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Cottrell CA, Hu X, Lee JH, Skog P, Luo S, Flynn CT, McKenney KR, Hurtado J, Kalyuzhniy O, Liguori A, Willis JR, Landais E, Raemisch S, Chen X, Baboo S, Himansu S, Diedrich JK, Duan H, Cheng C, Schiffner T, Bader DLV, Kulp DW, Tingle R, Georgeson E, Eskandarzadeh S, Alavi N, Lu D, Sincomb T, Kubitz M, Mullen TM, Yates JR, Paulson JC, Mascola JR, Alt FW, Briney B, Sok D, Schief WR. Heterologous prime-boost vaccination drives early maturation of HIV broadly neutralizing antibody precursors in humanized mice. Sci Transl Med 2024; 16:eadn0223. [PMID: 38753806 DOI: 10.1126/scitranslmed.adn0223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
A protective HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). Vaccination with the germline-targeting immunogen eOD-GT8 60mer adjuvanted with AS01B was found to induce VRC01-class bnAb precursors in 97% of vaccine recipients in the IAVI G001 phase 1 clinical trial; however, heterologous boost immunizations with antigens more similar to the native glycoprotein will be required to induce bnAbs. Therefore, we designed core-g28v2 60mer, a nanoparticle immunogen to be used as a first boost after eOD-GT8 60mer priming. We found, using a humanized mouse model approximating human conditions of VRC01-class precursor B cell diversity, affinity, and frequency, that both protein- and mRNA-based heterologous prime-boost regimens induced VRC01-class antibodies that gained key mutations and bound to near-native HIV envelope trimers lacking the N276 glycan. We further showed that VRC01-class antibodies induced by mRNA-based regimens could neutralize pseudoviruses lacking the N276 glycan. These results demonstrated that heterologous boosting can drive maturation toward VRC01-class bnAb development and supported the initiation of the IAVI G002 phase 1 trial testing mRNA-encoded nanoparticle prime-boost regimens.
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Affiliation(s)
- Christopher A Cottrell
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Therapeutics, Cambridge, MA 02139, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick Skog
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sai Luo
- HHMI, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia T Flynn
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katherine R McKenney
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sebastian Raemisch
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabyasachi Baboo
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongying Duan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Torben Schiffner
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel L V Bader
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Tingle
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nushin Alavi
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Danny Lu
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Troy Sincomb
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tina-Marie Mullen
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frederick W Alt
- HHMI, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Therapeutics, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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2
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Wang S, Chan KW, Wei D, Ma X, Liu S, Hu G, Park S, Pan R, Gu Y, Nazzari AF, Olia AS, Xu K, Lin BC, Louder MK, McKee K, Doria-Rose NA, Montefiori D, Seaman MS, Zhou T, Kwong PD, Arthos J, Kong XP, Lu S. Human CD4-binding site antibody elicited by polyvalent DNA prime-protein boost vaccine neutralizes cross-clade tier-2-HIV strains. Nat Commun 2024; 15:4301. [PMID: 38773089 PMCID: PMC11109196 DOI: 10.1038/s41467-024-48514-8] [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: 09/15/2023] [Accepted: 05/03/2024] [Indexed: 05/23/2024] Open
Abstract
The vaccine elicitation of HIV tier-2-neutralization antibodies has been a challenge. Here, we report the isolation and characterization of a CD4-binding site (CD4bs) specific monoclonal antibody, HmAb64, from a human volunteer immunized with a polyvalent DNA prime-protein boost HIV vaccine. HmAb64 is derived from heavy chain variable germline gene IGHV1-18 and light chain germline gene IGKV1-39. It has a third heavy chain complementarity-determining region (CDR H3) of 15 amino acids. On a cross-clade panel of 208 HIV-1 pseudo-virus strains, HmAb64 neutralized 20 (10%), including tier-2 strains from clades B, BC, C, and G. The cryo-EM structure of the antigen-binding fragment of HmAb64 in complex with a CNE40 SOSIP trimer revealed details of its recognition; HmAb64 uses both heavy and light CDR3s to recognize the CD4-binding loop, a critical component of the CD4bs. This study demonstrates that a gp120-based vaccine can elicit antibodies capable of tier 2-HIV neutralization.
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Affiliation(s)
- Shixia Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Danlan Wei
- Laboratory of Immune Regulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Xiuwen Ma
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Shuying Liu
- SYL Consulting, Thousand Oak, CA, 91320, USA
| | - Guangnan Hu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Saeyoung Park
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ying Gu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Alexandra F Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | | | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - James Arthos
- Laboratory of Immune Regulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Shan Lu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
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3
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Wang X, Cottrell CA, Hu X, Ray R, Bottermann M, Villavicencio PM, Yan Y, Xie Z, Warner JE, Ellis-Pugh JR, Kalyuzhniy O, Liguori A, Willis JR, Menis S, Rämisch S, Eskandarzadeh S, Kubitz M, Tingle R, Phelps N, Groschel B, Himansu S, Carfi A, Kirsch KH, Weldon SR, Nair U, Schief WR, Batista FD. mRNA-LNP prime boost evolves precursors toward VRC01-like broadly neutralizing antibodies in preclinical humanized mouse models. Sci Immunol 2024; 9:eadn0622. [PMID: 38753808 DOI: 10.1126/sciimmunol.adn0622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 05/18/2024]
Abstract
Germline-targeting (GT) protein immunogens to induce VRC01-class broadly neutralizing antibodies (bnAbs) to the CD4-binding site of the HIV envelope (Env) have shown promise in clinical trials. Here, we preclinically validated a lipid nanoparticle-encapsulated nucleoside mRNA (mRNA-LNP) encoding eOD-GT8 60mer as a soluble self-assembling nanoparticle in mouse models. In a model with three humanized B cell lineages bearing distinct VRC01-precursor B cell receptors (BCRs) with similar affinities for eOD-GT8, all lineages could be simultaneously primed and undergo diversification and affinity maturation without exclusionary competition. Boosts drove precursor B cell participation in germinal centers; the accumulation of somatic hypermutations, including in key VRC01-class positions; and affinity maturation to boost and native-like antigens in two of the three precursor lineages. We have preclinically validated a prime-boost regimen of soluble self-assembling nanoparticles encoded by mRNA-LNP, demonstrating that multiple lineages can be primed, boosted, and diversified along the bnAb pathway.
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Affiliation(s)
- Xuesong Wang
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Inc., Cambridge, MA 02139, USA
| | - Rashmi Ray
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Maria Bottermann
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Yu Yan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Zhenfei Xie
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - John E Warner
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sebastian Rämisch
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Tingle
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | - Kathrin H Kirsch
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Stephanie R Weldon
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Usha Nair
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - William R Schief
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Inc., Cambridge, MA 02139, USA
| | - Facundo D Batista
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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4
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Wiehe K, Saunders KO, Stalls V, Cain DW, Venkatayogi S, Martin Beem JS, Berry M, Evangelous T, Henderson R, Hora B, Xia SM, Jiang C, Newman A, Bowman C, Lu X, Bryan ME, Bal J, Sanzone A, Chen H, Eaton A, Tomai MA, Fox CB, Tam YK, Barbosa C, Bonsignori M, Muramatsu H, Alam SM, Montefiori DC, Williams WB, Pardi N, Tian M, Weissman D, Alt FW, Acharya P, Haynes BF. Mutation-guided vaccine design: A process for developing boosting immunogens for HIV broadly neutralizing antibody induction. Cell Host Microbe 2024; 32:693-709.e7. [PMID: 38670093 DOI: 10.1016/j.chom.2024.04.006] [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: 04/28/2023] [Revised: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
A major goal of HIV-1 vaccine development is the induction of broadly neutralizing antibodies (bnAbs). Although success has been achieved in initiating bnAb B cell lineages, design of boosting immunogens that select for bnAb B cell receptors with improbable mutations required for bnAb affinity maturation remains difficult. Here, we demonstrate a process for designing boosting immunogens for a V3-glycan bnAb B cell lineage. The immunogens induced affinity-matured antibodies by selecting for functional improbable mutations in bnAb precursor knockin mice. Moreover, we show similar success in prime and boosting with nucleoside-modified mRNA-encoded HIV-1 envelope trimer immunogens, with improved selection by mRNA immunogens of improbable mutations required for bnAb binding to key envelope glycans. These results demonstrate the ability of both protein and mRNA prime-boost immunogens for selection of rare B cell lineage intermediates with neutralizing breadth after bnAb precursor expansion, a key proof of concept and milestone toward development of an HIV-1 vaccine.
