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Xu J, Zhou T, McKee K, Zhang B, Liu C, Nazzari AF, Pegu A, Shen CH, Becker JE, Bender MF, Chan P, Changela A, Chaudhary R, Chen X, Einav T, Kwon YD, Lin BC, Louder MK, Merriam JS, Morano NC, O'Dell S, Olia AS, Rawi R, Roark RS, Stephens T, Teng IT, Tourtellott-Fogt E, Wang S, Yang ES, Shapiro L, Tsybovsky Y, Doria-Rose NA, Casellas R, Kwong PD. Ultrapotent Broadly Neutralizing Human-llama Bispecific Antibodies against HIV-1. Adv Sci (Weinh) 2024:e2309268. [PMID: 38704686 DOI: 10.1002/advs.202309268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/22/2024] [Indexed: 05/07/2024]
Abstract
Broadly neutralizing antibodies are proposed as therapeutic and prophylactic agents against HIV-1, but their potency and breadth are less than optimal. This study describes the immunization of a llama with the prefusion-stabilized HIV-1 envelope (Env) trimer, BG505 DS-SOSIP, and the identification and improvement of potent neutralizing nanobodies recognizing the CD4-binding site (CD4bs) of vulnerability. Two of the vaccine-elicited CD4bs-targeting nanobodies, G36 and R27, when engineered into a triple tandem format with llama IgG2a-hinge region and human IgG1-constant region (G36×3-IgG2a and R27×3-IgG2a), neutralized 96% of a multiclade 208-strain panel at geometric mean IC80s of 0.314 and 0.033 µg mL-1, respectively. Cryo-EM structures of these nanobodies in complex with Env trimer revealed the two nanobodies to neutralize HIV-1 by mimicking the recognition of the CD4 receptor. To enhance their neutralizing potency and breadth, nanobodies are linked to the light chain of the V2-apex-targeting broadly neutralizing antibody, CAP256V2LS. The resultant human-llama bispecific antibody CAP256L-R27×3LS exhibited ultrapotent neutralization and breadth exceeding other published HIV-1 broadly neutralizing antibodies, with pharmacokinetics determined in FcRn-Fc mice similar to the parent CAP256V2LS. Vaccine-elicited llama nanobodies, when combined with V2-apex broadly neutralizing antibodies, may therefore be able to fulfill anti-HIV-1 therapeutic and prophylactic clinical goals.
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Affiliation(s)
- Jianliang Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Laboratory of Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexandra F Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amarendra Pegu
- 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
| | - Jordan E Becker
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Payton Chan
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Anita Changela
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ridhi Chaudhary
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tal Einav
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jonah S Merriam
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicholas C Morano
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Sijy O'Dell
- 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
| | - Ryan S Roark
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emily Tourtellott-Fogt
- 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
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rafael Casellas
- Laboratory of Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
- Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
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2
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Kaiser JA, Nelson CE, Liu X, Park HS, Matsuoka Y, Luongo C, Santos C, Ahlers LRH, Herbert R, Moore IN, Wilder-Kofie T, Moore R, Walker A, Yang L, Munir S, Teng IT, Kwong PD, Dowdell K, Nguyen H, Kim J, Cohen JI, Johnson RF, Garza NL, Via LE, Barber DL, Buchholz UJ, Le Nouën C. Mucosal prime-boost immunization with live murine pneumonia virus-vectored SARS-CoV-2 vaccine is protective in macaques. Nat Commun 2024; 15:3553. [PMID: 38670948 PMCID: PMC11053155 DOI: 10.1038/s41467-024-47784-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Immunization via the respiratory route is predicted to increase the effectiveness of a SARS-CoV-2 vaccine. Here, we evaluate the immunogenicity and protective efficacy of one or two doses of a live-attenuated murine pneumonia virus vector expressing SARS-CoV-2 prefusion-stabilized spike protein (MPV/S-2P), delivered intranasally/intratracheally to male rhesus macaques. A single dose of MPV/S-2P is highly immunogenic, and a second dose increases the magnitude and breadth of the mucosal and systemic anti-S antibody responses and increases levels of dimeric anti-S IgA in the airways. MPV/S-2P also induces S-specific CD4+ and CD8+ T-cells in the airways that differentiate into large populations of tissue-resident memory cells within a month after the boost. One dose induces substantial protection against SARS-CoV-2 challenge, and two doses of MPV/S-2P are fully protective against SARS-CoV-2 challenge virus replication in the airways. A prime/boost immunization with a mucosally-administered live-attenuated MPV vector could thus be highly effective in preventing SARS-CoV-2 infection and replication.
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Affiliation(s)
- Jaclyn A Kaiser
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christine E Nelson
- T-Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xueqiao Liu
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hong-Su Park
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yumiko Matsuoka
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cindy Luongo
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Celia Santos
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura R H Ahlers
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard Herbert
- Experimental Primate Virology Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Poolesville, MD, USA
| | - Ian N Moore
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Temeri Wilder-Kofie
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Division of Assurances, Office of Laboratory Animal Welfare, National Institutes of Health, Bethesda, MD, USA
| | - Rashida Moore
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Emory National Primate Research Center, Environmental Health and Safety Office, Emory University, Atlanta, GA, USA
| | - April Walker
- Tuberculosis Imaging Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lijuan Yang
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shirin Munir
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kennichi Dowdell
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanh Nguyen
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - JungHyun Kim
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey I Cohen
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reed F Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole L Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura E Via
- Tuberculosis Imaging Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel L Barber
- T-Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril Le Nouën
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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3
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Awan SF, Pegu A, Strom L, Carter CA, Hendel CS, Holman LA, Costner PJ, Trofymenko O, Dyer R, Gordon IJ, Rothwell RSS, Hickman SP, Conan-Cibotti M, Doria-Rose NA, Lin BC, O'Connell S, Narpala SR, Almasri CG, Liu C, Ko S, Kwon YD, Namboodiri AM, Pandey JP, Arnold FJ, Carlton K, Gall JG, Kwong PD, Capparelli EV, Bailer RT, McDermott AB, Chen GL, Koup RA, Mascola JR, Coates EE, Ledgerwood JE, Gaudinski MR. Phase 1 trial evaluating safety and pharmacokinetics of HIV-1 broadly neutralizing mAbs 10E8VLS and VRC07-523LS. JCI Insight 2024; 9:e175375. [PMID: 38587079 DOI: 10.1172/jci.insight.175375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDBroadly neutralizing monoclonal antibodies (bNAbs) represent a promising strategy for HIV-1 immunoprophylaxis and treatment. 10E8VLS and VRC07-523LS are bNAbs that target the highly conserved membrane-proximal external region (MPER) and the CD4-binding site of the HIV-1 viral envelope glycoprotein, respectively.METHODSIn this phase 1, open-label trial, we evaluated the safety and pharmacokinetics of 5 mg/kg 10E8VLS administered alone, or concurrently with 5 mg/kg VRC07-523LS, via s.c. injection to healthy non-HIV-infected individuals.RESULTSEight participants received either 10E8VLS alone (n = 6) or 10E8VLS and VRC07-523LS in combination (n = 2). Five (n = 5 of 8, 62.5%) participants who received 10E8VLS experienced moderate local reactogenicity, and 1 participant (n = 1/8, 12.5%) experienced severe local reactogenicity. Further trial enrollment was stopped, and no participant received repeat dosing. All local reactogenicity resolved without sequelae. 10E8VLS retained its neutralizing capacity, and no functional anti-drug antibodies were detected; however, a serum t1/2 of 8.1 days was shorter than expected. Therefore, the trial was voluntarily stopped per sponsor decision (Vaccine Research Center, National Institute of Allergy and Infectious Diseases [NIAID], NIH). Mechanistic studies performed to investigate the underlying reason for the reactogenicity suggest that multiple mechanisms may have contributed, including antibody aggregation and upregulation of local inflammatory markers.CONCLUSION10E8VLS resulted in unexpected reactogenicity and a shorter t1/2 in comparison with previously tested bNAbs. These studies may facilitate identification of nonreactogenic second-generation MPER-targeting bNAbs, which could be an effective strategy for HIV-1 immunoprophylaxis and treatment.TRIAL REGISTRATIONClinicaltrials.gov, accession no. NCT03565315.FUNDINGDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH.
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Affiliation(s)
- Seemal F Awan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Larisa Strom
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cristina A Carter
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cynthia S Hendel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - LaSonji A Holman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Pamela J Costner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Olga Trofymenko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Renunda Dyer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ingelise J Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ro Shauna S Rothwell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Somia P Hickman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Michelle Conan-Cibotti
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sandeep R Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cassandra G Almasri
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sungyoul Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aryan M Namboodiri
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Janardan P Pandey
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Frank J Arnold
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin Carlton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason G Gall
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Edmund V Capparelli
- School of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Emily E Coates
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Julie E Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Martin R Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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4
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Ao Y, Grover JR, Gifford L, Han Y, Zhong G, Katte R, Li W, Bhattacharjee R, Zhang B, Sauve S, Qin W, Ghimire D, Haque MA, Arthos J, Moradi M, Mothes W, Lemke EA, Kwong PD, Melikyan GB, Lu M. Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging. Cell Chem Biol 2024; 31:487-501.e7. [PMID: 38232732 PMCID: PMC10960674 DOI: 10.1016/j.chembiol.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/13/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
Structural dynamics of human immunodeficiency virus 1 (HIV-1) envelope (Env) glycoprotein mediate cell entry and facilitate immune evasion. Single-molecule FRET using peptides for Env labeling revealed structural dynamics of Env, but peptide use risks potential effects on structural integrity/dynamics. While incorporating noncanonical amino acids (ncAAs) into Env by amber stop-codon suppression, followed by click chemistry, offers a minimally invasive approach, this has proved to be technically challenging for HIV-1. Here, we develope an intact amber-free HIV-1 system that overcomes hurdles of preexisting viral amber codons. We achieved dual-ncAA incorporation into Env on amber-free virions, enabling single-molecule Förster resonance energy transfer (smFRET) studies of click-labeled Env that validated the previous peptide-based labeling approaches by confirming the intrinsic propensity of Env to dynamically sample multiple conformational states. Amber-free click-labeled Env also enabled real-time tracking of single virion internalization and trafficking in cells. Our system thus permits in-virus bioorthogonal labeling of proteins, compatible with studies of virus entry, trafficking, and egress from cells.
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Affiliation(s)
- Yuanyun Ao
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Levi Gifford
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yang Han
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Guohua Zhong
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Revansiddha Katte
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Rajanya Bhattacharjee
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; International PhD Program of the Institute of Molecular Biology, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Wenyi Qin
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Dibya Ghimire
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Md Anzarul Haque
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory B Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA.
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5
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Lederhofer J, Tsybovsky Y, Nguyen L, Raab JE, Creanga A, Stephens T, Gillespie RA, Syeda HZ, Fisher BE, Skertic M, Yap C, Schaub AJ, Rawi R, Kwong PD, Graham BS, McDermott AB, Andrews SF, King NP, Kanekiyo M. Protective human monoclonal antibodies target conserved sites of vulnerability on the underside of influenza virus neuraminidase. Immunity 2024; 57:574-586.e7. [PMID: 38430907 PMCID: PMC10962683 DOI: 10.1016/j.immuni.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 12/02/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Continuously evolving influenza viruses cause seasonal epidemics and pose global pandemic threats. Although viral neuraminidase (NA) is an effective drug and vaccine target, our understanding of the NA antigenic landscape still remains incomplete. Here, we describe NA-specific human antibodies that target the underside of the NA globular head domain, inhibit viral propagation of a wide range of human H3N2, swine-origin variant H3N2, and H2N2 viruses, and confer both pre- and post-exposure protection against lethal H3N2 infection in mice. Cryo-EM structures of two such antibodies in complex with NA reveal non-overlapping epitopes covering the underside of the NA head. These sites are highly conserved among N2 NAs yet inaccessible unless the NA head tilts or dissociates. Our findings help guide the development of effective countermeasures against ever-changing influenza viruses by identifying hidden conserved sites of vulnerability on the NA underside.
