8. [PMID: 33453152 DOI: 10.1016/j.immuni.2020.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 11/24/2022]
Abstract
Vaccine elicitation of broadly neutralizing antibodies (bnAbs) is a key HIV-research goal. The VRC01 class of bnAbs targets the CD4-binding site on the HIV-envelope trimer and requires extensive somatic hypermutation (SHM) to neutralize effectively. Despite substantial progress, vaccine-induced VRC01-class antibodies starting from unmutated precursors have exhibited limited neutralization breadth, particularly against viruses bearing glycan on loop D residue N276 (glycan276), present on most circulating strains. Here, using sequential immunization of immunoglobulin (Ig)-humanized mice expressing diverse unmutated VRC01-class antibody precursors, we elicited serum responses capable of neutralizing viruses bearing glycan276 and isolated multiple lineages of VRC01-class bnAbs, including two with >50% breadth on a 208-strain panel. Crystal structures of representative bnAbs revealed the same mode of recognition as known VRC01-class bnAbs. Structure-function studies further pinpointed key mutations and correlated their induction with specific immunizations. VRC01-class bnAbs can thus be matured by sequential immunization from unmutated ancestors to >50% breadth, and we delineate immunogens and regimens inducing key SHM.
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27
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Ralph DK, Matsen FA. Using B cell receptor lineage structures to predict affinity. PLoS Comput Biol 2020; 16:e1008391. [PMID: 33175831 PMCID: PMC7682889 DOI: 10.1371/journal.pcbi.1008391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/23/2020] [Accepted: 08/30/2020] [Indexed: 11/18/2022] Open
Abstract
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis. Comments Please post comments or questions on this paper as new issues at https://git.io/Jvxkn.
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Affiliation(s)
- Duncan K. Ralph
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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28
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Chen CW, Saubi N, Joseph-Munné J. Design Concepts of Virus-Like Particle-Based HIV-1 Vaccines. Front Immunol 2020; 11:573157. [PMID: 33117367 PMCID: PMC7561392 DOI: 10.3389/fimmu.2020.573157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
Prophylactic vaccines remain the best approach for controlling the human immunodeficiency virus-1 (HIV-1) transmission. Despite the limited efficacy of the RV144 trial in Thailand, there is still no vaccine candidate that has been proven successful. Consequently, great efforts have been made to improve HIV-1 antigens design and discover delivery platforms for optimal immune elicitation. Owing to immunogenic, structural, and functional diversity, virus-like particles (VLPs) could act as efficient vaccine carriers to display HIV-1 immunogens and provide a variety of HIV-1 vaccine development strategies as well as prime-boost regimes. Here, we describe VLP-based HIV-1 vaccine candidates that have been enrolled in HIV-1 clinical trials and summarize current advances and challenges according to preclinical results obtained from five distinct strategies. This mini-review provides multiple perspectives to help in developing new generations of VLP-based HIV-1 vaccine candidates with better capacity to elicit specific anti-HIV immune responses.
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Affiliation(s)
- Chun-Wei Chen
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Narcís Saubi
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,EAVI2020 European AIDS Vaccine Initiative H2020 Research Programme, London, United Kingdom
| | - Joan Joseph-Munné
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,EAVI2020 European AIDS Vaccine Initiative H2020 Research Programme, London, United Kingdom.,Microbiology Department, Hospital Universitari de la Vall d'Hebron, Barcelona, Spain
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29
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B cells expressing authentic naive human VRC01-class BCRs can be recruited to germinal centers and affinity mature in multiple independent mouse models. Proc Natl Acad Sci U S A 2020; 117:22920-22931. [PMID: 32873644 PMCID: PMC7502816 DOI: 10.1073/pnas.2004489117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Rational development of successful vaccines requires utilization of predictive models of vaccination. One approach for development of an HIV vaccine has been to study broadly neutralizing antibodies (bnAbs) and revert the mutations back to germline. However, there are limitations to such models. Therefore, we generated three knockin mice expressing B cell receptors (BCRs) from authentic naive VRC01-class B cells from healthy human donors (“HuGL” mice). This approach revealed that human VRC01-class naive B cell BCRs are indeed competent for antigen-specific responses in vivo. Additionally, a series of experiments shows the importance of precursor frequency and affinity on B cell responses to vaccine antigens. Overall, these HuGL mouse models validate a central tenet of the germline-targeting approach to vaccine design. Animal models of human antigen-specific B cell receptors (BCRs) generally depend on “inferred germline” sequences, and thus their relationship to authentic naive human B cell BCR sequences and affinities is unclear. Here, BCR sequences from authentic naive human VRC01-class B cells from healthy human donors were selected for the generation of three BCR knockin mice. The BCRs span the physiological range of affinities found in humans, and use three different light chains (VK3-20, VK1-5, and VK1-33) found among subclasses of naive human VRC01-class B cells and HIV broadly neutralizing antibodies (bnAbs). The germline-targeting HIV immunogen eOD-GT8 60mer is currently in clinical trial as a candidate bnAb vaccine priming immunogen. To attempt to model human immune responses to the eOD-GT8 60mer, we tested each authentic naive human VRC01-class BCR mouse model under rare human physiological B cell precursor frequency conditions. B cells with high (HuGL18HL) or medium (HuGL17HL) affinity BCRs were primed, recruited to germinal centers, and they affinity matured, and formed memory B cells. Precursor frequency and affinity interdependently influenced responses. Taken together, these experiments utilizing authentic naive human VRC01-class BCRs validate a central tenet of germline-targeting vaccine design and extend the overall concept of the reverse vaccinology approach to vaccine development.