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Affiliation(s)
- Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Microbiology and Molecular Genetics, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua S Martin Beem
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tyler Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chuancang Jiang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cindy Bowman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mary E Bryan
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joena Bal
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aja Sanzone
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark A Tomai
- Corporate Research Materials Lab, 3M Company, St. Paul, MN 55144, USA
| | | | | | | | - Mattia Bonsignori
- Translational Immunobiology Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiromi Muramatsu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Norbert Pardi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ming Tian
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick W Alt
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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5
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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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6
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deCamp AC, Corcoran MM, Fulp WJ, Willis JR, Cottrell CA, Bader DLV, Kalyuzhniy O, Leggat DJ, Cohen KW, Hyrien O, Menis S, Finak G, Ballweber-Fleming L, Srikanth A, Plyler JR, Rahaman F, Lombardo A, Philiponis V, Whaley RE, Seese A, Brand J, Ruppel AM, Hoyland W, Mahoney CR, Cagigi A, Taylor A, Brown DM, Ambrozak DR, Sincomb T, Mullen TM, Maenza J, Kolokythas O, Khati N, Bethony J, Roederer M, Diemert D, Koup RA, Laufer DS, McElrath JM, McDermott AB, Karlsson Hedestam GB, Schief WR. Human immunoglobulin gene allelic variation impacts germline-targeting vaccine priming. NPJ Vaccines 2024; 9:58. [PMID: 38467663 DOI: 10.1038/s41541-024-00811-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Vaccine priming immunogens that activate germline precursors for broadly neutralizing antibodies (bnAbs) have promise for development of precision vaccines against major human pathogens. In a clinical trial of the eOD-GT8 60mer germline-targeting immunogen, higher frequencies of vaccine-induced VRC01-class bnAb-precursor B cells were observed in the high dose compared to the low dose group. Through immunoglobulin heavy chain variable (IGHV) genotyping, statistical modeling, quantification of IGHV1-2 allele usage and B cell frequencies in the naive repertoire for each trial participant, and antibody affinity analyses, we found that the difference between dose groups in VRC01-class response frequency was best explained by IGHV1-2 genotype rather than dose and was most likely due to differences in IGHV1-2 B cell frequencies for different genotypes. The results demonstrate the need to define population-level immunoglobulin allelic variations when designing germline-targeting immunogens and evaluating them in clinical trials.
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Affiliation(s)
- Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
| | - Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - William J Fulp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jordan R Willis
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Christopher A Cottrell
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Daniel L V Bader
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Oleksandr Kalyuzhniy
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - David J Leggat
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Sergey Menis
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Lamar Ballweber-Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Abhinaya Srikanth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason R Plyler
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Farhad Rahaman
- IAVI, 125 Broad Street, 9th floor, New York, NY, 10004, USA
| | | | | | - Rachael E Whaley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Joshua Brand
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexis M Ruppel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wesley Hoyland
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Celia R Mahoney
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison Taylor
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David M Brown
- The Foundation for the National Institutes of Health, North Bethesda, MD, USA
| | - David R Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Troy Sincomb
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tina-Marie Mullen
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Orpheus Kolokythas
- Department of Radiology, University of Washington, Seattle, WA, 98195, USA
| | - Nadia Khati
- Department of Radiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Jeffrey Bethony
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Diemert
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
- Department of Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dagna S Laufer
- IAVI, 125 Broad Street, 9th floor, New York, NY, 10004, USA
| | - Juliana M McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - William R Schief
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA.
- Moderna Inc., Cambridge, MA, 02139, USA.
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7
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Li K, Zhang Q. Eliminating the HIV tissue reservoir: current strategies and challenges. Infect Dis (Lond) 2024; 56:165-182. [PMID: 38149977 DOI: 10.1080/23744235.2023.2298450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/16/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Acquired immunodeficiency syndrome (AIDS) is still one of the most widespread and harmful infectious diseases in the world. The presence of reservoirs housing the human immunodeficiency virus (HIV) represents a significant impediment to the development of clinically applicable treatments on a large scale. The viral load in the blood can be effectively reduced to undetectable levels through antiretroviral therapy (ART), and a higher concentration of HIV is sequestered in various tissues throughout the body, forming the tissue reservoir - the source of viremia after interruption treatment. METHODS We take the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) as a guideline for this review. In June 2023, we used the Pubmed, Embase, and Scopus databases to search the relevant literature published in the last decade. RESULTS Here we review the current strategies and treatments for eliminating the HIV tissue reservoirs: early and intensive therapy, gene therapy (including ribozyme, RNA interference, RNA aptamer, zinc finger enzyme, transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/associated nuclease 9 (CRISPR/Cas9)), 'Shock and Kill', 'Block and lock', immunotherapy (including therapeutic vaccines, broadly neutralising antibodies (bNAbs), chimeric antigen receptor T-cell immunotherapy (CAR-T)), and haematopoietic stem cell transplantation (HSCT). CONCLUSION The existence of an HIV reservoir is the main obstacle to the complete cure of AIDS. Choosing the appropriate strategy to deplete the HIV reservoir and achieve a functional cure for AIDS is the focus and difficulty of current research. So far, there has been a lot of research and progress in reducing the HIV reservoir, but in general, the current research is still very preliminary. Much research is still needed to properly assess the reliability, effectiveness, and necessity of these strategies.
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Affiliation(s)
- Kangpeng Li
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhang
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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8
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Newby ML, Allen JD, Crispin M. Influence of glycosylation on the immunogenicity and antigenicity of viral immunogens. Biotechnol Adv 2024; 70:108283. [PMID: 37972669 PMCID: PMC10867814 DOI: 10.1016/j.biotechadv.2023.108283] [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: 02/24/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
A key aspect of successful viral vaccine design is the elicitation of neutralizing antibodies targeting viral attachment and fusion glycoproteins that embellish viral particles. This observation has catalyzed the development of numerous viral glycoprotein mimetics as vaccines. Glycans can dominate the surface of viral glycoproteins and as such, the viral glycome can influence the antigenicity and immunogenicity of a candidate vaccine. In one extreme, glycans can form an integral part of epitopes targeted by neutralizing antibodies and are therefore considered to be an important feature of key immunogens within an immunization regimen. In the other extreme, the existence of peptide and bacterially expressed protein vaccines shows that viral glycosylation can be dispensable in some cases. However, native-like glycosylation can indicate native-like protein folding and the presence of conformational epitopes. Furthermore, going beyond native glycan mimicry, in either occupancy of glycosylation sites or the glycan processing state, may offer opportunities for enhancing the immunogenicity and associated protection elicited by an immunogen. Here, we review key determinants of viral glycosylation and how recombinant immunogens can recapitulate these signatures across a range of enveloped viruses, including HIV-1, Ebola virus, SARS-CoV-2, Influenza and Lassa virus. The emerging understanding of immunogen glycosylation and its control will help guide the development of future vaccines in both recombinant protein- and nucleic acid-based vaccine technologies.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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9
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Stamatatos L. 'Immunization during ART and ATI for HIV-1 vaccine discovery/development'. Curr Opin HIV AIDS 2023; 18:309-314. [PMID: 37712859 PMCID: PMC10552831 DOI: 10.1097/coh.0000000000000817] [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] [Indexed: 09/16/2023]
Abstract
PURPOSE OF REVIEW Explore whether immunization with germline-targeting Env immunogens during ART, followed by ATI, leads to the identification of viral envelope glycoproteins (Envs) that promote and guide the full maturation of broadly neutralizing antibody responses. RECENT FINDINGS The HIV-1 envelope glycoprotein (Env) does not efficiently engage the germline precursors of broadly neutralizing antibodies (bnAbs). However, Env-derived proteins specifically designed to precisely do that, have been recently developed. These 'germline-targeting' Env immunogens activate naïve B cells that express the germline precursors of bnAbs but by themselves cannot guide their maturation towards their broadly neutralizing forms. This requires sequential immunizations with heterologous sets of Envs. These 'booster' Envs are currently unknown. SUMMARY Combining germline-targeting Env immunization approaches during ART with ATI could lead to the identification of natural Envs that are responsible for the maturation of broadly neutralizing antibody responses during infection. Such Envs could then serve as booster immunogens to guide the maturation of glBCRs that have become activated by germline-targeting immunogens in uninfected subjects.