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Affiliation(s)
- Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Lam Nguyen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Z Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian E Fisher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle Skertic
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Schaub
- 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
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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6
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Rimkute I, Chaimongkol N, Woods KD, Nagata BM, Darko S, Gudbole S, Henry AR, Sosnovtsev SV, Olia AS, Verardi R, Bok K, Todd JP, Woodward R, Kwong PD, Douek DC, Alves DA, Green KY, Roederer M. Publisher Correction: A non-human primate model for human norovirus infection. Nat Microbiol 2024; 9:877. [PMID: 38360987 DOI: 10.1038/s41564-024-01636-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Affiliation(s)
- Inga Rimkute
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Natthawan Chaimongkol
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kamron D Woods
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Bianca M Nagata
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, USA
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sucheta Gudbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stanislav V Sosnovtsev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Karin Bok
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ruth Woodward
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Derron A Alves
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, USA
| | - Kim Y Green
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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7
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Rimkute I, Chaimongkol N, Woods KD, Nagata BM, Darko S, Gudbole S, Henry AR, Sosnovtsev SV, Olia AS, Verardi R, Bok K, Todd JP, Woodward R, Kwong PD, Douek DC, Alves DA, Green KY, Roederer M. A non-human primate model for human norovirus infection. Nat Microbiol 2024; 9:776-786. [PMID: 38321182 DOI: 10.1038/s41564-023-01585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/12/2023] [Indexed: 02/08/2024]
Abstract
Norovirus infection can cause gastrointestinal disease in humans. Development of therapies and vaccines against norovirus have been limited by the lack of a suitable and reliable animal model. Here we established rhesus macaques as an animal model for human norovirus infection. We show that rhesus macaques are susceptible to oral infection with human noroviruses from two different genogroups. Variation in duration of virus shedding (days to weeks) between animals, evolution of the virus over the time of infection, induction of virus-specific adaptive immune responses, susceptibility to reinfection and preferential replication of norovirus in the jejunum of rhesus macaques was similar to infection reported in humans. We found minor pathological signs and changes in epithelial cell surface glycosylation patterns in the small intestine during infection. Detection of viral protein and RNA in intestinal biopsies confirmed the presence of the virus in chromogranin A-expressing epithelial cells, as it does in humans. Thus, rhesus macaques are a promising non-human primate model to evaluate vaccines and therapeutics against norovirus disease.
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Affiliation(s)
- Inga Rimkute
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Natthawan Chaimongkol
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kamron D Woods
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Bianca M Nagata
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, USA
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sucheta Gudbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stanislav V Sosnovtsev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Karin Bok
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ruth Woodward
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Derron A Alves
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, USA
| | - Kim Y Green
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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8
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Duan H, Corrigan AR, Cheng C, Biju A, Gonelli CA, Olia AS, Teng IT, Xu K, O’Dell S, Narpala S, Castro M, Serebryannyy L, Wang J, Parchment DK, Sarfo EK, van Schooten J, Todd JP, Wang S, Harris DR, Geng H, Jafari AJ, Woodward RA, Doria-Rose NA, Foulds KE, McDermott AB, van Gils MJ, Koup RA, Pierson TC, Kwong PD, Mascola JR. Long trimer-immunization interval and appropriate adjuvant reduce immune responses to the soluble HIV-1-envelope trimer base. iScience 2024; 27:108877. [PMID: 38318357 PMCID: PMC10839646 DOI: 10.1016/j.isci.2024.108877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Soluble 'SOSIP'-stabilized HIV-1 envelope glycoprotein (Env) trimers elicit dominant antibody responses targeting their glycan-free base regions, potentially diminishing neutralizing responses. Previously, using a nonhuman primate model, we demonstrated that priming with fusion peptide (FP)-carrier conjugate immunogens followed by boosting with Env trimers reduced the anti-base response. Further, we demonstrated that longer immunization intervals further reduced anti-base responses and increased neutralization breadth. Here, we demonstrate that long trimer-boosting intervals, but not long FP immunization intervals, reduce the anti-base response. Additionally, we identify that FP priming before trimer immunization enhances antibody avidity to the Env trimer. We also establish that adjuvants Matrix M and Adjuplex further reduce anti-base responses and increase neutralizing titers. FP priming, long trimer-immunization interval, and an appropriate adjuvant can thus reduce anti-base antibody responses and improve Env-directed vaccine outcomes.
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Affiliation(s)
- Hongying Duan
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela R. Corrigan
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher A. Gonelli
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S. Olia
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Xu
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O’Dell
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mike Castro
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leonid Serebryannyy
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Wang
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danealle K. Parchment
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward K. Sarfo
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jelle van Schooten
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam 1105AZ, the Netherlands
| | - John-Paul Todd
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui Geng
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander J. Jafari
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - VRC Production Program
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruth A. Woodward
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E. Foulds
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam 1105AZ, the Netherlands
| | - Richard A. Koup
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Theodore C. Pierson
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Jain S, Kumar S, Lai L, Linderman S, Malik AA, Ellis ML, Godbole S, Solis D, Sahoo MK, Bechnak K, Paredes I, Tanios R, Kazzi B, Dib SM, Litvack MB, Wimalasena ST, Ciric C, Rostad C, West R, Teng IT, Wang D, Edupuganti S, Kwong PD, Rouphael N, Pinsky BA, Douek DC, Wrammert J, Moreno A, Suthar MS. XBB.1.5 monovalent booster improves antibody binding and neutralization against emerging SARS-CoV-2 Omicron variants. bioRxiv 2024:2024.02.03.578771. [PMID: 38370837 PMCID: PMC10871242 DOI: 10.1101/2024.02.03.578771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The rapid emergence of divergent SARS-CoV-2 variants has led to an update of the COVID-19 booster vaccine to a monovalent version containing the XBB.1.5 spike. To determine the neutralization breadth following booster immunization, we collected blood samples from 24 individuals pre- and post-XBB.1.5 mRNA booster vaccination (∼1 month). The XBB.1.5 booster improved both neutralizing activity against the ancestral SARS-CoV-2 strain (WA1) and the circulating Omicron variants, including EG.5.1, HK.3, HV.1, XBB.1.5 and JN.1. Relative to the pre-boost titers, the XBB.1.5 monovalent booster induced greater total IgG and IgG subclass binding, particular IgG4, to the XBB.1.5 spike as compared to the WA1 spike. We evaluated antigen-specific memory B cells (MBCs) using either spike or receptor binding domain (RBD) probes and found that the monovalent booster largely increases non-RBD cross-reactive MBCs. These data suggest that the XBB.1.5 monovalent booster induces cross-reactive antibodies that neutralize XBB.1.5 and related Omicron variants.
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10
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Pegu A, Lovelace SE, DeMouth ME, Cully MD, Morris DJ, Li Y, Wang K, Schmidt SD, Choe M, Liu C, Chen X, Viox E, Rowshan A, Taft JD, Zhang B, Xu K, Duan H, Ou L, Todd JP, Kong R, Li H, Shaw GM, Doria-Rose NA, Kwong PD, Koup RA, Mascola JR. Antibodies targeting the fusion peptide on the HIV envelope provide protection to rhesus macaques against mucosal SHIV challenge. Sci Transl Med 2024; 16:eadh9039. [PMID: 38232141 DOI: 10.1126/scitranslmed.adh9039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/15/2023] [Indexed: 01/19/2024]
Abstract
The fusion peptide (FP) on the HIV-1 envelope (Env) trimer can be targeted by broadly neutralizing antibodies (bNAbs). Here, we evaluated the ability of a human FP-directed bNAb, VRC34.01, along with two vaccine-elicited anti-FP rhesus macaque mAbs, DFPH-a.15 and DF1W-a.01, to protect against simian-HIV (SHIV)BG505 challenge. VRC34.01 neutralized SHIVBG505 with a 50% inhibitory concentration (IC50) of 0.58 μg/ml, whereas DF1W-a.01 and DFPH-a.15 were 4- or 30-fold less potent, respectively. VRC34.01 was infused into four rhesus macaques at a dose of 10 mg/kg and four rhesus macaques at a dose of 2.5 mg/kg. The animals were intrarectally challenged 5 days later with SHIVBG505. In comparison with all 12 control animals that became infected, all four animals infused with VRC34.01 (10 mg/kg) and three out of four animals infused with VRC34.01 (2.5 mg/kg) remained uninfected. Because of the lower potency of DF1W-a.01 and DFPH-a.15 against SHIVBG505, we infused both Abs at a higher dose of 100 mg/kg into four rhesus macaques each, followed by SHIVBG505 challenge 5 days later. Three of four animals that received DF1W-a.01 were protected against infection, whereas all animals that received DFPH-a.15 were protected. Overall, the protective serum neutralization titers observed in these animals were similar to what has been observed for other bNAbs in similar SHIV infection models and in human clinical trials. In conclusion, FP-directed mAbs can thus provide dose-dependent in vivo protection against mucosal SHIV challenges, supporting the development of prophylactic vaccines targeting the HIV-1 Env FP.
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Affiliation(s)
- Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sarah E Lovelace
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Megan E DeMouth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Michelle D Cully
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Daniel J Morris
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keyun Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Elise Viox
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Ariana Rowshan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Justin D Taft
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Hongying Duan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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11
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Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA. Rapid Emergence and Evolution of SARS-CoV-2 Variants in Advanced HIV Infection. bioRxiv 2024:2024.01.05.574420. [PMID: 38313289 PMCID: PMC10836083 DOI: 10.1101/2024.01.05.574420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions1-4, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to ~103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/μL. In PWOH and PWH with CD4 counts ≥200 cells/μL, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pierce Radecki
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frida Belinky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Amoako
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Integrative Biology and Bioinformatics, College of Biological Sciences, University of Guelph, Ontario, Canada
| | - Vanessa Guerra Canedo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dikeledi Kekana
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Center for TB Research, Baltimore, MD 21218, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tatsiana Bylund
- 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
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Wolter
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Gorman J, Cheung CSF, Duan Z, Ou L, Wang M, Chen X, Cheng C, Biju A, Sun Y, Wang P, Yang Y, Zhang B, Boyington JC, Bylund T, Charaf S, Chen SJ, Du H, Henry AR, Liu T, Sarfo EK, Schramm CA, Shen CH, Stephens T, Teng IT, Todd JP, Tsybovsky Y, Verardi R, Wang D, Wang S, Wang Z, Zheng CY, Zhou T, Douek DC, Mascola JR, Ho DD, Ho M, Kwong PD. Cleavage-intermediate Lassa virus trimer elicits neutralizing responses, identifies neutralizing nanobodies, and reveals an apex-situated site-of-vulnerability. Nat Commun 2024; 15:285. [PMID: 38177144 PMCID: PMC10767048 DOI: 10.1038/s41467-023-44534-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024] Open
Abstract
Lassa virus (LASV) infection is expanding outside its traditionally endemic areas in West Africa, posing a pandemic biothreat. LASV-neutralizing antibodies, moreover, have proven difficult to elicit. To gain insight into LASV neutralization, here we develop a prefusion-stabilized LASV glycoprotein trimer (GPC), pan it against phage libraries comprising single-domain antibodies (nanobodies) from shark and camel, and identify one, D5, which neutralizes LASV. Cryo-EM analyses reveal D5 to recognize a cleavage-dependent site-of-vulnerability at the trimer apex. The recognized site appears specific to GPC intermediates, with protomers lacking full cleavage between GP1 and GP2 subunits. Guinea pig immunizations with the prefusion-stabilized cleavage-intermediate LASV GPC, first as trimer and then as a nanoparticle, induce neutralizing responses, targeting multiple epitopes including that of D5; we identify a neutralizing antibody (GP23) from the immunized guinea pigs. Collectively, our findings define a prefusion-stabilized GPC trimer, reveal an apex-situated site-of-vulnerability, and demonstrate elicitation of LASV-neutralizing responses by a cleavage-intermediate LASV trimer.
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Affiliation(s)
- Jason Gorman
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Zhijian Duan
- NCI Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yaping Sun
- NCI Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Yongping Yang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeffrey C Boyington
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sam Charaf
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Steven J Chen
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Haijuan Du
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Edward K Sarfo
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Danyi Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhantong Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cheng-Yan Zheng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Mitchell Ho
- NCI Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, 20892, USA.
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13
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Prabhakaran M, Matassoli F, Leggat D, Hoover A, Srikanth A, Wu W, Henry AR, Wang J, Lin BC, Teng IT, Schramm CA, Castro M, Serebryannyy L, Jean-Baptiste N, Moore C, Gajjala S, Todd JPM, McCarthy E, Narpala S, Francica J, Program VP, Corbett-Helaire KS, Douek DC, Kwong PD, Seder RA, Andrews SF, McDermott AB. Adjuvanted SARS-CoV-2 spike protein vaccination elicits long-lived plasma cells in nonhuman primates. Sci Transl Med 2024; 16:eadd5960. [PMID: 38170789 DOI: 10.1126/scitranslmed.add5960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Durable humoral immunity is mediated by long-lived plasma cells (LLPCs) that reside in the bone marrow. It remains unclear whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein vaccination is able to elicit and maintain LLPCs. Here, we describe a sensitive method to identify and isolate antigen-specific LLPCs by tethering antibodies secreted by these cells onto the cell surface. Using this method, we found that two doses of adjuvanted SARS-CoV-2 spike protein vaccination are able to induce spike protein-specific LLPC reservoirs enriched for receptor binding domain specificities in the bone marrow of nonhuman primates that are detectable for several months after vaccination. Immunoglobulin gene sequencing confirmed that several of these LLPCs were clones of memory B cells elicited 2 weeks after boost that had undergone further somatic hypermutation. Many of the antibodies secreted by these LLPCs also exhibited improved neutralization and cross-reactivity compared with earlier time points. These findings establish our method as a means to sensitively and reliably detect rare antigen-specific LLPCs and demonstrate that adjuvanted SARS-CoV-2 spike protein vaccination establishes spike protein-specific LLPC reservoirs.