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30
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Kumar S, Ju B, Shapero B, Lin X, Ren L, Zhang L, Li D, Zhou Z, Feng Y, Sou C, Mann CJ, Hao Y, Sarkar A, Hou J, Nunnally C, Hong K, Wang S, Ge X, Su B, Landais E, Sok D, Zwick MB, He L, Zhu J, Wilson IA, Shao Y. A V H1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. SCIENCE ADVANCES 2020; 6:eabb1328. [PMID: 32938661 PMCID: PMC7494343 DOI: 10.1126/sciadv.abb1328] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/31/2020] [Indexed: 05/03/2023]
Abstract
An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1-infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires. Monoclonal antibodies 438-B11 and 438-D5 were isolated that potently neutralize HIV-1 with moderate breadth, are encoded by the VH1-69 germline gene, and have a disulfide-linked long HCDR3 loop. Crystal structures of Env-bound and unbound antibodies revealed heavy chain-mediated recognition of the glycan supersite with a unique angle of approach and a critical role of the intra-HCDR3 disulfide. The mechanism of viral escape was examined via single-genome amplification/sequencing and glycan mutations around the N332 supersite. Our findings further emphasize the V3 glycan supersite as a prominent target for Env-based vaccine design.
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Affiliation(s)
- Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bin Ju
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
| | - Benjamin Shapero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Ren
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Lei Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Zehua Zhou
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin J Mann
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yanling Hao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiali Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Christian Nunnally
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Shuo Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Xiangyang Ge
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui Province 230601, China
| | - Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China.
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
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31
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Wen GP, He L, Tang ZM, Wang SL, Zhang X, Chen YZ, Lin X, Liu C, Chen JX, Ying D, Chen ZH, Wang YB, Luo WX, Huang SJ, Li SW, Zhang J, Zheng ZZ, Zhu J, Xia NS. Quantitative evaluation of protective antibody response induced by hepatitis E vaccine in humans. Nat Commun 2020; 11:3971. [PMID: 32769993 PMCID: PMC7414844 DOI: 10.1038/s41467-020-17737-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Efficacy evaluation through human trials is crucial for advancing a vaccine candidate to clinics. Next-generation sequencing (NGS) can be used to quantify B cell repertoire response and trace antibody lineages during vaccination. Here, we demonstrate this application with a case study of Hecolin®, the licensed vaccine for hepatitis E virus (HEV). Four subjects are administered the vaccine following a standard three-dose schedule. Vaccine-induced antibodies exhibit a high degree of clonal diversity, recognize five conformational antigenic sites of the genotype 1 HEV p239 antigen, and cross-react with other genotypes. Unbiased repertoire sequencing is performed for seven time points over six months of vaccination, with maturation pathways characterize for a set of vaccine-induced antibodies. In addition to dynamic repertoire profiles, NGS analysis reveals differential patterns of HEV-specific antibody lineages and highlights the necessity of the long vaccine boost. Together, our study presents a quantitative strategy for vaccine evaluation in small-scale human studies.
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Affiliation(s)
- Gui-Ping Wen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Zi-Min Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Si-Ling Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Xu Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Yuan-Zhi Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Jia-Xin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Dong Ying
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Zi-Hao Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Ying-Bin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Wen-Xin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Shou-Jie Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Shao-Wei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China
| | - Zi-Zheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China.
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Ning-Shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361005, Xiamen, Fujian, PR China.
- School of Life Sciences, Xiamen University, 361005, Xiamen, Fujian, PR China.
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32
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Abstract
PURPOSE OF REVIEW Exploring the molecular details of the coevolution of HIV-1 Envelope with broadly neutralizing antibodies (bNAbs) in infected individuals over time provides insights for vaccine design. Since mid-2017, the number of individuals described in such publications has nearly tripled. New publications have extended such studies to new epitopes on Env and provided more detail on previously known sites. RECENT FINDINGS Studies of two donors - one of them an infant, the other with three lineages targeting the same site - has deepened our understanding of V3-glycan-directed lineages. A V2-apex-directed lineage showed remarkable similarity to a lineage from a previously described donor, revealing general principles for this class of bNAbs. Understanding development of CD4 binding site antibodies has been enriched by the study of a VRC01-class lineage. Finally, the membrane-proximal external region is a new addition to the set of epitopes studied in this manner, with early development events explored in a study of three lineages from a single donor. SUMMARY These studies provide templates for immunogen design to elicit bNAbs against a widened set of epitopes, generating new directions in the quest for an HIV vaccine.
