1
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Suryadevara N, Otrelo-Cardoso AR, Kose N, Hu YX, Binshtein E, Wolters RM, Greninger AL, Handal LS, Carnahan RH, Moscona A, Jardetzky TS, Crowe JE. Functional and structural basis of human parainfluenza virus type 3 neutralization with human monoclonal antibodies. Nat Microbiol 2024:10.1038/s41564-024-01722-w. [PMID: 38858594 DOI: 10.1038/s41564-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 05/02/2024] [Indexed: 06/12/2024]
Abstract
Human parainfluenza virus type 3 (hPIV3) is a respiratory pathogen that can cause severe disease in older people and infants. Currently, vaccines against hPIV3 are in clinical trials but none have been approved yet. The haemagglutinin-neuraminidase (HN) and fusion (F) surface glycoproteins of hPIV3 are major antigenic determinants. Here we describe naturally occurring potently neutralizing human antibodies directed against both surface glycoproteins of hPIV3. We isolated seven neutralizing HN-reactive antibodies and a pre-fusion conformation F-reactive antibody from human memory B cells. One HN-binding monoclonal antibody (mAb), designated PIV3-23, exhibited functional attributes including haemagglutination and neuraminidase inhibition. We also delineated the structural basis of neutralization for two HN and one F mAbs. MAbs that neutralized hPIV3 in vitro protected against infection and disease in vivo in a cotton rat model of hPIV3 infection, suggesting correlates of protection for hPIV3 and the potential clinical utility of these mAbs.
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Affiliation(s)
| | | | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yao-Xiong Hu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elad Binshtein
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachael M Wolters
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Laura S Handal
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anne Moscona
- Departments of Pediatrics, Microbiology and Immunology, and Physiology and Cellular Biophysics, and Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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2
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Yang YR, Han J, Perrett HR, Richey ST, Rodriguez AJ, Jackson AM, Gillespie RA, O'Connell S, Raab JE, Cominsky LY, Chopde A, Kanekiyo M, Houser KV, Chen GL, McDermott AB, Andrews SF, Ward AB. Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. Cell Rep 2024; 43:114171. [PMID: 38717904 PMCID: PMC11156625 DOI: 10.1016/j.celrep.2024.114171] [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: 08/24/2023] [Revised: 03/25/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase 1 clinical trial investigating a ferritin nanoparticle vaccine displaying H2 hemagglutinin (HA) in H2-naive and H2-exposed adults enabled us to perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited. We temporally map the epitopes targeted by serum antibodies after vaccine prime and boost, revealing that previous H2 exposure results in higher responses to the variable HA head domain. In contrast, initial responses in H2-naive participants are dominated by antibodies targeting conserved epitopes. We use cryoelectron microscopy and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the HA head, including the receptor-binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses post-vaccination.
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Affiliation(s)
- Yuhe R Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailee R Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alesandra J Rodriguez
- Department of Integrative Structural and Computational Biology, 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
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah O'Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ankita Chopde
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA.
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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3
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Zhu Y, Ding W, Chen Y, Shan Y, Liu C, Fan X, Lin S, Chen PR. Genetically encoded bioorthogonal tryptophan decaging in living cells. Nat Chem 2024; 16:533-542. [PMID: 38418535 DOI: 10.1038/s41557-024-01463-7] [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: 07/05/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Tryptophan (Trp) plays a critical role in the regulation of protein structure, interactions and functions through its π system and indole N-H group. A generalizable method for blocking and rescuing Trp interactions would enable the gain-of-function manipulation of various Trp-containing proteins in vivo, but generating such a platform remains challenging. Here we develop a genetically encoded N1-vinyl-caged Trp capable of rapid and bioorthogonal decaging through an optimized inverse electron-demand Diels-Alder reaction, allowing site-specific activation of Trp on a protein of interest in living cells. This chemical activation of a genetically encoded caged-tryptophan (Trp-CAGE) strategy enables precise activation of the Trp of interest underlying diverse important molecular interactions. We demonstrate the utility of Trp-CAGE across various protein families, such as catalase-peroxidases and kinases, as translation initiators and posttranslational modification readers, allowing the modulation of epigenetic signalling in a temporally controlled manner. Coupled with computer-aided prediction, our strategy paves the way for bioorthogonal Trp activation on more than 28,000 candidate proteins within their native cellular settings.
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Affiliation(s)
- Yuchao Zhu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wenlong Ding
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Ye Shan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chao Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Xinyuan Fan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China.
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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4
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Hutchinson GB, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep 2023; 42:113552. [PMID: 38096058 PMCID: PMC10801709 DOI: 10.1016/j.celrep.2023.113552] [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: 06/20/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Geoffrey B Hutchinson
- 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, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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5
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Rijnink WF, Stadlbauer D, Puente-Massaguer E, Okba NMA, Kirkpatrick Roubidoux E, Strohmeier S, Mudd PA, Schmitz A, Ellebedy A, McMahon M, Krammer F. Characterization of non-neutralizing human monoclonal antibodies that target the M1 and NP of influenza A viruses. J Virol 2023; 97:e0164622. [PMID: 37916834 PMCID: PMC10688359 DOI: 10.1128/jvi.01646-22] [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: 10/25/2022] [Accepted: 10/08/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Currently, many groups are focusing on isolating both neutralizing and non-neutralizing antibodies to the mutation-prone hemagglutinin as a tool to treat or prevent influenza virus infection. Less is known about the level of protection induced by non-neutralizing antibodies that target conserved internal influenza virus proteins. Such non-neutralizing antibodies could provide an alternative pathway to induce broad cross-reactive protection against multiple influenza virus serotypes and subtypes by partially overcoming influenza virus escape mediated by antigenic drift and shift. Accordingly, more information about the level of protection and potential mechanism(s) of action of non-neutralizing antibodies targeting internal influenza virus proteins could be useful for the design of broadly protective and universal influenza virus vaccines.
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Affiliation(s)
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eduard Puente-Massaguer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nisreen M. A. Okba
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ericka Kirkpatrick Roubidoux
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip A. Mudd
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aaron Schmitz
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ali Ellebedy
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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6
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Teo QW, Wang Y, Lv H, Tan TJC, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. Cell Rep 2023; 42:113410. [PMID: 37976161 PMCID: PMC10872586 DOI: 10.1016/j.celrep.2023.113410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
IGHV1-69 is frequently utilized by broadly neutralizing influenza antibodies to the hemagglutinin (HA) stem. These IGHV1-69 HA stem antibodies have diverse complementarity-determining region (CDR) H3 sequences. Besides, their light chains have minimal to no contact with the epitope. Consequently, sequence determinants that confer IGHV1-69 antibodies with HA stem specificity remain largely elusive. Using high-throughput experiments, this study reveals the importance of light-chain sequence for the IGHV1-69 HA stem antibody CR9114, which is the broadest influenza antibody known to date. Moreover, we demonstrate that the CDR H3 sequences from many other IGHV1-69 antibodies, including those to the HA stem, are incompatible with CR9114. Along with mutagenesis and structural analysis, our results indicate that light-chain and CDR H3 sequences coordinately determine the HA stem specificity of IGHV1-69 antibodies. Overall, this work provides molecular insights into broadly neutralizing antibody responses to influenza virus, which have important implications for universal influenza vaccine development.