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Affiliation(s)
- Madhu Prabhakaran
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Flavio Matassoli
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Leggat
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Walter Reed Army Institute of Research, Military HIV Research Program, Silver Spring, MD 20910, USA
| | - Abigayle Hoover
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abhinaya Srikanth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Weiwei Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Jennifer Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mike Castro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leonid Serebryannyy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nazaire Jean-Baptiste
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Moore
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Suprabhath Gajjala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Astrazeneca, Washington, DC 20004, USA
| | | | - Kizzmekia S Corbett-Helaire
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Daniel C Douek
- 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
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Wang Z, Zhang B, Ou L, Qiu Q, Wang L, Bylund T, Kong WP, Shi W, Tsybovsky Y, Wu L, Zhou Q, Chaudhary R, Choe M, Dickey TH, El Anbari M, Olia AS, Rawi R, Teng IT, Wang D, Wang S, Tolia NH, Zhou T, Kwong PD. Extraordinary Titer and Broad Anti-SARS-CoV-2 Neutralization Induced by Stabilized RBD Nanoparticles from Strain BA.5. Vaccines (Basel) 2023; 12:37. [PMID: 38250850 PMCID: PMC10821209 DOI: 10.3390/vaccines12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike is a primary target of neutralizing antibodies and a key component of licensed vaccines. Substantial mutations in RBD, however, enable current variants to escape immunogenicity generated by vaccination with the ancestral (WA1) strain. Here, we produce and assess self-assembling nanoparticles displaying RBDs from WA1 and BA.5 strains by using the SpyTag:SpyCatcher system for coupling. We observed both WA1- and BA.5-RBD nanoparticles to degrade substantially after a few days at 37 °C. Incorporation of nine RBD-stabilizing mutations, however, increased yield ~five-fold and stability such that more than 50% of either the WA1- or BA.5-RBD nanoparticle was retained after one week at 37 °C. Murine immunizations revealed that the stabilized RBD-nanoparticles induced ~100-fold higher autologous neutralization titers than the prefusion-stabilized (S2P) spike at a 2 μg dose. Even at a 25-fold lower dose where S2P-induced neutralization titers were below the detection limit, the stabilized BA.5-RBD nanoparticle induced homologous titers of 12,795 ID50 and heterologous titers against WA1 of 1767 ID50. Assessment against a panel of β-coronavirus variants revealed both the stabilized BA.5-RBD nanoparticle and the stabilized WA1-BA.5-(mosaic)-RBD nanoparticle to elicit much higher neutralization breadth than the stabilized WA1-RBD nanoparticle. The extraordinary titer and high neutralization breadth elicited by stabilized RBD nanoparticles from strain BA.5 make them strong candidates for next-generation COVID-19 vaccines.
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Affiliation(s)
- Zhantong Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Qi Qiu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Lingyuan Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Qiong Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Ridhi Chaudhary
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Thayne H. Dickey
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (T.H.D.)
| | - Mohammed El Anbari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Danyi Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Niraj H. Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (T.H.D.)
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
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15
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Matassoli F, Cagigi A, Shen CH, Henry AR, Johnston TS, Schramm CA, Cottrell CA, Kalyuzhniy O, Spangler A, Eller L, Robb M, Eller M, Naluyima P, Kwong PD, Douek DC, Schief WR, Andrews SF, McDermott AB. High frequency of HIV precursor-target-specific B cells in sub-Saharan populations. Cell Rep 2023; 42:113450. [PMID: 38019653 PMCID: PMC10886445 DOI: 10.1016/j.celrep.2023.113450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/11/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
HIV gp120 engineered outer domain germline-targeting version 8 (eOD-GT8) was designed specifically to engage naive B cell precursors of VRC01-class antibodies. However, the frequency and affinity of naive B cell precursors able to recognize eOD-GT8 have been evaluated only in U.S. populations. HIV infection is disproportionally concentrated in sub-Saharan Africa, so we seek to characterize naive B cells able to recognize eOD-GT8 in sub-Saharan cohorts. We demonstrate that people from sub-Saharan Africa have a higher or equivalent frequency of naive B cells able to engage eOD-GT8 compared with people from the U.S. Genetically, the higher frequency of eOD-GT8-positive cells is accompanied by a higher level of naive B cells with gene signatures characteristic of the VRC01 class, as well as other CD4bs-directed antibodies. Our study demonstrates that vaccination with eOD-GT8 in sub-Saharan Africa could be successful at expanding and establishing a pool of CD4bs-directed memory B cells from naive precursors.
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Affiliation(s)
- Flavio Matassoli
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy S Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Abby Spangler
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leigh Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Merlin Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michael Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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16
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Schramm CA, Moon D, Peyton L, Lima NS, Wake C, Boswell KL, Henry AR, Laboune F, Ambrozak D, Darko SW, Teng IT, Foulds KE, Carfi A, Edwards DK, Kwong PD, Koup RA, Seder RA, Douek DC. Interaction dynamics between innate and adaptive immune cells responding to SARS-CoV-2 vaccination in non-human primates. Nat Commun 2023; 14:7961. [PMID: 38042809 PMCID: PMC10693617 DOI: 10.1038/s41467-023-43420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023] Open
Abstract
As SARS-CoV-2 variants continue evolving, testing updated vaccines in non-human primates remains important for guiding human clinical practice. To date, such studies have focused on antibody titers and antigen-specific B and T cell frequencies. Here, we extend our understanding by integrating innate and adaptive immune responses to mRNA-1273 vaccination in rhesus macaques. We sorted innate immune cells from a pre-vaccine time point, as well as innate immune cells and antigen-specific peripheral B and T cells two weeks after each of two vaccine doses and used single-cell sequencing to assess the transcriptomes and adaptive immune receptors of each cell. We show that a subset of S-specific T cells expresses cytokines critical for activating innate responses, with a concomitant increase in CCR5-expressing intermediate monocytes and a shift of natural killer cells to a more cytotoxic phenotype. The second vaccine dose, administered 4 weeks after the first, elicits an increase in circulating germinal center-like B cells 2 weeks later, which are more clonally expanded and enriched for epitopes in the receptor binding domain. Both doses stimulate inflammatory response genes associated with elevated antibody production. Overall, we provide a comprehensive picture of bidirectional signaling between innate and adaptive components of the immune system and suggest potential mechanisms for the enhanced response to secondary exposure.
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Affiliation(s)
- Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Damee Moon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lowrey Peyton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Noemia S Lima
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christian Wake
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristin L Boswell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Farida Laboune
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel W Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kathryn E Foulds
- 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
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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17
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Banach BB, Pletnev S, Olia AS, Xu K, Zhang B, Rawi R, Bylund T, Doria-Rose NA, Nguyen TD, Fahad AS, Lee M, Lin BC, Liu T, Louder MK, Madan B, McKee K, O'Dell S, Sastry M, Schön A, Bui N, Shen CH, Wolfe JR, Chuang GY, Mascola JR, Kwong PD, DeKosky BJ. Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site. Nat Commun 2023; 14:7593. [PMID: 37989731 PMCID: PMC10663459 DOI: 10.1038/s41467-023-42098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 09/25/2023] [Indexed: 11/23/2023] Open
Abstract
The HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we evolve the FP-targeting antibody VRC34.01 in vitro to enhance FP-neutralization using site saturation mutagenesis and yeast display. Successive rounds of directed evolution by iterative selection of antibodies for binding to resistant HIV-1 strains establish a variant, VRC34.01_mm28, as a best-in-class antibody with 10-fold enhanced potency compared to the template antibody and ~80% breadth on a cross-clade 208-strain neutralization panel. Structural analyses demonstrate that the improved paratope expands the FP binding groove to accommodate diverse FP sequences of different lengths while also recognizing the HIV-1 Env backbone. These data reveal critical antibody features for enhanced neutralization breadth and potency against the FP site of vulnerability and accelerate clinical development of broad HIV-1 FP-targeting vaccines and therapeutics.
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Affiliation(s)
- Bailey B Banach
- Bioengineering Graduate Program, The University of Kansas, Lawrence, KS, 66045, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Thuy Duong Nguyen
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Myungjin Lee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Arne Schön
- Department of Biology, John Hopkins University, Baltimore, MD, 21218, USA
| | - Natalie Bui
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Jacy R Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA.
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, 66045, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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18
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Gagne M, Flynn BJ, Andrew SF, Flebbe DR, Mychalowych A, Lamb E, Davis-Gardner ME, Burnett MR, Serebryannyy LA, Lin BC, Pessaint L, Todd JPM, Ziff ZE, Maule E, Carroll R, Naisan M, Jethmalani Y, Case JB, Dmitriev IP, Kashentseva EA, Ying B, Dodson A, Kouneski K, Doria-Rose NA, O'Dell S, Godbole S, Laboune F, Henry AR, Marquez J, Teng IT, Wang L, Zhou Q, Wali B, Ellis M, Zouantchangadou S, Ry AV, Lewis MG, Andersen H, Kwong PD, Curiel DT, Foulds KE, Nason MC, Suthar MS, Roederer M, Diamond MS, Douek DC, Seder RA. Mucosal Adenoviral-vectored Vaccine Boosting Durably Prevents XBB.1.16 Infection in Nonhuman Primates. bioRxiv 2023:2023.11.06.565765. [PMID: 37986823 PMCID: PMC10659340 DOI: 10.1101/2023.11.06.565765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Waning immunity and continued virus evolution have limited the durability of protection from symptomatic infection mediated by intramuscularly (IM)-delivered mRNA vaccines against COVID-19 although protection from severe disease remains high. Mucosal vaccination has been proposed as a strategy to increase protection at the site of SARS-CoV-2 infection by enhancing airway immunity, potentially reducing rates of infection and transmission. Here, we compared protection against XBB.1.16 virus challenge 5 months following IM or mucosal boosting in non-human primates (NHP) that had previously received a two-dose mRNA-1273 primary vaccine regimen. The mucosal boost was composed of a bivalent chimpanzee adenoviral-vectored vaccine encoding for both SARS-CoV-2 WA1 and BA.5 spike proteins (ChAd-SARS-CoV-2-S) and delivered either by an intranasal mist or an inhaled aerosol. An additional group of animals was boosted by the IM route with bivalent WA1/BA.5 spike-matched mRNA (mRNA-1273.222) as a benchmark control. NHP were challenged in the upper and lower airways 18 weeks after boosting with XBB.1.16, a heterologous Omicron lineage strain. Cohorts boosted with ChAd-SARS-CoV-2-S by an aerosolized or intranasal route had low to undetectable virus replication as assessed by levels of subgenomic SARS-CoV-2 RNA in the lungs and nose, respectively. In contrast, animals that received the mRNA-1273.222 boost by the IM route showed minimal protection against virus replication in the upper airway but substantial reduction of virus RNA levels in the lower airway. Immune analysis showed that the mucosal vaccines elicited more durable antibody and T cell responses than the IM vaccine. Protection elicited by the aerosolized vaccine was associated with mucosal IgG and IgA responses, whereas protection elicited by intranasal delivery was mediated primarily by mucosal IgA. Thus, durable immunity and effective protection against a highly transmissible heterologous variant in both the upper and lower airways can be achieved by mucosal delivery of a virus-vectored vaccine. Our study provides a template for the development of mucosal vaccines that limit infection and transmission against respiratory pathogens. Graphical abstract
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19
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Jia M, Zhao H, Morano NC, Lu H, Lui YM, Du H, Becker JE, Yuen KY, Ho DD, Kwong PD, Shapiro L, To KKW, Wu X. Allosteric Neutralization by Human H7N9 Antibodies. Res Sq 2023:rs.3.rs-3429355. [PMID: 37986867 PMCID: PMC10659534 DOI: 10.21203/rs.3.rs-3429355/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The avian influenza A virus H7N9 causes severe human infections with more than 30% fatality despite the use of neuraminidase inhibitors. Currently there is no H7N9-specific prevention or treatment for humans. From a 2013 H7N9 convalescent case occurred in Hong Kong, we isolated four H7 hemagglutinin (HA)-reactive monoclonal antibodies (mAbs) by single B cell cloning, with three mAbs directed to the HA globular head domain (HA1) and one to the HA stem region (HA2). Two clonally related HA1-directed mAbs, H7.HK1 and H7.HK2, potently neutralized H7N9 and protected mice from a lethal H7N9/AH1 challenge. Cryo-EM structures revealed that H7.HK1 and H7.HK2 bind to a β14-centered surface partially overlapping with the antigenic site D of HA1 and disrupt the 220-loop that makes hydrophobic contacts with sialic acid on the adjacent protomer, thus affectively blocking viral entry. The more potent mAb H7.HK2 retained full HA1 binding and neutralization capacity to later H7N9 isolates from 2016-2017, which is consistent with structural data showing that the antigenic mutations of 2016-2017 from the 2013 H7N9 only occurred at the periphery of the mAb epitope. The HA2-directed mAb H7.HK4 lacked neutralizing activity but protected mice from the lethal H7N9/AH1 challenge when engineered to mouse IgG2a enabling Fc effector function in mice. Used in combination with H7.HK2 at a suboptimal dose, H7.HK4 augmented mouse protection. Our data demonstrated an allosteric mechanism of mAb neutralization and augmented protection against H7N9 when a HA1-directed neutralizing mAb and a HA2-directed non-neutralizing mAb were combined.
