1
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Thakur B, Katte RH, Xu W, Janowska K, Sammour S, Henderson R, Lu M, Kwong PD, Acharya P. Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening. Nat Commun 2025; 16:4595. [PMID: 40382314 DOI: 10.1038/s41467-025-59721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 04/30/2025] [Indexed: 05/20/2025] Open
Abstract
The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminus of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41. The gp120/gp41 heterodimer assembles into a homotrimer, in which FP is accessible for antibody binding. Env conformational changes or "opening" that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibodies. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains, we visualize that the FP remains accessible for antibody binding despite substantial receptor-induced Env opening. We delineate stepwise Env opening from its closed state to a functional CD4-bound symmetrically open Env in which we show that FP was accessible for antibody binding. We define downstream re-organizations that lead to the formation of a gp120/gp41 cavity into which the FP buries to become inaccessible for antibody binding. These findings improve our understanding of HIV-1 entry and delineate the entry-related conformational trajectory of a key site of HIV vulnerability to neutralizing antibody.
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Affiliation(s)
- Bhishem Thakur
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Revansiddha H Katte
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Wang Xu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | | | - Salam Sammour
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Peter D Kwong
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University, Durham, NC, USA.
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2
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Dam KMA, Gristick HB, Li YE, Yang Z, Gnanapragasam PNP, West AP, Seaman MS, Bjorkman PJ. Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design. Cell Rep 2025; 44:115713. [PMID: 40378041 DOI: 10.1016/j.celrep.2025.115713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 03/17/2025] [Accepted: 04/25/2025] [Indexed: 05/18/2025] Open
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) targeting the CD4-binding site (CD4bs) contain rare features that pose challenges to elicit these bNAbs through vaccination. The IOMA class of CD4bs bNAbs includes fewer rare features and somatic hypermutations (SHMs) to achieve broad neutralization, thus presenting a potentially accessible pathway for vaccine-induced bNAb development. Here, we created a library of IOMA variants in which each SHM was individually reverted to the inferred germline counterpart to investigate the roles of SHMs in conferring IOMA's neutralization potency and breadth. Impacts on neutralization for each variant were evaluated, and this information was used to design minimally mutated IOMA-class variants (IOMAmin) that incorporated the fewest SHMs required for achieving IOMA's neutralization breadth. A cryoelectron microscopy (cryo-EM) structure of an IOMAmin variant bound to Env was used to further interpret characteristics of IOMA variants to elucidate how IOMA's structural features correlate with its neutralization mechanism, informing the design of IOMA-targeting immunogens.
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Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yancheng E Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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3
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Caniels TG, Prabhakaran M, Ozorowski G, MacPhee KJ, Wu W, van der Straten K, Agrawal S, Derking R, Reiss EIMM, Millard K, Turroja M, Desrosiers A, Bethony J, Malkin E, Liesdek MH, van der Veen A, Klouwens M, Snitselaar JL, Bouhuijs JH, Bronson R, Jean-Baptiste J, Gajjala S, Rikhtegaran Tehrani Z, Benner A, Ramaswami M, Duff MO, Liu YW, Sato AH, Kim JY, Baken IJL, Mendes Silva C, Bijl TPL, van Rijswijk J, Burger JA, Cupo A, Yasmeen A, Phulera S, Lee WH, Randall KN, Zhang S, Corcoran MM, Regadas I, Sullivan AC, Brown DM, Bohl JA, Greene KM, Gao H, Yates NL, Sawant S, Prins JM, Kootstra NA, Kaminsky SM, Barin B, Rahaman F, Meller M, Philiponis V, Laufer DS, Lombardo A, Mwoga L, Shotorbani S, Holman D, Koup RA, Klasse PJ, Karlsson Hedestam GB, Tomaras GD, van Gils MJ, Montefiori DC, McDermott AB, Hyrien O, Moore JP, Wilson IA, Ward AB, Diemert DJ, de Bree GJ, Andrews SF, Caskey M, Sanders RW. Precise targeting of HIV broadly neutralizing antibody precursors in humans. Science 2025:eadv5572. [PMID: 40373114 DOI: 10.1126/science.adv5572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Accepted: 05/01/2025] [Indexed: 05/17/2025]
Abstract
A protective HIV vaccine will need to induce broadly neutralizing antibodies (bnAbs) in humans, but priming rare bnAb precursor B cells has been challenging. In a double-blinded, placebo-controlled phase 1 human clinical trial, the recombinant, germline-targeting envelope glycoprotein (Env) trimer BG505 SOSIP.v4.1-GT1.1, adjuvanted with AS01B, induced bnAb precursors of the VRC01-class at a high frequency in the majority of vaccine recipients. These bnAb precursors, that target the CD4 receptor binding site, had undergone somatic hypermutation characteristic of the VRC01-class. A subset of isolated VRC01-class monoclonal antibodies neutralized wild-type pseudoviruses and was structurally extremely similar to bnAb VRC01. These results further support germline-targeting approaches for human HIV vaccine design and demonstrate atomic-level manipulation of B cell responses with rational vaccine design.
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Affiliation(s)
- Tom G Caniels
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Madhu Prabhakaran
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kellie J MacPhee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Weiwei Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karlijn van der Straten
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Sashank Agrawal
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ronald Derking
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Emma I M M Reiss
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Katrina Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Aimee Desrosiers
- Vaccine Research Unit, The George Washington University, Washington, DC, USA
| | - Jeffrey Bethony
- Vaccine Research Unit, The George Washington University, Washington, DC, USA
| | - Elissa Malkin
- Vaccine Research Unit, The George Washington University, Washington, DC, USA
| | - Marinus H Liesdek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Annelou van der Veen
- Department of Internal Medicine, Amsterdam UMC, location AMC, Amsterdam, Netherlands
| | - Michelle Klouwens
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam UMC, location AMC, Amsterdam, Netherlands
| | - Jonne L Snitselaar
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Joey H Bouhuijs
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Rhianna Bronson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jalen Jean-Baptiste
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Suprabhath Gajjala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zahra Rikhtegaran Tehrani
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison Benner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mukundhan Ramaswami
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael O Duff
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yung-Wen Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alicia H Sato
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ju Yeong Kim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Isabel J L Baken
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Catarina Mendes Silva
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Tom P L Bijl
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Jacqueline van Rijswijk
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Judith A Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Swastik Phulera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kipchoge N Randall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shiyu Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Regadas
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alex C Sullivan
- Foundation for the National Institutes of Health, Inc., Bethesda, MD, USA
| | - David M Brown
- Foundation for the National Institutes of Health, Inc., Bethesda, MD, USA
| | - Jennifer A Bohl
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kelli M Greene
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Nicole L Yates
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Sheetal Sawant
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Jan M Prins
- Department of Internal Medicine, Amsterdam UMC, location AMC, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, location AMC, Amsterdam, Netherlands
| | - Stephen M Kaminsky
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Farhad Rahaman
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | - Margaret Meller
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | | | - Dagna S Laufer
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | - Angela Lombardo
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | - Lindsey Mwoga
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Solmaz Shotorbani
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Drienna Holman
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | | | - Georgia D Tomaras
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
| | - David C Montefiori
- Foundation for the National Institutes of Health, Inc., Bethesda, MD, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - David J Diemert
- Vaccine Research Unit, The George Washington University, Washington, DC, USA
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, location AMC, Amsterdam, Netherlands
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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4
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Zhong L, Zhang W, Xiao R, He H, Wu Q, Hong J, Zeng MS, Zhao Q, Zheng Q, Chen YX, Zhang X. A Chimeric Virus-Like Particle Vaccine Presenting an Immunodominant Epitope of gB Elicited Potent Neutralizing Antibodies against EBV Infection In Vitro and In Vivo. ACS APPLIED MATERIALS & INTERFACES 2025; 17:26252-26262. [PMID: 40272901 DOI: 10.1021/acsami.5c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2025]
Abstract
Epstein-Barr Virus (EBV) as the first characterized tumorigenic virus in humans causes heavy disease burdens. An effective vaccine is urgently needed to block EBV infection. Glycoprotein B (gB) is the essential fusogen for EBV infection of all susceptible cell types. We previously demonstrated that neutralizing antibody 3A3 targeting gB effectively blocked EBV infection in a humanized mouse model, indicating that the epitope recognized by 3A3 is the potential immunogen candidate. Hence, we rationally designed a chimeric virus-like particle (cVLP) vaccine based on the hepatitis B core antigen (HBc149) to display gB peptide, αB, recognized by 3A3 (149-αB cVLP). The engineered 149-αB cVLP vaccine self-assembled into spherical particles presenting multiple copies of αB peptide. The 149-αB cVLP vaccine induced much higher antibody titers against αB peptides than gB protein immunization. Importantly, sera antibodies elicited by the 149-αB cVLP vaccine more efficiently blocked EBV infection and membrane fusion of epithelial cells and B cells. Sera from 149-αB cVLP vaccine-immunized rabbits conferred 100% protection against EBV infection in a humanized mouse model. We demonstrated that the 149-αB cVLP vaccine induced potent antigen-specific protective immune responses and shed light on the research of peptide-based vaccines against EBV infection.
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Affiliation(s)
- Ling Zhong
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wanlin Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Rui Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Huiping He
- Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, PR China
| | - Qian Wu
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Research Unit of Frontier Technology of Structural Vaccinology of the Chinese Academy of Medical Sciences, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Junping Hong
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Research Unit of Frontier Technology of Structural Vaccinology of the Chinese Academy of Medical Sciences, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Qinjian Zhao
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Qingbing Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Research Unit of Frontier Technology of Structural Vaccinology of the Chinese Academy of Medical Sciences, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Yi-Xin Chen
- State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Research Unit of Frontier Technology of Structural Vaccinology of the Chinese Academy of Medical Sciences, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Xiao Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
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5
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Sajadi MM, Abbasi A, Tehrani ZR, Siska C, Clark R, Chi W, Seaman MS, Mielke D, Wagh K, Liu Q, Jumpa T, Ketchem RR, Nguyen DN, Tolbert WD, Pierce BG, Atkinson B, Deming D, Sprague M, Asakawa A, Ferrer D, Dunn Y, Calvillo S, Yin R, Guest JD, Korber B, Mayer BT, Sato AH, Ouyang X, Foulke S, Habibzadeh P, Karimi M, Aslanabadi A, Hojabri M, Saadat S, Zareidoodeji R, Kędzior M, Pozharski E, Heredia A, Chen H, Montefiori D, Ferrari G, Pazgier M, Lewis GK, Jardine JG, Lusso P, DeVico A. A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV. Structure 2025:S0969-2126(25)00150-9. [PMID: 40373766 DOI: 10.1016/j.str.2025.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 03/20/2025] [Accepted: 04/18/2025] [Indexed: 05/17/2025]
Abstract
Anti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with "first-generation" bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of "enhanced" antibodies will be required for optimal clinical utility, while preserving or enhancing Current Good Manufacturing Practices (cGMP) manufacturing capability. Here, we report the engineering of an anti-CD4-binding site (CD4bs) bnAb, N49P9.3. Through a series of rational modifications, we produced a variant, N49P9.6-FR-LS, that demonstrates enhanced potency, superior antiviral activity in combination with other bnAbs, low polyreactivity, and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.
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Affiliation(s)
- Mohammad M Sajadi
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, Maryland VA Healthcare System, Baltimore, MD, USA.
| | - Abdolrahim Abbasi
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zahra Rikhtegaran Tehrani
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Christine Siska
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Rutilio Clark
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Woo Chi
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Qingbo Liu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Taylor Jumpa
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | | | - Dung N Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Ben Atkinson
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Derrick Deming
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Megan Sprague
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Andrew Asakawa
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - David Ferrer
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Yasmin Dunn
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Sarah Calvillo
- Just-Evotec Biologics, 401 Terry Avenue North, Seattle, WA, USA
| | - Rui Yin
- University of Maryland Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Johnathan D Guest
- University of Maryland Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Bette Korber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bryan T Mayer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alicia H Sato
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Xin Ouyang
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Scott Foulke
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Parham Habibzadeh
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maryam Karimi
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Arash Aslanabadi
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mahsa Hojabri
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Saman Saadat
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roza Zareidoodeji
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Edwin Pozharski
- University of Maryland Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alonso Heredia
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hegang Chen
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Montefiori
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Durham, NC, USA; Division of Surgical Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - George K Lewis
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joseph G Jardine
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Anthony DeVico
- Divisions of Vaccine Research and Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
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6
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Katte RH, Xu W, Han Y, Hong X, Lu M. Inter-protomer opening cooperativity of envelope trimers positively correlates with HIV-1 entry stoichiometry. mBio 2025; 16:e0275424. [PMID: 39998217 PMCID: PMC11980385 DOI: 10.1128/mbio.02754-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 01/29/2025] [Indexed: 02/26/2025] Open
Abstract
HIV-1 entry to host cells is fulfilled by fusion, mediated by surface glycoprotein envelope (Env) trimers upon interaction with host receptors. The entry stoichiometry (T) defining the number of Env trimers required for fusion remains elusive. Stoichiometry was previously estimated using mathematical modeling of infectivity curves of pseudoviruses surface-decorated with heterotrimers containing wild-type and entry-deficient Env. Nevertheless, previous models rarely co-considered inter-protomer opening cooperativity (S, reflecting how CD4-induced conformational changes in one protomer affect the opening of adjacent protomers) and virion trimer number distributions, while experiments were limited to pseudoviruses. Here, we factored these two parameters into our models and included replication-competent virions. We provided simultaneous estimates of T and S under varying trimer number distributions and offered 2D stoichiometry maps for different Env strains. Our results depicted the interplay between viral infectivity and stoichiometry tuned by the number of trimers per virion. The estimates for all tested Env strains were prevalently higher (T ≥ 7 for BG505 or JR-FL, T ≥ 13 for NL4-3) than reported. A high degree of inter-protomer opening cooperativity was observed for the neutralization-sensitive NL4-3, while neutralization-resistant BG505 and JR-FL showed a low to intermediate degree. Entry stoichiometry and opening cooperativity were strikingly positive-correlated, implying tied inter-protomer and inter-Env cooperative interactions. Our findings provided an in-depth view of Env cooperativities during HIV-1 entry.IMPORTANCEThe sparsely distributed envelope (Env) trimers on the surface of HIV-1 work collaboratively to mediate viral entry into the host, the early step of infection. The number of interacting trimers with host receptors required for entry awaits elucidation. Here, we explored the cooperative interplay among and within Env trimers, shedding light on a previously overlooked dimension of HIV-1 entry. For the first time, we presented distributions of estimated parameters depicting the number of Env trimers and degrees of inter-protomer opening cooperativities using biologically relevant mathematic models combined with virion infectivity measurements. Our results demonstrated that the quantity of required functional trimers positively correlates with inter-protomer opening cooperativity, a feature conserved across various strains. Our findings underscore cooperative behavior as an inherent characteristic of Env dynamics during HIV-1 entry. These insights enhance our understanding of HIV-1 infection mechanisms and could inform strategies for developing effective inhibitors or neutralizing agents.