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Affiliation(s)
- Qi Wen Teo
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin J Mao
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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7
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Yang YR, Han J, Perrett HR, Richey ST, Jackson AM, Rodriguez AJ, Gillespie RA, O’Connell S, Raab JE, Cominsky LY, Chopde A, Kanekiyo M, Houser KV, Chen GL, McDermott AB, Andrews SF, Ward AB. Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554525. [PMID: 37781590 PMCID: PMC10541104 DOI: 10.1101/2023.08.23.554525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses.
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Affiliation(s)
- Yuhe R. Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sara T. Richey
- Department of Integrative Structural and Computational Biology, 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
| | - Alesandra J. Rodriguez
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Rebecca A. Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah O’Connell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E. Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y. Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ankita Chopde
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V. Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L. Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sarah F. Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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8
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Piepenbrink M, Oladunni F, Nogales A, Khalil AM, Fitzgerald T, Basu M, Fucile C, Topham DJ, Rosenberg AF, Martinez-Sobrido L, Kobie JJ. Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies. Microbiol Spectr 2023; 11:e0472822. [PMID: 37318331 PMCID: PMC10433997 DOI: 10.1128/spectrum.04728-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/29/2023] [Indexed: 06/16/2023] Open
Abstract
Due to antigenic drift and shift of influenza A viruses (IAV) and the tendency to elicit predominantly strain-specific antibodies, humanity remains susceptible to new strains of seasonal IAV and is at risk from viruses with pandemic potential for which limited or no immunity may exist. The genetic drift of H3N2 IAV is specifically pronounced, resulting in two distinct clades since 2014. Here, we demonstrate that immunization with a seasonal inactivated influenza vaccine (IIV) results in increased levels of H3N2 IAV-specific serum antibodies against hemagglutinin (HA) and neuraminidase (NA). Detailed analysis of the H3N2 B cell response indicated expansion of H3N2-specific peripheral blood plasmablasts 7 days after IIV immunization which expressed monoclonal antibodies (MAbs) with broad and potent antiviral activity against many H3N2 IAV strains as well as prophylactic and therapeutic activity in mice. These H3N2-specific B cell clonal lineages persisted in CD138+ long-lived bone marrow plasma cells. These results demonstrate that IIV-induced H3N2 human MAbs can protect and treat influenza virus infection in vivo and suggest that IIV can induce a subset of IAV H3N2-specific B cells with broad protective potential, a feature that warrants further study for universal influenza vaccine development. IMPORTANCE Influenza A virus (IAV) infections continue to cause substantial morbidity and mortality despite the availability of seasonal vaccines. The extensive genetic variability in seasonal and potentially pandemic influenza strains necessitates new vaccine strategies that can induce universal protection by focusing the immune response on generating protective antibodies against conserved targets within the influenza virus hemagglutinin and neuraminidase proteins. We have demonstrated that seasonal immunization with inactivated influenza vaccine (IIV) stimulates H3N2-specific monoclonal antibodies in humans that are broad and potent in their neutralization of virus in vitro. These antibodies also provide protection from H3N2 IAV in a mouse model of infection. Furthermore, they persist in the bone marrow, where they are expressed by long-lived antibody-producing plasma cells. This significantly demonstrates that seasonal IIV can induce a subset of H3N2-specific B cells with broad protective potential, a process that if further studied and enhanced could aid in the development of a universal influenza vaccine.
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Affiliation(s)
- Michael Piepenbrink
- Heersink School of Medicine, Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Medicine, Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| | - Fatai Oladunni
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Ahmed M. Khalil
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Theresa Fitzgerald
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Madhubanti Basu
- Heersink School of Medicine, Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher Fucile
- Heersink School of Medicine, Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David J. Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - Alexander F. Rosenberg
- Heersink School of Medicine, Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Luis Martinez-Sobrido
- Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, USA
| | - James J. Kobie
- Heersink School of Medicine, Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Medicine, Infectious Diseases Division, University of Rochester, Rochester, New York, USA
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9
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Yuanyuan H, Zijian G, Subiaur S, Benegal A, Vahey MD. Antibody Inhibition of Influenza A Virus Assembly and Release. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552198. [PMID: 37609131 PMCID: PMC10441363 DOI: 10.1101/2023.08.08.552198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Antibodies are frontline defenders against influenza virus infection, providing protection through multiple complementary mechanisms. Although a subset of monoclonal antibodies (mAbs) have been shown to restrict replication at the level of virus assembly and release, it remains unclear how potent and pervasive this mechanism of protection is, due in part to the challenge of separating this effect from other aspects of antibody function. To address this question, we developed imaging-based assays to determine how effectively a broad range of mAbs against the IAV surface proteins can specifically restrict viral egress. We find that classically neutralizing antibodies against hemagglutinin are broadly multifunctional, inhibiting virus assembly and release at concentrations one- to twenty-fold higher than the concentrations at which they inhibit viral entry. These antibodies are also capable of altering the morphological features of shed virions, reducing the proportion of filamentous particles. We find that antibodies against neuraminidase and M2 also restrict viral egress, and that inhibition by anti-neuraminidase mAbs is only partly attributable to a loss in enzymatic activity. In all cases, antigen crosslinking - either on the surface of the infected cell, between the viral and cell membrane, or both - plays a critical role in inhibition, and we are able to distinguish between these modes experimentally and through a structure-based computational model. Together, these results provide a framework for dissecting antibody multifunctionality that could help guide the development of improved therapeutic antibodies or vaccines, and that can be extended to other viral families and antibody isotypes.