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Affiliation(s)
- Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center and University of Washington, Department of Global Health, Seattle, WA, USA
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10
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Dam KMA, Fan C, Yang Z, Bjorkman PJ. Intermediate conformations of CD4-bound HIV-1 Env heterotrimers. Nature 2023; 623:1017-1025. [PMID: 37993719 PMCID: PMC10686819 DOI: 10.1038/s41586-023-06639-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/13/2023] [Indexed: 11/24/2023]
Abstract
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120 and gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops1-4 and in fully saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops3-9. To investigate changes resulting from substoichiometric CD4 binding, we solved single-particle cryo-electron microscopy (cryo-EM) structures of soluble, native-like heterotrimeric Envs bound to one or two CD4 molecules. Most of the Env trimers bound to one CD4 adopted the closed, prefusion Env state, with a minority exhibiting a heterogeneous partially open Env conformation. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state10 that showed gp120 outward rotation but maintained the prefusion three-stranded gp120 bridging sheet with only partial V1V2 displacement and V3 exposure. We conclude that most of the engagements with one CD4 molecule were insufficient to stimulate CD4-induced conformational changes, whereas binding two CD4 molecules led to Env opening in CD4-bound protomers only. The substoichiometric CD4-bound soluble Env heterotrimer structures resembled counterparts derived from a cryo-electron tomography study of complexes between virion-bound Envs and membrane-anchored CD4 (ref. 11), validating their physiological relevance. Together, these results illuminate intermediate conformations of HIV-1 Env and illustrate its structural plasticity.
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Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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11
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Wang S, Chan KW, Wei D, Ma X, Liu S, Hu G, Park S, Pan R, Gu Y, Nazzari AF, Olia AS, Xu K, Lin BC, Louder MK, Doria-Rose NA, Montefiori D, Seaman MS, Zhou T, Kwong PD, Arthos J, Kong XP, Lu S. Human CD4-Binding Site Antibody Elicited by Polyvalent DNA Prime-Protein Boost Vaccine Neutralizes Cross-Clade Tier-2-HIV Strains. RESEARCH SQUARE 2023:rs.3.rs-3360161. [PMID: 37886518 PMCID: PMC10602183 DOI: 10.21203/rs.3.rs-3360161/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The vaccine elicitation of HIV-neutralizing antibodies with tier-2-neutralization breadth has been a challenge. Here, we report the isolation and characteristics of a CD4-binding site specific monoclonal antibody, HmAb64, from a human volunteer immunized with a polyvalent gp120 DNA prime-protein boost vaccine. HmAb64 derived from heavy chain variable germline gene IGHV1-18, light chain germline gene IGKV1-39, and had a 3rd heavy chain complementarity determining region (CDR H3) of 15 amino acids. On a cross-clade panel of 208 HIV-1 pseudo-virus strains, HmAb64 neutralized 21 (10%), including tier-2 neutralization resistant strains from clades B, BC, C, and G. The cryo-EM structure of the antigen-binding fragment of HmAb64 bound to a conformation between prefusion closed and occluded open forms of envelope trimer, using both heavy and light CDR3s to recognize the CD4-binding loop, a critical component of the CD4-binding site. A gp120 subunit-based vaccine can thus elicit an antibody capable of tier 2-HIV neutralization.
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Affiliation(s)
- Shixia Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Danlan Wei
- Laboratory of Immune Regulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Xiuwen Ma
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | | | - Guangnan Hu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Saeyoung Park
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Gu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandra F Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - James Arthos
- Laboratory of Immune Regulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Shan Lu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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12
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Radford CE, Schommers P, Gieselmann L, Crawford KHD, Dadonaite B, Yu TC, Dingens AS, Overbaugh J, Klein F, Bloom JD. Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning. Cell Host Microbe 2023; 31:1200-1215.e9. [PMID: 37327779 PMCID: PMC10351223 DOI: 10.1016/j.chom.2023.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/18/2023]
Abstract
Understanding the specificities of human serum antibodies that broadly neutralize HIV can inform prevention and treatment strategies. Here, we describe a deep mutational scanning system that can measure the effects of combinations of mutations to HIV envelope (Env) on neutralization by antibodies and polyclonal serum. We first show that this system can accurately map how all functionally tolerated mutations to Env affect neutralization by monoclonal antibodies. We then comprehensively map Env mutations that affect neutralization by a set of human polyclonal sera that neutralize diverse strains of HIV and target the site engaging the host receptor CD4. The neutralizing activities of these sera target different epitopes, with most sera having specificities reminiscent of individual characterized monoclonal antibodies, but one serum targeting two epitopes within the CD4-binding site. Mapping the specificity of the neutralizing activity in polyclonal human serum will aid in assessing anti-HIV immune responses to inform prevention strategies.
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Affiliation(s)
- Caelan E Radford
- Molecular and Cellular Biology Graduate Program, University of Washington and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy C Yu
- Molecular and Cellular Biology Graduate Program, University of Washington and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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13
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Capella-Pujol J, de Gast M, Radić L, Zon I, Chumbe A, Koekkoek S, Olijhoek W, Schinkel J, van Gils MJ, Sanders RW, Sliepen K. Signatures of V H1-69-derived hepatitis C virus neutralizing antibody precursors defined by binding to envelope glycoproteins. Nat Commun 2023; 14:4036. [PMID: 37419906 PMCID: PMC10328973 DOI: 10.1038/s41467-023-39690-0] [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: 11/09/2022] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
An effective preventive vaccine for hepatitis C virus (HCV) remains a major unmet need. Antigenic region 3 (AR3) on the E1E2 envelope glycoprotein complex overlaps with the CD81 receptor binding site and represents an important epitope for broadly neutralizing antibodies (bNAbs) and is therefore important for HCV vaccine design. Most AR3 bNAbs utilize the VH1-69 gene and share structural features that define the AR3C-class of HCV bNAbs. In this work, we identify recombinant HCV glycoproteins based on a permuted E2E1 trimer design that bind to the inferred VH1-69 germline precursors of AR3C-class bNAbs. When presented on nanoparticles, these recombinant E2E1 glycoproteins efficiently activate B cells expressing inferred germline AR3C-class bNAb precursors as B cell receptors. Furthermore, we identify critical signatures in three AR3C-class bNAbs that represent two subclasses of AR3C-class bNAbs that will allow refined protein design. These results provide a framework for germline-targeting vaccine design strategies against HCV.
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Affiliation(s)
- Joan Capella-Pujol
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Marlon de Gast
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Laura Radić
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Ian Zon
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Wouter Olijhoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10065, USA.
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands.
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14
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Zhang X, Zhou Z. The Mechanism of bnAb Production and Its Application in Mutable Virus Broad-Spectrum Vaccines: Inspiration from HIV-1 Broad Neutralization Research. Vaccines (Basel) 2023; 11:1143. [PMID: 37514959 PMCID: PMC10384589 DOI: 10.3390/vaccines11071143] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Elite controllers among HIV-1-infected individuals have demonstrated a stronger ability to control the viral load in their bodies. Scientists have isolated antibodies with strong neutralizing ability from these individuals, which can neutralize HIV-1 variations; these are known as broadly neutralizing antibodies. The nucleic acid of some viruses will constantly mutate during replication (such as SARS-CoV-2), which will reduce the protective ability of the corresponding vaccines. The immune escape caused by this mutation is the most severe challenge faced by humans in the battle against the virus. Therefore, developing broad-spectrum vaccines that can induce broadly neutralizing antibodies against various viruses and their mutated strains is the best way to combat virus mutations. Exploring the mechanism by which the human immune system produces broadly neutralizing antibodies and its induction strategies is crucial in the design process of broad-spectrum vaccines.