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33
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Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature 2020; 584:115-119. [PMID: 32454513 DOI: 10.1038/s41586-020-2380-z] [Citation(s) in RCA: 1208] [Impact Index Per Article: 302.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/18/2020] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a global health emergency that is in urgent need of intervention1-3. The entry of SARS-CoV-2 into its target cells depends on binding between the receptor-binding domain (RBD) of the viral spike protein and its cellular receptor, angiotensin-converting enzyme 2 (ACE2)2,4-6. Here we report the isolation and characterization of 206 RBD-specific monoclonal antibodies derived from single B cells from 8 individuals infected with SARS-CoV-2. We identified antibodies that potently neutralize SARS-CoV-2; this activity correlates with competition with ACE2 for binding to RBD. Unexpectedly, the anti-SARS-CoV-2 antibodies and the infected plasma did not cross-react with the RBDs of SARS-CoV or Middle East respiratory syndrome-related coronavirus (MERS-CoV), although there was substantial plasma cross-reactivity to their trimeric spike proteins. Analysis of the crystal structure of RBD-bound antibody revealed that steric hindrance inhibits viral engagement with ACE2, thereby blocking viral entry. These findings suggest that anti-RBD antibodies are largely viral-species-specific inhibitors. The antibodies identified here may be candidates for development of clinical interventions against SARS-CoV-2.
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34
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Cao W, Li B, Liu H, Cheng X, Liu Y, Zhao X, Qiao Y. CD4 binding loop responsible for the neutralization of human monoclonal neutralizing antibody Y498. Virus Res 2020; 285:198001. [PMID: 32413370 DOI: 10.1016/j.virusres.2020.198001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
Broad and potent human monoclonal neutralizing antibodies have considerable potential in the prevention and treatment of acquired immunodeficiency syndrome (AIDS). To identify the key amino acid recognition site contacted with neutralizing antibody Y498, peptides were panned from the PhD-12 peptide library and predicted using online software. Then, four key amino acid sites, G367, D368, E370, and V372 located on the CD4 binding loop on gp120 of envelope of human immunodeficiency virus-1 (HIV-1), were found to determine the neutralization of antibody Y498. Residue E370 is in the deep part of the CD4 binding loop, which affects Y498-mediated neutralization. This form of recognition leads to a somewhat limiting neutralization spectrum of neutralizing antibody Y498, although it has some neutralization ability. Further study of the interactions between the neutralizing antibody Y498 and its epitope on the surface of the virus may facilitate vaccine development and so prevent new AIDS cases.
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Affiliation(s)
- Weiyou Cao
- Binzhou Medical University, Yantai, Shandong Province, China.
| | - Boqing Li
- Binzhou Medical University, Yantai, Shandong Province, China.
| | - Huan Liu
- Binzhou Medical University, Yantai, Shandong Province, China.
| | - Xue Cheng
- Binzhou Medical University, Yantai, Shandong Province, China.
| | - Yezi Liu
- Binzhou Medical University, Yantai, Shandong Province, China.
| | - Xueqing Zhao
- Binzhou Medical University, Yantai, Shandong Province, China.
| | - Yuanyuan Qiao
- Binzhou Medical University, Yantai, Shandong Province, China; MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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35
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Zhou C, Chen Z, Zhang L, Yan D, Mao T, Tang K, Qiu T, Cao Z. SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens. Nucleic Acids Res 2020; 47:W388-W394. [PMID: 31114919 PMCID: PMC6602482 DOI: 10.1093/nar/gkz413] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 01/19/2023] Open
Abstract
B-cell epitope information is critical to immune therapy and vaccine design. Protein epitopes can be significantly affected by glycosylation, while no methods have considered this till now. Based on previous versions of Spatial Epitope Prediction of Protein Antigens (SEPPA), we here present an enhanced tool SEPPA 3.0, enabling glycoprotein antigens. Parameters were updated based on the latest and largest dataset. Then, additional micro-environmental features of glycosylation triangles and glycosylation-related amino acid indexes were added as important classifiers, coupled with final calibration based on neighboring antigenicity. Logistic regression model was retained as SEPPA 2.0. The AUC value of 0.794 was obtained through 10-fold cross-validation on internal validation. Independent testing on general protein antigens resulted in AUC of 0.740 with BA (balanced accuracy) of 0.657 as baseline of SEPPA 3.0. Most importantly, when tested on independent glycoprotein antigens only, SEPPA 3.0 gave an AUC of 0.749 and BA of 0.665, leading the top performance among peers. As the first server enabling accurate epitope prediction for glycoproteins, SEPPA 3.0 shows significant advantages over popular peers on both general protein and glycoprotein antigens. It can be accessed at http://bidd2.nus.edu.sg/SEPPA3/ or at http://www.badd-cao.net/seppa3/index.html. Batch query is supported.