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Affiliation(s)
- He Yuanyuan
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Guo Zijian
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sofie Subiaur
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ananya Benegal
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael D. Vahey
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, Missouri, USA
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10
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Gholami S, Mafakher L, Fotouhi F, Bambai B, Cohan RA, Mehrbod P, Shokouhi H, Farahmand B. Computational peptide engineering approach for selection of the new C05 antibody-driven peptide with potency to blocking influenza a virus attachment; from in silico to in vivo. J Biomol Struct Dyn 2023:1-17. [PMID: 37553776 DOI: 10.1080/07391102.2023.2241554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Antiviral drugs are currently used to prevent or treat viral infections like influenza A Virus (IAV). Nonetheless, annual genetic mutations of influenza viruses make them resistant to efficient treatment by current medications. Antiviral peptides have recently attracted researchers' attention and can potentially supplant the current medications. This study aimed to design peptides against IAV propagation. For this purpose, P2 and P3 peptides were computationally designed based on the HCDR3 region of the C05 antibody (a monoclonal antibody that neutralizes influenza HA protein and inhibits the virus attachment). The synthesized peptides were tested against the influenza A virus (A/Puerto Rico/8/34 (H1N1)) in vitro, and the most efficient peptide was selected for in vivo experiments. It was shown that the designed peptide shows much more prophylactic and therapeutic effects against the virus. These findings demonstrated that the designed peptide can control the virus infection without any cytotoxicity effect. Antiviral peptide design is acknowledged as a critical tactic to manage viral infections by preventing viral binding to the host cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shima Gholami
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Fotouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Bijan Bambai
- Department of Systems Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Parvaneh Mehrbod
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Hadiseh Shokouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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11
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Capella-Pujol J, de Gast M, Radić L, Zon I, Chumbe A, Koekkoek S, Olijhoek W, Schinkel J, van Gils MJ, Sanders RW, Sliepen K. Signatures of V H1-69-derived hepatitis C virus neutralizing antibody precursors defined by binding to envelope glycoproteins. Nat Commun 2023; 14:4036. [PMID: 37419906 PMCID: PMC10328973 DOI: 10.1038/s41467-023-39690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
An effective preventive vaccine for hepatitis C virus (HCV) remains a major unmet need. Antigenic region 3 (AR3) on the E1E2 envelope glycoprotein complex overlaps with the CD81 receptor binding site and represents an important epitope for broadly neutralizing antibodies (bNAbs) and is therefore important for HCV vaccine design. Most AR3 bNAbs utilize the VH1-69 gene and share structural features that define the AR3C-class of HCV bNAbs. In this work, we identify recombinant HCV glycoproteins based on a permuted E2E1 trimer design that bind to the inferred VH1-69 germline precursors of AR3C-class bNAbs. When presented on nanoparticles, these recombinant E2E1 glycoproteins efficiently activate B cells expressing inferred germline AR3C-class bNAb precursors as B cell receptors. Furthermore, we identify critical signatures in three AR3C-class bNAbs that represent two subclasses of AR3C-class bNAbs that will allow refined protein design. These results provide a framework for germline-targeting vaccine design strategies against HCV.
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Affiliation(s)
- Joan Capella-Pujol
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Marlon de Gast
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Laura Radić
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Ian Zon
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Wouter Olijhoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10065, USA.
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands.
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12
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Teo QW, Wang Y, Lv H, Tan TJ, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547908. [PMID: 37461670 PMCID: PMC10350038 DOI: 10.1101/2023.07.06.547908] [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: 07/25/2023]
Abstract
IGHV1-69 is frequently utilized by broadly neutralizing influenza antibodies to the hemagglutinin (HA) stem. These IGHV1-69 HA stem antibodies have diverse complementarity-determining region (CDR) H3 sequences. Besides, their light chains have minimal to no contact with the epitope. Consequently, sequence determinants that confer IGHV1-69 antibodies with HA stem specificity remain largely elusive. Using high-throughput experiments, this study revealed the importance of light chain sequence for the IGHV1-69 HA stem antibody CR9114, which is the broadest influenza antibody known to date. Moreover, we demonstrated that the CDR H3 sequences from many other IGHV1-69 antibodies, including those to HA stem, were incompatible with CR9114. Along with mutagenesis and structural analysis, our results indicate that light chain and CDR H3 sequences coordinately determine the HA stem specificity of IGHV1-69 antibodies. Overall, this work provides molecular insights into broadly neutralizing antibody responses to influenza virus, which have important implications for universal influenza vaccine development.
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Affiliation(s)
- Qi Wen Teo
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin J. Mao
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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13
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541980. [PMID: 37292995 PMCID: PMC10245855 DOI: 10.1101/2023.05.23.541980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses to enable the creation of next-generation vaccines with improved potency and breadth. However, our understanding of the relationship between immunogen structure and immunogenicity is limited. Here we use computational protein design to generate a self-assembling nanoparticle vaccine platform based on the head domain of influenza hemagglutinin (HA) that enables precise control of antigen conformation, flexibility, and spacing on the nanoparticle exterior. Domain-based HA head antigens were presented either as monomers or in a native-like closed trimeric conformation that prevents exposure of trimer interface epitopes. These antigens were connected to the underlying nanoparticle by a rigid linker that was modularly extended to precisely control antigen spacing. We found that nanoparticle immunogens with decreased spacing between closed trimeric head antigens elicited antibodies with improved hemagglutination inhibition (HAI) and neutralization potency as well as binding breadth across diverse HAs within a subtype. Our "trihead" nanoparticle immunogen platform thus enables new insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used to generate next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- 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, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A. Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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14
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Dzimianski JV, Han J, Sautto GA, O'Rourke SM, Cruz JM, Pierce SR, Ecker JW, Carlock MA, Nagashima KA, Mousa JJ, Ross TM, Ward AB, DuBois RM. Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine. Commun Biol 2023; 6:454. [PMID: 37185989 PMCID: PMC10126545 DOI: 10.1038/s42003-023-04793-3] [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: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally optimized broadly reactive antigen (COBRA) hemagglutinin (HA) proteins is a promising vaccine strategy to protect against a wide range of current and future influenza viruses. Though effective in preclinical studies, the mechanistic basis driving the broad reactivity of COBRA proteins remains to be elucidated. Here, we report the crystal structure of the COBRA HA termed P1 and identify antigenic and glycosylation properties that contribute to its immunogenicity. We further report the cryo-EM structure of the P1-elicited broadly neutralizing antibody 1F8 bound to COBRA P1, revealing 1F8 to recognize an atypical receptor binding site epitope via an unexpected mode of binding.
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Affiliation(s)
- John V Dzimianski
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Giuseppe A Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Sara M O'Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph M Cruz
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Spencer R Pierce
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jeffrey W Ecker
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Michael A Carlock
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Kaito A Nagashima
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jarrod J Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
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15
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Zhang Y, Li Q, Luo L, Duan C, Shen J, Wang Z. Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis. Biotechnol Adv 2023; 65:108143. [PMID: 37023966 DOI: 10.1016/j.biotechadv.2023.108143] [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: 01/13/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Qing Li
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Changfei Duan
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China.
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16
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Ricci AD, Bracco L, Salas-Sarduy E, Ramsey JM, Nolan MS, Lynn MK, Altcheh J, Ballering GE, Torrico F, Kesper N, Villar JC, Marcipar IS, Marco JD, Agüero F. The Trypanosoma cruzi Antigen and Epitope Atlas: antibody specificities in Chagas disease patients across the Americas. Nat Commun 2023; 14:1850. [PMID: 37012236 PMCID: PMC10070320 DOI: 10.1038/s41467-023-37522-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
During an infection the immune system produces pathogen-specific antibodies. These antibody repertoires become specific to the history of infections and represent a rich source of diagnostic markers. However, the specificities of these antibodies are mostly unknown. Here, using high-density peptide arrays we examined the human antibody repertoires of Chagas disease patients. Chagas disease is a neglected disease caused by Trypanosoma cruzi, a protozoan parasite that evades immune mediated elimination and mounts long-lasting chronic infections. We describe a proteome-wide search for antigens, characterised their linear epitopes, and show their reactivity on 71 individuals from diverse human populations. Using single-residue mutagenesis we revealed the core functional residues for 232 of these epitopes. Finally, we show the diagnostic performance of identified antigens on challenging samples. These datasets enable the study of the Chagas antibody repertoire at an unprecedented depth and granularity, while also providing a rich source of serological biomarkers.