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Affiliation(s)
- Xinyu Zhang
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- College of Life Science, Jilin University, Changchun 130012, China
| | - Zehua Zhou
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
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15
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Joyce C, Murrell S, Murrell B, Omorodion O, Ver LS, Carrico N, Bastidas R, Nedellec R, Bick M, Woehl J, Zhao F, Burns A, Barman S, Appel M, Ramos A, Wickramasinghe L, Eren K, Vollbrecht T, Smith DM, Kosakovsky Pond SL, McBride R, Worth C, Batista F, Sok D, Poignard P, Briney B, Wilson IA, Landais E, Burton DR. Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies. PLoS Pathog 2023; 19:e1011416. [PMID: 37384622 PMCID: PMC10309625 DOI: 10.1371/journal.ppat.1011416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/10/2023] [Indexed: 07/01/2023] Open
Abstract
Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population "arms" that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.
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Affiliation(s)
- Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sasha Murrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ben Murrell
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Oluwarotimi Omorodion
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lorena S. Ver
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Nancy Carrico
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Raiza Bastidas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Michael Bick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Alison Burns
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Shawn Barman
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Michael Appel
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Alejandra Ramos
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Lalinda Wickramasinghe
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Kemal Eren
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Thomas Vollbrecht
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Charli Worth
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Facundo Batista
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | | | - Pascal Poignard
- Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat à l’Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ian A. Wilson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Elise Landais
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
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16
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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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17
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Radford CE, Schommers P, Gieselmann L, Crawford KHD, Dadonaite B, Yu TC, Dingens AS, Overbaugh J, Klein F, Bloom JD. Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533993. [PMID: 36993197 PMCID: PMC10055425 DOI: 10.1101/2023.03.23.533993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Understanding the specificities of human serum antibodies that broadly neutralize HIV can inform prevention and treatment strategies. Here we describe a deep mutational scanning system that can measure the effects of combinations of mutations to HIV envelope (Env) on neutralization by antibodies and polyclonal serum. We first show that this system can accurately map how all functionally tolerated mutations to Env affect neutralization by monoclonal antibodies. We then comprehensively map Env mutations that affect neutralization by a set of human polyclonal sera known to target the CD4-binding site that neutralize diverse strains of HIV. The neutralizing activities of these sera target different epitopes, with most sera having specificities reminiscent of individual characterized monoclonal antibodies, but one sera targeting two epitopes within the CD4 binding site. Mapping the specificity of the neutralizing activity in polyclonal human serum will aid in assessing anti-HIV immune responses to inform prevention strategies.
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18
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deCamp AC, Corcoran MM, Fulp WJ, Willis JR, Cottrell CA, Bader DLV, Kalyuzhniy O, Leggat DJ, Cohen KW, Hyrien O, Menis S, Finak G, Ballweber-Fleming L, Srikanth A, Plyler JR, Rahaman F, Lombardo A, Philiponis V, Whaley RE, Seese A, Brand J, Ruppel AM, Hoyland W, Mahoney CR, Cagigi A, Taylor A, Brown DM, Ambrozak DR, Sincomb T, Mullen TM, Maenza J, Kolokythas O, Khati N, Bethony J, Roederer M, Diemert D, Koup RA, Laufer DS, McElrath JM, McDermott AB, Hedestam GBK, Schief WR. Human immunoglobulin gene allelic variation impacts germline-targeting vaccine priming. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.10.23287126. [PMID: 36993183 PMCID: PMC10055468 DOI: 10.1101/2023.03.10.23287126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Vaccine priming immunogens that activate germline precursors for broadly neutralizing antibodies (bnAbs) have promise for development of precision vaccines against major human pathogens. In a clinical trial of the eOD-GT8 60mer germline-targeting immunogen, higher frequencies of vaccine-induced VRC01-class bnAb-precursor B cells were observed in the high dose compared to the low dose group. Through immunoglobulin heavy chain variable (IGHV) genotyping, statistical modeling, quantification of IGHV1-2 allele usage and B cell frequencies in the naive repertoire for each trial participant, and antibody affinity analyses, we found that the difference between dose groups in VRC01-class response frequency was best explained by IGHV1-2 genotype rather than dose and was most likely due to differences in IGHV1-2 B cell frequencies for different genotypes. The results demonstrate the need to define population-level immunoglobulin allelic variations when designing germline-targeting immunogens and evaluating them in clinical trials. One-Sentence Summary Human genetic variation can modulate the strength of vaccine-induced broadly neutralizing antibody precursor B cell responses.
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19
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA. .,Department of Medicine, Duke University School of Medicine, Durham, NC, USA. .,Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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20
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Gristick HB, Hartweger H, Loewe M, van Schooten J, Ramos V, Oliviera TY, Nishimura Y, Koranda NS, Wall A, Yao KH, Poston D, Gazumyan A, Wiatr M, Horning M, Keeffe JR, Hoffmann MA, Yang Z, Abernathy ME, Dam KMA, Gao H, Gnanapragasam PN, Kakutani LM, Pavlovitch-Bedzyk AJ, Seaman MS, Howarth M, McGuire AT, Stamatatos L, Martin MA, West AP, Nussenzweig MC, Bjorkman PJ. CD4 binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wild-type animals. Sci Immunol 2023; 8:eade6364. [PMID: 36763635 PMCID: PMC10202037 DOI: 10.1126/sciimmunol.ade6364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023]
Abstract
Passive transfer of broadly neutralizing anti-HIV-1 antibodies (bNAbs) protects against infection, and therefore, eliciting bNAbs by vaccination is a major goal of HIV-1 vaccine efforts. bNAbs that target the CD4 binding site (CD4bs) on HIV-1 Env are among the most broadly active, but to date, responses elicited against this epitope in vaccinated animals have lacked potency and breadth. We hypothesized that CD4bs bNAbs resembling the antibody IOMA might be easier to elicit than other CD4bs antibodies that exhibit higher somatic mutation rates, a difficult-to-achieve mechanism to accommodate Env's N276gp120 N-glycan, and rare five-residue light chain complementarity-determining region 3. As an initial test of this idea, we developed IOMA germline-targeting Env immunogens and evaluated a sequential immunization regimen in transgenic mice expressing germline-reverted IOMA. These mice developed CD4bs epitope-specific responses with heterologous neutralization, and cloned antibodies overcame neutralization roadblocks, including accommodating the N276gp120 glycan, with some neutralizing selected HIV-1 strains more potently than IOMA. The immunization regimen also elicited CD4bs-specific responses in mice containing polyclonal antibody repertoires as well as rabbits and rhesus macaques. Thus, germline targeting of IOMA-class antibody precursors represents a potential vaccine strategy to induce CD4bs bNAbs.
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Affiliation(s)
- Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Maximilian Loewe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jelle van Schooten
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y. Oliviera
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas S. Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Abigail Wall
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Wiatr
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marcel Horning
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magnus A.G. Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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21
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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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22
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Dam KMA, Fan C, Yang Z, Bjorkman PJ. Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525985. [PMID: 36747804 PMCID: PMC9900888 DOI: 10.1101/2023.01.27.525985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops, and in fully-saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops. To investigate changes resulting from sub-stoichiometric CD4 binding, we solved 3.4Å and 3.9Å single-particle cryo-EM structures of soluble, native-like Envs bound to one or two CD4 molecules. Env trimer bound to one CD4 adopted the closed, prefusion Env state. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state that included gp120 outward rotation but maintained the prefusion, three-stranded gp120 bridging sheet and showed only partial V1V2 displacement and V3 exposure. We conclude that engagement of one CD4 molecule was insufficient to stimulate CD4-induced conformational changes, while binding two CD4 molecules led to Env opening in CD4-bound protomers only. Together, these results illuminate HIV-1 Env intermediate conformations and illustrate the structural plasticity of HIV-1 Env.