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Affiliation(s)
- Chen Zhou
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zikun Chen
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lu Zhang
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Deyu Yan
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Tiantian Mao
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kailin Tang
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Tianyi Qiu
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 200433, China
| | - Zhiwei Cao
- Shanghai 10th People's Hospital & School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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36
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Galkin A, Chen Y, Guenaga J, O'Dell S, Acevedo R, Steinhardt JJ, Wang Y, Wilson R, Chiang CI, Doria-Rose N, Grishaev AV, Mascola JR, Li Y. HIV-1 gp120-CD4-Induced Antibody Complex Elicits CD4 Binding Site-Specific Antibody Response in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:1543-1561. [PMID: 32066595 PMCID: PMC7065964 DOI: 10.4049/jimmunol.1901051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/31/2019] [Indexed: 11/19/2022]
Abstract
Elicitation of broadly neutralizing Ab (bNAb) responses toward the conserved HIV-1 envelope (Env) CD4 binding site (CD4bs) by vaccination is an important goal for vaccine development and yet to be achieved. The outcome of previous immunogenicity studies suggests that the limited accessibility of the CD4bs and the presence of predominant nonneutralizing determinants (nND) on Env may impede the elicitation of bNAbs and their precursors by vaccination. In this study, we designed a panel of novel immunogens that 1) preferentially expose the CD4bs by selective elimination of glycosylation sites flanking the CD4bs, and 2) minimize the nND immune response by engineering fusion proteins consisting of gp120 Core and one or two CD4-induced (CD4i) mAbs for masking nND epitopes, referred to as gp120-CD4i fusion proteins. As expected, the fusion proteins possess improved antigenicity with retained affinity for VRC01-class, CD4bs-directed bNAbs and dampened affinity for nonneutralizing Abs. We immunized C57BL/6 mice with these fusion proteins and found that overall the fusion proteins elicit more focused CD4bs Ab response than prototypical gp120 Core by serological analysis. Consistently, we found that mice immunized with selected gp120-CD4i fusion proteins have higher frequencies of germinal center-activated B cells and CD4bs-directed memory B cells than those inoculated with parental immunogens. We isolated three mAbs from mice immunized with selected gp120-CD4i fusion proteins and found that their footprints on Env are similar to VRC01-class bNAbs. Thus, using gp120-CD4i fusion proteins with selective glycan deletion as immunogens could focus Ab response toward CD4bs epitope.
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MESH Headings
- AIDS Vaccines/administration & dosage
- AIDS Vaccines/genetics
- AIDS Vaccines/immunology
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Binding Sites, Antibody/genetics
- Binding Sites, Antibody/immunology
- CD4 Antigens/immunology
- CD4 Antigens/metabolism
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Female
- HIV Antibodies/blood
- HIV Antibodies/immunology
- HIV Envelope Protein gp120/genetics
- HIV Envelope Protein gp120/immunology
- HIV Infections/blood
- HIV Infections/immunology
- HIV Infections/prevention & control
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/immunology
- Humans
- Immunogenicity, Vaccine
- Mice
- Models, Animal
- Recombinant Fusion Proteins/administration & dosage
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
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Affiliation(s)
- Andrey Galkin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
- Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Yajing Chen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037
| | - Javier Guenaga
- International AIDS Vaccine Initiative Neutralizing Antibody Center at Scripps Research, La Jolla, CA 92037
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Roderico Acevedo
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - James J Steinhardt
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Richard Wilson
- International AIDS Vaccine Initiative Neutralizing Antibody Center at Scripps Research, La Jolla, CA 92037
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Alexander V Grishaev
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850;
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
- Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201
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37
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Zhang L, Irimia A, He L, Landais E, Rantalainen K, Leaman DP, Vollbrecht T, Stano A, Sands DI, Kim AS, Poignard P, Burton DR, Murrell B, Ward AB, Zhu J, Wilson IA, Zwick MB. An MPER antibody neutralizes HIV-1 using germline features shared among donors. Nat Commun 2019; 10:5389. [PMID: 31772165 PMCID: PMC6879610 DOI: 10.1038/s41467-019-12973-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC50). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.
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Affiliation(s)
- Lei Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- CTK Biotech, Inc., 3855 Stowe Drive, Poway, California, 92064, USA
| | - Adriana Irimia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Lingling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel P Leaman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Thomas Vollbrecht
- Department of Medicine, University of California, San Diego, California, 92093, USA
| | - Armando Stano
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel I Sands
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Arthur S Kim
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- Departments of Medicine, Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Pascal Poignard
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative, New York, New York, 10004, USA
- Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044, Grenoble, France
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachussetts, 02114, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, California, 92093, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Jiang Zhu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, 92037, USA.