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Affiliation(s)
- Alejandro D Ricci
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | - Leonel Bracco
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | - Janine M Ramsey
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, México
| | - Melissa S Nolan
- Laboratory of Vector-borne and Zoonotic Diseases, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - M Katie Lynn
- Laboratory of Vector-borne and Zoonotic Diseases, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Jaime Altcheh
- Hospital de Niños "Ricardo Gutierrez", Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP) - GCBA-CONICET, Buenos Aires, Argentina
| | - Griselda E Ballering
- Hospital de Niños "Ricardo Gutierrez", Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | | | - Norival Kesper
- LIM-49, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Juan C Villar
- Facultad de Ciencias de la Salud, Universidad Autónoma de Bucaramanga y Fundación Cardioinfantil - Instituto de Cardiología, Bogotá, Colombia
| | - Iván S Marcipar
- Facultad de Ciencias Médicas y Facultad de Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jorge D Marco
- Instituto de Patología Experimental, Universidad Nacional de Salta - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina.
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina.
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17
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Jiao C, Wang B, Chen P, Jiang Y, Liu J. Analysis of the conserved protective epitopes of hemagglutinin on influenza A viruses. Front Immunol 2023; 14:1086297. [PMID: 36875062 PMCID: PMC9981632 DOI: 10.3389/fimmu.2023.1086297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
The conserved protective epitopes of hemagglutinin (HA) are essential to the design of a universal influenza vaccine and new targeted therapeutic agents. Over the last 15 years, numerous broadly neutralizing antibodies (bnAbs) targeting the HA of influenza A viruses have been isolated from B lymphocytes of human donors and mouse models, and their binding epitopes identified. This work has brought new perspectives for identifying conserved protective epitopes of HA. In this review, we succinctly analyzed and summarized the antigenic epitopes and functions of more than 70 kinds of bnAb. The highly conserved protective epitopes are concentrated on five regions of HA: the hydrophobic groove, the receptor-binding site, the occluded epitope region of the HA monomers interface, the fusion peptide region, and the vestigial esterase subdomain. Our analysis clarifies the distribution of the conserved protective epitope regions on HA and provides distinct targets for the design of novel vaccines and therapeutics to combat influenza A virus infection.
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Affiliation(s)
- Chenchen Jiao
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bo Wang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Pucheng Chen
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongping Jiang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinxiong Liu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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18
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Xu D, Li C, Utz A, Weidenbacher PA, Tang S, Sanyal M, Pulendran B, Kim PS. Designing epitope-focused vaccines via antigen reorientation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.20.521291. [PMID: 36597536 PMCID: PMC9810212 DOI: 10.1101/2022.12.20.521291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A.B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Bali Pulendran
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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19
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Xu D, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Kim PS. Designing epitope-focused vaccines via antigen reorientation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 36597536 DOI: 10.1101/2022.09.08.507187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
UNLABELLED A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates. GRAPHICAL ABSTRACT Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an "upside-down" configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.
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20
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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21
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Mechanistic dissection of antibody inhibition of influenza entry yields unexpected heterogeneity. Biophys J 2022:S0006-3495(22)00864-5. [DOI: 10.1016/j.bpj.2022.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022] Open
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22
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Kar U, Khaleeq S, Garg P, Bhat M, Reddy P, Vignesh VS, Upadhyaya A, Das M, Chakshusmathi G, Pandey S, Dutta S, Varadarajan R. Comparative Immunogenicity of Bacterially Expressed Soluble Trimers and Nanoparticle Displayed Influenza Hemagglutinin Stem Immunogens. Front Immunol 2022; 13:890622. [PMID: 35720346 PMCID: PMC9204493 DOI: 10.3389/fimmu.2022.890622] [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: 03/06/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Current influenza vaccines need to be updated annually due to mutations in the globular head of the viral surface protein, hemagglutinin (HA). To address this, vaccine candidates have been designed based on the relatively conserved HA stem domain and have shown protective efficacy in animal models. Oligomerization of the antigens either by fusion to oligomerization motifs or display on self-assembling nanoparticle scaffolds, can induce more potent immune responses compared to the corresponding monomeric antigen due to multivalent engagement of B-cells. Since nanoparticle display can increase manufacturing complexity, and often involves one or more mammalian cell expressed components, it is important to characterize and compare various display and oligomerization scaffolds. Using a structure guided approach, we successfully displayed multiple copies of a previously designed soluble, trimeric influenza stem domain immunogen, pH1HA10, on the ferritin like protein, MsDps2 (12 copies), Ferritin (24 copies) and Encapsulin (180 copies). All proteins were expressed in Escherichia coli. The nanoparticle fusion immunogens were found to be well folded and bound to the influenza stem directed broadly neutralizing antibodies with high affinity. An 8.5 Å Cryo-EM map of Msdps2-pH1HA10 confirmed the successful design of the nanoparticle fusion immunogen. Mice immunization studies with the soluble trimeric stem and nanoparticle fusion constructs revealed that all of them were immunogenic, and protected mice against homologous (A/Belgium/145-MA/2009) and heterologous (A/Puerto Rico/8/1934) challenge with 10MLD50 mouse adapted virus. Although nanoparticle display conferred a small but statistically significant improvement in protection relative to the soluble trimer in a homologous challenge, heterologous protection was similar in both nanoparticle-stem immunized and trimeric stem immunized groups. Such rapidly producible, bacterially expressed antigens and nanoparticle scaffolds are useful modalities to tackle future influenza pandemics.
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Affiliation(s)
- Uddipan Kar
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Sara Khaleeq
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Priyanka Garg
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Madhuraj Bhat
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Poorvi Reddy
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | | | - Aditya Upadhyaya
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Mili Das
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Ghadiyaram Chakshusmathi
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Suman Pandey
- Mynvax Private Limited, ES12, Entrepreneurship Centre, Society for Innovation and Development (SID), Indian Institute of Science, Bengaluru, India
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
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23
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Abstract
Antibodies have been used to prevent or treat viral infections since the nineteenth century, but the full potential to use passive immunization for infectious diseases has yet to be realized. The advent of efficient methods for isolating broad and potently neutralizing human monoclonal antibodies is enabling us to develop antibodies with unprecedented activities. The discovery of IgG Fc region modifications that extend antibody half-life in humans to three months or more suggests that antibodies could become the principal tool with which we manage future viral epidemics. Antibodies for members of most virus families that cause severe disease in humans have been isolated, and many of them are in clinical development, an area that has accelerated during the effort to prevent or treat COVID-19 (coronavirus disease 2019). Broad and potently neutralizing antibodies are also important research reagents for identification of protective epitopes that can be engineered into active vaccines through structure-based reverse vaccinology. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James E Crowe
- Vanderbilt Vaccine Center, Department of Pediatrics, and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
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24
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Cheung CSF, Fruehwirth A, Paparoditis PCG, Shen CH, Foglierini M, Joyce MG, Leung K, Piccoli L, Rawi R, Silacci-Fregni C, Tsybovsky Y, Verardi R, Wang L, Wang S, Yang ES, Zhang B, Zhang Y, Chuang GY, Corti D, Mascola JR, Shapiro L, Kwong PD, Lanzavecchia A, Zhou T. Identification and Structure of a Multidonor Class of Head-Directed Influenza-Neutralizing Antibodies Reveal the Mechanism for Its Recurrent Elicitation. Cell Rep 2021; 32:108088. [PMID: 32877670 DOI: 10.1016/j.celrep.2020.108088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/12/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
Multidonor antibodies are of interest for vaccine design because they can in principle be elicited in the general population by a common set of immunogens. For influenza, multidonor antibodies have been observed against the hemagglutinin (HA) stem, but not the immunodominant HA head. Here, we identify and characterize a multidonor antibody class (LPAF-a class) targeting the HA head. This class exhibits potent viral entry inhibition against H1N1 A/California/04/2009 (CA09) virus. LPAF-a class antibodies derive from the HV2-70 gene and contain a "Tyr-Gly-Asp"-motif, which occludes the HA-sialic acid binding site as revealed by a co-crystal structure with HA. Both germline-reverted and mature LPAF antibodies potently neutralize CA09 virus and have nanomolar affinities for CA09 HA. Moreover, increased frequencies for LPFA-a class antibodies are observed in humans after a single vaccination. Overall, this work highlights the identification of a multidonor class of head-directed influenza-neutralizing antibodies and delineates the mechanism of their recurrent elicitation in humans.