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Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Department of Molecular and Cell Biology, University of California, 13 Berkeley, CA 94720, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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23
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Luo S, Jing C, Ye AY, Kratochvil S, Cottrell CA, Koo JH, Chapdelaine Williams A, Francisco LV, Batra H, Lamperti E, Kalyuzhniy O, Zhang Y, Barbieri A, Manis JP, Haynes BF, Schief WR, Batista FD, Tian M, Alt FW. Humanized V(D)J-rearranging and TdT-expressing mouse vaccine models with physiological HIV-1 broadly neutralizing antibody precursors. Proc Natl Acad Sci U S A 2023; 120:e2217883120. [PMID: 36574685 PMCID: PMC9910454 DOI: 10.1073/pnas.2217883120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Antibody heavy chain (HC) and light chain (LC) variable region exons are assembled by V(D)J recombination. V(D)J junctional regions encode complementarity-determining-region 3 (CDR3), an antigen-contact region immensely diversified through nontemplated nucleotide additions ("N-regions") by terminal deoxynucleotidyl transferase (TdT). HIV-1 vaccine strategies seek to elicit human HIV-1 broadly neutralizing antibodies (bnAbs), such as the potent CD4-binding site VRC01-class bnAbs. Mice with primary B cells that express receptors (BCRs) representing bnAb precursors are used as vaccination models. VRC01-class bnAbs uniformly use human HC VH1-2 and commonly use human LCs Vκ3-20 or Vκ1-33 associated with an exceptionally short 5-amino-acid (5-aa) CDR3. Prior VRC01-class models had nonphysiological precursor levels and/or limited precursor diversity. Here, we describe VRC01-class rearranging mice that generate more physiological primary VRC01-class BCR repertoires via rearrangement of VH1-2, as well as Vκ1-33 and/or Vκ3-20 in association with diverse CDR3s. Human-like TdT expression in mouse precursor B cells increased LC CDR3 length and diversity and also promoted the generation of shorter LC CDR3s via N-region suppression of dominant microhomology-mediated Vκ-to-Jκ joins. Priming immunization with eOD-GT8 60mer, which strongly engages VRC01 precursors, induced robust VRC01-class germinal center B cell responses. Vκ3-20-based responses were enhanced by N-region addition, which generates Vκ3-20-to-Jκ junctional sequence combinations that encode VRC01-class 5-aa CDR3s with a critical E residue. VRC01-class-rearranging models should facilitate further evaluation of VRC01-class prime and boost immunogens. These new VRC01-class mouse models establish a prototype for the generation of vaccine-testing mouse models for other HIV-1 bnAb lineages that employ different HC or LC Vs.
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Affiliation(s)
- Sai Luo
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Changbin Jing
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Adam Yongxin Ye
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Sven Kratochvil
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
| | - Christopher A. Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA92037
| | - Ja-Hyun Koo
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
| | - Aimee Chapdelaine Williams
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Lucas Vieira Francisco
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Himanshu Batra
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Edward Lamperti
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA92037
| | - Yuxiang Zhang
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Alessandro Barbieri
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA02115
| | - John P. Manis
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA02115
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC27710
- Department of Medicine, Duke University School of Medicine, Durham, NC27710
- Department of Immunology, Duke University School of Medicine, Durham, NC27710
| | - William R. Schief
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA92037
| | - Facundo D. Batista
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Immunology, Harvard Medical School, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Ming Tian
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Frederick W. Alt
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
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24
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Leggat DJ, Cohen KW, Willis JR, Fulp WJ, deCamp AC, Kalyuzhniy O, Cottrell CA, Menis S, Finak G, Ballweber-Fleming L, Srikanth A, Plyler JR, Schiffner T, Liguori A, Rahaman F, Lombardo A, Philiponis V, Whaley RE, Seese A, Brand J, Ruppel AM, Hoyland W, Yates NL, Williams LD, Greene K, Gao H, Mahoney CR, Corcoran MM, Cagigi A, Taylor A, Brown DM, Ambrozak DR, Sincomb T, Hu X, Tingle R, Georgeson E, Eskandarzadeh S, Alavi N, Lu D, Mullen TM, Kubitz M, Groschel B, Maenza J, Kolokythas O, Khati N, Bethony J, Crotty S, Roederer M, Karlsson Hedestam GB, Tomaras GD, Montefiori D, Diemert D, Koup RA, Laufer DS, McElrath MJ, McDermott AB, Schief WR. Vaccination induces HIV broadly neutralizing antibody precursors in humans. Science 2022; 378:eadd6502. [PMID: 36454825 PMCID: PMC11103259 DOI: 10.1126/science.add6502] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) can protect against HIV infection but have not been induced by human vaccination. A key barrier to bnAb induction is vaccine priming of rare bnAb-precursor B cells. In a randomized, double-blind, placebo-controlled phase 1 clinical trial, the HIV vaccine-priming candidate eOD-GT8 60mer adjuvanted with AS01B had a favorable safety profile and induced VRC01-class bnAb precursors in 97% of vaccine recipients with median frequencies reaching 0.1% among immunoglobulin G B cells in blood. bnAb precursors shared properties with bnAbs and gained somatic hypermutation and affinity with the boost. The results establish clinical proof of concept for germline-targeting vaccine priming, support development of boosting regimens to induce bnAbs, and encourage application of the germline-targeting strategy to other targets in HIV and other pathogens.
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Affiliation(s)
- David J. Leggat
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jordan R. Willis
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William J. Fulp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Allan C. deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Oleksandr Kalyuzhniy
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A. Cottrell
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lamar Ballweber-Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Abhinaya Srikanth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason R. Plyler
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Torben Schiffner
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Farhad Rahaman
- IAVI, 125 Broad Street, 9th floor, New York, NY 10004, USA
| | | | | | - Rachael E. Whaley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Aaron Seese
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Joshua Brand
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexis M. Ruppel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wesley Hoyland
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole L. Yates
- Center for Human Systems Immunology; Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Duke University, Durham, NC 27701, USA
| | - LaTonya D. Williams
- Center for Human Systems Immunology; Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Duke University, Durham, NC 27701, USA
| | - Kelli Greene
- Duke University Medical Center, Durham NC 27701, USA
| | - Hongmei Gao
- Duke University Medical Center, Durham NC 27701, USA
| | - Celia R. Mahoney
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Martin M. Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison Taylor
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David M. Brown
- The Foundation for the National Institutes of Health, North Bethesda, MD, USA
| | - David R. Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Troy Sincomb
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Tingle
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nushin Alavi
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Danny Lu
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tina-Marie Mullen
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Nadia Khati
- Department of Radiology, School of Medicine and Health Sciences, The George Washington University, Washington DC, USA
| | - Jeffrey Bethony
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington DC, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Georgia D. Tomaras
- Center for Human Systems Immunology; Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Duke University, Durham, NC 27701, USA
| | | | - David Diemert
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington DC, USA
- Department of Medicine, School of Medicine and Health Sciences, The George Washington University, Washington DC, USA
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - William R. Schief
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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25
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Knudsen ML, Agrawal P, MacCamy A, Parks KR, Gray MD, Takushi BN, Khechaduri A, Salladay KR, Coler RN, LaBranche CC, Montefiori D, Stamatatos L. Adjuvants influence the maturation of VRC01-like antibodies during immunization. iScience 2022; 25:105473. [PMID: 36405776 PMCID: PMC9667313 DOI: 10.1016/j.isci.2022.105473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/26/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Once naive B cells expressing germline VRC01-class B cell receptors become activated by germline-targeting immunogens, they enter germinal centers and undergo affinity maturation. Booster immunizations with heterologous Envs are required for the full maturation of VRC01-class antibodies. Here, we examined whether and how three adjuvants, Poly(I:C), GLA-LSQ, or Rehydragel, that activate different pathways of the innate immune system, influence the rate and type of somatic mutations accumulated by VRC01-class BCRs that become activated by the germline-targeting 426c.Mod.Core immunogen and the heterologous HxB2.WT.Core booster immunogen. We report that although the adjuvant used had no influence on the durability of plasma antibody responses after the prime, it influenced the plasma VRC01 antibody titers after the boost and the accumulation of somatic mutations on the elicited VRC01 antibodies.
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Affiliation(s)
- Maria L. Knudsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Parul Agrawal
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anna MacCamy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - K. Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Matthew D. Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Brittany N. Takushi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Arineh Khechaduri
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kelsey R. Salladay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rhea N. Coler
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - David Montefiori
- Division of Surgical Sciences, Duke University, Durham, NC 27710, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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26
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HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design. Nat Commun 2022; 13:6123. [PMID: 36253376 PMCID: PMC9576718 DOI: 10.1038/s41467-022-33860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/04/2022] [Indexed: 02/08/2023] Open
Abstract
BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we report 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures reveal critical Env contacts by BG24iGL and identify antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24iGL variants bound to Envs with CD4bs glycans present provide insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276gp120 glycan. Together, these findings reveal Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.