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Affiliation(s)
- Revansiddha H. Katte
- Department of Cellular and Molecular Biology, School of Medicine, The University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Wang Xu
- Department of Cellular and Molecular Biology, School of Medicine, The University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Yang Han
- Department of Cellular and Molecular Biology, School of Medicine, The University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Xinyu Hong
- Department of Cellular and Molecular Biology, School of Medicine, The University of Texas at Tyler Health Science Center, Tyler, Texas, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, The University of Texas at Tyler Health Science Center, Tyler, Texas, USA
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7
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Qi Y, Zhang S, Wang K, Ding H, Zhang Z, Anang S, Nguyen HT, Kappes JC, Sodroski J, Mao Y. The membrane-proximal external region of human immunodeficiency virus (HIV-1) envelope glycoprotein trimers in A18-lipid nanodiscs. Commun Biol 2025; 8:442. [PMID: 40089599 PMCID: PMC11910548 DOI: 10.1038/s42003-025-07852-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 02/28/2025] [Indexed: 03/17/2025] Open
Abstract
During human immunodeficiency virus (HIV-1) entry, the metastable pretriggered envelope glycoprotein (Env) trimer ((gp120/gp41)3) opens asymmetrically. We present cryo-EM structures of cleaved asymmetric Env trimers in amphipol-lipid nanodiscs. The gp41 membrane-proximal external region (MPER) could be traced in Env protomers that remained close to the nanodisc despite Env tilting. The MPER interacts with the gp120 C-termini and gp41 α9 helices at the base of the Env trimer. MPER conformation is coupled with the tilt angles of the α9 helices, the helicity of the gp41 heptad repeat (HR1N) regions, and the opening angles between the protomers of the asymmetric trimers. Our structural models explain the stabilizing effects of MPER integrity and Env proteolytic maturation on the pretriggered Env conformation. Superimposed on the asymmetry of the Env protomers, variation in the glycans at the trimer apex creates substantial structural heterogeneity in the V2 quaternary epitopes of difficult-to-elicit broadly neutralizing antibodies.
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Affiliation(s)
- Yi Qi
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Kunyu Wang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China
- Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Zhiqing Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Hanh T Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Youdong Mao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
- Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China.
- National Biomedical Imaging Center, Peking University, Beijing, China.
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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8
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Lee YZ, Zhang YN, Newby ML, Ward G, Gomes KB, Auclair S, DesRoberts C, Allen JD, Ward AB, Stanfield RL, He L, Crispin M, Wilson IA, Zhu J. Rational design of next-generation filovirus vaccines with glycoprotein stabilization, nanoparticle display, and glycan modification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.02.641072. [PMID: 40060701 PMCID: PMC11888476 DOI: 10.1101/2025.03.02.641072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/16/2025]
Abstract
Filoviruses pose a significant threat to human health with frequent outbreaks and high mortality. Although two vector-based vaccines are available for Ebola virus, a broadly protective filovirus vaccine remains elusive. In this study, we evaluate a general strategy for stabilizing glycoprotein (GP) structures of Ebola, Sudan, and Bundibugyo ebolaviruses and Ravn marburgvirus. A 3.2 Å-resolution crystal structure provides atomic details for the redesigned Ebola virus GP, and cryo-electron microscopy reveals how a pan-ebolavirus neutralizing antibody targets a conserved site on the Sudan virus GP (3.13 Å-resolution), in addition to a low-resolution model of antibody-bound Ravn virus GP. A self-assembling protein nanoparticle (SApNP), I3-01v9, is redesigned at the N-terminus to allow the optimal surface display of filovirus GP trimers. Following detailed in vitro characterization, the lymph node dynamics of Sudan virus GP and GP-presenting SApNPs are investigated in a mouse model. Compared with soluble GP trimer, SApNPs show ~112 times longer retention in lymph node follicles, up-to-28 times greater presentation on follicular dendritic cell dendrites, and up-to-3 times stronger germinal center reactions. Functional antibody responses induced by filovirus GP trimers and SApNPs bearing wildtype and modified glycans are assessed in mice. Our study provides a foundation for next-generation filovirus vaccine development.
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Affiliation(s)
- Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maddy L. Newby
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Garrett Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Sarah Auclair
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Connor DesRoberts
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joel D. Allen
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Uvax Bio, LLC, Newark, DE 19702, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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9
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Hesselman MC, Zeeb M, Rusert P, Pasin C, Mamrosh J, Kariuki S, Pichler I, Sickmann M, Kaufmann MM, Schmidt D, Friedrich N, Metzner KJ, Rindler A, Kuster H, Adams C, Thebus R, Huber M, Yerly S, Leuzinger K, Perreau M, Koller R, Dollenmaier G, Frigerio S, Westfall DH, Deng W, deCamp AC, Juraska M, Edupuganti S, Mgodi N, Murrell H, Garrett N, Wagh K, Mullins JI, Williamson C, Moore PL, Günthard HF, Kouyos RD, Trkola A. Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development. Cell Host Microbe 2025; 33:279-293.e6. [PMID: 39909038 DOI: 10.1016/j.chom.2025.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 11/26/2024] [Accepted: 01/09/2025] [Indexed: 02/07/2025]
Abstract
Identifying HIV-1 envelope (Env) traits associated with neutralization cross-reactivity is crucial for vaccine design. Variable loops 1 and 2 (V1V2), positioned at the Env trimer apex, are key regions linked to neutralization. We describe non-canonical cysteine (Cys) residues in V1 that are enriched in individuals with elite neutralization breadth. Analyzing over 65,000 V1 sequences from the CATNAP database, AMP trials, and longitudinal HIV-1 cohorts (SHCS, ZPHI, and CAPRISA), we found that Env variants with extra V1 Cys are present at low levels and fluctuate over time. Extra V1 Cys associate with elite plasma neutralization, and two additional Cys are preferred, suggesting stabilization through disulfide bonds. Among 34 broadly neutralizing antibody (bnAb)-inducer Envs, 17.6% had elongated V1 regions with extra Cys. These extra Cys moderately increased neutralization resistance and altered bnAb epitope accessibility. Collectively, altering epitope exposure alongside Env stabilization renders the V1 twin Cys motif a promising feature for HIV-1 bnAb immunogens.
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Affiliation(s)
- Maria C Hesselman
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Marius Zeeb
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Jennifer Mamrosh
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Samuel Kariuki
- Department of Biological Sciences, School of Science, University of Eldoret, 30100 Eldoret, Kenya; Institute for Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, 7925 Cape Town, South Africa
| | - Ian Pichler
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Michèle Sickmann
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Masako M Kaufmann
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Daniel Schmidt
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Nikolas Friedrich
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Audrey Rindler
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Herbert Kuster
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Craig Adams
- Institute for Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, 7925 Cape Town, South Africa
| | - Ruwayhida Thebus
- Institute for Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, 7925 Cape Town, South Africa
| | - Michael Huber
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, 1205 Geneva, Switzerland
| | | | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, 1011 Lausanne, Switzerland
| | - Roger Koller
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | | | - Simona Frigerio
- Institute of Laboratory Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
| | - Dylan H Westfall
- Department of Microbiology at the University of Washington, Seattle, WA 98195, USA
| | - Wenjie Deng
- Department of Microbiology at the University of Washington, Seattle, WA 98195, USA
| | | | | | - Srilatha Edupuganti
- Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
| | - Nyaradzo Mgodi
- University of Zimbabwe Clinical Trials Research Centre, Harare, Zimbabwe; University of California, San Francisco, San Francisco, CA 94115, USA
| | - Hugh Murrell
- Institute for Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, 7925 Cape Town, South Africa
| | - Nigel Garrett
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, 4041 Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Kshitij Wagh
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James I Mullins
- Department of Microbiology at the University of Washington, Seattle, WA 98195, USA
| | - Carolyn Williamson
- Institute for Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, 7925 Cape Town, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Penny L Moore
- SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, 2050 Johannesburg, South Africa; National Institute for Communicable Disease of the National Health Laboratory Services, 2192 Johannesburg, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), 8091 Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), 8057 Zurich, Switzerland.
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10
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Pollock KM, Cheeseman HM, McFarlane LR, Day S, Tolazzi M, Turner HL, Joypooranachandran J, Shramko K, Dispinseri S, Mundsperger P, Bontjer I, Lemm NM, Coelho S, Tanaka M, Cole T, Korber B, Katinger D, Sattentau QJ, Ward AB, Scarlatti G, Sanders RW, Shattock RJ. Experimental medicine study with stabilised native-like HIV-1 Env immunogens drives long-term antibody responses, but lacks neutralising breadth. EBioMedicine 2025; 112:105544. [PMID: 39753033 PMCID: PMC11753977 DOI: 10.1016/j.ebiom.2024.105544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 11/19/2024] [Accepted: 12/19/2024] [Indexed: 01/26/2025] Open
Abstract
BACKGROUND We report findings from an experimental medicine study of rationally designed prefusion stabilised native-like HIV envelope glycoprotein (Env) immunogens, representative of global circulating strains, delivered by sequential intramuscular injection. METHODS Healthy adult volunteers were enrolled into one of five groups (A to E) each receiving a different schedule of one of two consensus Env immunogens (ConM SOSIP, ConS UFO, either unmodified or stabilised by chemical cross-linking, followed by a boost with two mosaic Env immunogens (Mos3.1 and Mos3.2). All immunogens were co-formulated with liposomal Monophosphoryl-Lipid A (MPLA) adjuvant, and volunteers were followed up for 28 days post final Mosaic booster injection. Participants gave written informed consent to join the study. The study is registered on ClinicalTrials.gov ID NCT03816137. FINDINGS Fifty-one participants (men n = 23 and women n = 28) aged 18-55 were enrolled. The seroconversion rate against Env was 100% with all participants having measurable anti-Env IgG antibodies after their second injection and throughout the study. Neutralisation was detected against the ConM pseudovirus in sera of those who had received both ConM and ConS immunogens. However, this activity was limited in breadth and was neither boosted nor broadened in those receiving the Mos3.1 and Mos3.2 immunogens. Neutralising antibody function correlated with binding to V1/V3 and V5 epitopes and peaked after the third injection. INTERPRETATION Rationally designed prefusion-stabilised native-like Env trimers are robustly immunogenic in a prime-boost schedule. When given alone they are insufficient to induce neutralising antibody titres of significant breadth, but they represent potentially valuable polishing immunogens after germline-targeting. FUNDING European Aids Vaccine initiative (EAVI2020) received funding from EU Horizon 2020, grant number 681137. Structural studies were supported by the Bill and Melinda Gates Foundation (INV-002916).
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Affiliation(s)
- Katrina M Pollock
- Imperial College London, Department of Infectious Disease, UK; NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK
| | | | | | - Suzanne Day
- Imperial College London, Department of Infectious Disease, UK
| | - Monica Tolazzi
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - Stefania Dispinseri
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Ilja Bontjer
- Department of Medical Microbiology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands
| | - Nana-Marie Lemm
- NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK
| | - Sofia Coelho
- NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK
| | - Maniola Tanaka
- NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK
| | - Tom Cole
- NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK
| | | | - Dietmar Katinger
- Polymun Scientific Immunbiologische Forschung GmbH, Klosterneuburg, Austria
| | - Quentin J Sattentau
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands
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11
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Boomgarden AC, Upadhyay C. Progress and Challenges in HIV-1 Vaccine Research: A Comprehensive Overview. Vaccines (Basel) 2025; 13:148. [PMID: 40006695 PMCID: PMC11860913 DOI: 10.3390/vaccines13020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 01/20/2025] [Accepted: 01/28/2025] [Indexed: 02/27/2025] Open
Abstract
The development of an effective HIV-1 vaccine remains a formidable challenge in biomedical research. Despite significant advancements in our understanding of HIV biology and pathogenesis, progress has been impeded by factors such as the virus's genetic diversity, high mutation rates, and its ability to establish latent reservoirs. Recent innovative approaches, including mosaic vaccines and mRNA technology to induce broadly neutralizing antibodies, have shown promise. However, the efficacy of these vaccines has been modest, with the best results achieving approximately 30% effectiveness. Ongoing research emphasizes the necessity of a multifaceted strategy to overcome these obstacles and achieve a breakthrough in HIV-1 vaccine development. This review summarizes current approaches utilized to further understand HIV-1 biology and to create a global vaccine. We discuss the impact of these approaches on vaccine development for other diseases, including COVID-19, influenza, and Zika virus. Additionally, we highlight the specific limitations faced with each approach and present the methods researchers employ to overcome these challenges. These innovative techniques, which have demonstrated preclinical and clinical success, have advanced the field closer to the ultimate goal of developing a global HIV-1 vaccine. Leveraging these advancements will enable significant strides in combating HIV-1 and other infectious diseases, ultimately improving global health outcomes.