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Affiliation(s)
- Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander Fruehwirth
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chiara Silacci-Fregni
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Corti
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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25
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Liu WJ, Xiao H, Dai L, Liu D, Chen J, Qi X, Bi Y, Shi Y, Gao GF, Liu Y. Avian influenza A (H7N9) virus: from low pathogenic to highly pathogenic. Front Med 2021; 15:507-527. [PMID: 33860875 PMCID: PMC8190734 DOI: 10.1007/s11684-020-0814-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022]
Abstract
The avian influenza A (H7N9) virus is a zoonotic virus that is closely associated with live poultry markets. It has caused infections in humans in China since 2013. Five waves of the H7N9 influenza epidemic occurred in China between March 2013 and September 2017. H7N9 with low-pathogenicity dominated in the first four waves, whereas highly pathogenic H7N9 influenza emerged in poultry and spread to humans during the fifth wave, causing wide concern. Specialists and officials from China and other countries responded quickly, controlled the epidemic well thus far, and characterized the virus by using new technologies and surveillance tools that were made possible by their preparedness efforts. Here, we review the characteristics of the H7N9 viruses that were identified while controlling the spread of the disease. It was summarized and discussed from the perspectives of molecular epidemiology, clinical features, virulence and pathogenesis, receptor binding, T-cell responses, monoclonal antibody development, vaccine development, and disease burden. These data provide tools for minimizing the future threat of H7N9 and other emerging and re-emerging viruses, such as SARS-CoV-2.
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Affiliation(s)
- William J Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518114, China.
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Haixia Xiao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences (CAS), Tianjin, 300308, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Chinese Academy of Sciences, Wuhan, 430071, China
- National Virus Resource Center, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy Sciences, Beijing, 100049, China
- Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Chinese Academy of Sciences, Wuhan, 430071, China
- National Virus Resource Center, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy Sciences, Beijing, 100049, China
- Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaopeng Qi
- Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuhai Bi
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518114, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy Sciences, Beijing, 100049, China
- Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Shi
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518114, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy Sciences, Beijing, 100049, China
- Center for Influenza Research and Early Warning, Chinese Academy of Sciences, Beijing, 100101, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518114, China.
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26
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Sangesland M, Lingwood D. Antibody Focusing to Conserved Sites of Vulnerability: The Immunological Pathways for 'Universal' Influenza Vaccines. Vaccines (Basel) 2021; 9:vaccines9020125. [PMID: 33562627 PMCID: PMC7914524 DOI: 10.3390/vaccines9020125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Influenza virus remains a serious public health burden due to ongoing viral evolution. Vaccination remains the best measure of prophylaxis, yet current seasonal vaccines elicit strain-specific neutralizing responses that favor the hypervariable epitopes on the virus. This necessitates yearly reformulations of seasonal vaccines, which can be limited in efficacy and also shortchange pandemic preparedness. Universal vaccine development aims to overcome these deficits by redirecting antibody responses to functionally conserved sites of viral vulnerability to enable broad coverage. However, this is challenging as such antibodies are largely immunologically silent, both following vaccination and infection. Defining and then overcoming the immunological basis for such subdominant or ‘immuno-recessive’ antibody targeting has thus become an important aspect of universal vaccine development. This, coupled with structure-guided immunogen design, has led to proof-of-concept that it is possible to rationally refocus humoral immunity upon normally ‘unseen’ broadly neutralizing antibody targets on influenza virus.
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27
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Do PC, Nguyen TH, Vo UHM, Le L. iBRAB: In silico based-designed broad-spectrum Fab against H1N1 influenza A virus. PLoS One 2020; 15:e0239112. [PMID: 33382708 PMCID: PMC7774956 DOI: 10.1371/journal.pone.0239112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
Influenza virus A is a significant agent involved in the outbreak of worldwide epidemics, causing millions of fatalities around the world by respiratory diseases and seasonal illness. Many projects had been conducting to investigate recovered infected patients for therapeutic vaccines that have broad-spectrum activity. With the aid of the computational approach in biology, the designation for a vaccine model is more accessible. We developed an in silico protocol called iBRAB to design a broad-reactive Fab on a wide range of influenza A virus. The Fab model was constructed based on sequences and structures of available broad-spectrum Abs or Fabs against a wide range of H1N1 influenza A virus. As a result, the proposed Fab model followed iBRAB has good binding affinity over 27 selected HA of different strains of H1 influenza A virus, including wild-type and mutated ones. The examination also took by computational tools to fasten the procedure. This protocol could be applied for a fast-designed therapeutic vaccine against different types of threats.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Binding Sites
- Computer Simulation
- Drug Design
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/biosynthesis
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Molecular Docking Simulation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Sequence Alignment
- Sequence Homology, Amino Acid
- Thermodynamics
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Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
| | - Trung H. Nguyen
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
| | - Uyen H. M. Vo
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
| | - Ly Le
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
- Vingroup Big Data Institute, Hai Ba Trung District, Ha Noi, Vietnam
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28
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Rujas E, Cui H, Sicard T, Semesi A, Julien JP. Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies. Nat Commun 2020; 11:5066. [PMID: 33033255 PMCID: PMC7545189 DOI: 10.1038/s41467-020-18828-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
The inducible co-stimulator (ICOS) is a member of the CD28/B7 superfamily, and delivers a positive co-stimulatory signal to activated T cells upon binding to its ligand (ICOS-L). Dysregulation of this pathway has been implicated in autoimmune diseases and cancer, and is currently under clinical investigation as an immune checkpoint blockade. Here, we describe the molecular interactions of the ICOS/ICOS-L immune complex at 3.3 Å resolution. A central FDPPPF motif and residues within the CC' loop of ICOS are responsible for the specificity of the interaction with ICOS-L, with a distinct receptor binding orientation in comparison to other family members. Furthermore, our structure and binding data reveal that the ICOS N110 N-linked glycan participates in ICOS-L binding. In addition, we report crystal structures of ICOS and ICOS-L in complex with monoclonal antibodies under clinical evaluation in immunotherapy. Strikingly, antibody paratopes closely mimic receptor-ligand binding core interactions, in addition to contacting peripheral residues to confer high binding affinities. Our results uncover key molecular interactions of an immune complex central to human adaptive immunity and have direct implications for the ongoing development of therapeutic interventions targeting immune checkpoint receptors.