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27
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Barnes CO, Schoofs T, Gnanapragasam PN, Golijanin J, Huey-Tubman KE, Gruell H, Schommers P, Suh-Toma N, Lee YE, Cetrulo Lorenzi JC, Piechocka-Trocha A, Scheid JF, West AP, Walker BD, Seaman MS, Klein F, Nussenzweig MC, Bjorkman PJ. A naturally arising broad and potent CD4-binding site antibody with low somatic mutation. SCIENCE ADVANCES 2022; 8:eabp8155. [PMID: 35960796 PMCID: PMC9374330 DOI: 10.1126/sciadv.abp8155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | | | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nina Suh-Toma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Erica Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Johannes F. Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, 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
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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28
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A key F27I substitution within HCDR1 facilitates the rapid maturation of P2C-1F11-like neutralizing antibodies in a SARS-CoV-2-infected donor. Cell Rep 2022; 40:111335. [PMID: 36057256 PMCID: PMC9395280 DOI: 10.1016/j.celrep.2022.111335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
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29
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Miller NL, Raman R, Clark T, Sasisekharan R. Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies. Front Immunol 2022; 13:904609. [PMID: 35784339 PMCID: PMC9247215 DOI: 10.3389/fimmu.2022.904609] [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: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
The dynamic interplay between virus and host plays out across many interacting surfaces as virus and host evolve continually in response to one another. In particular, epitope-paratope interactions (EPIs) between viral antigen and host antibodies drive much of this evolutionary race. In this review, we describe a series of recent studies examining aspects of epitope complexity that go beyond two interacting protein surfaces as EPIs are typically understood. To structure our discussion, we present a framework for understanding epitope complexity as a spectrum along a series of axes, focusing primarily on 1) epitope biochemical complexity (e.g., epitopes involving N-glycans) and 2) antigen conformational/dynamic complexity (e.g., epitopes with differential properties depending on antigen state or fold-axis). We highlight additional epitope complexity factors including epitope tertiary/quaternary structure, which contribute to epistatic relationships between epitope residues within- or adjacent-to a given epitope, as well as epitope overlap resulting from polyclonal antibody responses, which is relevant when assessing antigenic pressure against a given epitope. Finally, we discuss how these different forms of epitope complexity can limit EPI analyses and therapeutic antibody development, as well as recent efforts to overcome these limitations.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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30
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Gray MD, Feng J, Weidle CE, Cohen KW, Ballweber-Fleming L, MacCamy AJ, Huynh CN, Trichka JJ, Montefiori D, Ferrari G, Pancera M, McElrath MJ, Stamatatos L. Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain. SCIENCE ADVANCES 2022; 8:eabm3948. [PMID: 35507661 PMCID: PMC9067929 DOI: 10.1126/sciadv.abm3948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Broadly HIV-1-neutralizing VRC01-class antibodies bind the CD4-binding site of Env and contain VH1-2*02-derived heavy chains paired with light chains expressing five-amino acid-long CDRL3s. Their unmutated germline forms do not recognize HIV-1 Env, and their lack of elicitation in human clinical trials could be due to the absence of activation of the corresponding naïve B cells by the vaccine immunogens. To address this point, we examined Env-specific B cell receptor sequences from participants in the HVTN 100 clinical trial. Of all the sequences analyzed, only one displayed homology to VRC01-class antibodies, but the corresponding antibody (FH1) recognized the C1C2 gp120 domain. For FH1 to switch epitope recognition to the CD4-binding site, alterations in the CDRH3 and CDRL3 were necessary. Only germ line-targeting Env immunogens efficiently activated VRC01 B cells, even in the presence of FH1 B cells. Our findings support the use of these immunogens to activate VRC01 B cells in humans.
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Affiliation(s)
- Matthew D. Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Junli Feng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Connor E. Weidle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lamar Ballweber-Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anna J. MacCamy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Crystal N. Huynh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Josephine J. Trichka
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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31
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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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Hanke L, Sheward DJ, Pankow A, Vidakovics LP, Karl V, Kim C, Urgard E, Smith NL, Astorga-Wells J, Ekström S, Coquet JM, McInerney GM, Murrell B. Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies. SCIENCE ADVANCES 2022; 8:eabm0220. [PMID: 35333580 PMCID: PMC8956255 DOI: 10.1126/sciadv.abm0220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Conventional approaches to isolate and characterize nanobodies are laborious. We combine phage display, multivariate enrichment, next-generation sequencing, and a streamlined screening strategy to identify numerous anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nanobodies. We characterize their potency and specificity using neutralization assays and hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most potent nanobodies bind to the receptor binding motif of the receptor binding domain (RBD), and we identify two exceptionally potent members of this category (with monomeric half-maximal inhibitory concentrations around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the Beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 μg/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L. Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juan Astorga-Wells
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Simon Ekström
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Jonathan M. Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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33
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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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Abstract
Antibody immunodominance refers to the preferential and asymmetric elicitation of antibodies against specific epitopes on a complex protein antigen. Traditional vaccination approaches for rapidly evolving pathogens have had limited success in part because of this phenomenon, as elicited antibodies preferentially target highly variable regions of antigens, and thus do not confer long lasting protection. While antibodies targeting functionally conserved epitopes have the potential to be broadly protective, they often make up a minority of the overall repertoire. Here, we discuss recent protein engineering strategies used to favorably alter patterns of immunodominance, and selectively focus antibody responses toward broadly protective epitopes in the pursuit of next-generation vaccines for rapidly evolving pathogens.
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35
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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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36
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Mahomed S, Garrett N, Baxter C, Abdool Karim Q, Abdool Karim SS. Clinical Trials of Broadly Neutralizing Monoclonal Antibodies for Human Immunodeficiency Virus Prevention: A Review. J Infect Dis 2021; 223:370-380. [PMID: 32604408 PMCID: PMC8508778 DOI: 10.1093/infdis/jiaa377] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/23/2020] [Indexed: 11/14/2022] Open
Abstract
Passive immunization with broadly neutralizing antibodies (bnAbs) is a promising approach to reduce the 1.7 million annual human immunodeficiency virus (HIV) infections globally. Early studies on bnAbs showed safety in humans, but short elimination half-lives and low potency and breadth. Since 2010, several new highly potent bnAbs have been assessed in clinical trials alone or in combination for HIV prevention. Published data indicate that these bnAbs are safe and have a half-life ranging from 15 to 71 days. Only intravenous VRC01 has advanced to an efficacy trial, with results expected in late 2020. If bnAbs are shown to be effective in preventing HIV infection, they could fast-track vaccine development as correlates of protection, and contribute as passive immunization to achieving the goal of epidemic control. The purpose of the current review is to describe the current status and provide a synopsis of the available data on bnAbs in clinical trials for HIV prevention.
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Affiliation(s)
- Sharana Mahomed
- CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Nigel Garrett
- CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.,Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Cheryl Baxter
- CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Quarraisha Abdool Karim
- CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.,Department of Epidemiology, Mailman School of Public Health, Columba University, New York, New York, USA
| | - Salim S Abdool Karim
- CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.,Department of Epidemiology, Mailman School of Public Health, Columba University, New York, New York, USA
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37
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Lee JH, Toy L, Kos JT, Safonova Y, Schief WR, Havenar-Daughton C, Watson CT, Crotty S. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells. NPJ Vaccines 2021; 6:113. [PMID: 34489473 PMCID: PMC8421370 DOI: 10.1038/s41541-021-00376-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
A successful HIV vaccine eliciting broadly neutralizing antibodies (bnAbs) must overcome the hurdle of being able to activate naive precursor B cells encoding features within their germline B cell receptors (BCR) that allow recognition of broadly neutralizing epitopes. Knowledge of whether bnAb precursor B cells are circulating at sufficient frequencies within individuals in communities heavily impacted by HIV may be important. Using a germline-targeting eOD-GT8 immunogen and high-throughput droplet-based single-cell BCR sequencing, we demonstrate that large numbers of paired BCR sequences from multiple donors can be efficiently screened to elucidate precursor frequencies of rare, naive VRC01-class B cells. Further, we analyzed IGHV1-2 allelic usage among three different cohorts; we find that IGHV1-2 alleles traditionally thought to be incompatible with VRC01-class responses are relatively common in various human populations and that germline variation within IGHV1-2 associates with gene usage frequencies in the naive BCR repertoire.