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38
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Gao F, Lin X, He L, Wang R, Wang H, Shi X, Zhang F, Yin C, Zhang L, Zhu J, Yu L. Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human. Front Immunol 2019; 10:2424. [PMID: 31708914 PMCID: PMC6821881 DOI: 10.3389/fimmu.2019.02424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Zika virus (ZIKV) specific neutralizing antibodies hold great promise for antibody-based interventions and vaccine design against ZIKV infection. However, their development in infected patients remains unclear. Here, we applied next-generation sequencing (NGS) to probe the dynamic development of a potent and protective ZIKV E DIII-specific antibody ZK2B10 isolated from a ZIKV convalescent individual. The unbiased repertoire analysis showed dramatic changes in the usage of antibody variable region germline genes. However, lineage tracing of ZK2B10 revealed limited somatic hypermutation and transient expansion during the 12 months following the onset of symptoms. The NGS-derived, germline-like ZK2B10 somatic variants neutralized ZIKV potently and protected mice from lethal challenge of ZIKV without detectable cross-reactivity with Dengue virus (DENV). Site-directed mutagenesis identified two residues within the λ chain, N31 and S91, that are essential to the functional maturation of ZK2B10. The repertoire and lineage features unveiled here will help elucidate the developmental process and protective potential of E DIII-directed antibodies against ZIKV infection.
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Affiliation(s)
- Fei Gao
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Linling He
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruoke Wang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Han Wang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xuanling Shi
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Fuchun Zhang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chibiao Yin
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Linqi Zhang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Lei Yu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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39
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Umotoy J, Bagaya BS, Joyce C, Schiffner T, Menis S, Saye-Francisco KL, Biddle T, Mohan S, Vollbrecht T, Kalyuzhniy O, Madzorera S, Kitchin D, Lambson B, Nonyane M, Kilembe W, Poignard P, Schief WR, Burton DR, Murrell B, Moore PL, Briney B, Sok D, Landais E. Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan. Immunity 2019; 51:141-154.e6. [PMID: 31315032 PMCID: PMC6642152 DOI: 10.1016/j.immuni.2019.06.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/31/2019] [Accepted: 06/06/2019] [Indexed: 11/25/2022]
Abstract
The VH1-2 restricted VRC01-class of antibodies targeting the HIV envelope CD4 binding site are a major focus of HIV vaccine strategies. However, a detailed analysis of VRC01-class antibody development has been limited by the rare nature of these responses during natural infection and the lack of longitudinal sampling of such responses. To inform vaccine strategies, we mapped the development of a VRC01-class antibody lineage (PCIN63) in the subtype C infected IAVI Protocol C neutralizer PC063. PCIN63 monoclonal antibodies had the hallmark VRC01-class features and demonstrated neutralization breadth similar to the prototype VRC01 antibody, but were 2- to 3-fold less mutated. Maturation occurred rapidly within ∼24 months of emergence of the lineage and somatic hypermutations accumulated at key contact residues. This longitudinal study of broadly neutralizing VRC01-class antibody lineage reveals early binding to the N276-glycan during affinity maturation, which may have implications for vaccine design.
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Affiliation(s)
- Jeffrey Umotoy
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Bernard S Bagaya
- UVRI-IAVI HIV Vaccine Program, Entebbe, Uganda; Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala-Uganda
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID) The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Karen L Saye-Francisco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trevor Biddle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sanjay Mohan
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA
| | - Thomas Vollbrecht
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA
| | - Oleksander Kalyuzhniy
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Sharon Madzorera
- Centre for HIV and STIs, National Institute for Communicable Diseases, of the National Health Laboratory Service (NHLS), Johannesburg 2131, South Africa
| | - Dale Kitchin
- Centre for HIV and STIs, National Institute for Communicable Diseases, of the National Health Laboratory Service (NHLS), Johannesburg 2131, South Africa
| | - Bronwen Lambson
- Centre for HIV and STIs, National Institute for Communicable Diseases, of the National Health Laboratory Service (NHLS), Johannesburg 2131, South Africa
| | - Molati Nonyane
- Centre for HIV and STIs, National Institute for Communicable Diseases, of the National Health Laboratory Service (NHLS), Johannesburg 2131, South Africa
| | | | - Pascal Poignard
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044 Grenoble, France
| | - William R Schief
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID) The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID) The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02114, USA
| | - Ben Murrell
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA; Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases, of the National Health Laboratory Service (NHLS), Johannesburg 2131, South Africa; School of Pathology Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2050, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of Kwa-Zulu Natal, Durban 4013, South Africa
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID) The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID) The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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40
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Zhang D, Zou S, Hu Y, Hou J, Hu X, Ren L, Ma L, He X, Shao Y, Hong K. Characteristics of Envelope Genes in a Chinese Chronically HIV-1 Infected Patient With Broadly Neutralizing Activity. Front Microbiol 2019; 10:1096. [PMID: 31178836 PMCID: PMC6543928 DOI: 10.3389/fmicb.2019.01096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Exploring the characteristics of the HIV-1 envelope glycoprotein (env) gene in a natural HIV-1 infected individual, with broadly neutralizing activity, may provide insight into the generation of such broadly neutralizing antibodies and initiate the design of an appropriate immunogen. Recently, a chronically HIV-1 infected patient with broadly neutralization activity was identified and a VRC01-class neutralizing antibody DRVIA7 (A7) was isolated from the patient. In the present study, 155 full length HIV-1 env gene fragments (including 68 functionally Env clones) were amplified longitudinally from the plasma of six time points spanning over 5 years in this donor. Viral features were analyzed by comparing Env clones of different time points, as well as 165 Chinese HIV-1 subtype B env sequences from HIV Sequence Database (Chinese B_database). Shorter V1 length, less potential glycan and a lower ratio of NXT: NXS in gp160 were observed in the first five time points compared to that from the last time points, as well that from the Chinese B_database. A sequence analysis and a neutralization assay of Env-pseudoviruses showed that the increasing diversity of env sequences in the patient was consistent with the appearance and maturation of A7 lineage antibodies. The potent neutralization activity and viruses that escaped from the neutralization of the concurrent autologous plasma, are consistent with higher residue variations at the antibody recognition sites. Almost all viruses from the plasmas were neutralization-resistant to VRC01 and A7 lineage antibodies. For a chronically HIV-1 infected individual over 10 years, we found that greater viral diversity, short V1 sequences and less potential N-linked glycosylation (PNGS) in V1, might be associated with the development of broadly neutralizing antibody responses.