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Affiliation(s)
- Edurne Rujas
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.,Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Anthony Semesi
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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29
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Identification of Antibodies Targeting the H3N2 Hemagglutinin Receptor Binding Site following Vaccination of Humans. Cell Rep 2020; 29:4460-4470.e8. [PMID: 31875553 PMCID: PMC6953393 DOI: 10.1016/j.celrep.2019.11.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/26/2019] [Accepted: 11/20/2019] [Indexed: 11/26/2022] Open
Abstract
Antibodies targeting the receptor binding site (RBS) of the influenza virus hemagglutinin (HA) protein are usually not broadly reactive because their footprints are typically large and extend to nearby variable HA residues. Here, we identify several human H3N2 HA RBS-targeting monoclonal antibodies (mAbs) that are sensitive to substitutions in conventional antigenic sites and are therefore not broadly reactive. However, we also identify an H3N2 HA RBS-targeting mAb that is exceptionally broadly reactive despite being sensitive to substitutions in residues outside of the RBS. We show that similar antibodies are present at measurable levels in the sera of some individuals but that they are inefficiently elicited by conventional vaccines. Our data indicate that HA RBS-targeting antibodies can be effective against variable viral strains even when they are somewhat sensitive to substitutions in HA residues adjacent to the RBS. Zost et al. show that most antibodies targeting the RBS of the H3N2 HAs are not broadly reactive. They identify one broadly reactive H3 HA RBS antibody that is tolerant of substitutions in adjacent antigenic sites but show that these types of antibodies are not efficiently elicited by vaccination.
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30
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Wu NC, Wilson IA. Influenza Hemagglutinin Structures and Antibody Recognition. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038778. [PMID: 31871236 DOI: 10.1101/cshperspect.a038778] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hemagglutinin (HA) is most abundant glycoprotein on the influenza virus surface. Influenza HA promotes viral entry by engaging the receptor and mediating virus-host membrane fusion. At the same time, HA is the major antigen of the influenza virus. HA antigenic shift can result in pandemics, whereas antigenic drift allows human circulating strains to escape herd immunity. Most antibody responses against HA are strain-specific. However, antibodies that have neutralizing activities against multiple strains or even subtypes have now been discovered and characterized. These broadly neutralizing antibodies (bnAbs) target conserved regions on HA, such as the receptor-binding site and the stem domain. Structural studies of such bnAbs have provided important insight into universal influenza vaccine and therapeutic design. This review discusses the HA functions as well as HA-antibody interactions from a structural perspective.
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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31
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Nath Neerukonda S, Vassell R, Weiss CD. Neutralizing Antibodies Targeting the Conserved Stem Region of Influenza Hemagglutinin. Vaccines (Basel) 2020; 8:E382. [PMID: 32664628 PMCID: PMC7563823 DOI: 10.3390/vaccines8030382] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza continues to be a public health threat despite the availability of annual vaccines. While vaccines are generally effective at inducing strain-specific immunity, they are sub-optimal or ineffective when drifted or novel pandemic strains arise due to sequence changes in the major surface glycoprotein hemagglutinin (HA). The discovery of a large number of antibodies targeting the highly conserved stem region of HAs that are capable of potently neutralizing a broad range of virus strains and subtypes suggests new ways to protect against influenza. The structural characterization of HA stem epitopes and broadly neutralizing antibody paratopes has enabled the design of novel proteins, mini-proteins, and peptides targeting the HA stem, thus providing a foundation for the design of new vaccines. In this narrative, we comprehensively review the current knowledge about stem-directed broadly neutralizing antibodies and the structural features contributing to virus neutralization.
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Affiliation(s)
| | | | - Carol D. Weiss
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (S.N.N.); (R.V.)
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32
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Qiu T, Qiu J, Yang Y, Zhang L, Mao T, Zhang X, Xu J, Cao Z. A benchmark dataset of protein antigens for antigenicity measurement. Sci Data 2020; 7:212. [PMID: 32632108 PMCID: PMC7338539 DOI: 10.1038/s41597-020-0555-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/12/2020] [Indexed: 01/03/2023] Open
Abstract
Antigenicity measurement plays a fundamental role in vaccine design, which requires antigen selection from a large number of mutants. To augment traditional cross-reactivity experiments, computational approaches for predicting the antigenic distance between multiple protein antigens are highly valuable. The performance of in silico models relies heavily on large-scale benchmark datasets, which are scattered among public databases and published articles or reports. Here, we present the first benchmark dataset of protein antigens with experimental evidence to guide in silico antigenicity calculations. This dataset includes (1) standard haemagglutination-inhibition (HI) tests for 3,867 influenza A/H3N2 strain pairs, (2) standard HI tests for 559 influenza virus B strain pairs, and (3) neutralization titres derived from 1,073 Dengue virus strain pairs. All of these datasets were collated and annotated with experimentally validated antigenicity relationships as well as sequence information for the corresponding protein antigens. We anticipate that this work will provide a benchmark dataset for in silico antigenicity prediction that could be further used to assist in epidemic surveillance and therapeutic vaccine design for viruses with variable antigenicity.
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Affiliation(s)
- Tianyi Qiu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jingxuan Qiu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yiyan Yang
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Lu Zhang
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Tiantian Mao
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China.
| | - Zhiwei Cao
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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33
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Li Y, Wang L, Si H, Yu Z, Tian S, Xiang R, Deng X, Liang R, Jiang S, Yu F. Influenza virus glycoprotein-reactive human monoclonal antibodies. Microbes Infect 2020; 22:263-271. [PMID: 32569735 PMCID: PMC7303604 DOI: 10.1016/j.micinf.2020.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 11/05/2022]
Abstract
Influenza continues to be a significant public health challenge. Two glycoproteins on the surface of influenza virus, hemagglutinin and neuraminidase, play a prominent role in the process of influenza virus infection and release. Monoclonal antibodies targeting glycoproteins can effectively prevent the spread of the virus. In this review, we summarized currently reported human monoclonal antibodies targeting glycoproteins of influenza A and B viruses.
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Affiliation(s)
- Yanbai Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Helong Si
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhengsen Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shijun Tian
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Rong Xiang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China.