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Affiliation(s)
| | - Chitra Upadhyay
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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12
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Mason RD, Zhang B, Morano NC, Shen CH, McKee K, Heimann A, Du R, Nazzari AF, Hodges S, Kanai T, Lin BC, Louder MK, Doria-Rose NA, Zhou T, Shapiro L, Roederer M, Kwong PD, Gorman J. Structural development of the HIV-1 apex-directed PGT145-PGDM1400 antibody lineage. Cell Rep 2025; 44:115223. [PMID: 39826122 PMCID: PMC11883830 DOI: 10.1016/j.celrep.2024.115223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 11/23/2024] [Accepted: 12/29/2024] [Indexed: 01/22/2025] Open
Abstract
Broadly neutralizing antibodies (bNAbs) targeting the apex of the HIV-1-envelope (Env) trimer comprise the most potent category of HIV-1 bNAbs and have emerged as promising therapeutics. Here, we investigate the development of the HIV-1 apex-directed PGT145-PGDM1400 antibody lineage and report cryo-EM structures at 3.4 Å resolution of PGDM1400 and of an improved PGT145 variant (PGT145-R100aS), each bound to the BG505 Env trimer. Cross-species-based engineering improves PGT145 IC80 breadth to near that of PGDM1400. Despite similar breadth and potency, the two antibodies differ in their residue-level interactions with important apex features, including N160 glycans and apex cavity, with residue 100i of PGT145 (sulfated tyrosine) penetrating ∼7 Å farther than residue 100i of PGDM1400 (aspartic acid). While apex-directed bNAbs from other donors use maturation pathways that often converge on analogous residue-level recognition, our results demonstrate that divergent residue-level recognition can occur within the same lineage, thereby enabling improved coverage of escape variants.
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Affiliation(s)
- Rosemarie D Mason
- 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
| | - Nicholas C Morano
- Aaron Diamond AIDS Research Center and Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Chen-Hsiang Shen
- 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
| | - Ashley Heimann
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renguang Du
- 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
| | - Shelby Hodges
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Tapan Kanai
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, 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
| | - Nicole A Doria-Rose
- 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
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center and 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
| | - 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 and Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
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13
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Ramezani-Rad P, Cottrell CA, Marina-Zárate E, Liguori A, Landais E, Torres JL, Myers A, Lee JH, Baboo S, Flynn C, McKenney K, Salcedo E, Zhou X, Kalyuzhniy O, Georgeson E, Phelps N, Lu D, Eskandarzadeh S, Menis S, Kubitz M, Groschel B, Alavi N, Jackson AM, Lee WH, Tran AS, Ben-Akiva E, Michaels KK, Diedrich JK, Enemuo CA, Lewis V, Pradhan A, Kasturi SP, Schiffner T, Steichen JM, Carnathan DG, Himansu S, Yates JR, Paulson JC, Ozorowski G, Irvine DJ, Silvestri G, Sok D, Ward AB, Crotty S, Schief WR. Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.24.634423. [PMID: 39896562 PMCID: PMC11785158 DOI: 10.1101/2025.01.24.634423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. Nearly all vaccine strategies to induce bnAbs require the use of relatively complex immunization regimens involving a series of different immunogens, most of which are Env trimers. Producing protein-based clinical material to evaluate such relatively complex regimens in humans presents major challenges in cost and time. Furthermore, immunization with HIV trimers as soluble proteins induces strong non-neutralizing responses to the trimer base, which is normally occluded on the virion. These base responses could potentially detract from the induction of nAbs and the eventual induction of bnAbs. mRNA vaccine platforms offer potential advantages over protein delivery for HIV vaccine development, including increased production speed, reduced cost, and the ability to deliver membrane-bound trimers that might facilitate improved immuno-focusing to non-base epitopes. We report the design of mRNA-delivered soluble and membrane-bound forms of a stabilized native-like Env trimer (BG505 MD39.3), initial immunogenicity evaluation in rabbits that triggered clinical evaluation, and more comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates. mRNA-encoded membrane-bound Env immunization elicited reduced off-target base-directed Env responses and stronger neutralizing antibody responses, compared with mRNA-encoded soluble Env. Overall, mRNA delivery of membrane-bound Env appears promising for enhancing B cell responses to subdominant epitopes and facilitating rapid translation to clinical testing, which should assist HIV vaccine development.
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Affiliation(s)
- Parham Ramezani-Rad
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A. Cottrell
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ester Marina-Zárate
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Elise Landais
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amber Myers
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeong Hyun Lee
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Sabyasachi Baboo
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Claudia Flynn
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Katherine McKenney
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Eugenia Salcedo
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Xiaoya Zhou
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Oleksandr Kalyuzhniy
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Erik Georgeson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole Phelps
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Danny Lu
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Michael Kubitz
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Nushin Alavi
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Abigail M. Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andy S. Tran
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elana Ben-Akiva
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Jolene K. Diedrich
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chiamaka A. Enemuo
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Vanessa Lewis
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Arpan Pradhan
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Sudhir Pai Kasturi
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Torben Schiffner
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Jon M. Steichen
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Diane G. Carnathan
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | | | - John R. Yates
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C. Paulson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Darrell J. Irvine
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Guido Silvestri
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
| | - Andrew B. Ward
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - William R. Schief
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, San Diego, CA 92121, USA
- Moderna, Inc. Cambridge, MA 02139, USA
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14
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Kumar S, del Moral-Sánchez I, Singh S, Newby ML, Allen JD, Bijl TPL, Vaghani Y, Jing L, Lodha R, Ortlund EA, Crispin M, Patel A, Sanders RW, Luthra K. The Design and Immunogenicity of an HIV-1 Clade C Pediatric Envelope Glycoprotein Stabilized by Multiple Platforms. Vaccines (Basel) 2025; 13:110. [PMID: 40006657 PMCID: PMC11860714 DOI: 10.3390/vaccines13020110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 01/08/2025] [Accepted: 01/20/2025] [Indexed: 02/27/2025] Open
Abstract
BACKGROUND Elite-neutralizer-derived HIV-1 envelopes (Envs), which induce broadly neutralizing antibodies (bnAbs), can inform HIV-1 vaccine design by serving as templates for bnAb-eliciting vaccines. Since single Env-based immunizations are insufficient to induce bnAb responses, sequential regimens using multivalent immunogens or Env cocktails hold greater promise. This underscores the need to develop stable Env trimers from diverse HIV-1 strains, particularly clade-C, which accounts for 50% of global infections and over 90% in India and South Africa. While various platforms exist to stabilize soluble Env trimers for use as antigenic baits and vaccines, stabilizing clade C trimers remains challenging. METHODS We stabilized an HIV-1 clade C trimer based on an Env isolated from a pediatric elite neutralizer (AIIMS_329) using multiple platforms, including SOSIP.v8.2, ferritin nanoparticles (NPs) and I53-50 two-component NPs, followed by characterization of their biophysical, antigenic, and immunogenic properties. RESULTS The stabilized 329 Envs showed binding to multiple HIV-1 bnAbs, with negligible binding to non-neutralizing antibodies. Negative-stain electron microscopy confirmed the native-like conformation of the Envs. Multimerization of 329 SOSIP.v8.2 on ferritin and two-component I53-50 NPs improved the affinity to HIV-1 bnAbs and showed higher immunogenicity in rabbits. CONCLUSIONS The soluble 329 Env protein could serve as an antigenic bait, and multimeric 329 NP Envs are potential vaccine candidates.
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Affiliation(s)
- Sanjeev Kumar
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.K.); (I.d.M.-S.); (T.P.L.B.)
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India;
- Department of Pediatrics, Division of Infectious Diseases, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Iván del Moral-Sánchez
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.K.); (I.d.M.-S.); (T.P.L.B.)
- Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, The Netherlands
| | - Swarandeep Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India;
| | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (M.L.N.); (J.D.A.); (M.C.)
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (M.L.N.); (J.D.A.); (M.C.)
| | - Tom P. L. Bijl
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.K.); (I.d.M.-S.); (T.P.L.B.)
- Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, The Netherlands
| | - Yog Vaghani
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; (Y.V.); (L.J.); (E.A.O.); (A.P.)
| | - Liang Jing
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; (Y.V.); (L.J.); (E.A.O.); (A.P.)
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India;
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; (Y.V.); (L.J.); (E.A.O.); (A.P.)
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; (M.L.N.); (J.D.A.); (M.C.)
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; (Y.V.); (L.J.); (E.A.O.); (A.P.)
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.K.); (I.d.M.-S.); (T.P.L.B.)
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India;
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15
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Jamieson PJ, Shen X, Abu-Shmais AA, Wasdin PT, Janowska K, Edwards RJ, Scapellato G, Richardson SI, Manamela NP, Liu S, Barr M, Gillespie RA, Mimms J, Suryadevara N, Sornberger TA, Zost S, Parks R, Flaherty S, Janke AK, Howard BN, Suresh YP, Ruprecht RM, Crowe JE, Carnahan RH, Bailey JR, Masaru K, Haynes BF, Moore PL, Acharya P, Montefiori DC, Kalams SA, Lu S, Georgiev IS. Glycan-reactive antibodies isolated from human HIV-1 vaccine trial participants show broad pathogen cross-reactivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.17.633475. [PMID: 39896680 PMCID: PMC11785028 DOI: 10.1101/2025.01.17.633475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
HIV-1 continues to pose a significant global health challenge, requiring ongoing research into effective prevention and treatment strategies. Understanding the B cell repertoire that can be engaged upon vaccination in humans is crucial for the development of future preventive vaccines. In this study, PBMCs from HIV-negative participants in the multivalent HVTN124 human HIV-1 vaccine clinical trial were interrogated for HIV-reactive B cells using LIBRA-seq, a high-throughput B cell mapping technology. We report the discovery of glycan-reactive antibodies capable of neutralizing diverse heterologous HIV-1 virus strains. Further, isolated antibodies showed broad cross-reactivity against antigens from a variety of other pathogens, while remaining mostly negative on autoreactivity assays. The emerging class of glycan-reactive virus-neutralizing antibodies with exceptional breadth of pathogen cross-reactivity may present an effective target for vaccination at the population level.
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Affiliation(s)
- Parker J Jamieson
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alexandra A Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Perry T Wasdin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Katarzyna Janowska
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Garrett Scapellato
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Simone I Richardson
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Nelia P Manamela
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Shuying Liu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica Mimms
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Ty A Sornberger
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Seth Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shelby Flaherty
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alexis K Janke
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bethany N Howard
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yukthi P Suresh
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Ruth M Ruprecht
- Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Justin R Bailey
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kanekiyo Masaru
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Penny L Moore
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Priyamvada Acharya
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Spyros A Kalams
- Infectious Diseases Unit, Department of Internal Medicine; Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shan Lu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
- Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
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16
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Brown S, Antanasijevic A, Sewall LM, Garcia DM, Ferguson J, Brouwer PJM, Sanders RW, Ward AB. Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens. Sci Immunol 2025; 10:eadp5218. [PMID: 39823319 PMCID: PMC12057571 DOI: 10.1126/sciimmunol.adp5218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 12/10/2024] [Indexed: 01/19/2025]
Abstract
Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required.
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Affiliation(s)
- Sharidan Brown
- Department of Integrative, Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | | | - Leigh M. Sewall
- Department of Integrative, Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Daniel Montiel Garcia
- Department of Integrative, Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - James Ferguson
- Department of Integrative, Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Philip J. M. Brouwer
- Department of Integrative, Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam; Amsterdam, The Netherlands
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
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17
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Gristick HB, Hartweger H, Nishimura Y, Gavor E, Nagashima K, Koranda NS, Gnanapragasam PNP, Kakutani LM, Segovia L, Donau O, Keeffe JR, West AP, Martin MA, Nussenzweig MC, Bjorkman PJ. Design and characterization of HIV-1 vaccine candidates to elicit antibodies targeting multiple epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.632013. [PMID: 39829910 PMCID: PMC11741423 DOI: 10.1101/2025.01.08.632013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
A primary goal in the development of an AIDS vaccine is the elicitation of broadly neutralizing antibodies (bNAbs) that protect against diverse HIV-1 strains. To this aim, germline-targeting immunogens have been developed to activate bNAb precursors and initiate the induction of bNAbs. While most pre-clinical germline-targeting HIV-1 vaccine candidates only target a single bNAb precursor epitope, an effective HIV-1 vaccine will likely require bNAbs that target multiple epitopes on Env. Here, we report a newly designed germline-targeting Env SOSIP trimer, named 3nv.2, that targets three bNAb epitopes on Env: the CD4bs, V3, and V2 epitopes. 3nv.2 forms a stable trimeric Env and binds to bNAb precursors from each one of the desired epitopes. Importantly, immunization experiments in rhesus macaques and mice demonstrate 3nv.2 elicits the combined effects of its parent immunogens. Our results reported here provide a proof-of-concept for using a germline-targeting immunogen that targets three or more bNAb precursors and present a framework to develop improved next-generation HIV-1 vaccine candidates.