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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 (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Toy
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Justin T Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Yana Safonova
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
- Computer Science and Engineering Department, University of California San Diego, San Diego, CA, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Colin Havenar-Daughton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 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 (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA.
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38
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Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody. Proc Natl Acad Sci U S A 2021; 118:2011653118. [PMID: 33649208 DOI: 10.1073/pnas.2011653118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Vaccine-based elicitation of broadly neutralizing antibodies holds great promise for preventing HIV-1 transmission. However, the key biophysical markers of improved antibody recognition remain uncertain in the diverse landscape of potential antibody mutation pathways, and a more complete understanding of anti-HIV-1 fusion peptide (FP) antibody development will accelerate rational vaccine designs. Here we survey the mutational landscape of the vaccine-elicited anti-FP antibody, vFP16.02, to determine the genetic, structural, and functional features associated with antibody improvement or fitness. Using site-saturation mutagenesis and yeast display functional screening, we found that 1% of possible single mutations improved HIV-1 envelope trimer (Env) affinity, but generally comprised rare somatic hypermutations that may not arise frequently in vivo. We observed that many single mutations in the vFP16.02 Fab could enhance affinity >1,000-fold against soluble FP, although affinity improvements against the HIV-1 trimer were more measured and rare. The most potent variants enhanced affinity to both soluble FP and Env, had mutations concentrated in antibody framework regions, and achieved up to 37% neutralization breadth compared to 28% neutralization of the template antibody. Altered heavy- and light-chain interface angles and conformational dynamics, as well as reduced Fab thermal stability, were associated with improved HIV-1 neutralization breadth and potency. We also observed parallel sets of mutations that enhanced viral neutralization through similar structural mechanisms. These data provide a quantitative understanding of the mutational landscape for vaccine-elicited FP-directed broadly neutralizing antibody and demonstrate that numerous antigen-distal framework mutations can improve antibody function by enhancing affinity simultaneously toward HIV-1 Env and FP.
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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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40
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Membrane Env Liposomes Facilitate Immunization with Multivalent Full-Length HIV Spikes. J Virol 2021; 95:e0000521. [PMID: 33883221 DOI: 10.1128/jvi.00005-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A major goal of HIV vaccine design is to elicit broadly neutralizing antibodies (bNAbs). Such bNAbs target HIV's trimeric, membrane-embedded envelope glycoprotein spikes (mEnv). Soluble Env (sEnv) trimers have been used as vaccines, but engineering sEnvs for stability, multivalency, and desired antigenicity is problematic and deletes key neutralizing epitopes on glycoprotein 41 (gp41) while creating neoepitopes that elicit unwanted antibodies. Meanwhile, multivalent mEnv vaccines are challenging to develop due to trimer instability and low mEnv copy number amid other extraneous proteins on virus-like particles. Here, we describe a multivalent mEnv vaccine platform that does not require protein engineering or extraneous proteins. mEnv trimers were fixed, purified, and combined with naked liposomes in mild detergent. On removal of detergent, mEnv spikes were observed embedded in liposome particles (mean diameter, 133 nm) in correct orientation. These particles were recognized by HIV bNAbs and not non-NAbs and are designated mEnv liposomes (MELs). Following a sequential immunization scheme in rabbits, MELs elicited antibodies that neutralized tier 2 HIV isolates. Analysis of serum antibody specificities, including those to epitopes involving a missing conserved N-glycosylation site at position 197 near the CD4 binding site on two of the immunogens, provides clues on how NAb responses can be improved with modified immunogens. In sum, MELs are a biochemically defined platform that enables rational immunization strategies to elicit HIV bNAbs using multimerized mEnv. IMPORTANCE A vaccine that induced broadly neutralizing antibodies against HIV would likely end the AIDS pandemic. Such antibodies target membrane-embedded envelope glycoprotein spikes (mEnv) that HIV uses to enter cells. Due to HIV Env's low expression and instability, soluble stabilized Env trimers have been used as vaccine candidates, but these have an altered base that disrupts targets of HIV broadly neutralizing antibodies that bind near the membrane and are not available for all HIV isolates. Here, we describe membrane Env liposomes (MELs) that display a multivalent array of stable mEnvs on liposome particles. MELs showed the expected antibody recognition properties, including targeting parts of mEnv missing on soluble Envs. Immunization with MELs elicited antibodies that neutralized diverse HIV isolates. The MEL platform facilitates vaccine development with potentially any HIV Env at high valency, and a similar approach may be useful for eliciting antibodies to membrane-embedded targets of therapeutic interest.
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Chuang GY, Shen CH, Cheung CSF, Gorman J, Creanga A, Joyce MG, Leung K, Rawi R, Wang L, Yang ES, Yang Y, Zhang B, Zhang Y, Kanekiyo M, Zhou T, DeKosky BJ, Graham BS, Mascola JR, Kwong PD. Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses. Front Immunol 2021; 12:662909. [PMID: 34135892 PMCID: PMC8201785 DOI: 10.3389/fimmu.2021.662909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly protective vaccine strategies. Antibodies of the same class share similar recognition modes and developmental pathways, and several antibody classes have been identified that neutralize diverse group 1- and group 2-influenza A viruses and have been observed in multiple human donors. One such multidonor antibody class, the HV6-1-derived class, targets the stem region of hemagglutinin with extraordinary neutralization breadth. Here, we use an iterative process to combine informatics, biochemical, and structural analyses to delineate an improved sequence signature for HV6-1-class antibodies. Based on sequence and structure analyses of known HV6-1 class antibodies, we derived a more inclusive signature (version 1), which we used to search for matching B-cell transcripts from published next-generation sequencing datasets of influenza vaccination studies. We expressed selected antibodies, evaluated their function, and identified amino acid-level requirements from which to refine the sequence signature (version 2). The cryo-electron microscopy structure for one of the signature-identified antibodies in complex with hemagglutinin confirmed motif recognition to be similar to known HV6-1-class members, MEDI8852 and 56.a.09, despite differences in recognition-loop length. Threading indicated the refined signature to have increased accuracy, and signature-identified heavy chains, when paired with the light chain of MEDI8852, showed neutralization comparable to the most potent members of the class. Incorporating sequences of additional class members thus enables an improved sequence signature for HV6-1-class antibodies, which can identify class members with increased accuracy.
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Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry and Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Seydoux E, Wan YH, Feng J, Wall A, Aljedani S, Homad LJ, MacCamy AJ, Weidle C, Gray MD, Brumage L, Taylor JJ, Pancera M, Stamatatos L, McGuire AT. Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies. Cell Rep 2021; 35:109084. [PMID: 33951425 PMCID: PMC8127986 DOI: 10.1016/j.celrep.2021.109084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/08/2021] [Accepted: 04/13/2021] [Indexed: 10/27/2022] Open
Abstract
An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs). Broad and potent VRC01-class bNAbs have been isolated from multiple infected individuals, suggesting that they could be reproducibly elicited by vaccination. Several HIV-1 envelope-derived germline-targeting immunogens have been designed to engage naive VRC01-class precursor B cells. However, they also present off-target epitopes that could hinder development of VRC01-class bNAbs. We characterize a panel of anti-idiotypic monoclonal antibodies (ai-mAbs) raised against inferred-germline (iGL) VRC01-class antibodies. By leveraging binding, structural, and B cell sorting data, we engineered a bispecific molecule derived from two ai-mAbs; one specific for VRC01-class heavy chains and one specific for VRC01-class light chains. The bispecific molecule preferentially activates iGL-VRC01 B cells in vitro and induces specific antibody responses in a murine adoptive transfer model with a diverse polyclonal B cell repertoire. This molecule represents an alternative non-envelope-derived germline-targeting immunogen that can selectively activate VRC01-class precursors in vivo.