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34
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Abstract
Understanding antigenic variation in influenza virus strains and how the human immune system recognizes strains are central challenges for vaccinologists. Antibodies directed to the 2 major viral surface membrane proteins, hemagglutinin (HA) and neuraminidase (NA), mediate protection against reinfection following natural infection or vaccination, but HA and NA protein sequences in field strains are highly variable. The central questions are how to achieve protective antibody responses in a higher proportion of individuals and how to induce responses with more breadth and durability. Studies using isolation of human monoclonal antibodies followed by structural and functional characterization revealed conserved antigenic sites recognized by broadly cross-reactive antibodies. The antigenic landscape on HA and NA proteins is coming into focus to inform studies of the correlates and mechanisms of immunity. Understanding the antibody determinants of influenza immunity points the way toward development and testing of next-generation vaccines with potential to confer broadly protective immunity.
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Affiliation(s)
- James E Crowe
- Vanderbilt Vaccine Center, Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
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35
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Zost SJ, Wu NC, Hensley SE, Wilson IA. Immunodominance and Antigenic Variation of Influenza Virus Hemagglutinin: Implications for Design of Universal Vaccine Immunogens. J Infect Dis 2020; 219:S38-S45. [PMID: 30535315 DOI: 10.1093/infdis/jiy696] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Influenza viruses routinely acquire mutations in their hemagglutinin (HA) and neuraminidase (NA) glycoproteins that abrogate binding of pre-existing antibodies in a process known as antigenic drift. Most human antibodies against HA and NA are directed against epitopes that are hypervariable and not against epitopes that are conserved among different influenza virus strains. Universal influenza vaccines are currently being developed to elicit protective responses against functionally conserved sites on influenza proteins where viral escape mutations can result in large fitness costs [1]. Universal vaccine targets include the highly conserved HA stem domain [2-12], the less conserved HA receptor-binding site (RBS) [13-16], as well as conserved sites on NA [17-19]. One central challenge of universal vaccine efforts is to steer human antibody responses away from immunodominant, variable epitopes and towards subdominant, functionally conserved sites. Overcoming this challenge will require further understanding of the structural basis of broadly neutralizing HA and NA antibody binding epitopes and factors that influence immunodominance hierarchies of human antibody responses.
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Affiliation(s)
- Seth J Zost
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California
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36
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Mapping of a Novel H3-Specific Broadly Neutralizing Monoclonal Antibody Targeting the Hemagglutinin Globular Head Isolated from an Elite Influenza Virus-Immunized Donor Exhibiting Serological Breadth. J Virol 2020; 94:JVI.01035-19. [PMID: 31826999 DOI: 10.1128/jvi.01035-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/05/2019] [Indexed: 11/20/2022] Open
Abstract
The discovery of potent and broadly protective influenza virus epitopes could lead to improved vaccines that are resistant to antigenic drift. Here, we describe human antibody C585, isolated from a vaccinee with remarkable serological breadth as measured by hemagglutinin inhibition (HAI). C585 binds and neutralizes multiple H3N2 strains isolated between 1968 and 2016, including strains that emerged up to 4 years after B cells were isolated from the vaccinated donor. The crystal structure of C585 Fab in complex with the HA from A/Switzerland/9715293/2013 (H3N2) shows that the antibody binds to a novel and well-conserved epitope on the globular head of H3 HA and that it differs from other antibodies not only in its epitope but in its binding geometry and hypermutated framework 3 region, thereby explaining its breadth and ability to mediate hemagglutination inhibition across decades of H3N2 strains. The existence of epitopes such as the one elucidated by C585 has implications for rational vaccine design.IMPORTANCE Influenza viruses escape immunity through continuous antigenic changes that occur predominantly on the viral hemagglutinin (HA). Induction of broadly neutralizing antibodies (bnAbs) targeting conserved epitopes following vaccination is a goal of universal influenza vaccines and advantageous in protecting hosts against virus evolution and antigenic drift. To date, most of the discovered bnAbs bind either to conserved sites in the stem region or to the sialic acid-binding pocket. Generally, antibodies targeting the stem region offer broader breadth with low potency, while antibodies targeting the sialic acid-binding pocket cover narrower breadth but usually have higher potency. In this study, we identified a novel neutralizing epitope in the head region recognized by a broadly neutralizing human antibody against a broad range of H3N2 with high potency. This epitope may provide insights for future universal vaccine design.
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37
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Portnoff AD, Patel N, Massare MJ, Zhou H, Tian JH, Zhou B, Shinde V, Glenn GM, Smith G. Influenza Hemagglutinin Nanoparticle Vaccine Elicits Broadly Neutralizing Antibodies against Structurally Distinct Domains of H3N2 HA. Vaccines (Basel) 2020; 8:vaccines8010099. [PMID: 32098409 PMCID: PMC7157642 DOI: 10.3390/vaccines8010099] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022] Open
Abstract
Influenza vaccine effectiveness varies annually due to the fast evolving seasonal influenza A(H3N2) strain and egg-derived mutations—both of which can cause a mismatch between the vaccine and circulating strains. To address these limitations, we have developed a hemagglutinin (HA)-based protein-detergent nanoparticle influenza vaccine (NIV) with a saponin-based Matrix-M™ adjuvant. In a phase 1 clinical trial of older adults, the vaccine demonstrated broadly cross-reactive A(H3N2) HA antibody responses. Two broadly neutralizing monoclonal antibodies derived from NIV-immunized mice were characterized by transmission electron microscopy (TEM), antibody competition assays, fluorescence-activated cell sorting (FACS) analysis, and protein–protein docking. These antibodies recognize two conserved regions of the head domain, namely the receptor binding site and the vestigial esterase subdomain, thus demonstrating the potential for an HA subunit vaccine to elicit antibodies targeting structurally and antigenically distinct but conserved sites. Antibody competition studies with sera from the phase 1 trial in older adults confirmed that humans also make antibodies to these two head domains and against the highly conserved stem domain. This data supports the potential of an adjuvanted recombinant HA nanoparticle vaccine to induce broadly protective immunity and improved vaccine efficacy.
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38
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Wei CJ, Crank MC, Shiver J, Graham BS, Mascola JR, Nabel GJ. Next-generation influenza vaccines: opportunities and challenges. Nat Rev Drug Discov 2020; 19:239-252. [PMID: 32060419 PMCID: PMC7223957 DOI: 10.1038/s41573-019-0056-x] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Seasonal influenza vaccines lack efficacy against drifted or pandemic influenza strains. Developing improved vaccines that elicit broader immunity remains a public health priority. Immune responses to current vaccines focus on the haemagglutinin head domain, whereas next-generation vaccines target less variable virus structures, including the haemagglutinin stem. Strategies employed to improve vaccine efficacy involve using structure-based design and nanoparticle display to optimize the antigenicity and immunogenicity of target antigens; increasing the antigen dose; using novel adjuvants; stimulating cellular immunity; and targeting other viral proteins, including neuraminidase, matrix protein 2 or nucleoprotein. Improved understanding of influenza antigen structure and immunobiology is advancing novel vaccine candidates into human trials. Current seasonal influenza vaccines lack efficacy against drifted or pandemic virus strains, and the development of novel vaccines that elicit broader immunity represents a public health priority. Here, Nabel and colleagues discuss approaches to improve vaccine efficacy which harness new insights from influenza antigen structure and human immunity, highlighting major targets, vaccines in development and ongoing challenges.