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Affiliation(s)
- Dai Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.,The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Sen Zou
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Yuanyuan Hu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Jiali Hou
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Xintao Hu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Liying Ma
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Xiang He
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Kunxue Hong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
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41
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Conti S, Karplus M. Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning. PLoS Comput Biol 2019; 15:e1006954. [PMID: 30970017 PMCID: PMC6457539 DOI: 10.1371/journal.pcbi.1006954] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
HIV is a highly mutable virus for which all attempts to develop a vaccine have been unsuccessful. Nevertheless, few long-infected patients develop antibodies, called broadly neutralizing antibodies (bnAbs), that have a high breadth and can neutralize multiple variants of the virus. This suggests that a universal HIV vaccine should be possible. A measure of the efficacy of a HIV vaccine is the neutralization breadth of the antibodies it generates. The breadth is defined as the fraction of viruses in the Seaman panel that are neutralized by the antibody. Experimentally the neutralization ability is measured as the half maximal inhibitory concentration of the antibody (IC50). To avoid such time-consuming experimental measurements, we developed a computational approach to estimate the IC50 and use it to determine the antibody breadth. Given that no direct method exists for calculating IC50 values, we resort to a combination of atomistic modeling and machine learning. For each antibody/virus complex, an all-atoms model is built using the amino acid sequence and a known structure of a related complex. Then a series of descriptors are derived from the atomistic models, and these are used to train a Multi-Layer Perceptron (an Artificial Neural Network) to predict the value of the IC50 (by regression), or if the antibody binds or not to the virus (by classification). The neural networks are trained by use of experimental IC50 values collected in the CATNAP database. The computed breadths obtained by regression and classification are reported and the importance of having some related information in the data set for obtaining accurate predictions is analyzed. This approach is expected to prove useful for the design of HIV bnAbs, where the computation of the potency must be accompanied by a computation of the breadth, and for evaluating the efficiency of potential vaccination schemes developed through modeling and simulation.
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Affiliation(s)
- Simone Conti
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
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42
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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43
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Tzarum N, Giang E, Kong L, He L, Prentoe J, Augestad E, Hua Y, Castillo S, Lauer GM, Bukh J, Zhu J, Wilson IA, Law M. Genetic and structural insights into broad neutralization of hepatitis C virus by human V H1-69 antibodies. SCIENCE ADVANCES 2019; 5:eaav1882. [PMID: 30613781 PMCID: PMC6314831 DOI: 10.1126/sciadv.aav1882] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
An effective vaccine to the antigenically diverse hepatitis C virus (HCV) must target conserved immune epitopes. Here, we investigate cross-neutralization of HCV genotypes by broadly neutralizing antibodies (bNAbs) encoded by the relatively abundant human gene family V H 1-69. We have deciphered the molecular requirements for cross-neutralization by this unique class of human antibodies from crystal structures of HCV E2 in complex with bNAbs. An unusually high binding affinity is found for germ line-reverted versions of VH1-69 precursor antibodies, and neutralization breadth is acquired during affinity maturation. Deep sequencing analysis of an HCV-immune B cell repertoire further demonstrates the importance of the V H 1-69 gene family in the generation of HCV bNAbs. This study therefore provides critical insights into immune recognition of HCV with important implications for rational vaccine design.
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Affiliation(s)
- Netanel Tzarum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erick Giang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Leopold Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elias Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shaun Castillo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Georg M. Lauer
- Gastrointestinal Unit and Liver Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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44
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Borst AJ, Weidle CE, Gray MD, Frenz B, Snijder J, Joyce MG, Georgiev IS, Stewart-Jones GB, Kwong PD, McGuire AT, DiMaio F, Stamatatos L, Pancera M, Veesler D. Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. eLife 2018; 7:37688. [PMID: 30403372 PMCID: PMC6237438 DOI: 10.7554/elife.37688] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/11/2018] [Indexed: 12/31/2022] Open
Abstract
VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4BS) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1–3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.