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Affiliation(s)
- Emilie Seydoux
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Junli Feng
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Abigail Wall
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Safia Aljedani
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Connor Weidle
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Matthew D Gray
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Lauren Brumage
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Justin J Taylor
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA; University of Washington, Department of Immunology, Seattle, WA 98109, USA
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA.
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA.
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43
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Lin YR, Parks KR, Weidle C, Naidu AS, Khechaduri A, Riker AO, Takushi B, Chun JH, Borst AJ, Veesler D, Stuart A, Agrawal P, Gray M, Pancera M, Huang PS, Stamatatos L. HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors. Immunity 2021; 53:840-851.e6. [PMID: 33053332 DOI: 10.1016/j.immuni.2020.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/12/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023]
Abstract
Activating precursor B cell receptors of HIV-1 broadly neutralizing antibodies requires specifically designed immunogens. Here, we compared the abilities of three such germline-targeting immunogens against the VRC01-class receptors to activate the targeted B cells in transgenic mice expressing the germline VH of the VRC01 antibody but diverse mouse light chains. Immunogen-specific VRC01-like B cells were isolated at different time points after immunization, their VH and VL genes were sequenced, and the corresponding antibodies characterized. VRC01 B cell sub-populations with distinct cross-reactivity properties were activated by each immunogen, and these differences correlated with distinct biophysical and biochemical features of the germline-targeting immunogens. Our study indicates that the design of effective immunogens to activate B cell receptors leading to protective HIV-1 antibodies will require a better understanding of how the biophysical properties of the epitope and its surrounding surface on the germline-targeting immunogen influence its interaction with the available receptor variants in vivo.
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Affiliation(s)
- Yu-Ru Lin
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - K Rachael Parks
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; University of Washington, Department of Global Health, Seattle, WA, USA
| | - Connor Weidle
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Anika S Naidu
- Stanford University, Department of Bioengineering, Stanford, CA, USA
| | - Arineh Khechaduri
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Andrew O Riker
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Brittany Takushi
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Jung-Ho Chun
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Andrew J Borst
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - David Veesler
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Andrew Stuart
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Parul Agrawal
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Matthew Gray
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA.
| | - Po-Ssu Huang
- Stanford University, Department of Bioengineering, Stanford, CA, USA.
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; University of Washington, Department of Global Health, Seattle, WA, USA.
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44
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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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45
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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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46
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Abstract
HIV is a virus that remains a major health concern and results in an infection that has no cure even after over 30 years since its discovery. As such, HIV vaccine discovery continues to be an area of intensive research. In this review, we summarize the most recent HIV vaccine efficacy trials, clinical trials initiated within the last 3 years, and discuss prominent improvements that have been made in prophylactic HIV vaccine designs.
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Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA.
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47
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Chakraborty S, Berndsen ZT, Hengartner NW, Korber BT, Ward AB, Gnanakaran S. Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail. iScience 2020; 23:101836. [PMID: 33319171 PMCID: PMC7724196 DOI: 10.1016/j.isci.2020.101836] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/22/2020] [Accepted: 11/17/2020] [Indexed: 01/09/2023] Open
Abstract
Dense surface glycosylation on the HIV-1 envelope (Env) protein acts as a shield from the adaptive immune system. However, the molecular complexity and flexibility of glycans make experimental studies a challenge. Here we have integrated high-throughput atomistic modeling of fully glycosylated HIV-1 Env with graph theory to capture immunologically important features of the shield topology. This is the first complete all-atom model of HIV-1 Env SOSIP glycan shield that includes both oligomannose and complex glycans, providing physiologically relevant insights of the glycan shield. This integrated approach including quantitative comparison with cryo-electron microscopy data provides hitherto unexplored details of the native shield architecture and its difference from the high-mannose glycoform. We have also derived a measure to quantify the shielding effect over the antigenic protein surface that defines regions of relative vulnerability and resilience of the shield and can be harnessed for rational immunogen design.
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Affiliation(s)
- Srirupa Chakraborty
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Center for Non-Linear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Zachary T. Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicolas W. Hengartner
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette T. Korber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - S. Gnanakaran
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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48
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Wang X, Ray R, Kratochvil S, Melzi E, Lin YC, Giguere S, Xu L, Warner J, Cheon D, Liguori A, Groschel B, Phelps N, Adachi Y, Tingle R, Wu L, Crotty S, Kirsch KH, Nair U, Schief WR, Batista FD. Multiplexed CRISPR/CAS9-mediated engineering of pre-clinical mouse models bearing native human B cell receptors. EMBO J 2020; 40:e105926. [PMID: 33258500 PMCID: PMC7809789 DOI: 10.15252/embj.2020105926] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022] Open
Abstract
B‐cell receptor (BCR) knock‐in (KI) mouse models play an important role in vaccine development and fundamental immunological studies. However, the time required to generate them poses a bottleneck. Here we report a one‐step CRISPR/Cas9 KI methodology to combine the insertion of human germline immunoglobulin heavy and light chains at their endogenous loci in mice. We validate this technology with the rapid generation of three BCR KI lines expressing native human precursors, instead of computationally inferred germline sequences, to HIV broadly neutralizing antibodies. We demonstrate that B cells from these mice are fully functional: upon transfer to congenic, wild type mice at controlled frequencies, such B cells can be primed by eOD‐GT8 60mer, a germline‐targeting immunogen currently in clinical trials, recruited to germinal centers, secrete class‐switched antibodies, undergo somatic hypermutation, and differentiate into memory B cells. KI mice expressing functional human BCRs promise to accelerate the development of vaccines for HIV and other infectious diseases.
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Affiliation(s)
- Xuesong Wang
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Rashmi Ray
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Sven Kratochvil
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Eleonora Melzi
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Ying-Cing Lin
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Sophie Giguere
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Liling Xu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - John Warner
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Diane Cheon
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Lin Wu
- Genome Modification Facility, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Shane Crotty
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.,Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Usha Nair
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - William R Schief
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.,Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Facundo D Batista
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Immunology, Harvard Medical School, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
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van Regenmortel MHV. What does it mean to develop an HIV vaccine by rational design? Arch Virol 2020; 166:27-33. [PMID: 33251565 DOI: 10.1007/s00705-020-04884-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/03/2020] [Indexed: 12/29/2022]
Abstract
This review argues that the three popular concepts of design, rationality and reductionism, which guided vaccine research for many years, actually contributed to the inability of vaccinologists to develop an effective HIV vaccine. The strong goal-directed intentionality inherent in the concept of design together with excessive confidence in the power of rational thinking convinced investigators that the accumulated structural knowledge on HIV epitopes, derived from crystallographic studies of complexes of neutralizing antibodies bound to HIV Env epitopes, would allow them to rationally design complementary immunogens capable of inducing anti-HIV protective antibodies. This strategy failed because it was not appreciated that the structures observed in epitope-paratope crystallographic complexes result from mutually induced fit between the two partners and do not represent structures present in the free disordered molecules before they had interacted. In addition, reductionist thinking led investigators to accept that biology could be reduced to chemistry, and this made them neglect the fundamental difference between chemical antigenicity and biological immunogenicity. As a result, they did not investigate which inherent constituents of immune systems controlled the induction of protective antibodies and focused instead only on the steric complementarity that exists between bound epitopes and paratopes.
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Abstract
The vaccine field is pursuing diverse approaches to translate the molecular insights from analyses of effective antibodies and their targeted epitopes into immunogens capable of eliciting protective immune responses. Here we review current antibody-guided strategies including conformation-based, epitope-based, and lineage-based vaccine approaches, which are yielding promising vaccine candidates now being evaluated in clinical trials. We summarize directions being employed by the field, including the use of sequencing technologies to monitor and track developing immune responses for understanding and improving antibody-based immunity. We review opportunities and challenges to transform powerful new discoveries into safe and effective vaccines, which are encapsulated by vaccine efforts against a variety of pathogens including HIV-1, influenza A virus, malaria parasites, respiratory syncytial virus, and SARS-CoV-2. Overall, this review summarizes the extensive progress that has been made to realize antibody-guided structure-based vaccines, the considerable challenges faced, and the opportunities afforded by recently developed molecular approaches to vaccine development.
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