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Affiliation(s)
- Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of Rockefeller University, New York, NY 10016, USA
| | - Hanjun Zhao
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
| | - Nicholas C. Morano
- Department of Biochemistry, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of Rockefeller University, New York, NY 10016, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yin-Ming Lui
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Haijuan Du
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan E. Becker
- Department of Biochemistry, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Affiliate of Rockefeller University, New York, NY 10016, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Peter D. Kwong
- Department of Biochemistry, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Department of Biochemistry, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of Rockefeller University, New York, NY 10016, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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20
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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Ou L, Chen SJ, Teng IT, Yang L, Zhang B, Zhou T, Biju A, Cheng C, Kong WP, Morano NC, Stancofski ESD, Todd JP, Tsybovsky Y, Wang S, Zheng CY, Mascola JR, Shapiro L, Woodward RA, Buchholz UJ, Kwong PD. Structure-based design of a single-chain triple-disulfide-stabilized fusion-glycoprotein trimer that elicits high-titer neutralizing responses against human metapneumovirus. PLoS Pathog 2023; 19:e1011584. [PMID: 37738240 PMCID: PMC10516418 DOI: 10.1371/journal.ppat.1011584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/29/2023] [Indexed: 09/24/2023] Open
Abstract
The Pneumoviridae family of viruses includes human metapneumovirus (HMPV) and respiratory syncytial virus (RSV). The closely related Paramyxoviridae family includes parainfluenza viruses (PIVs). These three viral pathogens cause acute respiratory tract infections with substantial disease burden in the young, the elderly, and the immune-compromised. While promising subunit vaccines are being developed with prefusion-stabilized forms of the fusion glycoproteins (Fs) of RSV and PIVs, for which neutralizing titers elicited by the prefusion (pre-F) conformation of F are much higher than for the postfusion (post-F) conformation, with HMPV, pre-F and post-F immunogens described thus far elicit similar neutralizing responses, and it has been unclear which conformation, pre-F or post-F, would be the most effective HMPV F-vaccine immunogen. Here, we investigate the impact of further stabilizing HMPV F in the pre-F state. We replaced the furin-cleavage site with a flexible linker, creating a single chain F that yielded increased amounts of pre-F stabilized trimers, enabling the generation and assessment of F trimers stabilized by multiple disulfide bonds. Introduced prolines could increase both expression yields and antigenic recognition by the pre-F specific antibody, MPE8. The cryo-EM structure of a triple disulfide-stabilized pre-F trimer with the variable region of antibody MPE8 at 3.25-Å resolution confirmed the formation of designed disulfides and provided structural details on the MPE8 interface. Immunogenicity assessments in naïve mice showed the triple disulfide-stabilized pre-F trimer could elicit high titer neutralization, >10-fold higher than elicited by post-F. Immunogenicity assessments in pre-exposed rhesus macaques showed the triple disulfide-stabilized pre-F could recall high neutralizing titers after a single immunization, with little discrimination in the recall response between pre-F and post-F immunogens. However, the triple disulfide-stabilized pre-F adsorbed HMPV-directed responses from commercially available pooled human immunoglobulin more fully than post-F. Collectively, these results suggest single-chain triple disulfide-stabilized pre-F trimers to be promising HMPV-vaccine antigens.
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Affiliation(s)
- Li Ou
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Steven J. Chen
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lijuan Yang
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wing-Pui Kong
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicholas C. Morano
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, United States of America
| | | | - John-Paul Todd
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cheng-Yan Zheng
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, United States of America
| | - Ruth A. Woodward
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ursula J. Buchholz
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
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22
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Glögl M, Friedrich N, Cerutti G, Lemmin T, Kwon YD, Gorman J, Maliqi L, Mittl PRE, Hesselman MC, Schmidt D, Weber J, Foulkes C, Dingens AS, Bylund T, Olia AS, Verardi R, Reinberg T, Baumann NS, Rusert P, Dreier B, Shapiro L, Kwong PD, Plückthun A, Trkola A. Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat Struct Mol Biol 2023; 30:1323-1336. [PMID: 37605043 PMCID: PMC10497408 DOI: 10.1038/s41594-023-01062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023]
Abstract
The third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein trimer is indispensable for virus cell entry. Conformational masking of V3 within the trimer allows efficient neutralization via V3 only by rare, broadly neutralizing glycan-dependent antibodies targeting the closed prefusion trimer but not by abundant antibodies that access the V3 crown on open trimers after CD4 attachment. Here, we report on a distinct category of V3-specific inhibitors based on designed ankyrin repeat protein (DARPin) technology that reinstitute the CD4-bound state as a key neutralization target with up to >90% breadth. Broadly neutralizing DARPins (bnDs) bound V3 solely on open envelope and recognized a four-turn amphipathic α-helix in the carboxy-terminal half of V3 (amino acids 314-324), which we termed 'αV3C'. The bnD contact surface on αV3C was as conserved as the CD4 binding site. Molecular dynamics and escape mutation analyses underscored the functional relevance of αV3C, highlighting the potential of αV3C-based inhibitors and, more generally, of postattachment inhibition of HIV-1.
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Affiliation(s)
- Matthias Glögl
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Nikolas Friedrich
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Thomas Lemmin
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liridona Maliqi
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Maria C Hesselman
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Daniel Schmidt
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Jacqueline Weber
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Adam S Dingens
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Nicolas S Baumann
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peter Rusert
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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23
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Yang Y, Kong WP, Liu C, Ruckwardt TJ, Tsybovsky Y, Wang L, Wang S, Biner DW, Chen M, Liu T, Merriam J, Olia AS, Ou L, Qiu Q, Shi W, Stephens T, Yang ES, Zhang B, Zhang Y, Zhou Q, Rawi R, Koup RA, Mascola JR, Kwong PD. Enhancing Anti-SARS-CoV-2 Neutralizing Immunity by Genetic Delivery of Enveloped Virus-like Particles Displaying SARS-CoV-2 Spikes. Vaccines (Basel) 2023; 11:1438. [PMID: 37766115 PMCID: PMC10537688 DOI: 10.3390/vaccines11091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/19/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
New vaccine delivery technologies, such as mRNA, have played a critical role in the rapid and efficient control of SARS-CoV-2, helping to end the COVID-19 pandemic. Enveloped virus-like particles (eVLPs) are often more immunogenic than protein subunit immunogens and could be an effective vaccine platform. Here, we investigated whether the genetic delivery of eVLPs could achieve strong immune responses in mice as previously reported with the immunization of in vitro purified eVLPs. We utilized Newcastle disease virus-like particles (NDVLPs) to display SARS-CoV-2 prefusion-stabilized spikes from the WA-1 or Beta variant (S-2P or S-2Pᵦ, respectively) and evaluated neutralizing murine immune responses achieved by a single-gene-transcript DNA construct for the WA-1 or Beta variant (which we named S-2P-NDVLP-1T and S-2Pᵦ-NDVLP-1T, respectively), by multiple-gene-transcript DNA constructs for the Beta variant (S-2Pᵦ-NDVLP-3T), and by a protein subunit-DNA construct for the WA-1 or Beta variant (S-2P-TM or S-2Pᵦ-TM, respectively). The genetic delivery of S-2P-NDVLP-1T or S-2Pᵦ-NDVLP-1T yielded modest neutralizing responses after a single immunization and high neutralizing responses after a second immunization, comparable to previously reported results in mice immunized with in vitro purified S-2P-NDVLPs. Notably, genetic delivery of S-2Pᵦ-NDVLP-3T yielded significantly higher neutralizing responses in mice after a second immunization than S-2Pᵦ-NDVLP-1T or S-2Pᵦ-TM. Genetic delivery also elicited high spike-specific T-cell responses. Collectively, these results indicate that genetic delivery can provide an effective means to immunize eVLPs and that a multiple-gene transcript eVLP platform may be especially efficacious and inform the design of improved vaccines.
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Affiliation(s)
- Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Daniel W. Biner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Jonah Merriam
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Qi Qiu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Qiong Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Y.Y.)
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24
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Olia AS, Cheng C, Zhou T, Biju A, Harris DR, Changela A, Duan H, Ivleva VB, Kong WP, Ou L, Rawi R, Tsybovsky Y, Van Wazer DJ, Corrigan AR, Gonelli CA, Lee M, McKee K, Narpala S, O’Dell S, Parchment DK, Stancofski ESD, Stephens T, Tan I, Teng IT, Wang S, Wei Q, Yang Y, Yang Z, Zhang B, Novak J, Renfrow MB, Doria-Rose NA, Koup RA, McDermott AB, Gall JG, Lei QP, Mascola JR, Kwong PD. Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases. iScience 2023; 26:107403. [PMID: 37554450 PMCID: PMC10404741 DOI: 10.1016/j.isci.2023.107403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/23/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023] Open
Abstract
Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential N-linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response.
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Affiliation(s)
- Adam S. Olia
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anita Changela
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongying Duan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vera B. Ivleva
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - David J. Van Wazer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela R. Corrigan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Myungjin Lee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O’Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ivy Tan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qing Wei
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yongping Yang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhengrong Yang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Richard A. Koup
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason G. Gall
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Q. Paula Lei
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
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25
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Liu C, Wang L, Merriam JS, Shi W, Yang ES, Zhang Y, Chen M, Kong WP, Cheng C, Tsybovsky Y, Stephens T, Verardi R, Leung K, Stein C, Olia AS, Harris DR, Choe M, Zhang B, Graham BS, Kwong PD, Koup RA, Pegu A, Mascola JR. Self-assembling SARS-CoV-2 spike-HBsAg nanoparticles elicit potent and durable neutralizing antibody responses via genetic delivery. NPJ Vaccines 2023; 8:111. [PMID: 37553406 PMCID: PMC10409857 DOI: 10.1038/s41541-023-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/12/2023] [Indexed: 08/10/2023] Open
Abstract
While several COVID-19 vaccines have been in use, more effective and durable vaccines are needed to combat the ongoing COVID-19 pandemic. Here, we report highly immunogenic self-assembling SARS-CoV-2 spike-HBsAg nanoparticles displaying a six-proline-stabilized WA1 (wild type, WT) spike S6P on a HBsAg core. These S6P-HBsAgs bound diverse domain-specific SARS-CoV-2 monoclonal antibodies. In mice with and without a HBV pre-vaccination, DNA immunization with S6P-HBsAgs elicited significantly more potent and durable neutralizing antibody (nAb) responses against diverse SARS-CoV-2 strains than that of soluble S2P or S6P, or full-length S2P with its coding sequence matching mRNA-1273. The nAb responses elicited by S6P-HBsAgs persisted substantially longer than by soluble S2P or S6P and appeared to be enhanced by HBsAg pre-exposure. These data show that genetic delivery of SARS-CoV-2 S6P-HBsAg nanoparticles can elicit greater and more durable nAb responses than non-nanoparticle forms of stabilized spike. Our findings highlight the potential of S6P-HBsAgs as next generation genetic vaccine candidates against SARS-CoV-2.
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Affiliation(s)
- Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Jonah S Merriam
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Cody Stein
- 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
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | - Barney S Graham
- 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
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA.