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18
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Odidika S, Pirkl M, Lengauer T, Schommers P. Current methods for detecting and assessing HIV-1 antibody resistance. Front Immunol 2025; 15:1443377. [PMID: 39835119 PMCID: PMC11743526 DOI: 10.3389/fimmu.2024.1443377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 12/10/2024] [Indexed: 01/22/2025] Open
Abstract
Antiretroviral therapy is the standard treatment for HIV, but it requires daily use and can cause side effects. Despite being available for decades, there are still 1.5 million new infections and 700,000 deaths each year, highlighting the need for better therapies. Broadly neutralizing antibodies (bNAbs), which are highly active against HIV-1, represent a promising new approach and clinical trials have demonstrated the potential of bNAbs in the treatment and prevention of HIV-1 infection. However, HIV-1 antibody resistance (HIVAR) due to variants in the HIV-1 envelope glycoproteins (HIV-1 Env) is not well understood yet and poses a critical problem for the clinical use of bNAbs in treatment. HIVAR also plays an important role in the future development of an HIV-1 vaccine, which will require elicitation of bNAbs to which the circulating strains are sensitive. In recent years, a variety of methods have been developed to detect, characterize and predict HIVAR. Structural analysis of antibody-HIV-1 Env complexes has provided insight into viral residues critical for neutralization, while testing of viruses for antibody susceptibility has verified the impact of some of these residues. In addition, in vitro viral neutralization and adaption assays have shaped our understanding of bNAb susceptibility based on the envelope sequence. Furthermore, in vivo studies in animal models have revealed the rapid emergence of escape variants to mono- or combined bNAb treatments. Finally, similar variants were found in the first clinical trials testing bNAbs for the treatment of HIV-1-infected patients. These structural, in vitro, in vivo and clinical studies have led to the identification and validation of HIVAR for almost all available bNAbs. However, defined assays for the detection of HIVAR in patients are still lacking and for some novel, highly potent and broad-spectrum bNAbs, HIVAR have not been clearly defined. Here, we review currently available approaches for the detection, characterization and prediction of HIVAR.
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Affiliation(s)
- Stanley Odidika
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
| | - Martin Pirkl
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Informatics and Saarland Informatics Campus, Saarbrücken, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
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19
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Foulkes C, Friedrich N, Ivan B, Stiegeler E, Magnus C, Schmidt D, Karakus U, Weber J, Günthard HF, Pasin C, Rusert P, Trkola A. Assessing bnAb potency in the context of HIV-1 envelope conformational plasticity. PLoS Pathog 2025; 21:e1012825. [PMID: 39836706 PMCID: PMC11774494 DOI: 10.1371/journal.ppat.1012825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 01/28/2025] [Accepted: 12/13/2024] [Indexed: 01/23/2025] Open
Abstract
For use in prevention and treatment, HIV-1 broadly neutralizing antibodies (bnAbs) have to overcome Env conformational heterogeneity of viral quasispecies and neutralize with constant high potency. Comparative analysis of neutralization data from the CATNAP database revealed a nuanced relationship between bnAb activity and Env conformational flexibility, with substantial epitope-specific variation of bnAb potency ranging from increased to decreased activity against open, neutralization-sensitive Env. To systematically investigate the impact of variability in Env conformation on bnAb potency we screened 126 JR-CSF point mutants for generalized neutralization sensitivity to weakly neutralizing antibodies (weak-nAbs) depending on trimer opening and plasma from people with chronic HIV-1 infection. 23 mutations resulted in a highly neutralization sensitive phenotype, which was associated with de-stabilization of the closed, prefusion conformation. Including 19 of these mutants into a Sensitivity Env mutant panel (SENSE-19), we classified bnAbs according to potency variations in response to trimer opening. To verify that these sensitivity patterns are independent of the in vitro assay system, replication-competent SENSE-19 mutant viruses were tested on primary CD4 T cells. While loss of potency on SENSE-19 was registered for bnAbs from several classes recognizing quaternary epitopes on pre-triggered Env, structural destabilization benefitted MPER bnAbs and other inhibitors known to have post-CD4 attachment neutralization activity. Importantly, for a subset of CD4bs bnAbs, and the interface bnAb PGT151, particularly low potency variation was noted, suggesting that Env conformational tolerance can be achieved but is not the rule. In summary, SENSE-19 screens revealed distinct tolerance levels to Env conformational intermediates between bnAbs that provide mechanistic insights in their function and broaden current neutralization breadth assessments.
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Affiliation(s)
- Caio Foulkes
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Nikolas Friedrich
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Branislav Ivan
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Emanuel Stiegeler
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Carsten Magnus
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Daniel Schmidt
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Jacqueline Weber
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Huldrych F. Günthard
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), University of Zurich (UZH), Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), University of Zurich (UZH), Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
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20
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Rai P, Mehrotra S, Prajapati VK. Exploring immunotherapy to control human infectious diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 144:389-429. [PMID: 39978973 DOI: 10.1016/bs.apcsb.2024.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2025]
Abstract
Infectious diseases continue to pose significant challenges to global health, especially with the rise of antibiotic resistance and emerging pathogens. Traditional treatments, while effective, are often limited in the face of rapidly evolving pathogens. Immunotherapy, which harnesses and enhances the body's immune response, offers a promising alternative to conventional approaches for the treatment of infectious diseases. By employing use of monoclonal antibodies, vaccines, cytokine therapies, and immune checkpoint inhibitors, immunotherapy has demonstrated considerable potential in overcoming treatment resistance and improving patient outcomes. Key innovations, including the development of mRNA vaccines, use of immune modulators, adoptive cell transfer, and chimeric antigen receptor (CAR)-T cell therapy are paving the way for more targeted pathogen clearance. Further, combining immunotherapy with conventional antibiotic treatment has demonstrated effectiveness against drug-resistant strains, but this chapter explores the evolving field of immunotherapy for the treatment of bacterial, viral, fungal, and parasitic infections. The chapter also explores the recent breakthroughs and ongoing clinical trials in infectious disease immunotherapy.
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Affiliation(s)
- Praveen Rai
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, India.
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21
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Ding H, Nguyen HT, Li W, Deshpande A, Zhang S, Jiang F, Zhang Z, Anang S, Mothes W, Sodroski J, Kappes JC. Inducible cell lines producing replication-defective human immunodeficiency virus particles containing envelope glycoproteins stabilized in a pretriggered conformation. J Virol 2024; 98:e0172024. [PMID: 39508605 PMCID: PMC11650979 DOI: 10.1128/jvi.01720-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 10/16/2024] [Indexed: 11/15/2024] Open
Abstract
During the process by which human immunodeficiency virus (HIV-1) enters cells, the envelope glycoprotein (Env) trimer on the virion surface engages host cell receptors. Binding to the receptor CD4 induces Env to undergo transitions from a pretriggered, "closed" (State-1) conformation to more "open" (State 2/3) conformations. Most broadly neutralizing antibodies (bNAbs), which are difficult to elicit, recognize the pretriggered (State-1) conformation. More open Env conformations are recognized by poorly neutralizing antibodies (pNAbs), which are readily elicited during natural infection and vaccination with current Env immunogens. Env heterogeneity likely contributes to HIV-1 persistence by skewing antibody responses away from the pretriggered conformation. The conformationally flexible gp160 Env precursor on the infected cell or virion surface potentially presents multiple pNAb epitopes to the host immune system. Although proteolytic cleavage to produce the functional, mature Env trimer [(gp120/gp41)3] stabilizes State-1, many primary HIV-1 Envs spontaneously sample more open conformations. Here, we establish inducible cell lines that produce replication-defective HIV-1 particles with Env trimers stabilized in a pretriggered conformation. The mature Env is enriched on virus-like particles (VLPs). Using complementary approaches, we estimate an average of 25-50 Env trimers on each VLP. The stabilizing changes in Env limit the natural conformational heterogeneity of the VLP Env trimers, allowing recognition by bNAbs but not pNAbs. These defective VLPs provide a more homogeneous source of pretriggered Env trimers in a native membrane environment. Thus, these VLPs may facilitate the characterization of this functionally important Env conformation and its interaction with the immune system.IMPORTANCEA major impediment to the development of an effective HIV/AIDS vaccine is the inefficiency with which human immunodeficiency virus (HIV-1) envelope glycoproteins elicit antibodies that neutralize multiple virus strains. Neutralizing antibodies recognize a particular shape of the envelope glycoproteins that resides on the viral membrane before the virus engages the host cell. Here, we report the creation of stable cell lines that inducibly produce non-infectious HIV-like particles. The normally flexible envelope glycoprotein spikes on these virus-like particles have been stabilized in a conformation that is recognized by broadly neutralizing antibodies. These virus-like particles allow the study of the envelope glycoprotein conformation, its modification by sugars, and its ability to elicit desired neutralizing antibodies.
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Affiliation(s)
- Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hanh T. Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Ashlesha Deshpande
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Fan Jiang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zhiqing Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, Alabama, USA
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22
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Wang H, Cheng C, Dal Santo JL, Shen CH, Bylund T, Henry AR, Howe CA, Hwang J, Morano NC, Morris DJ, Pletnev S, Roark RS, Zhou T, Hansen BT, Hoyt FH, Johnston TS, Wang S, Zhang B, Ambrozak DR, Becker JE, Bender MF, Changela A, Chaudhary R, Corcoran M, Corrigan AR, Foulds KE, Guo Y, Lee M, Li Y, Lin BC, Liu T, Louder MK, Mandolesi M, Mason RD, McKee K, Nair V, O'Dell S, Olia AS, Ou L, Pegu A, Raju N, Rawi R, Roberts-Torres J, Sarfo EK, Sastry M, Schaub AJ, Schmidt SD, Schramm CA, Schwartz CL, Smith SC, Stephens T, Stuckey J, Teng IT, Todd JP, Tsybovsky Y, Van Wazer DJ, Wang S, Doria-Rose NA, Fischer ER, Georgiev IS, Karlsson Hedestam GB, Sheng Z, Woodward RA, Douek DC, Koup RA, Pierson TC, Shapiro L, Shaw GM, Mascola JR, Kwong PD. Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques. Cell 2024; 187:7214-7231.e23. [PMID: 39471811 PMCID: PMC11645223 DOI: 10.1016/j.cell.2024.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/03/2024] [Accepted: 10/02/2024] [Indexed: 11/01/2024]
Abstract
An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the fusion-peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45%-77% breadth (geometric mean 50% inhibitory dilution [ID50] ∼100) on a 208-strain panel. Molecular dissection of these responses by antibody isolation and cryo-electron microscopy (cryo-EM) structure determination revealed 15 of 16 antibody lineages with cross-clade neutralization to be directed toward the fusion-peptide site of vulnerability. In each macaque, isolated antibodies from memory B cells recapitulated the plasma-neutralizing response, with fusion-peptide-binding antibodies reaching breadths of 40%-60% (50% inhibitory concentration [IC50] < 50 μg/mL) and total lineage-concentrations estimates of 50-200 μg/mL. Longitudinal mapping indicated that these responses arose prior to SHIV infection. Collectively, these results provide in vivo molecular examples for one to a few B cell lineages affording potent, broadly neutralizing plasma responses.
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Affiliation(s)
- Hua Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James L Dal Santo
- 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
| | - Tatsiana Bylund
- 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
| | - Colin A Howe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juyun Hwang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas C Morano
- Department of Biochemistry and Molecular Biophysics and 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
| | - Daniel J Morris
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan S Roark
- Department of Biochemistry and Molecular Biophysics and 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
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bryan T Hansen
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Forrest H Hoyt
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Timothy S Johnston
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan E Becker
- Department of Biochemistry and Molecular Biophysics and 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
| | - Michael F Bender
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, 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
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Angela R Corrigan
- 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
| | - Yicheng Guo
- Department of Biochemistry and Molecular Biophysics and 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
| | - Myungjin Lee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bob C Lin
- 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
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rosemarie D Mason
- 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
| | - Vinod Nair
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, 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
| | - Li Ou
- 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
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesmine Roberts-Torres
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward K Sarfo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- 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
| | - Stephen D Schmidt
- 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
| | - Cindi L Schwartz
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Sarah C Smith
- 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
| | - Jonathan Stuckey
- 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
| | - John-Paul Todd
- 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
| | - David J Van Wazer
- 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
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth R Fischer
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics and 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
| | - Ruth A Woodward
- 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
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Theodore C Pierson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics and 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
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Modex Therapeutics Inc., Natick, MA 01760, 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 and 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.
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23
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Smith JC, Arunachalam PS, Legere TH, Cavacini LA, Hunter E, Pulendran B, Amara RR, Kozlowski PA. Induction of Tier 2 HIV-Neutralizing IgA Antibodies in Rhesus Macaques Vaccinated with BG505.664 SOSIP. Vaccines (Basel) 2024; 12:1386. [PMID: 39772048 PMCID: PMC11680376 DOI: 10.3390/vaccines12121386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 12/04/2024] [Accepted: 12/07/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND A goal of mucosal human immunodeficiency virus type 1 (HIV-1) vaccines is to generate mucosal plasma cells producing polymeric IgA (pIgA)-neutralizing antibodies at sites of viral entry. However, vaccine immunogens capable of eliciting IgA neutralizing antibodies (nAbs) that recognize tier 2 viral isolates have not yet been identified. METHODS To determine if stabilized native-like HIV-1 envelope (Env) trimers could generate IgA nAbs, we purified total IgA and IgG from the banked sera of six rhesus macaques that had been found in a previous study to develop serum nAbs after subcutaneous immunization with BG505.664 SOSIP and 3M-052 adjuvant, which is a TLR7/8 agonist. The neutralization of autologous tier 2 BG505 T332N pseudovirus by the IgA and IgG preparations was measured using the TZM-bl assay. Anti-SOSIP binding antibodies (bAbs) were measured by ELISA. RESULTS The IgG samples were found to have significantly greater levels of both nAb and bAb. However, after normalizing the nAb titer relative to the concentration of bAb, SOSIP-specific IgA purified from 2/6 animals was found to neutralize just as effectively as SOSIP-specific IgG, and in 3/6 animals, neutralization by the specific IgA was significantly greater. The more potent neutralization by IgA in these three animals was associated with a higher percentage of anti-SOSIP J chain-bound (polymeric) antibody. CONCLUSIONS The parenteral vaccination of nonhuman primates with BG505.664 SOSIP generates HIV-1 tier 2 IgA nAbs in serum, including SOSIP-specific polymeric IgA, which appears to neutralize more efficiently than monomeric IgA or IgG. Mucosal delivery of this SOSIP or other stable Env trimers could generate locally synthesized polymeric IgA nAbs in mucosal tissues and secretions.