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Affiliation(s)
- Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Connor E Weidle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Matthew D Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Brandon Frenz
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Joost Snijder
- Department of Biochemistry, University of Washington, Seattle, United States
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Guillaume Be Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Global Health, University of Washington, Seattle, United States
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, United States
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45
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Ju B, Li D, Ren L, Hou J, Hao Y, Liang H, Wang S, Zhu J, Wei M, Shao Y. Identification of a novel broadly HIV-1-neutralizing antibody from a CRF01_AE-infected Chinese donor. Emerg Microbes Infect 2018; 7:174. [PMID: 30382080 PMCID: PMC6210191 DOI: 10.1038/s41426-018-0175-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 01/13/2023]
Abstract
The isolation and characterization of monoclonal broadly neutralizing antibodies (nAbs) from natural HIV-1-infected individuals play very important roles in understanding nAb responses to HIV-1 infection and designing vaccines and therapeutics. Many broadly nAbs have been isolated from individuals infected with HIV-1 clade A, B, C, etc., but, as an important recombinant virus, the identification of broadly nAbs in CRF01_AE-infected individuals remains elusive. In this study, we used antigen-specific single B-cell sorting and monoclonal antibody expression to isolate monoclonal antibodies from a CRF01_AE-infected Chinese donor (GX2016EU04), a broad neutralizer based on neutralizing activity against a cross-clade virus panel. We identified a series of HIV-1 monoclonal cross-reactive nAbs, termed F2, H6, BF8, F4, F8, BE7, and F6. F6 could neutralize 21 of 37 tested HIV-1 Env-pseudotyped viruses (57%) with a geometric mean value of 12.15 μg/ml. Heavy and light chains of F6 were derived from IGHV4-34 and IGKV 2-28 germlines, complementarity determining region (CDR) 3 loops were composed of 18 and 9 amino acids, and somatic hypermutations (SHMs) were 16.14% and 11.83% divergent from their respective germline genes. F6 was a GP120-specific nAb and recognized the linear epitope. We identified for the first time a novel broadly HIV-1-neutralizing antibody, termed F6, from a CRF01_AE-infected donor, which could enrich the research of HIV-1 nAbs and provide useful insights for designing vaccine immunogens and antibody-based therapeutics.
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Affiliation(s)
- Bin Ju
- School of Medicine, Nankai University, 300071, Tianjin, China.,Nankai University Second People's Hospital, School of Medicine, Nankai University, 300071, Tianjin, China.,State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Jiali Hou
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Hua Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China
| | - Jiang Zhu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Min Wei
- School of Medicine, Nankai University, 300071, Tianjin, China. .,Nankai University Second People's Hospital, School of Medicine, Nankai University, 300071, Tianjin, China.
| | - Yiming Shao
- School of Medicine, Nankai University, 300071, Tianjin, China. .,State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206, Beijing, China.
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Abstract
A large array of broadly neutralizing antibodies (bnAbs) against HIV have been isolated and described, particularly in the last decade. This continually expanding array of bnAbs has crucially led to the identification of novel epitopes on the HIV envelope protein via which antibodies can block a broad range of HIV strains. Moreover, these studies have produced high-resolution understanding of these sites of vulnerability on the envelope protein. They have also clarified the mechanisms of action of bnAbs and provided detailed descriptions of B cell ontogenies from which they arise. However, it is still not possible to predict which HIV-infected individuals will go onto develop breath nor is it possible to induce neutralization breadth by immunization in humans. This review aims to discuss the major insights gained so far and also to evaluate the requirement to continue isolating and characterizing new bnAbs. While new epitopes may remain to be uncovered, a clearer probable benefit of further bnAb characterization is a greater understanding of key decision points in bnAb development within the anti-HIV immune response. This in turn may lead to new insights into how to trigger bnAbs by immunization and more clearly define the challenges to using bnAbs as therapeutic agents.
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Affiliation(s)
- Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK.
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47
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Landais E, Moore PL. Development of broadly neutralizing antibodies in HIV-1 infected elite neutralizers. Retrovirology 2018; 15:61. [PMID: 30185183 PMCID: PMC6125991 DOI: 10.1186/s12977-018-0443-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/23/2018] [Indexed: 12/20/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs), able to prevent viral entry by diverse global viruses, are a major focus of HIV vaccine design, with data from animal studies confirming their ability to prevent HIV infection. However, traditional vaccine approaches have failed to elicit these types of antibodies. During chronic HIV infection, a subset of individuals develops bNAbs, some of which are extremely broad and potent. This review describes the immunological and virological factors leading to the development of bNAbs in such "elite neutralizers". The features, targets and developmental pathways of bNAbs from their precursors have been defined through extraordinarily detailed within-donor studies. These have enabled the identification of epitope-specific commonalities in bNAb precursors, their intermediates and Env escape patterns, providing a template for vaccine discovery. The unusual features of bNAbs, such as high levels of somatic hypermutation, and precursors with unusually short or long antigen-binding loops, present significant challenges in vaccine design. However, the use of new technologies has led to the isolation of more than 200 bNAbs, including some with genetic profiles more representative of the normal immunoglobulin repertoire, suggesting alternate and shorter pathways to breadth. The insights from these studies have been harnessed for the development of optimized immunogens, novel vaccine regimens and improved delivery schedules, which are providing encouraging data that an HIV vaccine may soon be a realistic possibility.