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26
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Wang S, Matassoli F, Zhang B, Liu T, Shen CH, Bylund T, Johnston T, Henry AR, Teng IT, Tripathi P, Becker JE, Changela A, Chaudhary R, Cheng C, Gaudinski M, Gorman J, Harris DR, Lee M, Morano NC, Novik L, O'Dell S, Olia AS, Parchment DK, Rawi R, Roberts-Torres J, Stephens T, Tsybovsky Y, Wang D, Van Wazer DJ, Zhou T, Doria-Rose NA, Koup RA, Shapiro L, Douek DC, McDermott AB, Kwong PD. HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide. Cell Rep 2023; 42:112755. [PMID: 37436899 PMCID: PMC10491024 DOI: 10.1016/j.celrep.2023.112755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023] Open
Abstract
Elicitation of antibodies that neutralize the tier-2 neutralization-resistant isolates that typify HIV-1 transmission has been a long-sought goal. Success with prefusion-stabilized envelope trimers eliciting autologous neutralizing antibodies has been reported in multiple vaccine-test species, though not in humans. To investigate elicitation of HIV-1 neutralizing antibodies in humans, here, we analyze B cells from a phase I clinical trial of the "DS-SOSIP"-stabilized envelope trimer from strain BG505, identifying two antibodies, N751-2C06.01 and N751-2C09.01 (named for donor-lineage.clone), that neutralize the autologous tier-2 strain, BG505. Though derived from distinct lineages, these antibodies form a reproducible antibody class that targets the HIV-1 fusion peptide. Both antibodies are highly strain specific, which we attribute to their partial recognition of a BG505-specific glycan hole and to their binding requirements for a few BG505-specific residues. Prefusion-stabilized envelope trimers can thus elicit autologous tier-2 neutralizing antibodies in humans, with initially identified neutralizing antibodies recognizing the fusion-peptide site of vulnerability.
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Affiliation(s)
- Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Flavio Matassoli
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy Johnston
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prabhanshu Tripathi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan E Becker
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Anita Changela
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ridhi Chaudhary
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin Gaudinski
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myungjin Lee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas C Morano
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Laura Novik
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Danyi Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Van Wazer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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27
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Holt GT, Gorman J, Wang S, Lowegard AU, Zhang B, Liu T, Lin BC, Louder MK, Frenkel MS, McKee K, O'Dell S, Rawi R, Shen CH, Doria-Rose NA, Kwong PD, Donald BR. Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design. Cell Rep 2023; 42:112711. [PMID: 37436900 PMCID: PMC10528384 DOI: 10.1016/j.celrep.2023.112711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Broadly neutralizing antibodies (bNAbs) against HIV can reduce viral transmission in humans, but an effective therapeutic will require unusually high breadth and potency of neutralization. We employ the OSPREY computational protein design software to engineer variants of two apex-directed bNAbs, PGT145 and PG9RSH, resulting in increases in potency of over 100-fold against some viruses. The top designed variants improve neutralization breadth from 39% to 54% at clinically relevant concentrations (IC80 < 1 μg/mL) and improve median potency (IC80) by up to 4-fold over a cross-clade panel of 208 strains. To investigate the mechanisms of improvement, we determine cryoelectron microscopy structures of each variant in complex with the HIV envelope trimer. Surprisingly, we find the largest increases in breadth to be a result of optimizing side-chain interactions with highly variable epitope residues. These results provide insight into mechanisms of neutralization breadth and inform strategies for antibody design and improvement.
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Affiliation(s)
- Graham T Holt
- Department of Computer Science, Duke University, Durham, NC, USA; Program in Computational Biology & Bioinformatics, Duke University, Durham, NC, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Siyu Wang
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC, USA
| | - Anna U Lowegard
- Department of Computer Science, Duke University, Durham, NC, USA; Program in Computational Biology & Bioinformatics, Duke University, Durham, NC, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Bruce R Donald
- Department of Computer Science, Duke University, Durham, NC, USA; Department of Biochemistry, Duke University, Durham, NC, USA; Department of Mathematics, Duke University, Durham, NC, USA; Department of Chemistry, Duke University, Durham, NC, USA.
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28
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Gagne M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ, McCormick L, Van Ry A, McCarthy E, Todd JPM, Bao S, Teng IT, Marciano S, Rudich Y, Li C, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H, Zahradník J, Nason MC, Foulds KE, Kwong PD, Roederer M, Schreiber G, Seder RA, Douek DC. RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways. bioRxiv 2023:2023.06.09.544432. [PMID: 37503026 PMCID: PMC10370179 DOI: 10.1101/2023.06.09.544432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
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29
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Percze K, Tolnai ZJ, Eleveld M, Ou L, Du H, Olia AS, Kwong PD, de Jonge MI, Mészáros T. Tryptophan-like side chain holding aptamers inhibit respiratory syncytial virus infection of lung epithelial cells. Sci Rep 2023; 13:9403. [PMID: 37296186 PMCID: PMC10251311 DOI: 10.1038/s41598-023-36428-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of serious and even fatal acute lower respiratory tract infections in infants and in the elderly. Potent RSV neutralization has been achieved by antibodies that selectively bind the prefusion form of the viral fusion (F) protein. We hypothesised that similar potent neutralization could be achieved using F protein targeting aptamers. Aptamers have yet to reach their translational potential for therapeutics or diagnostics due to their short half-life and limited range of target-aptamer interactions; these shortcomings can, however, be ameliorated by application of amino acid-like side chain holding nucleotides. In this study, a stabilized version of the prefusion RSV F protein was targeted by aptamer selection using an oligonucleotide library holding a tryptophan-like side chain. This process resulted in aptamers that bound the F protein with high affinity and differentiated between its pre- and postfusion conformation. Identified aptamers inhibited viral infection of lung epithelial cells. Moreover, introduction of modified nucleotides extended aptamer half-lives. Our results suggest that targeting aptamers to the surface of viruses could yield effective drug candidates, which could keep pace with the continuously evolving pathogens.
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Affiliation(s)
- Krisztina Percze
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zoltán János Tolnai
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Marc Eleveld
- Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Haijuan Du
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marien I de Jonge
- Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tamás Mészáros
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.
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30
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Sutton MS, Pletnev S, Callahan V, Ko S, Tsybovsky Y, Bylund T, Casner RG, Cerutti G, Gardner CL, Guirguis V, Verardi R, Zhang B, Ambrozak D, Beddall M, Lei H, Yang ES, Liu T, Henry AR, Rawi R, Schön A, Schramm CA, Shen CH, Shi W, Stephens T, Yang Y, Florez MB, Ledgerwood JE, Burke CW, Shapiro L, Fox JM, Kwong PD, Roederer M. Vaccine elicitation and structural basis for antibody protection against alphaviruses. Cell 2023; 186:2672-2689.e25. [PMID: 37295404 PMCID: PMC10411218 DOI: 10.1016/j.cell.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/03/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses.
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Affiliation(s)
- Matthew S Sutton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria Callahan
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sungyoul Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan G Casner
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Christina L Gardner
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Veronica Guirguis
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Beddall
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong Lei
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Henry
- 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
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chaim A Schramm
- 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
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Burgos Florez
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie E Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Crystal W Burke
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Julie M Fox
- Laboratory of Viral Diseases, 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 Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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Sastry M, Changela A, Gorman J, Xu K, Chuang GY, Shen CH, Cheng C, Geng H, O'Dell S, Ou L, Rawi R, Reveiz M, Stewart-Jones GBE, Wang S, Zhang B, Zhou T, Biju A, Chambers M, Chen X, Corrigan AR, Lin BC, Louder MK, McKee K, Nazzari AF, Olia AS, Parchment DK, Sarfo EK, Stephens T, Stuckey J, Tsybovsky Y, Verardi R, Wang Y, Zheng CY, Chen Y, Doria-Rose NA, McDermott AB, Mascola JR, Kwong PD. Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization. J Virol 2023; 97:e0160422. [PMID: 37098956 PMCID: PMC10234334 DOI: 10.1128/jvi.01604-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/21/2023] [Indexed: 04/27/2023] Open
Abstract
While neutralizing antibodies that target the HIV-1 fusion peptide have been elicited in mice by vaccination, antibodies reported thus far have been from only a single antibody class that could neutralize ~30% of HIV-1 strains. To explore the ability of the murine immune system to generate cross-clade neutralizing antibodies and to investigate how higher breadth and potency might be achieved, we tested 17 prime-boost regimens that utilized diverse fusion peptide-carrier conjugates and HIV-1 envelope trimers with different fusion peptides. We observed priming in mice with fusion peptide-carrier conjugates of variable peptide length to elicit higher neutralizing responses, a result we confirmed in guinea pigs. From vaccinated mice, we isolated 21 antibodies, belonging to 4 distinct classes of fusion peptide-directed antibodies capable of cross-clade neutralization. Top antibodies from each class collectively neutralized over 50% of a 208-strain panel. Structural analyses - both X-ray and cryo-EM - revealed each antibody class to recognize a distinct conformation of fusion peptide and to have a binding pocket capable of accommodating diverse fusion peptides. Murine vaccinations can thus elicit diverse neutralizing antibodies, and altering peptide length during prime can improve the elicitation of cross-clade responses targeting the fusion peptide site of HIV-1 vulnerability. IMPORTANCE The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence. We found that variation in peptide length during prime elicits enhanced neutralizing responses in mice and guinea pigs. We identified vaccine-elicited murine monoclonal antibodies from distinct classes capable of cross-clade neutralization and of diverse fusion peptide recognition. Our findings lend insight into improved immunogens and regimens for HIV-1 vaccine development.
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Affiliation(s)
- Mallika Sastry
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Anita Changela
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason Gorman
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Kai Xu
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Hui Geng
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Li Ou
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Mateo Reveiz
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Chambers
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela R. Corrigan
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Bob C. Lin
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark K. Louder
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Krisha McKee
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Adam S. Olia
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Edward K. Sarfo
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, USA
| | - Jonathan Stuckey
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Yiran Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Cheng-Yan Zheng
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Adrian B. McDermott
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, USA
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32
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Stamos JD, Rahman MA, Gorini G, Silva de Castro I, Becerra-Flores M, Van Wazer DJ, N’Guessan KF, Clark NM, Bissa M, Gutowska A, Mason RD, Kim J, Rao M, Roederer M, Paquin-Proulx D, Evans DT, Cicala C, Arthos J, Kwong PD, Zhou T, Cardozo T, Franchini G. Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β-Sheet Conformations on Time of SIV mac251 Acquisition. J Virol 2023; 97:e0186422. [PMID: 36976017 PMCID: PMC10134845 DOI: 10.1128/jvi.01864-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vaccinated macaque that was protected from multiple simian immunodeficiency virus (SIV) challenges, both target an overlapping, conformationally dynamic epitope in SIV envelope variable region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a β-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIVmac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIVmac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation. IMPORTANCE Studies suggest that the protection against SIV/simian-human immunodeficiency virus (SHIV) acquisition afforded by the SIV/HIV V1 deletion-containing envelope immunogens, delivered by the DNA/ALVAC vaccine platform, requires multiple innate and adaptive host responses. Anti-inflammatory macrophages and tolerogenic dendritic cells (DC-10), together with CD14+ efferocytes, are consistently found to correlate with a vaccine-induced decrease in the risk of SIV/SHIV acquisition. Similarly, V2-specific antibody responses mediating ADCC, Th1 and Th2 cells expressing no or low levels of CCR5, and envelope-specific NKp44+ cells producing interleukin 17 (IL-17) also are reproducible correlates of decreased risk of virus acquisition. We focused on the function and the antiviral potential of two monoclonal antibodies (NCI05 and NCI09) isolated from vaccinated animals that differ in antiviral function in vitro and recognize V2 in a linear (NCI09) or coil/helical (NCI05) conformation. We demonstrate that NCI05, but not NCI09, delays SIVmac251 acquisition, highlighting the complexity of antibody responses to V2.