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Affiliation(s)
- Justin C. Smith
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94304, USA;
| | - Traci H. Legere
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA;
| | - Lisa A. Cavacini
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA;
| | - Eric Hunter
- Emory Vaccine Center, Department of Pathology and Laboratory Medicine, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA;
| | - Bali Pulendran
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA;
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Rama R. Amara
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA;
| | - Pamela A. Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA;
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24
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DeLaitsch AT, Keeffe JR, Gristick HB, Lee JA, Ding W, Liu W, Skelly AN, Shaw GM, Hahn BH, Björkman PJ. Neutralizing antibodies elicited in macaques recognize V3 residues on altered conformations of HIV-1 Env trimer. NPJ Vaccines 2024; 9:240. [PMID: 39638818 PMCID: PMC11621127 DOI: 10.1038/s41541-024-01038-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 11/26/2024] [Indexed: 12/07/2024] Open
Abstract
Eliciting broadly neutralizing antibodies that protect against diverse HIV-1 strains is a primary goal of AIDS vaccine research. We characterized Ab1456 and Ab1271, two heterologously-neutralizing antibodies elicited in non-human primates by priming with an engineered V3-targeting SOSIP Env immunogen and boosting with increasingly native-like SOSIP Envs derived from different strain backgrounds. Structures of Env trimers in complex with these antibodies revealed V3 targeting, but on conformational states of Env distinct from the typical closed, prefusion trimeric SOSIP structure. Env trimers bound by Ab1456 adopted conformations resembling CD4-bound open Env states in the absence of soluble CD4, whereas trimers bound by Ab1271 exhibited a trimer apex-altered conformation to accommodate antibody binding. The finding that elicited antibodies cross-neutralized by targeting altered, non-closed, prefusion Env trimer conformations provides important information about Env dynamics that is relevant for HIV-1 vaccine design aimed at raising antibodies to desired epitopes on closed pre-fusion Env trimers.
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Affiliation(s)
- Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Juliet A Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wenge Ding
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Weimin Liu
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashwin N Skelly
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Pamela J Björkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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25
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Grobben M, Bakker M, Schriek AI, Levels LJ, Umotoy JC, Tejjani K, van Breemen MJ, Lin RN, de Taeye SW, Ozorowski G, Kootstra NA, Ward AB, Kent SJ, Hogarth PM, Wines BD, Sanders RW, Chung AW, van Gils MJ. Polyfunctionality and breadth of HIV-1 antibodies are associated with delayed disease progression. PLoS Pathog 2024; 20:e1012739. [PMID: 39661636 PMCID: PMC11634010 DOI: 10.1371/journal.ppat.1012739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 11/09/2024] [Indexed: 12/13/2024] Open
Abstract
HIV-1 infection leads to chronic disease requiring life-long treatment and therefore alternative therapeutics, a cure and/or a protective vaccine are needed. Antibody-mediated effector functions could have a role in the fight against HIV-1. However, the properties underlying the potential beneficial effects of antibodies during HIV-1 infection are poorly understood. To identify a specific profile of antibody features associated with delayed disease progression, we studied antibody polyfunctionality during untreated HIV-1 infection in the well-documented Amsterdam Cohort Studies. Serum samples were analyzed from untreated individuals with HIV-1 at approximately 6 months (n = 166) and 3 years (n = 382) post-seroconversion (post-SC). A Luminex antibody Fc array was used to profile 15 different Fc features for serum antibodies against 20 different HIV-1 envelope glycoprotein antigens and the resulting data was also compared with data on neutralization breadth. We found that high HIV-1 specific IgG1 levels and low IgG2 and IgG4 levels at 3 years post-SC were associated with delayed disease progression. Moreover, delayed disease progression was associated with a broad and polyfunctional antibody response. Specifically, the capacity to interact with all Fc γ receptors (FcγRs) and C1q, and in particular with FcγRIIa, correlated positively with delayed disease progression. There were strong correlations between antibody Fc features and neutralization breadth and several antibody features that were associated with delayed disease progression were also associated with the development of broad and potent antibody neutralization. In summary, we identified a strong association between broad, polyfunctional antibodies and delayed disease progression. These findings contribute new information for the fight against HIV-1, especially for new antibody-based therapy and cure strategies.
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Affiliation(s)
- Marloes Grobben
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Margreet Bakker
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Angela I. Schriek
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Liesbeth J.J. Levels
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Jeffrey C. Umotoy
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Khadija Tejjani
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Mariëlle J. van Breemen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Ryan N. Lin
- The Scripps Research Institute, Department of Structural Biology and Computational Biology, La Jolla, California, United States of America
| | - Steven W. de Taeye
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Gabriel Ozorowski
- The Scripps Research Institute, Department of Structural Biology and Computational Biology, La Jolla, California, United States of America
| | - Neeltje A. Kootstra
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Experimental Immunology, Amsterdam, The Netherlands
| | - Andrew B. Ward
- The Scripps Research Institute, Department of Structural Biology and Computational Biology, La Jolla, California, United States of America
| | - Stephen J. Kent
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Department of Microbiology and Immunology, Melbourne, Australia
- Alfred Hospital and Central Clinical School, Monash University, Melbourne Sexual Health Centre and Department of Infectious Diseases, Melbourne, Australia
| | - P. Mark Hogarth
- Burnet Institute, Immune Therapies Group, Melbourne, Australia
- Central Clinical School, Monash University, Department of Immunology, Melbourne, Australia
| | - Bruce D. Wines
- Burnet Institute, Immune Therapies Group, Melbourne, Australia
- Central Clinical School, Monash University, Department of Immunology, Melbourne, Australia
| | - Rogier W. Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Weill Medical College of Cornell University, Department of Microbiology and Immunology, New York, New York, United States of America
| | - Amy W. Chung
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Department of Microbiology and Immunology, Melbourne, Australia
| | - Marit J. van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
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26
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Gupta A, Rudra A, Reed K, Langer R, Anderson DG. Advanced technologies for the development of infectious disease vaccines. Nat Rev Drug Discov 2024; 23:914-938. [PMID: 39433939 DOI: 10.1038/s41573-024-01041-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2024] [Indexed: 10/23/2024]
Abstract
Vaccines play a critical role in the prevention of life-threatening infectious disease. However, the development of effective vaccines against many immune-evading pathogens such as HIV has proven challenging, and existing vaccines against some diseases such as tuberculosis and malaria have limited efficacy. The historically slow rate of vaccine development and limited pan-variant immune responses also limit existing vaccine utility against rapidly emerging and mutating pathogens such as influenza and SARS-CoV-2. Additionally, reactogenic effects can contribute to vaccine hesitancy, further undermining the ability of vaccination campaigns to generate herd immunity. These limitations are fuelling the development of novel vaccine technologies to more effectively combat infectious diseases. Towards this end, advances in vaccine delivery systems, adjuvants, antigens and other technologies are paving the way for the next generation of vaccines. This Review focuses on recent advances in synthetic vaccine systems and their associated challenges, highlighting innovation in the field of nano- and nucleic acid-based vaccines.
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Affiliation(s)
- Akash Gupta
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arnab Rudra
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kaelan Reed
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Langer
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel G Anderson
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA.
- Harvard and MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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27
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Pratap PP, Cottrell CA, Quinn J, Carnathan DG, Bader DLV, Tran AS, Enemuo CA, Ngo JT, Richey ST, Gao H, Shen X, Greene KM, Hurtado J, Michaels KK, Ben-Akiva E, Allen JD, Ozorowski G, Crispin M, Briney B, Montefiori D, Silvestri G, Irvine DJ, Crotty S, Ward AB. Immunofocusing on the conserved fusion peptide of HIV envelope glycoprotein in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.27.625755. [PMID: 39651156 PMCID: PMC11623688 DOI: 10.1101/2024.11.27.625755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
During infection, the fusion peptide (FP) of HIV envelope glycoprotein (Env) serves a central role in viral fusion with the host cell. As such, the FP is highly conserved and therefore an attractive epitope for vaccine design. Here, we describe a vaccination study in non-human primates (NHPs) where glycan deletions were made on soluble HIV Env to increase FP epitope exposure. When delivered via implantable osmotic pumps, this immunogen primed immune responses against the FP, which were then boosted with heterologous trimers resulting in a focused immune response targeting the conserved FP epitope. Although autologous immunizations did not elicit high affinity FP-targeting antibodies, the conserved FP epitope on a heterologous trimer further matured the lower affinity, FP-targeting B cells. This study suggests using epitope conservation strategies on distinct Env trimer immunogens can focus humoral responses on desired neutralizing epitopes and suppress immune-distracting antibody responses against non-neutralizing epitopes.
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28
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Mishra N, Avillion G, Callaghan S, DiBiase C, Hurtado J, Liendo N, Burbach S, Messmer T, Briney B. Conformational ensemble-based framework enables rapid development of Lassa virus vaccine candidates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.21.624760. [PMID: 39605488 PMCID: PMC11601624 DOI: 10.1101/2024.11.21.624760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Lassa virus (LASV), an arenavirus endemic to West Africa, poses a significant public health threat due to its high pathogenicity and expanding geographic risk zone. LASV glycoprotein complex (GPC) is the only known target of neutralizing antibodies, but its inherent metastability and conformational flexibility have hindered the development of GPC-based vaccines. We employed a variant of AlphaFold2 (AF2), called subsampled AF2, to generate diverse structures of LASV GPC that capture an array of potential conformational states using MSA subsampling and dropout layers. Conformational ensembles identified several metamorphic domains-areas of significant conformational flexibility-that could be targeted to stabilize the GPC in its immunogenic prefusion state. ProteinMPNN was then used to redesign GPC sequences to minimize the mobility of metamorphic domains. These redesigned sequences were further filtered using subsampled AF2, leading to the identification of promising GPC variants for further testing. A small library of redesigned GPC sequences was experimentally validated and showed significantly increased protein yields compared to controls. Antigenic profiles indicated these variants preserved essential epitopes for effective immune response, suggesting their potential for broad protective efficacy. Our results demonstrate that AI-driven approaches can predict the conformational landscape of complex pathogens. This knowledge can be used to stabilize viral proteins, such as LASV GPC, in their prefusion conformation, optimizing them for stability and expression, and offering a streamlined framework for vaccine design. Our deep learning / machine learning enabled framework contributes to global efforts to combat LASV and has broader implications for vaccine design and pandemic preparedness.
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Affiliation(s)
- Nitesh Mishra
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Gabriel Avillion
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Charlotte DiBiase
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Jonathan Hurtado
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Nathan Liendo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sarah Burbach
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Terrence Messmer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
- Multi-Omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA 92037 USA
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037 USA
- San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA 92037 USA
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29
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Lee YZ, Han J, Zhang YN, Ward G, Braz Gomes K, Auclair S, Stanfield RL, He L, Wilson IA, Zhu J. Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus. Nat Commun 2024; 15:9939. [PMID: 39550381 PMCID: PMC11569192 DOI: 10.1038/s41467-024-54287-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 11/04/2024] [Indexed: 11/18/2024] Open
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause human respiratory diseases and are major targets for vaccine development. In this study, we design uncleaved prefusion-closed (UFC) trimers for the fusion protein (F) of both viruses by examining mutations critical to F metastability. For RSV, we assess four previous prefusion F designs, including the first and second generations of DS-Cav1, SC-TM, and 847A. We then identify key mutations that can maintain prefusion F in a native-like, closed trimeric form (up to 76%) without introducing any interprotomer disulfide bond. For hMPV, we develop a stable UFC trimer with a truncated F2-F1 linkage and an interprotomer disulfide bond. Dozens of UFC constructs are characterized by negative-stain electron microscopy (nsEM), x-ray crystallography (11 RSV-F structures and one hMPV-F structure), and antigenic profiling. Using an optimized RSV-F UFC trimer as bait, we identify three potent RSV neutralizing antibodies (NAbs) from a phage-displayed human antibody library, with a public NAb lineage targeting sites Ø and V and two cross-pneumovirus NAbs recognizing site III. In mouse immunization, rationally designed RSV-F and hMPV-F UFC trimers induce robust antibody responses with high neutralizing titers. Our study provides a foundation for future prefusion F-based RSV and hMPV vaccine development.