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Affiliation(s)
- Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,International AIDS Vaccine Initiative, New York, NY, 10004, USA
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. .,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.
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48
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Zhao C, Xu J. Toward universal influenza virus vaccines: from natural infection to vaccination strategy. Curr Opin Immunol 2018; 53:1-6. [PMID: 29604600 DOI: 10.1016/j.coi.2018.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 10/17/2022]
Abstract
Conceptually, a universal influenza vaccine should elicit broadly protective antibody responses targeting highly conserved epitope(s) shared by various virus strains. Strategically directing antibody immunity to the conserved hemagglutinin stalk has recently emerged as a promising approach that is substantiated by the identification of naturally occurring, stalk-reactive human antibodies capable of conferring broad protection against influenza virus challenge in animal models. Despite all the advancements, future realization of this strategy still faces many challenges, particularly whether it is able to induce enough of cross-reactive antibody response to protect against pandemic viruses. In this respect, recent in-depth dissections of human immune responses to H7N9 virus and vaccination provide much-needed new insights.
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Affiliation(s)
- Chen Zhao
- Shanghai Public Health Clinic Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Jianqing Xu
- Shanghai Public Health Clinic Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, China; State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, China.
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Freund NT, Wang H, Scharf L, Nogueira L, Horwitz JA, Bar-On Y, Golijanin J, Sievers SA, Sok D, Cai H, Cesar Lorenzi JC, Halper-Stromberg A, Toth I, Piechocka-Trocha A, Gristick HB, van Gils MJ, Sanders RW, Wang LX, Seaman MS, Burton DR, Gazumyan A, Walker BD, West AP, Bjorkman PJ, Nussenzweig MC. Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller. Sci Transl Med 2018; 9:9/373/eaal2144. [PMID: 28100831 DOI: 10.1126/scitranslmed.aal2144] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/14/2016] [Accepted: 12/08/2016] [Indexed: 12/13/2022]
Abstract
Some HIV-1-infected patients develop broad and potent HIV-1 neutralizing antibodies (bNAbs) that when passively transferred to mice or macaques can treat or prevent infection. However, bNAbs typically fail to neutralize coexisting autologous viruses due to antibody-mediated selection against sensitive viral strains. We describe an HIV-1 controller expressing HLA-B57*01 and HLA-B27*05 who maintained low viral loads for 30 years after infection and developed broad and potent serologic activity against HIV-1. Neutralization was attributed to three different bNAbs targeting nonoverlapping sites on the HIV-1 envelope trimer (Env). One of the three, BG18, an antibody directed against the glycan-V3 portion of Env, is the most potent member of this class reported to date and, as revealed by crystallography and electron microscopy, recognizes HIV-1 Env in a manner that is distinct from other bNAbs in this class. Single-genome sequencing of HIV-1 from serum samples obtained over a period of 9 years showed a diverse group of circulating viruses, 88.5% (31 of 35) of which remained sensitive to at least one of the temporally coincident autologous bNAbs and the individual's serum. Thus, bNAb-sensitive strains of HIV-1 coexist with potent neutralizing antibodies that target the virus and may contribute to control in this individual. When administered as a mix, the three bNAbs controlled viremia in HIV-1YU2-infected humanized mice. Our finding suggests that combinations of bNAbs may contribute to control of HIV-1 infection.
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Affiliation(s)
- Natalia T Freund
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Louise Scharf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Joshua A Horwitz
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Yotam Bar-On
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Stuart A Sievers
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, and International AIDS Vaccine Initiative Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hui Cai
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742, USA
| | | | | | - Ildiko Toth
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, and International AIDS Vaccine Initiative Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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50
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HIV Broadly Neutralizing Antibodies: VRC01 and Beyond. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1075:53-72. [PMID: 30030789 DOI: 10.1007/978-981-13-0484-2_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Developing an effective prophylaxis HIV-1 vaccine is likely to require the elicitation of broadly neutralizing antibodies (bnAbs). As the HIV-1 envelope (Env) glycoprotein - the sole target of bnAbs - has evolved multiple mechanisms to evade antibody neutralization, the processes for bnAb generation are highly selective and time-consuming. Benefiting from antibody isolation technologies of single B cell culturing and direct single B cell sorting and cloning, a new generation of monoclonal bnAbs has been isolated since 2009, exhibiting remarkable breadths and potencies, thus breaking through a nearly 20-year-long limit of four monoclonal bnAbs with moderate breadth and potency. The discovery of a long list of monoclonal bnAbs has provided in-depth understanding of the sites of vulnerability on the HIV-1 Env and the complexity of human B cell immunology to generate such responses, thus presenting both guidance and challenges to move the Env immunogen design effort forward.
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