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Affiliation(s)
- James D. Stamos
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Mohammad Arif Rahman
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Giacomo Gorini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Isabela Silva de Castro
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Manuel Becerra-Flores
- New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - David J. Van Wazer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kombo F. N’Guessan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Innate Immunology Laboratory, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Natasha M. Clark
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Anna Gutowska
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Rosemarie D. Mason
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiae Kim
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Innate Immunology Laboratory, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - David T. Evans
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Timothy Cardozo
- New York University Grossman School of Medicine, NYU Langone Health, New York, New York, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, National Cancer Institute, Bethesda, Maryland, USA
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Andrews SF, Cominsky LY, Shimberg GD, Gillespie RA, Gorman J, Raab JE, Brand J, Creanga A, Gajjala SR, Narpala S, Cheung CSF, Harris DR, Zhou T, Gordon I, Holman L, Mendoza F, Houser KV, Chen GL, Mascola JR, Graham BS, Kwong PD, Widge A, Dropulic LK, Ledgerwood JE, Kanekiyo M, McDermott AB. An influenza H1 hemagglutinin stem-only immunogen elicits a broadly cross-reactive B cell response in humans. Sci Transl Med 2023; 15:eade4976. [PMID: 37075126 DOI: 10.1126/scitranslmed.ade4976] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Current yearly seasonal influenza vaccines primarily induce an antibody response directed against the immunodominant but continually diversifying hemagglutinin (HA) head region. These antibody responses provide protection against the vaccinating strain but little cross-protection against other influenza strains or subtypes. To focus the immune response on subdominant but more conserved epitopes on the HA stem that might protect against a broad range of influenza strains, we developed a stabilized H1 stem immunogen lacking the immunodominant head displayed on a ferritin nanoparticle (H1ssF). Here, we evaluated the B cell response to H1ssF in healthy adults ages 18 to 70 in a phase 1 clinical trial (NCT03814720). We observed both a strong plasmablast response and sustained elicitation of cross-reactive HA stem-specific memory B cells after vaccination with H1ssF in individuals of all ages. The B cell response was focused on two conserved epitopes on the H1 stem, with a highly restricted immunoglobulin repertoire unique to each epitope. On average, two-thirds of the B cell and serological antibody response recognized a central epitope on the H1 stem and exhibited broad neutralization across group 1 influenza virus subtypes. The remaining third recognized an epitope near the viral membrane anchor and was largely limited to H1 strains. Together, we demonstrate that an H1 HA immunogen lacking the immunodominant HA head produces a robust and broadly neutralizing HA stem-directed B cell response.
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Affiliation(s)
- Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Geoffrey D Shimberg
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Joshua Brand
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Suprabhath R Gajjala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Crystal S F Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ingelise Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - LaSonji Holman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Floreliz Mendoza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Alicia Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lesia K Dropulic
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
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Tripathi P, Bender MF, Lei H, Da Silva Pereira L, Shen CH, Bonilla B, Dillon M, Ou L, Pancera M, Wang LT, Zhang B, Batista FD, Idris AH, Seder RA, Kwong PD. Cryo-EM structures of anti-malarial antibody L9 with circumsporozoite protein reveal trimeric L9 association and complete 27-residue epitope. Structure 2023; 31:480-491.e4. [PMID: 36931276 PMCID: PMC10237622 DOI: 10.1016/j.str.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/17/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023]
Abstract
Monoclonal antibody L9 recognizes the Plasmodium falciparum circumsporozoite protein (PfCSP) and is highly protective following controlled human malaria challenge. To gain insight into its function, we determined cryoelectron microscopy (cryo-EM) structures of L9 in complex with full-length PfCSP and assessed how this recognition influenced protection by wild-type and mutant L9s. Cryo-EM reconstructions at 3.6- and 3.7-Å resolution revealed L9 to recognize PfCSP as an atypical trimer. Each of the three L9s in the trimer directly recognized an Asn-Pro-Asn-Val (NPNV) tetrapeptide on PfCSP and interacted homotypically to facilitate L9-trimer assembly. We analyzed peptides containing different repeat tetrapeptides for binding to wild-type and mutant L9s to delineate epitope and homotypic components of L9 recognition; we found both components necessary for potent malaria protection. Last, we found the 27-residue stretch recognized by L9 to be highly conserved in P. falciparum isolates, suggesting the newly revealed complete L9 epitope to be an attractive vaccine target.
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Affiliation(s)
- Prabhanshu Tripathi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haotian Lei
- Research Technology Branch Electron Microscopy Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lais Da Silva Pereira
- 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
| | - Brian Bonilla
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marlon Dillon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lawrence T Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Facundo D Batista
- Departments of Immunology and Microbiology, Harvard Medical School, Boston, MA 02139, USA
| | - Azza H Idris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- 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.
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35
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Ao Y, Grover JR, Han Y, Zhong G, Qin W, Ghimire D, Haque A, Bhattacharjee R, Zhang B, Arthos J, Lemke EA, Kwong PD, Lu M. An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics. bioRxiv 2023:2023.02.28.530526. [PMID: 36909529 PMCID: PMC10002649 DOI: 10.1101/2023.02.28.530526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
The HIV-1 envelope (Env) glycoprotein is conformationally dynamic and mediates membrane fusion required for cell entry. Single-molecule fluorescence resonance energy transfer (smFRET) of Env using peptide tags has provided mechanistic insights into the dynamics of Env conformations. Nevertheless, using peptide tags risks potential effects on structural integrity. Here, we aim to establish minimally invasive smFRET systems of Env on the virus by combining genetic code expansion and bioorthogonal click chemistry. Amber stop-codon suppression allows site-specifically incorporating noncanonical/unnatural amino acids (ncAAs) at introduced amber sites into proteins. However, ncAA incorporation into Env (or other HIV-1 proteins) in the virus context has been challenging due to low copies of Env on virions and incomplete amber suppression in mammalian cells. Here, we developed an intact amber-free virus system that overcomes impediments from preexisting ambers in HIV-1. Using this system, we successfully incorporated dual ncAAs at amber-introduced sites into Env on intact virions. Dual-ncAA incorporated Env retained similar neutralization sensitivities to neutralizing antibodies as wildtype. smFRET of click-labeled Env on intact amber-free virions recapitulated conformational profiles of Env. The amber-free HIV-1 infectious system also permits in-virus protein bioorthogonal labeling, compatible with various advanced microscopic studies of virus entry, trafficking, and egress in living cells. Amber-free HIV-1 infectious systems actualized minimal invasive Env tagging for smFRET, versatile for in-virus bioorthogonal click labeling in advanced microscopic studies of virus-host interactions.
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Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z. A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins. Nat Chem Biol 2023; 19:284-291. [PMID: 36411391 PMCID: PMC10294592 DOI: 10.1038/s41589-022-01193-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022]
Abstract
We report the engineering and selection of two synthetic proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon. Despite selection by a spike protein from a now historical SARS-CoV-2 strain, FSR16m and FSR22 exhibit broad-spectrum neutralization of SARS-CoV-2 strains, inhibiting authentic B.1.351, B.1.617.2 and BA.1.1 viruses, with respective IC50 values of 3.4, 2.2 and 7.4 ng ml-1 for FSR16m. Cryo-EM structures revealed that these DARPins recognize a region of the receptor-binding domain (residues 456, 475, 486, 487 and 489) overlapping a critical portion of the angiotensin-converting enzyme 2 (ACE2)-binding surface. K18-hACE2 transgenic mice inoculated with B.1.617.2 and receiving intranasally administered FSR16m showed less weight loss and 10-100-fold lower viral burden in upper and lower respiratory tracts. The strong and broad neutralization potency makes FSR16m and FSR22 promising candidates for the prevention and treatment of infection by SARS-CoV-2.
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Affiliation(s)
- Vikas Chonira
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Ryan G Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Stephens
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hannah Boyd
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai (ISMMS), New York City, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, ISMMS, New York City, NY, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Pathology and Immunology, Department of Molecular Microbiology, and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA.
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Bibollet-Ruche F, Russell RM, Ding W, Liu W, Li Y, Wagh K, Wrapp D, Habib R, Skelly AN, Roark RS, Sherrill-Mix S, Wang S, Rando J, Lindemuth E, Cruickshank K, Park Y, Baum R, Carey JW, Connell AJ, Li H, Giorgi EE, Song GS, Ding S, Finzi A, Newman A, Hernandez GE, Machiele E, Cain DW, Mansouri K, Lewis MG, Montefiori DC, Wiehe KJ, Alam SM, Teng IT, Kwong PD, Andrabi R, Verkoczy L, Burton DR, Korber BT, Saunders KO, Haynes BF, Edwards RJ, Shaw GM, Hahn BH. A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies. mBio 2023; 14:e0337022. [PMID: 36629414 PMCID: PMC9973348 DOI: 10.1128/mbio.03370-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
HIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germ line-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these animals identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, nonneutralizing antibodies revealed that SCIV-expressed, but not wild-type SIVcpz Envs, as well as a subset of primary HIV-1 Envs, preferentially adopted a more open trimeric state. These results reveal the existence of a cryptic V2 epitope that is exposed in occluded-open SIVcpz and HIV-1 Env trimers and elicits cross-neutralizing responses of limited breadth and potency. IMPORTANCE An effective HIV-1 vaccination strategy will need to stimulate rare precursor B cells of multiple bNAb lineages and affinity mature them along desired pathways. Here, we searched for V2-apex germ line-targeting Envs among a large set of diverse primate lentiviruses and identified minimally modified versions of one chimpanzee SIV Env that bound several human V2-apex bNAb precursors and stimulated one of these in a V2-apex bNAb precursor-expressing knock-in mouse. We also generated chimeric simian-chimpanzee immunodeficiency viruses and showed that they elicit low-titer V2-directed heterologous plasma breadth in six of seven infected rhesus macaques. Characterization of this antibody response identified a new class of weakly cross-reactive neutralizing antibodies that target the V2-apex, but only in occluded-open Env trimers. The existence of this cryptic epitope, which in some Env backgrounds is immunodominant, needs to be considered in immunogen design.
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Affiliation(s)
- Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronnie M. Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wenge Ding
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Daniel Wrapp
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rumi Habib
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ashwin N. Skelly
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ryan S. Roark
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Juliette Rando
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily Lindemuth
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kendra Cruickshank
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Younghoon Park
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rachel Baum
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John W. Carey
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elena E. Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Ge S. Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Emily Machiele
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - David C. Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kevin J. Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Laurent Verkoczy
- San Diego Biomedical Research Institute, San Diego, California, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, Harvard and MIT, Cambridge, Massachusetts, USA
| | - Bette T. Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H. Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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38
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Samsel J, Boswell KL, Watkins T, Ambrozak DR, Mason R, Yamamoto T, Ko S, Yang Y, Zhou T, Doria-Rose NA, Foulds KE, Roederer M, Mascola JR, Kwong PD, Gama L, Koup RA. Rhesus macaque Bcl-6/Bcl-xL B cell immortalization: Discovery of HIV-1 neutralizing antibodies from lymph node. J Immunol Methods 2023; 516:113445. [PMID: 36848985 DOI: 10.1016/j.jim.2023.113445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Many HIV-1 vaccines are designed to elicit neutralizing antibodies, and pre-clinical testing is often carried out in rhesus macaques (RMs). We have therefore adapted a method of B cell immortalization for use with RM B cells. In this system, RM B cells are activated with CD40 ligand and RM IL-21 before transduction with a retroviral vector encoding Bcl-6, Bcl-xL, and green fluorescent protein. Importantly, RM B cells from lymph nodes are more effectively immortalized by this method than B cells from PBMC, a difference not seen in humans. We suggest the discrepancy between these two tissues is due to increased expression of CD40 on RM lymph node B cells. Immortalized RM B cells expand long-term, undergo minimal somatic hypermutation, express surface B cell receptor, and secrete antibodies into culture. This allows for the identification of cells based on antigen specificity and/or functional assays. Here, we show the characterization of this system and its application for the isolation of HIV-1 neutralizing antibodies from a SHIV.CH505-infected animal, both with and without antigen probe. Taken together, we show that Bcl-6/xL immortalization is a valuable and flexible tool for antibody discovery in RMs, but with important distinctions from application of the system in human cells.
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Affiliation(s)
- Jakob Samsel
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America; Institute for Biomedical Sciences, George Washington University, Washington, D.C., United States of America.
| | - Kristin L Boswell
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - Timothy Watkins
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - David R Ambrozak
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - Rosemarie Mason
- ImmunoTechnology Section, VRC; Humoral Immunology Section, VRC
| | - Takuya Yamamoto
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | | | | | | | | | | | | | | | | | - Lucio Gama
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
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39
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Cable J, Saphire EO, Hayday AC, Wiltshire TD, Mousa JJ, Humphreys DP, Breij ECW, Bruhns P, Broketa M, Furuya G, Hauser BM, Mahévas M, Carfi A, Cantaert T, Kwong PD, Tripathi P, Davis JH, Brewis N, Keyt BA, Fennemann FL, Dussupt V, Sivasubramanian A, Kim PM, Rawi R, Richardson E, Leventhal D, Wolters RM, Geuijen CAW, Sleeman MA, Pengo N, Donnellan FR. Antibodies as drugs-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1519:153-166. [PMID: 36382536 PMCID: PMC10103175 DOI: 10.1111/nyas.14915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Therapeutic antibodies have broad indications across diverse disease states, such as oncology, autoimmune diseases, and infectious diseases. New research continues to identify antibodies with therapeutic potential as well as methods to improve upon endogenous antibodies and to design antibodies de novo. On April 27-30, 2022, experts in antibody research across academia and industry met for the Keystone symposium "Antibodies as Drugs" to present the state-of-the-art in antibody therapeutics, repertoires and deep learning, bispecific antibodies, and engineering.