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Affiliation(s)
- Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jerome Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Garrett Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Sarah Auclair
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Uvax Bio, LLC, Newark, DE, 19702, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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30
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Umotoy JC, Kroon PZ, Man S, van Dort KA, Atabey T, Schriek AI, Dekkers G, Herrera-Carrillo E, Geijtenbeek TB, Heukers R, Kootstra NA, van Gils MJ, de Taeye SW. Inhibition of HIV-1 replication by nanobodies targeting tetraspanin CD9. iScience 2024; 27:110958. [PMID: 39391729 PMCID: PMC11465043 DOI: 10.1016/j.isci.2024.110958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/05/2024] [Accepted: 09/10/2024] [Indexed: 10/12/2024] Open
Abstract
HIV-1 alters the dynamics and distribution of tetraspanins, a group of proteins integral to membrane organization, to facilitate both entry and egress. Notably, the tetraspanin CD9 is dysregulated during HIV-1 infection, correlating with multifaceted effects on viral replication. Here, we generated llama-derived nanobodies against CD9 to restrict HIV-1 replication. We immunized llamas with recombinant large extracellular loop of CD9 and identified eight clonally distinct nanobodies targeting CD9, each exhibiting a range of affinities and differential binding to cell surface-expressed CD9. Notably, nanobodies T2C001 and T2C002 demonstrated low nanomolar affinities and exhibited differential sensitivities against endogenous and overexpressed CD9 on the cell surface. Although CD9-directed nanobodies did not impede the early stages of HIV-1 life cycle, they effectively inhibited virus-induced syncytia formation and virus replication in T cells and monocyte-derived macrophages. This discovery opens new avenues for host-targeted therapeutic strategies, potentially augmenting existing antiretroviral treatments for HIV-1.
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Affiliation(s)
- Jeffrey C. Umotoy
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Pascal Z. Kroon
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Shirley Man
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Karel A. van Dort
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Tugba Atabey
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Angela I. Schriek
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Gillian Dekkers
- QVQ Holding BV, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Elena Herrera-Carrillo
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Teunis B.H. Geijtenbeek
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Raimond Heukers
- QVQ Holding BV, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
| | - Steven W. de Taeye
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, the Netherlands
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31
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Sajadi MM, Abbasi A, Tehrani ZR, Siska C, Clark R, Chi W, Seaman MS, Mielke D, Wagh K, Liu Q, Jumpa T, Ketchem RR, Nguyen DN, Tolbert WD, Pierce BG, Atkinson B, Deming D, Sprague M, Asakawa A, Ferrer D, Dunn Y, Calvillo S, Yin R, Guest JD, Korber B, Mayer BT, Sato AH, Ouyang X, Foulke S, Habibzadeh P, Karimi M, Aslanabadi A, Hojabri M, Saadat S, Zareidoodeji R, Kędzior M, Pozharski E, Heredia A, Montefiori D, Ferrari G, Pazgier M, Lewis GK, Jardine JG, Lusso P, DeVico A. A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618178. [PMID: 39464103 PMCID: PMC11507801 DOI: 10.1101/2024.10.14.618178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Anti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with "first generation" bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of "enhanced" antibodies will be required for optimal clinical utility, while preserving or enhancing cGMP manufacturing capability. Here we report the engineering of an anti-CD4 binding-site (CD4bs) bnAb, N49P9.3, purified from the plasma of an HIV elite-neutralizer. Through a series of rational modifications we produced a variant that demonstrates: enhanced potency; superior antiviral activity in combination with other bnAbs; low polyreactivity; and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.
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32
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Lembo A, Molinaro A, De Castro C, Berti F, Biagini M. Impact of glycosylation on viral vaccines. Carbohydr Polym 2024; 342:122402. [PMID: 39048237 DOI: 10.1016/j.carbpol.2024.122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.
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Affiliation(s)
- Antonio Lembo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy; GSK, Siena, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
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33
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Haryadi R, Chan KF, Lin PC, Tan YL, Wan C, Shahreel W, Tay SJ, Nguyen-Khuong T, Walsh I, Song Z. Generating and characterizing a comprehensive panel of CHO cells glycosylation mutants for advancing glycobiology and biotechnology research. Sci Rep 2024; 14:23068. [PMID: 39367021 PMCID: PMC11452509 DOI: 10.1038/s41598-024-73722-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 09/20/2024] [Indexed: 10/06/2024] Open
Abstract
This report describes the development and characterization of a comprehensive collection of CHO cell glycosylation mutants with significant potential for advancing glycobiology and biotechnology. EPO-Fc and trastuzumab, two model molecules, were produced using these mutants to assess the effects of mutated glycogenes, and LC-MS/MS analysis was employed to quantitatively analyse their N-glycans. EPO-Fc exhibited exclusively homogeneous Man9 glycans only when nearly all α-mannosidases in the genome were inactivated, except lysosomal MAN2B1. Some mutants lacking GnT-I activity produce mostly Man5 N-glycans, while their O-glycan and glycolipid profiles can differ due to other mutations in the cell. GnT-II deficiency prevents GnT-V from adding GlcNAc to the core N-glycan, resulting in branches attaching solely to the α1,3-linked mannose, leaving the α1,6-linked mannose free. The mutant-produced antibody's single-branched glycan contains more sialic acid than the dual-branched glycans produced in CHO-K1 cells. Trastuzumab produced in these mutants provided insights into how Fc N-glycans impact the antibody's interaction with FcγR1 and FcγR2a, FcγR3a, and their influence on antibody-dependent cellular cytotoxicity (ADCC). In the study of Fc glycans in Fc-FcγR1 and FcγR2a interactions, we observed a consistent glycan-related impact on binding to both receptors, indicating a common interaction mechanism between Fc glycans and both FcγRI and FcγRIIa. CHO mutants produced trimeric gp120 demonstrated distinct reactivity with multiple broadly neutralizing anti-HIV antibodies, confirming the involvement of gp120 glycans in interactions with specific broadly neutralizing antibodies. Finally, one of the mutants produced human β-glucocerebrosidase with uniform Man5 N-glycans, showcasing its potential for glycoengineered production and enhancement in therapeutic efficacy.
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Affiliation(s)
- Ryan Haryadi
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Kah Fai Chan
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Pao Chun Lin
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Yun Lei Tan
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Corrine Wan
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Wahyu Shahreel
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Terry Nguyen-Khuong
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Ian Walsh
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
| | - Zhiwei Song
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01, Centros, 138668, Singapore.
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Brinkkemper M, Kerster G, Brouwer PJM, Tran AS, Torres JL, Ettema RA, Nijhuis H, Allen JD, Zhu W, Gao H, Lee WH, Bijl TPL, Snitselaar JL, Burger JA, Bontjer I, Olijhoek W, Ravichandran R, van Breemen MJ, Del Moral-Sánchez I, Derking R, Sliepen K, Ozorowski G, Crispin M, Montefiori DC, Claireaux M, Ward AB, van Gils MJ, King NP, Sanders RW. Mosaic and mixed HIV-1 glycoprotein nanoparticles elicit antibody responses to broadly neutralizing epitopes. PLoS Pathog 2024; 20:e1012558. [PMID: 39361585 PMCID: PMC11449375 DOI: 10.1371/journal.ppat.1012558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 09/02/2024] [Indexed: 10/05/2024] Open
Abstract
An effective human immunodeficiency virus 1 (HIV-1) vaccine will most likely have to elicit broadly neutralizing antibodies (bNAbs) to overcome the sequence diversity of the envelope glycoprotein (Env). So far, stabilized versions of Env, such as SOSIP trimers, have been able to induce neutralizing antibody (NAb) responses, but those responses are mainly strain-specific. Here we attempted to broaden NAb responses by using a multivalent vaccine and applying a number of design improvements. First, we used highly stabilized SOSIP.v9 trimers. Second, we removed any holes in the glycan shields and optimized glycan occupancy to avoid strain-specific glycan hole responses. Third, we selected five sequences from the same clade (B), as we observed previously that combining Env trimers from clade A, B and C did not improve cross-reactive responses, as they might have been too diverse. Fourth, to improve antibody (Ab) responses, the Env trimers were displayed on two-component I53-50 nanoparticles (NPs). Fifth, to favor activation of cross-reactive B cells, the five Env trimers were co-displayed on mosaic NPs. Sixth, we immunized rabbits four times with long intervals between vaccinations. These efforts led to the induction of cross-reactive B cells and cross-reactive binding Ab responses, but we only sporadically detected cross-neutralizing responses. We conclude that stabilized HIV-1 Env trimers that are not modified specifically for priming naive B cells are unable to elicit strong bNAb responses, and infer that sequential immunization regimens, most likely starting with specific germline-targeting immunogens, will be necessary to overcome Env's defenses against the induction of NAbs. The antigens described here could be excellent boosting immunogens in a sequential immunization regimen, as responses to bNAb epitopes were induced.
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Affiliation(s)
- Mitch Brinkkemper
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Gius Kerster
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Philip J M Brouwer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Andy S Tran
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Roos A Ettema
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Haye Nijhuis
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Wenwen Zhu
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Hongmei Gao
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tom P L Bijl
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Jonne L Snitselaar
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Judith A Burger
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Marielle J van Breemen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Iván Del Moral-Sánchez
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Ronald Derking
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - David C Montefiori
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Mathieu Claireaux
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marit J van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Rogier W Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
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35
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Upadhyay C, Rao P, Behzadi MA, Feyznezhad R, Lambert GS, Kumar R, Kumar M, Yang W, Jiang X, Luo CC, Nadas A, Arthos J, Kong XP, Zhang H, Hioe CE, Duty JA. Signal peptide exchange alters HIV-1 envelope antigenicity and immunogenicity. Front Immunol 2024; 15:1476924. [PMID: 39380992 PMCID: PMC11458420 DOI: 10.3389/fimmu.2024.1476924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 09/09/2024] [Indexed: 10/10/2024] Open
Abstract
Introduction HIV-1 envelope (Env) is the key target for antibodies (Abs) against the virus and thus an important HIV-1 vaccine component. Env is synthesized from a gp160 precursor with a signal peptide (SP) at its N-terminus. This study investigated the influence of the SP on Env antigenicity and immunogenicity. Methods Env proteins from two HIV-1 isolates, AA05 and AC02, were analyzed as gp120 and gp160 in their native wild-type (WT) forms and as chimeras with swapped SPs (AA05-02 and AC02-05). The WT and chimeric Env were assessed for antigenicity and glycosylation using monoclonal antibodies (mAbs) and glycan probes. Immunogenicity was tested in mice using three vaccine types: gp120 protein, gp120 DNA+gp120 protein, and gp120 DNA+gp160 DNA. Results The recombinant AC02 gp120 protein was antigenically superior to AA05 as indicated by higher reactivity with most mAbs tested. When SPs were swapped, the antigenicity of the chimeric gp120s (AA05-02 and AC02-05) resembled that of the gp120s from which the SPs were derived; AA05-02 was similar to AC02 and vice versa. Glycan probe reactivity followed a similar pattern: AA05-02 and AC02 showed similar affinity to high-mannose specific mAbs and lectins. Interestingly, the antigenicity of gp160s showed an opposite pattern; membrane-bound gp160 expressed with the AA05 SP (AA05 and AC02-05) showed greater mAb binding than gp160 with the AC02 SP (AC02 and AA05-02). Mice immunized with gp120 protein showed that AA05-02 induced stronger cross-reactive binding Ab responses than AA05 WT, and AC02 elicited stronger responses than AC02-05, indicating AC02 SP enhanced gp120 immunogenicity. However, when DNA vaccines were included (gp120 DNA+gp120 protein and gp120 DNA+gp160 DNA), the use of heterologous SPs diminished the immunogenicity of the WT immunogens. Among the three vaccine regimens tested, only gp120 DNA+gp160 DNA immunization elicited low-level Tier 2 neutralizing Abs, with AA05 WT inducing Abs with greater neutralization capabilities than AA05-02. Conclusion These data demonstrate that the SP can significantly impact the antigenicity and immunogenicity of HIV-1 Env proteins. Hence, while SP swapping is a common practice in constructing Env immunogens, this study highlights the importance of careful consideration of the effects of replacing native SPs on the immunogenicity of Env vaccines.
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Affiliation(s)
- Chitra Upadhyay
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Priyanka Rao
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mohammad Amin Behzadi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Roya Feyznezhad
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gregory S. Lambert
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Rajnish Kumar
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Madhu Kumar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Xunqing Jiang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Christina C. Luo
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Arthur Nadas
- Department of Environment Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - James Arthos
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Catarina E. Hioe
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Research Service, James J. Peters VA Medical Center, Bronx, NY, United States
| | - J. Andrew Duty
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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36
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Gao Y, Zhu S, Li H, Hao X, Chen W, Pan D, Qian Z. AntigenBoost: enhanced mRNA-based antigen expression through rational amino acid substitution. Brief Bioinform 2024; 25:bbae468. [PMID: 39400114 PMCID: PMC11472322 DOI: 10.1093/bib/bbae468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/29/2024] [Accepted: 09/09/2024] [Indexed: 10/15/2024] Open
Abstract
Messenger RNA (mRNA) vaccines represent a groundbreaking advancement in immunology and public health, particularly highlighted by their role in combating the COVID-19 pandemic. Optimizing mRNA-based antigen expression is a crucial focus in this emerging industry. We have developed a bioinformatics tool named AntigenBoost to address the challenge posed by destabilizing dipeptides that hinder ribosomal translation. AntigenBoost identifies these dipeptides within specific antigens and provides a range of potential amino acid substitution strategies using a two-dimensional scoring system. Through a combination of bioinformatics analysis and experimental validation, we significantly enhanced the in vitro expression of mRNA-derived Respiratory Syncytial Virus fusion glycoprotein and Influenza A Hemagglutinin antigen. Notably, a single amino acid substitution improved the immune response in mice, underscoring the effectiveness of AntigenBoost in mRNA vaccine design.