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Affiliation(s)
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA.,Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Adrian C Hayday
- Peter Gorer Department of Immunobiology, King's College London, London, UK.,Cancer Research UK Cancer Immunotherapy Accelerator, London, UK.,Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | | | - Jarrod J Mousa
- Department of Infectious Diseases and Center for Vaccines and Immunology, College of Veterinary Medicine, Athens, Georgia, USA.,Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, USA.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Esther C W Breij
- Translational Research and Precision Medicine, Genmab BV, Utrecht, the Netherlands
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Matteo Broketa
- Institut Pasteur, Université de Paris, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Genta Furuya
- Department of Preventive Medicine and Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Matthieu Mahévas
- Service de Médecine Interne, Centre de Référence des Cytopénies Auto-immunes de l'adulte, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est Créteil, Créteil, France
| | - Andrea Carfi
- Moderna Inc., Cambridge, Massachusetts, USA.,Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Tineke Cantaert
- Immunology Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Prabhanshu Tripathi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Bruce A Keyt
- IGM Biosciences, Inc., Mountainview, California, USA
| | | | - Vincent Dussupt
- Emerging Infectious Diseases Branch, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | | | - Philip M Kim
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eve Richardson
- Department of Statistics, University of Oxford, Oxford, UK
| | | | - Rachael M Wolters
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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40
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Kwon YD, Pegu A, Yang ES, Zhang B, Bender MF, Asokan M, Liu Q, McKee K, Lin BC, Liu T, Louder MK, Rawi R, Reveiz M, Schaub AJ, Shen CH, Doria-Rose NA, Lusso P, Mascola JR, Kwong PD. Improved pharmacokinetics of HIV-neutralizing VRC01-class antibodies achieved by reduction of net positive charge on variable domain. MAbs 2023; 15:2223350. [PMID: 37345226 DOI: 10.1080/19420862.2023.2223350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
The amino-acid composition of the immunoglobulin variable region has been observed to impact antibody pharmacokinetics (PK). Here, we sought to improve the PK of the broad HIV-1-neutralizing VRC01-class antibodies, VRC07-523LS and N6LS, by reducing the net positive charge in their variable domains. We used a structure-guided approach to generate a panel of antibody variants incorporating select Arg or Lys substituted to Asp, Gln, Glu, or Ser. The engineered variants exhibited reduced affinity to heparin, reduced polyreactivity, and improved PK in human FcRn-transgenic mice. One variant, VRC07-523LS.v34, with three charge substitutions, had an observed in vivo half-life and an estimated human half-life of 10.8 and 60 days, respectively (versus 5.4 and 38 days for VRC07-523LS) and retained functionality, neutralizing 92% of a 208-strain panel at a geometric mean IC80 <1 µg/mL. Another variant, N6LS.C49, with two charge substitutions, had an observed in vivo half-life and an estimated human half-life of 14.5 and 80 days (versus 9.0 and 44 days for N6LS) and neutralized ~80% of 208 strains at a geometric mean IC80 <1 µg/mL. Since Arg and Lys residues are prevalent in human antibodies, we propose substitution of select Arg or Lys with Asp, Gln, Glu, or Ser in the framework region as a general means to improve PK of therapeutic antibodies.
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Affiliation(s)
- Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mangaiarkarasi Asokan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Qingbo Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mateo Reveiz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Schaub
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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41
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Zhang B, Gorman J, Kwon YD, Pegu A, Chao CW, Liu T, Asokan M, Bender MF, Bylund T, Damron L, Gollapudi D, Lei P, Li Y, Liu C, Louder MK, McKee K, Olia AS, Rawi R, Schön A, Wang S, Yang ES, Yang Y, Carlton K, Doria-Rose NA, Shapiro L, Seaman MS, Mascola JR, Kwong PD. Bispecific antibody CAP256.J3LS targets V2-apex and CD4-binding sites with high breadth and potency. MAbs 2023; 15:2165390. [PMID: 36729903 PMCID: PMC9897750 DOI: 10.1080/19420862.2023.2165390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antibody CAP256-VRC26.25 targets the second hypervariable region (V2) at the apex of the HIV envelope (Env) trimer with extraordinary neutralization potency, although less than optimal breadth. To improve breadth, we linked the light chain of CAP256V2LS, an optimized version of CAP256-VRC26.25 currently under clinical evaluation, to the llama nanobody J3, which has broad CD4-binding site-directed neutralization. The J3-linked bispecific antibody exhibited improved breadth and potency over both J3 and CAP256V2LS, indicative of synergistic neutralization. The cryo-EM structure of the bispecific antibody in complex with a prefusion-closed Env trimer revealed simultaneous binding of J3 and CAP256V2LS. We further optimized the pharmacokinetics of the bispecific antibody by reducing the net positive charge of J3. The optimized bispecific antibody, which we named CAP256.J3LS, had a half-life similar to CAP256V2LS in human FcRn knock-in mice and exhibited suitable auto-reactivity, manufacturability, and biophysical risk. CAP256.J3LS neutralized over 97% of a multiclade 208-strain panel (geometric mean concentration for 80% inhibition (IC80) 0.079 μg/ml) and 100% of a 100-virus clade C panel (geometric mean IC80 of 0.05 μg/ml), suggesting its anti-HIV utility especially in regions where clade C dominates.
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Affiliation(s)
- Baoshan Zhang
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Young D. Kwon
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Amarendra Pegu
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Cara W. Chao
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Tracy Liu
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | | | - Michael F. Bender
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Tatsiana Bylund
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Leland Damron
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Deepika Gollapudi
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Paula Lei
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Yile Li
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Cuiping Liu
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Mark K. Louder
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Krisha McKee
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Adam S. Olia
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Shuishu Wang
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Eun Sung Yang
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Yongping Yang
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Carlton
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence Shapiro
- Department of Biochemistry, Columbia University, New York, NY, USA
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - John R. Mascola
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA
| | - Peter D. Kwong
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, USA,Department of Biochemistry, Columbia University, New York, NY, USA,CONTACT Peter D. Kwong Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD20892, USA
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42
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Curreli F, Kwon YD, Nicolau I, Burgos G, Altieri A, Kurkin AV, Verardi R, Kwong PD, Debnath AK. Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists. Int J Mol Sci 2022; 23:ijms232415999. [PMID: 36555641 PMCID: PMC9784924 DOI: 10.3390/ijms232415999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
As part of our effort to discover drugs that target HIV-1 entry, we report the antiviral activity and crystal structures of two novel inhibitors in a complex with a gp120 core. NBD-14204 showed similar antiviral activity against all the clinical isolates tested. The IC50 values were in the range of 0.24-0.9 µM with an overall mean of 0.47 ± 0.03 µM, showing slightly better activity against the clinical isolates than against the lab-adapted HIV-1HXB2 (IC50 = 0.96 ± 0.1 µM). Moreover, the antiviral activity of NBD-14208 was less consistent, showing a wider range of IC50 values (0.66-5.7 µM) with an overall mean of 3 ± 0.25 µM and better activity against subtypes B and D (Mean IC50 2.2-2.5 µM) than the A, C and Rec viruses (Mean IC50 2.9-3.9 µM). SI of NBD-14204 was about 10-fold higher than NBD-14208, making it a better lead compound for further optimization. In addition, we tested these compounds against S375Y and S375H mutants of gp120, which occurred in some clades and observed these to be sensitive to NBD-14204 and NBD-14208. These inhibitors also showed modest activity against HIV-1 reverse transcriptase. Furthermore, we determined the crystal structures of both inhibitors in complexes with gp120 cores. As expected, both NBD-14204 and NBD-14208 bind primarily within the Phe43 cavity. It is noteworthy that the electron density of the thiazole ring in both structures was poorly defined due to the flexibility of this scaffold, suggesting that these compounds maintain substantial entropy, even when bound to the Phe43 cavity.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Young D. Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Isabella Nicolau
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Giancarla Burgos
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Andrea Altieri
- EDASA Scientific srls, Via Stingi 37, 66050 San Salvo, Italy
| | | | - Raffaello Verardi
- 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
| | - Asim K. Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
- Correspondence:
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43
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Boswell KL, Watkins TA, Cale EM, Samsel J, Andrews SF, Ambrozak DR, Driscoll JI, Messina MA, Narpala S, Hopp CS, Cagigi A, Casazza JP, Yamamoto T, Zhou T, Schief WR, Crompton PD, Ledgerwood JE, Connors M, Gama L, Kwong PD, McDermott A, Mascola JR, Koup RA. Application of B cell immortalization for the isolation of antibodies and B cell clones from vaccine and infection settings. Front Immunol 2022; 13:1087018. [PMID: 36582240 PMCID: PMC9794141 DOI: 10.3389/fimmu.2022.1087018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The isolation and characterization of neutralizing antibodies from infection and vaccine settings informs future vaccine design, and methodologies that streamline the isolation of antibodies and the generation of B cell clones are of great interest. Retroviral transduction to express Bcl-6 and Bcl-xL and transform primary B cells has been shown to promote long-term B cell survival and antibody secretion in vitro, and can be used to isolate antibodies from memory B cells. However, application of this methodology to B cell subsets from different tissues and B cells from chronically infected individuals has not been well characterized. Here, we characterize Bcl-6/Bcl-xL B cell immortalization across multiple tissue types and B cell subsets in healthy and HIV-1 infected individuals, as well as individuals recovering from malaria. In healthy individuals, naïve and memory B cell subsets from PBMCs and tonsil tissue transformed with similar efficiencies, and displayed similar characteristics with respect to their longevity and immunoglobulin secretion. In HIV-1-viremic individuals or in individuals with recent malaria infections, the exhausted CD27-CD21- memory B cells transformed with lower efficiency, but the transformed B cells expanded and secreted IgG with similar efficiency. Importantly, we show that this methodology can be used to isolate broadly neutralizing antibodies from HIV-infected individuals. Overall, we demonstrate that Bcl-6/Bcl-xL B cell immortalization can be used to isolate antibodies and generate B cell clones from different B cell populations, albeit with varying efficiencies.
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Affiliation(s)
- Kristin L. Boswell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States,*Correspondence: Kristin L. Boswell,
| | - Timothy A. Watkins
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Evan M. Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jakob Samsel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States,Institute for Biomedical Sciences, George Washington University, Washington, DC, United States
| | - Sarah F. Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - David R. Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jefferson I. Driscoll
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael A. Messina
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Christine S. Hopp
- Malaria Infection Biology and Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Joseph P. Casazza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Takuya Yamamoto
- 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
| | - William R. Schief
- Department of Immunology and Microbial Science, IAVI Neutralizing Antibody Center and Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Julie E. Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mark Connors
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lucio Gama
- 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
| | - Adrian McDermott
- 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
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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44
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Wang P, Casner RG, Nair MS, Yu J, Guo Y, Wang M, Chan JFW, Cerutti G, Iketani S, Liu L, Sheng Z, Chen Z, Yuen KY, Kwong PD, Huang Y, Shapiro L, Ho DD. A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect 2022; 11:147-157. [PMID: 34836485 PMCID: PMC8725896 DOI: 10.1080/22221751.2021.2011623] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023]
Abstract
The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378 T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.