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Affiliation(s)
- Yumiao Gao
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
| | - Siran Zhu
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
| | - Huichun Li
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
| | - Xueting Hao
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
| | - Wen Chen
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
| | - Deng Pan
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
| | - Zhikang Qian
- NanoRibo (Shanghai) Biotechnology Co., Ltd., No. 1188 Lianhang Road, Minhang District, Shanghai 200003, China
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Kumar S, del Moral-Sánchez I, Singh S, Newby ML, Allen JD, Bijl TPL, Vaghani Y, Jing L, Ortlund EA, Crispin M, Patel A, Sanders RW, Luthra K. Design and immunogenicity of an HIV-1 clade C pediatric envelope glycoprotein stabilized by multiple platforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.14.613016. [PMID: 39345501 PMCID: PMC11429718 DOI: 10.1101/2024.09.14.613016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Various design platforms are available to stabilize soluble HIV-1 envelope (Env) trimers, which can be used as antigenic baits and vaccine antigens. However, stabilizing HIV-1 clade C trimers can be challenging. Here, we stabilized an HIV-1 clade C trimer based on an Env isolated from a pediatric elite-neutralizer (AIIMS_329) using multiple platforms, including SOSIP.v8.2, ferritin nanoparticles (NP) and an I53-50 two-component NP, followed by characterization of their biophysical, antigenic, and immunogenic properties. The stabilized 329 Envs showed binding affinity to trimer-specific HIV-1 broadly neutralizing antibodies (bnAbs), with negligible binding to non-neutralizing antibodies (non-nAbs). Negative-stain electron microscopy (nsEM) confirmed the native-like conformation of the Envs. Multimerization of 329 SOSIP.v8.2 on ferritin and two-component I53-50 NPs improved the overall affinity to HIV-1 bnAbs and immunogenicity in rabbits. These stabilized HIV-1 clade C 329 Envs demonstrate the potential to be used as antigenic baits and as components of multivalent vaccine candidates in future.
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Affiliation(s)
- Sanjeev Kumar
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Iván del Moral-Sánchez
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, 1105AZ, The Netherlands
| | - Swarandeep Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom P. L. Bijl
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, 1105AZ, The Netherlands
| | - Yog Vaghani
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Liang Jing
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, 1105AZ, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
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38
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Rappuoli R, Alter G, Pulendran B. Transforming vaccinology. Cell 2024; 187:5171-5194. [PMID: 39303685 PMCID: PMC11736809 DOI: 10.1016/j.cell.2024.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 09/22/2024]
Abstract
The COVID-19 pandemic placed the field of vaccinology squarely at the center of global consciousness, emphasizing the vital role of vaccines as transformative public health tools. The impact of vaccines was recently acknowledged by the award of the 2023 Nobel Prize in Physiology or Medicine to Katalin Kariko and Drew Weissman for their seminal contributions to the development of mRNA vaccines. Here, we provide a historic perspective on the key innovations that led to the development of some 27 licensed vaccines over the past two centuries and recent advances that promise to transform vaccines in the future. Technological revolutions such as reverse vaccinology, synthetic biology, and structure-based design transformed decades of vaccine failures into successful vaccines against meningococcus B and respiratory syncytial virus (RSV). Likewise, the speed and flexibility of mRNA vaccines profoundly altered vaccine development, and the advancement of novel adjuvants promises to revolutionize our ability to tune immunity. Here, we highlight exciting new advances in the field of systems immunology that are transforming our mechanistic understanding of the human immune response to vaccines and how to predict and manipulate them. Additionally, we discuss major immunological challenges such as learning how to stimulate durable protective immune response in humans.
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Affiliation(s)
| | - Galit Alter
- Moderna Therapeutics, Cambridge, MA 02139, USA.
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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39
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Li D, Liu L, Ye X, Chen Y, Ren Q, Xu S, Ren Y, Cao H, Wang T. Intermediate open state of CD4-bound HIV-1 env heterotrimers in asia CRFs. Biochem Biophys Res Commun 2024; 725:150249. [PMID: 38880081 DOI: 10.1016/j.bbrc.2024.150249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 06/18/2024]
Abstract
The HIV-1 envelope glycoprotein (Env) plays crucial role in viral infection by facilitating viral attachment to host cells and inducing fusion of the virus with the host cell membrane. This fusion allows the HIV-1 viral genome to enter the target cell then triggering various stages of the viral life cycle. The native Env directly interacts with the main receptor CD4 and the co-receptor (CCR5 or CXCR4) in human cell membrane then induces membrane fusion. The elucidation of the structure of Env with CD4 and co-receptors in different HIV-1 subtypes is essential for the understanding of the mechanism of virus entry. Here we report the Cryo-EM structure of the CD4-bound HIV-1 heterotrimeric Env from Asia prevalent CRF07_BC CH119 strain. In this structure, the binding of three CD4 molecules with Env induced extensively conformational changes in gp120, resulting in the transformation of the Env from close state to intermediate open state. Additionally, the conformational shift of V1/V2 loops of the heterotrimeric Env allosterically expose the V3 loop and promoting the further interactions with co-receptor CCR5 or CXCR4. These findings not only illustrate the structural complexity and plasticity of HIV-1 Env but also give new insights how the biological trimeric Env initialize the immune recognition and membrane fusion.
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Affiliation(s)
- Dan Li
- School of basic medical Sciences, Capital Medical University, 10 Xitoutiao You'anMen Street, Beijing, 100069, China; Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - Li Liu
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China; Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China
| | - Xuejun Ye
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - Yuyang Chen
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - Qiaoju Ren
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - ShaoJian Xu
- Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China
| | - Yan Ren
- Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China
| | - He Cao
- Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China.
| | - Tao Wang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China; Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China; Key Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Nanshan District, Shenzhen, 518055, China.
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40
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Thakur B, Katte RH, Xu W, Janowska K, Sammour S, Henderson R, Lu M, Kwong PD, Acharya P. Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.14.613076. [PMID: 39314380 PMCID: PMC11419153 DOI: 10.1101/2024.09.14.613076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminal stretch of the envelope (Env) gp41 subunit 1-3 . The receptor-binding gp120 subunit of Env forms a heterodimer with gp41 and assembles into a trimer, in which FP is accessible for antibody binding 3 . Env conformational changes or "opening" that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibody 4 . The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains 5 , we visualized atomic-level details of a functional entry intermediate, where partially open Env was bound to receptor CD4, co-receptor mimetic antibody 17b, and FP-targeting antibody VRC34.01, demonstrating that FP remains antibody accessible despite substantial receptor-induced Env opening. We determined a series of structures delineating stepwise opening of Env from its closed state to a newly resolved intermediate and defining downstream re-organizations of the gp120-gp41 interface that ultimately resulted in FP burial in an antibody-inaccessible configuration. Our studies improve our understanding of HIV-1 entry and provide information on entry-related conformation reorganization of a key site of HIV vulnerability to neutralizing antibody.
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41
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Govindan R, Stephenson KE. HIV Vaccine Development at a Crossroads: New B and T Cell Approaches. Vaccines (Basel) 2024; 12:1043. [PMID: 39340073 PMCID: PMC11435826 DOI: 10.3390/vaccines12091043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 09/03/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
Despite rigorous scientific efforts over the forty years since the onset of the global HIV pandemic, a safe and effective HIV-1 vaccine remains elusive. The challenges of HIV vaccine development have proven immense, in large part due to the tremendous sequence diversity of HIV and its ability to escape from antiviral adaptive immune responses. In recent years, several phase 3 efficacy trials have been conducted, testing a similar hypothesis, e.g., that non-neutralizing antibodies and classical cellular immune responses could prevent HIV-1 acquisition. These studies were not successful. As a result, the field has now pivoted to bold novel approaches, including sequential immunization strategies to drive the generation of broadly neutralizing antibodies and human CMV-vectored vaccines to elicit MHC-E-restricted CD8+ T cell responses. Many of these vaccine candidates are now in phase 1 trials, with early promising results.
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Affiliation(s)
- Ramesh Govindan
- Division of Infectious Diseases and Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA;
| | - Kathryn E. Stephenson
- Division of Infectious Diseases and Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA;
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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42
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Altman PX, Ozorowski G, Stanfield RL, Haakenson J, Appel M, Parren M, Lee WH, Sang H, Woehl J, Saye-Francisco K, Sewall LM, Joyce C, Song G, Porter K, Landais E, Andrabi R, Wilson IA, Ward AB, Mwangi W, Smider VV, Burton DR, Sok D. Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire. PLoS Pathog 2024; 20:e1012042. [PMID: 39250525 PMCID: PMC11412654 DOI: 10.1371/journal.ppat.1012042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 09/19/2024] [Accepted: 08/12/2024] [Indexed: 09/11/2024] Open
Abstract
The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.
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Affiliation(s)
- Pilar X Altman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jeremy Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Applied Biomedical Science Institute, San Diego, California, United States of America
| | - Michael Appel
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Huldah Sang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medical, Kansas State University, Manhattan, Kansas, United States of America
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Karen Saye-Francisco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ian A Wilson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medical, Kansas State University, Manhattan, Kansas, United States of America
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Applied Biomedical Science Institute, San Diego, California, United States of America
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Global Health Investment Corporation, New York, New York, United States of America
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43
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Peter AS, Hoffmann DS, Klier J, Lange CM, Moeller J, Most V, Wüst CK, Beining M, Gülesen S, Junker H, Brumme B, Schiffner T, Meiler J, Schoeder CT. Strategies of rational and structure-driven vaccine design for Arenaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105626. [PMID: 38908736 PMCID: PMC12010953 DOI: 10.1016/j.meegid.2024.105626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/16/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
The COVID-19 outbreak has highlighted the importance of pandemic preparedness for the prevention of future health crises. One virus family with high pandemic potential are Arenaviruses, which have been detected almost worldwide, particularly in Africa and the Americas. These viruses are highly understudied and many questions regarding their structure, replication and tropism remain unanswered, making the design of an efficacious and molecularly-defined vaccine challenging. We propose that structure-driven computational vaccine design will contribute to overcome these challenges. Computational methods for stabilization of viral glycoproteins or epitope focusing have made progress during the last decades and particularly during the COVID-19 pandemic, and have proven useful for rational vaccine design and the establishment of novel diagnostic tools. In this review, we summarize gaps in our understanding of Arenavirus molecular biology, highlight challenges in vaccine design and discuss how structure-driven and computationally informed strategies will aid in overcoming these obstacles.
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Affiliation(s)
- Antonia Sophia Peter
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Dieter S Hoffmann
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Johannes Klier
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Christina M Lange
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Johanna Moeller
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
| | - Victoria Most
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Christina K Wüst
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Molecular Medicine Studies, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Max Beining
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; SECAI, School of Embedded Composite Artificial Intelligence, Dresden/Leipzig, Germany
| | - Sevilay Gülesen
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Hannes Junker
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Birke Brumme
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Torben Schiffner
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; The Scripps Research Institute, Department for Immunology and Microbiology, La Jolla, CA, United States
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany; Department of Chemistry, Vanderbilt University, Nashville, TN, United States; Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Clara T Schoeder
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany.
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44
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Nelson AN, Shen X, Vekatayogi S, Zhang S, Ozorowski G, Dennis M, Sewall LM, Milligan E, Davis D, Cross KA, Chen Y, van Schooten J, Eudailey J, Isaac J, Memon S, Weinbaum C, Gao H, Stanfield-Oakley S, Byrd A, Chutkan S, Berendam S, Cronin K, Yasmeen A, Alam S, LaBranche CC, Rogers K, Shirreff L, Cupo A, Derking R, Villinger F, Klasse PJ, Ferrari G, Williams WB, Hudgens MG, Ward AB, Montefiori DC, Van Rompay KKA, Wiehe K, Moore JP, Sanders RW, De Paris K, Permar SR. Immunization with germ line-targeting SOSIP trimers elicits broadly neutralizing antibody precursors in infant macaques. Sci Immunol 2024; 9:eadm7097. [PMID: 39213340 DOI: 10.1126/sciimmunol.adm7097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Adolescents are a growing population of people living with HIV. The period between weaning and sexual debut presents a low-risk window for HIV acquisition, making early childhood an ideal time for implementing an immunization regimen. Because the elicitation of broadly neutralizing antibodies (bnAbs) is critical for an effective HIV vaccine, our goal was to assess the ability of a bnAb B cell lineage-designed HIV envelope SOSIP (protein stabilized by a disulfide bond between gp120-gp41-named "SOS"-and an isoleucine-to-proline point mutation-named "IP"-at residue 559) to induce precursor CD4 binding site (CD4bs)-targeting bnAbs in early life. Infant rhesus macaques received either a BG505 SOSIP, based on the infant BG505 transmitted/founder virus, or the CD4bs germ line-targeting BG505 SOSIP GT1.1 (n = 5 per group). Although both strategies induced durable, high-magnitude plasma autologous virus neutralization responses, only GT1.1-immunized infants (n = 3 of 5) exhibited VRC01-like CD4bs bnAb precursor development. Thus, a multidose immunization regimen with bnAb lineage-designed SOSIPs shows promise for inducing early B cell responses with the potential to mature into protective HIV bnAbs before sexual debut.