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Affiliation(s)
- Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Ryan G Casner
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jasper F-W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Gabriele Cerutti
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Vaccine Research Center, National Institutes of Health, Bethesda, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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Misasi J, Wei RR, Wang L, Pegu A, Wei CJ, Oloniniyi OK, Zhou T, Moliva JI, Zhao B, Choe M, Yang ES, Zhang Y, Boruszczak M, Chen M, Leung K, Li J, Yang ZY, Andersen H, Carlton K, Godbole S, Harris DR, Henry AR, Ivleva VB, Lei P, Liu C, Longobardi L, Merriam JS, Nase D, Olia AS, Pessaint L, Porto M, Shi W, Wolff JJ, Douek DC, Suthar MS, Gall J, Koup RA, Kwong PD, Mascola JR, Nabel GJ, Sullivan NJ. A multispecific antibody prevents immune escape and confers pan-SARS-CoV-2 neutralization. bioRxiv 2022:2022.07.29.502029. [PMID: 35982683 PMCID: PMC9387125 DOI: 10.1101/2022.07.29.502029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite effective countermeasures, SARS-CoV-2 persists worldwide due to its ability to diversify and evade human immunity1. This evasion stems from amino-acid substitutions, particularly in the receptor-binding domain of the spike, that confer resistance to vaccines and antibodies 2-16. To constrain viral escape through resistance mutations, we combined antibody variable regions that recognize different receptor binding domain (RBD) sites17,18 into multispecific antibodies. Here, we describe multispecific antibodies, including a trispecific that prevented virus escape >3000-fold more potently than the most effective clinical antibody or mixtures of the parental antibodies. Despite being generated before the evolution of Omicron, this trispecific antibody potently neutralized all previous variants of concern and major Omicron variants, including the most recent BA.4/BA.5 strains at nanomolar concentrations. Negative stain electron microscopy revealed that synergistic neutralization was achieved by engaging different epitopes in specific orientations that facilitated inter-spike binding. An optimized trispecific antibody also protected Syrian hamsters against Omicron variants BA.1, BA.2 and BA.5, each of which uses different amino acid substitutions to mediate escape from therapeutic antibodies. Such multispecific antibodies decrease the likelihood of SARS-CoV-2 escape, simplify treatment, and maximize coverage, providing a strategy for universal antibody therapies that could help eliminate pandemic spread for this and other pathogens.
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Affiliation(s)
- John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronnie R. Wei
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chih-Jen Wei
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Olamide K. Oloniniyi
- 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
| | - Juan I. Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bingchun Zhao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marika Boruszczak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwan Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan Li
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Zhi-Yong Yang
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | | | - Kevin Carlton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R. Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vera B. Ivleva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paula Lei
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lindsay Longobardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonah S. Merriam
- 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
| | | | | | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeremy J. Wolff
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jason Gall
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A. Koup
- 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
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gary J. Nabel
- Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Ou L, Gulla K, Biju A, Biner DW, Bylund T, Changela A, Chen SJ, Zheng CY, Cibelli N, Corrigan AR, Duan H, Gonelli CA, Kong WP, Cheng C, O’Dell S, Sarfo EK, Shaddeau A, Wang S, Vinitsky A, Yang Y, Zhang B, Zhang Y, Koup RA, Doria-Rose NA, Gall JG, Mascola JR, Kwong PD. Assessment of Crosslinkers between Peptide Antigen and Carrier Protein for Fusion Peptide-Directed Vaccines against HIV-1. Vaccines (Basel) 2022; 10:vaccines10111916. [PMID: 36423012 PMCID: PMC9698951 DOI: 10.3390/vaccines10111916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Conjugate-vaccine immunogens require three components: a carrier protein, an antigen, and a crosslinker, capable of coupling antigen to carrier protein, while preserving both T-cell responses from carrier protein and B-cell responses from antigen. We previously showed that the N-terminal eight residues of the HIV-1 fusion peptide (FP8) as an antigen could prime for broad cross-clade neutralizing responses, that recombinant heavy chain of tetanus toxin (rTTHC) as a carrier protein provided optimal responses, and that choice of crosslinker could impact both antigenicity and immunogenicity. Here, we delve more deeply into the impact of varying the linker between FP8 and rTTHC. In specific, we assessed the physical properties, the antigenicity, and the immunogenicity of conjugates for crosslinkers ranging in spacer-arm length from 1.5 to 95.2 Å, with varying hydrophobicity and crosslinking-functional groups. Conjugates coupled with different degrees of multimerization and peptide-to-rTTHC stoichiometry, but all were well recognized by HIV-fusion-peptide-directed antibodies VRC34.01, VRC34.05, PGT151, and ACS202 except for the conjugate with the longest linker (24-PEGylated SMCC; SM(PEG)24), which had lower affinity for ACS202, as did the conjugate with the shortest linker (succinimidyl iodoacetate; SIA), which also had the lowest peptide-to-rTTHC stoichiometry. Murine immunizations testing seven FP8-rTTHC conjugates elicited fusion-peptide-directed antibody responses, with SIA- and SM(PEG)24-linked conjugates eliciting lower responses than the other five conjugates. After boosting with prefusion-closed envelope trimers from strains BG505 clade A and consensus clade C, trimer-directed antibody-binding responses were lower for the SIA-linked conjugate; elicited neutralizing responses were similar, however, though statistically lower for the SM(PEG)24-linked conjugate, when tested against a strain especially sensitive to fusion-peptide-directed responses. Overall, correlation analyses revealed the immunogenicity of FP8-rTTHC conjugates to be negatively impacted by hydrophilicity and extremes of length or low peptide-carrier stoichiometry, but robust to other linker parameters, with several commonly used crosslinkers yielding statistically indistinguishable serological results.
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Affiliation(s)
- Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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47
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Buckner CM, Kardava L, El Merhebi O, Narpala SR, Serebryannyy L, Lin BC, Wang W, Zhang X, Lopes de Assis F, Kelly SE, Teng IT, McCormack GE, Praiss LH, Seamon CA, Rai MA, Kalish H, Kwong PD, Proschan MA, McDermott AB, Fauci AS, Chun TW, Moir S. Interval between prior SARS-CoV-2 infection and booster vaccination impacts magnitude and quality of antibody and B cell responses. Cell 2022; 185:4333-4346.e14. [PMID: 36257313 PMCID: PMC9513331 DOI: 10.1016/j.cell.2022.09.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 01/26/2023]
Abstract
SARS-CoV-2 mRNA booster vaccines provide protection from severe disease, eliciting strong immunity that is further boosted by previous infection. However, it is unclear whether these immune responses are affected by the interval between infection and vaccination. Over a 2-month period, we evaluated antibody and B cell responses to a third-dose mRNA vaccine in 66 individuals with different infection histories. Uninfected and post-boost but not previously infected individuals mounted robust ancestral and variant spike-binding and neutralizing antibodies and memory B cells. Spike-specific B cell responses from recent infection (<180 days) were elevated at pre-boost but comparatively less so at 60 days post-boost compared with uninfected individuals, and these differences were linked to baseline frequencies of CD27lo B cells. Day 60 to baseline ratio of BCR signaling measured by phosphorylation of Syk was inversely correlated to days between infection and vaccination. Thus, B cell responses to booster vaccines are impeded by recent infection.
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Affiliation(s)
- Clarisa M. Buckner
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Omar El Merhebi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep R. Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leonid Serebryannyy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C. Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaozhen Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Felipe Lopes de Assis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sophie E.M. Kelly
- Bioengineering and Physical Sciences Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Genevieve E. McCormack
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren H. Praiss
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine A. Seamon
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - M. Ali Rai
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heather Kalish
- Bioengineering and Physical Sciences Shared Resource, National Institute of Biomedical Imaging and Bioengineering, 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
| | - Michael A. Proschan
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony S. Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author
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48
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Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P. Potent monoclonal antibodies neutralize Omicron sublineages and other SARS-CoV-2 variants. Cell Rep 2022; 41:111528. [PMID: 36302375 PMCID: PMC9554601 DOI: 10.1016/j.celrep.2022.111528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/29/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence and global spread of the SARS-CoV-2 Omicron variants, which carry an unprecedented number of mutations, raise serious concerns due to the reduced efficacy of current vaccines and resistance to therapeutic antibodies. Here, we report the generation and characterization of two potent human monoclonal antibodies, NA8 and NE12, against the receptor-binding domain of the SARS-CoV-2 spike protein. NA8 interacts with a highly conserved region and has a breadth of neutralization with picomolar potency against the Beta variant and the Omicron BA.1 and BA.2 sublineages and nanomolar potency against BA.2.12.1 and BA.4. Combination of NA8 and NE12 retains potent neutralizing activity against the major SARS-CoV-2 variants of concern. Cryo-EM analysis provides the structural basis for the broad and complementary neutralizing activity of these two antibodies. We confirm the in vivo protective and therapeutic efficacies of NA8 and NE12 in the hamster model. These results show that broad and potent human antibodies can overcome the continuous immune escape of evolving SARS-CoV-2 variants.
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Affiliation(s)
- Zhaochun Chen
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Peng Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yumiko Matsuoka
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kamille West
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Celia Santos
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanh Nguyen
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Pomerenke
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Stephens
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Robin Gross
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Elena Postnikova
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Nicole L Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reed F Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Harvey J Alter
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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49
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Gorman J, Wang C, Mason RD, Nazzari AF, Welles HC, Zhou T, Bess JW, Bylund T, Lee M, Tsybovsky Y, Verardi R, Wang S, Yang Y, Zhang B, Rawi R, Keele BF, Lifson JD, Liu J, Roederer M, Kwong PD. Cryo-EM structures of prefusion SIV envelope trimer. Nat Struct Mol Biol 2022; 29:1080-1091. [PMID: 36344847 PMCID: PMC10606957 DOI: 10.1038/s41594-022-00852-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 09/25/2022] [Indexed: 11/09/2022]
Abstract
Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion stabilization and cryo-EM structures of soluble envelope (Env) trimers from rhesus macaque SIV (SIVmac) in complex with neutralizing antibodies. These structures provide residue-level definition for SIV-specific disulfide-bonded variable loops (V1 and V2), which we used to delineate variable-loop coverage of the Env trimer. The defined variable loops enabled us to investigate assembled Env-glycan shields throughout SIV, which we found to comprise both N- and O-linked glycans, the latter emanating from V1 inserts, which bound the O-link-specific lectin jacalin. We also investigated in situ SIVmac-Env trimers on virions, determining cryo-electron tomography structures at subnanometer resolutions for an antibody-bound complex and a ligand-free state. Collectively, these structures define the prefusion-closed structure of the SIV-Env trimer and delineate variable-loop and glycan-shielding mechanisms of immune evasion conserved throughout SIV evolution.
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Affiliation(s)
- Jason Gorman
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Chunyan Wang
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Hugh C Welles
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Julian W Bess
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Myungjin Lee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Yongping Yang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
| | - Mario Roederer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA.
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50
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Zhang B, Gollapudi D, Gorman J, O’Dell S, Damron LF, McKee K, Asokan M, Yang ES, Pegu A, Lin BC, Chao CW, Chen X, Gama L, Ivleva VB, Law WH, Liu C, Louder MK, Schmidt SD, Shen CH, Shi W, Stein JA, Seaman MS, McDermott AB, Carlton K, Mascola JR, Kwong PD, Lei QP, Doria-Rose NA. Engineering of HIV-1 neutralizing antibody CAP256V2LS for manufacturability and improved half life. Sci Rep 2022; 12:17876. [PMID: 36284200 PMCID: PMC9596707 DOI: 10.1038/s41598-022-22435-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/14/2022] [Indexed: 01/20/2023] Open
Abstract
The broadly neutralizing antibody (bNAb) CAP256-VRC26.25 has exceptional potency against HIV-1 and has been considered for clinical use. During the characterization and production of this bNAb, we observed several unusual features. First, the antibody appeared to adhere to pipette tips, requiring tips to be changed during serial dilution to accurately measure potency. Second, during production scale-up, proteolytic cleavage was discovered to target an extended heavy chain loop, which was attributed to a protease in spent medium from 2-week culture. To enable large scale production, we altered the site of cleavage via a single amino acid change, K100mA. The resultant antibody retained potency and breadth while avoiding protease cleavage. We also added the half-life extending mutation LS, which improved the in vivo persistence in animal models, but did not impact neutralization activity; we observed the same preservation of neutralization for bNAbs VRC01, N6, and PGDM1400 with LS on a 208-virus panel. The final engineered antibody, CAP256V2LS, retained the extraordinary neutralization potency of the parental antibody, had a favorable pharmacokinetic profile in animal models, and was negative in in vitro assessment of autoreactivity. CAP256V2LS has the requisite potency, developability and suitability for scale-up, allowing its advancement as a clinical candidate.
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Affiliation(s)
- Baoshan Zhang
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Deepika Gollapudi
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Jason Gorman
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Sijy O’Dell
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Leland F. Damron
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Krisha McKee
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Mangaiarkarasi Asokan
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Eun Sung Yang
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Amarendra Pegu
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Bob C. Lin
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Cara W. Chao
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Xuejun Chen
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Lucio Gama
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Vera B. Ivleva
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - William H. Law
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Cuiping Liu
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Mark K. Louder
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Stephen D. Schmidt
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Chen-Hsiang Shen
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Wei Shi
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Judith A. Stein
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Michael S. Seaman
- grid.239395.70000 0000 9011 8547Beth Israel Deaconess Medical Center, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Adrian B. McDermott
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Kevin Carlton
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - John R. Mascola
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Peter D. Kwong
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Q. Paula Lei
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
| | - Nicole A. Doria-Rose
- grid.94365.3d0000 0001 2297 5165Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892 USA
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