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Affiliation(s)
- Ashley N Nelson
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Xiaoying Shen
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Sravani Vekatayogi
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Shiyu Zhang
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Maria Dennis
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Emma Milligan
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dominique Davis
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kaitlyn A Cross
- Gillings School of Public Health and Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Chen
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Jelle van Schooten
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, Netherlands
| | - Joshua Eudailey
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - John Isaac
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Saad Memon
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Carolyn Weinbaum
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Hongmei Gao
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | | | - Alliyah Byrd
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Suni Chutkan
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Stella Berendam
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Kenneth Cronin
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - S Alam
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Celia C LaBranche
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Kenneth Rogers
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Lisa Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Ronald Derking
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Guido Ferrari
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Wilton B Williams
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Michael G Hudgens
- Gillings School of Public Health and Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - David C Montefiori
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Kevin Wiehe
- Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Kristina De Paris
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
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45
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Caniels TG, Medina-Ramìrez M, Zhang S, Kratochvil S, Xian Y, Koo JH, Derking R, Samsel J, van Schooten J, Pecetta S, Lamperti E, Yuan M, Carrasco MR, Sanchez IDM, Allen JD, Bouhuijs JH, Yasmeen A, Ketas TJ, Snitselaar JL, Bijl TPL, Martin IC, Torres JL, Cupo A, Shirreff L, Rogers K, Mason RD, Roederer M, Greene KM, Gao H, Silva CM, Baken IJL, Tian M, Alt FW, Pulendran B, Seaman MS, Crispin M, van Gils MJ, Montefiori DC, McDermott AB, Villinger FJ, Koup RA, Moore JP, Klasse PJ, Ozorowski G, Batista FD, Wilson IA, Ward AB, Sanders RW. Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site. Sci Immunol 2024; 9:eadk9550. [PMID: 39213338 PMCID: PMC11783328 DOI: 10.1126/sciimmunol.adk9550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/09/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.
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Affiliation(s)
- Tom G Caniels
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Max Medina-Ramìrez
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Shiyu Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sven Kratochvil
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Yuejiao Xian
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ja-Hyun Koo
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ronald Derking
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jakob Samsel
- Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA
- Institute for Biomedical Sciences, The George Washington University, Washington DC, USA
| | - Jelle van Schooten
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Simone Pecetta
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Edward Lamperti
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - María Ríos Carrasco
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Iván del Moral Sanchez
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Joey H Bouhuijs
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Jonne L Snitselaar
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom PL Bijl
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Isabel Cuella Martin
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Lisa Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Kenneth Rogers
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | | | - Mario Roederer
- Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA
| | | | - Hongmei Gao
- Duke University Medical Center, Durham, NC, USA
| | - Catarina Mendes Silva
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Isabel JL Baken
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Ming Tian
- HHMI, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Frederick W Alt
- HHMI, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Marit J van Gils
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | | | | | - François J Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Richard A Koup
- Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rogier W Sanders
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
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46
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Richard J, Grunst MW, Niu L, Díaz-Salinas MA, Tolbert WD, Marchitto L, Zhou F, Bourassa C, Yang D, Chiu TJ, Chen HC, Benlarbi M, Guillaume-Beaudoin-Buissières, Gottumukkala S, Li W, Dionne K, Bélanger É, Chatterjee D, Medjahed H, Hendrickson WA, Sodroski J, Lang ZC, Morton AJ, Huang RK, Matthies D, Smith AB, Mothes W, Munro JB, Pazgier M, Finzi A. The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609961. [PMID: 39253431 PMCID: PMC11383012 DOI: 10.1101/2024.08.27.609961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
HIV-1 envelope glycoproteins (Env) from primary HIV-1 isolates typically adopt a pretriggered "closed" conformation that resists to CD4-induced (CD4i) non-neutralizing antibodies (nnAbs) mediating antibody-dependent cellular cytotoxicity (ADCC). CD4-mimetic compounds (CD4mcs) "open-up" Env allowing binding of CD4i nnAbs, thereby sensitizing HIV-1-infected cells to ADCC. Two families of CD4i nnAbs, the anti-cluster A and anti-coreceptor binding site (CoRBS) Abs, are required to mediate ADCC in combination with the indane CD4mc BNM-III-170. Recently, new indoline CD4mcs with improved potency and breadth have been described. Here, we show that the lead indoline CD4mc, CJF-III-288, sensitizes HIV-1-infected cells to ADCC mediated by anti-CoRBS Abs alone, contributing to improved ADCC activity. Structural and conformational analyses reveal that CJF-III-288, in combination with anti-CoRBS Abs, potently stabilizes an asymmetric "open" State-3 Env conformation, This Env conformation orients the anti-CoRBS Ab to improve ADCC activity and therapeutic potential.
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Affiliation(s)
- Jonathan Richard
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Michael W. Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Ling Niu
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Marco A. Díaz-Salinas
- Department of Microbiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - William D. Tolbert
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Lorie Marchitto
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | | | - Derek Yang
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Ta Jung Chiu
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Hung-Ching Chen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Guillaume-Beaudoin-Buissières
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Suneetha Gottumukkala
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Katrina Dionne
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Étienne Bélanger
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Debashree Chatterjee
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | | | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Zabrina C. Lang
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, USA
| | - Abraham J. Morton
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, USA
| | - Rick K. Huang
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, USA
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Amos B. Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - James B. Munro
- Department of Microbiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
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47
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Zhang P, Gorman J, Tsybovsky Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia AS, Chuang GY, Geng H, Lai YT, Zhou T, Mascola JR, Mothes W, Kwong PD, Lusso P. Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation. Cell Rep 2024; 43:114518. [PMID: 39028623 PMCID: PMC11459465 DOI: 10.1016/j.celrep.2024.114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
Soluble HIV-1 envelope (Env) trimers may serve as effective vaccine immunogens. The widely utilized SOSIP trimers have been paramount for structural studies, but the disulfide bond they feature between gp120 and gp41 constrains intersubunit mobility and may alter antigenicity. Here, we report an alternative strategy to generate stabilized soluble Env trimers free of covalent gp120-gp41 bonds. Stabilization was achieved by introducing an intrasubunit disulfide bond between the inner and outer domains of gp120, defined as interdomain lock (IDL). Correctly folded IDL trimers displaying a native-like antigenic profile were produced for HIV-1 Envs of different clades. Importantly, the IDL design abrogated CD4 binding while not affecting recognition by potent neutralizing antibodies to the CD4-binding site. By cryoelectron microscopy, IDL trimers were shown to adopt a closed prefusion configuration, while single-molecule fluorescence resonance energy transfer documented a high prevalence of native-like conformation. Thus, IDL trimers may be promising candidates as vaccine immunogens.
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Affiliation(s)
- Peng Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Qingbo Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Vinay Gopan
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mamta Singh
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yin Lin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huiyi Miao
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuna Seo
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alice Kwon
- Laboratory of Immunoregulation, 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
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yen-Ting Lai
- 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
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; ModeX Therapeutics, 20 Riverside Road, Weston, MA 02493, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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48
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Rodrigues KA, Zhang YJ, Aung A, Morgan DM, Maiorino L, Yousefpour P, Gibson G, Ozorowski G, Gregory JR, Amlashi P, Buckley M, Ward AB, Schief WR, Love JC, Irvine DJ. Vaccines combining slow delivery and follicle targeting of antigens increase germinal center B cell clonal diversity and clonal expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608655. [PMID: 39229011 PMCID: PMC11370361 DOI: 10.1101/2024.08.19.608655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Vaccines incorporating slow delivery, multivalent antigen display, or immunomodulation through adjuvants have an important role to play in shaping the humoral immune response. Here we analyzed mechanisms of action of a clinically relevant combination adjuvant strategy, where phosphoserine (pSer)-tagged immunogens bound to aluminum hydroxide (alum) adjuvant (promoting prolonged antigen delivery to draining lymph nodes) are combined with a potent saponin nanoparticle adjuvant termed SMNP (which alters lymph flow and antigen entry into lymph nodes). When employed with a stabilized HIV Env trimer antigen in mice, this combined adjuvant approach promoted substantial enhancements in germinal center (GC) and antibody responses relative to either adjuvant alone. Using scRNA-seq and scBCR-seq, we found that the alum-pSer/SMNP combination both increased the diversity of GC B cell clones and increased GC B cell clonal expansion, coincident with increases in the expression of Myc and the proportion of S-phase GC B cells. To gain insight into the source of these changes in the GC response, we analyzed antigen biodistribution and structural integrity in draining lymph nodes and found that the combination adjuvant approach, but not alum-pSer delivery or SMNP alone, promoted accumulation of highly intact antigen on follicular dendritic cells, reflecting an integration of the slow antigen delivery and altered lymph node uptake effects of these two adjuvants. These results demonstrate how adjuvants with complementary mechanisms of action impacting vaccine biodistribution and kinetics can synergize to enhance humoral immunity.
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Affiliation(s)
- Kristen A. Rodrigues
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Harvard-MIT Health Sciences and Technology Program, Institute for Medical Engineering and Science; Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Yiming J. Zhang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Aereas Aung
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Duncan M. Morgan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Department of Chemical Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Laura Maiorino
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Parisa Yousefpour
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Grace Gibson
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Gabriel Ozorowski
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Justin R. Gregory
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Parastoo Amlashi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - Maureen Buckley
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Andrew B. Ward
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037 USA
| | - William R. Schief
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Department of Chemical Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
| | - Darrell J. Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University; Cambridge, MA 02139 USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute; La Jolla, CA 92037 USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139 USA
- Howard Hughes Medical Institute; Chevy Chase, MD 20815 USA
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49
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de Taeye SW, Schriek AI, Umotoy JC, Grobben M, Burger JA, Sanders RW, Vidarsson G, Wuhrer M, Falck D, Kootstra NA, van Gils MJ. Afucosylated broadly neutralizing antibodies enhance clearance of HIV-1 infected cells through cell-mediated killing. Commun Biol 2024; 7:964. [PMID: 39122901 PMCID: PMC11316088 DOI: 10.1038/s42003-024-06659-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) have the capacity to delay viral rebound when administered to people with HIV-1 (PWH) during anti-retroviral therapy (ART) interruption. To further enhance the performance of bNAbs through their Fc effector functions, in particular NK cell-mediated killing of HIV-1 infected cells, we have produced a panel of glyco-engineered (afucosylated) bNAbs with enhanced affinity for Fc gamma receptor IIIa. These afucosylated anti-HIV-1 bNAbs enhance NK cell activation and degranulation compared to fucosylated counterparts even at low antigen density. NK cells from PWH expressing exhaustion markers PD-1 and TIGIT are activated in a similar fashion by afucosylated bNAbs as NK cell from HIV-1 negative individuals. Killing of HIV-1 infected cells is most effective with afucosylated bNAbs 2G12, N6, PGT151 and PGDM1400, whereas afucosylated PGT121 and non-neutralizing antibody A32 only induce minor NK cell-mediated killing. These data indicate that the approach angle and affinity of Abs influence the capacity to induce antibody-dependent cellular cytotoxicity. Thus, afucosylated bNAbs have the capacity to induce NK cell-mediated killing of infected cells, which warrants further investigation of afucosylated bNAb administration in vivo, aiming for reduction of the viral reservoir and ART free durable control.
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Affiliation(s)
- Steven W de Taeye
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands.
| | - Angela I Schriek
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands
| | - Jeffrey C Umotoy
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands
| | - Marloes Grobben
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands
| | - Judith A Burger
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands
| | - Rogier W Sanders
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands
- Weill Medical College of Cornell University, Department of Microbiology and Immunology, New York, NY, 10065, USA
| | - Gestur Vidarsson
- Sanquin Research and Landsteiner, Amsterdam UMC location University of Amsterdam, Immunoglobulin Research Laboratory, Department of Experimental Immunohematology, 1066 CX, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Neeltje A Kootstra
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Institute for Immunology and Infectious diseases, Infectious diseases, Amsterdam, The Netherlands.
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van der Straten K, Guerra D, Kerster G, Claireaux M, Grobben M, Schriek AI, Boyd A, van Rijswijk J, Tejjani K, Eggink D, Beaumont T, de Taeye SW, de Bree GJ, Sanders RW, van Gils MJ. Primary SARS-CoV-2 variant of concern infections elicit broad antibody Fc-mediated effector functions and memory B cell responses. PLoS Pathog 2024; 20:e1012453. [PMID: 39146376 PMCID: PMC11349224 DOI: 10.1371/journal.ppat.1012453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/27/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024] Open
Abstract
Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by human sera is a strong correlate of protection against symptomatic and severe Coronavirus Disease 2019 (COVID-19). The emergence of antigenically distinct SARS-CoV-2 variants of concern (VOCs) and the relatively rapid waning of serum antibody titers, however, raises questions about the sustainability of serum protection. In addition to serum neutralization, other antibody functionalities and the memory B cell (MBC) response are suggested to help maintaining this protection. In this study, we investigate the breadth of spike (S) protein-specific serum antibodies that mediate effector functions by interacting with Fc-gamma receptor IIa (FcγRIIa) and FcγRIIIa, and of the receptor binding domain (RBD)-specific MBCs, following a primary SARS-CoV-2 infection with the D614G, Alpha, Beta, Gamma, Delta, Omicron BA.1 or BA.2 variant. Irrespectively of the variant causing the infection, the breadth of S protein-specific serum antibodies that interact with FcγRIIa and FcγRIIIa and the RBD-specific MBC responses exceeded the breadth of serum neutralization, although the Alpha-induced B cell response seemed more strain-specific. Between VOC groups, both quantitative and qualitative differences in the immune responses were observed, suggesting differences in immunogenicity. Overall, this study contributes to the understanding of protective humoral and B cell responses in the light of emerging antigenically distinct VOCs, and highlights the need to study the immune system beyond serum neutralization to gain a better understanding of the protection against emerging variants.
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Affiliation(s)
- Karlijn van der Straten
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Denise Guerra
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Gius Kerster
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu Claireaux
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Marloes Grobben
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Angela I. Schriek
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Anders Boyd
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Stichting HIV monitoring, Amsterdam, the Netherlands
| | - Jacqueline van Rijswijk
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Khadija Tejjani
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Dirk Eggink
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Tim Beaumont
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Steven W. de Taeye
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Godelieve J. de Bree
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Amsterdam UMC, location Academic Medical Center, Department of Internal Medicine, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Marit J. van Gils
- Amsterdam UMC, location Academic Medical Center, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
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