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Affiliation(s)
- Chih-Jen Wei
- Sanofi Global Research and Development, Cambridge, MA, USA
| | - Michelle C Crank
- Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Barney S Graham
- Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gary J Nabel
- Sanofi Global Research and Development, Cambridge, MA, USA.
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39
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Bangaru S, Lang S, Schotsaert M, Vanderven HA, Zhu X, Kose N, Bombardi R, Finn JA, Kent SJ, Gilchuk P, Gilchuk I, Turner HL, García-Sastre A, Li S, Ward AB, Wilson IA, Crowe JE. A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface. Cell 2020; 177:1136-1152.e18. [PMID: 31100268 DOI: 10.1016/j.cell.2019.04.011] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/25/2019] [Accepted: 04/04/2019] [Indexed: 12/17/2022]
Abstract
Here, we describe the discovery of a naturally occurring human antibody (Ab), FluA-20, that recognizes a new site of vulnerability on the hemagglutinin (HA) head domain and reacts with most influenza A viruses. Structural characterization of FluA-20 with H1 and H3 head domains revealed a novel epitope in the HA trimer interface, suggesting previously unrecognized dynamic features of the trimeric HA protein. The critical HA residues recognized by FluA-20 remain conserved across most subtypes of influenza A viruses, which explains the Ab's extraordinary breadth. The Ab rapidly disrupted the integrity of HA protein trimers, inhibited cell-to-cell spread of virus in culture, and protected mice against challenge with viruses of H1N1, H3N2, H5N1, or H7N9 subtypes when used as prophylaxis or therapy. The FluA-20 Ab has uncovered an exceedingly conserved protective determinant in the influenza HA head domain trimer interface that is an unexpected new target for anti-influenza therapeutics and vaccines.
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Affiliation(s)
- Sandhya Bangaru
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shanshan Lang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hillary A Vanderven
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica A Finn
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Iuliia Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sheng Li
- Department of Medicine and Biomedical Sciences, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Andrew B Ward
- 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; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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40
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A Complex Dance: Measuring the Multidimensional Worlds of Influenza Virus Evolution and Anti-Influenza Immune Responses. Pathogens 2019; 8:pathogens8040238. [PMID: 31731815 PMCID: PMC6963821 DOI: 10.3390/pathogens8040238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 11/17/2022] Open
Abstract
The human antibody response to influenza virus infection or vaccination is as complicated as it is essential for protection against flu. The constant antigenic changes of the virus to escape human herd immunity hinder the yearly selection of vaccine strains since it is hard to predict which virus strains will circulate for the coming flu season. A "universal" influenza vaccine that could induce broad cross-influenza subtype protection would help to address this issue. However, the human antibody response is intricate and often obscure, with factors such as antigenic seniority or original antigenic sin (OAS), and back-boosting ensuring that each person mounts a unique immune response to infection or vaccination with any new influenza virus strain. Notably, the effects of existing antibodies on cross-protective immunity after repeated vaccinations are unclear. More research is needed to characterize the mechanisms at play, but traditional assays such as hemagglutinin inhibition (HAI) and microneutralization (MN) are excessively limited in scope and too resource-intensive to effectively meet this challenge. In the past ten years, new multiple dimensional assays (MDAs) have been developed to help overcome these problems by simultaneously measuring antibodies against a large panel of influenza hemagglutinin (HA) proteins with a minimal amount of sample in a high throughput way. MDAs will likely be a powerful tool for accelerating the study of the humoral immune response to influenza vaccination and the development of a universal influenza vaccine.
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41
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Ning T, Nie J, Huang W, Li C, Li X, Liu Q, Zhao H, Wang Y. Antigenic Drift of Influenza A(H7N9) Virus Hemagglutinin. J Infect Dis 2019; 219:19-25. [PMID: 29982588 DOI: 10.1093/infdis/jiy408] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/28/2018] [Indexed: 01/03/2023] Open
Abstract
Background Since the emergence of influenza A(H7N9) virus in 2013, there have been 5 waves of influenza A(H7N9) epidemics in China. However, evolution of the hemagglutinin (HA) protein antigenicity has not been systematically investigated. Methods To better understand how antigenic drift in HA proteins of influenza (A)H7N9 virus occurs, 902 influenza A(H7N9) virus HA protein sequences from a public database were retrieved and analyzed. Fifty-three mutants with single amino acid substitutions in HA protein were introduced into pseudoviruses, and their antigenic characteristics were analyzed using pseudovirus-based assays. Results The frequencies of 9 mutations incrementally increased over the past 5 years, with mutations identified at multiple sites. While mean neutralization titers of most variants remained unchanged, 3 mutations, A143V, A143T, and R148K, displayed a median 4-fold lower susceptibility to neutralization by antisera against influenza A/Anhui/1/2013(H7N9) virus. Notably, A143V and A143T were located outside the previously reported antigenic sites. The most dominant variant (A143V/R148K) in the most recent season constituted 74.11% of all mutations and demonstrated a 10-fold reduction in its reactivity to influenza A/Anhui/1/2013(H7N9) virus antisera. Importantly, compared with the DNA construct without the corresponding HA protein mutation, DNA vaccine encoding the A143V/R148K mutant induced a 5-fold increase in the neutralizing activity against this circulating virus. Conclusions An appropriate vaccine strain should be considered in response to increasing antigenic drift in influenza A(H7N9) virus HA protein.
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Affiliation(s)
- Tingting Ning
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Beijing, China
| | - Weijin Huang
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Beijing, China
| | - Changgui Li
- Division of Respiratory Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Canada
| | - Qiang Liu
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Beijing, China
| | - Hui Zhao
- Division of Respiratory Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
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42
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Crowe JE. Influenza Virus-Specific Human Antibody Repertoire Studies. THE JOURNAL OF IMMUNOLOGY 2019; 202:368-373. [PMID: 30617118 DOI: 10.4049/jimmunol.1801459] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022]
Abstract
The diversity of Ag-specific adaptive receptors on the surface of B cells and in the population of secreted Abs is enormous, but increasingly, we are acquiring the technical capability to interrogate Ab repertoires in great detail. These Ab technologies have been especially pointed at understanding the complex issues of immunity to infection and disease caused by influenza virus, one of the most common and vexing medical problems in man. Influenza immunity is particularly interesting as a model system because the antigenic diversity of influenza strains and proteins is high and constantly evolving. Discovery of canonical features in the subset of the influenza repertoire response that is broadly reactive for diverse influenza strains has spurred the recent optimism for creating universal influenza vaccines. Using new technologies for sequencing Ab repertoires at great depth is helping us to understand the central features of influenza immunity.
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Affiliation(s)
- James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232; .,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232; and .,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232
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43
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Butler AL, Fallon JK, Alter G. A Sample-Sparing Multiplexed ADCP Assay. Front Immunol 2019; 10:1851. [PMID: 31456799 PMCID: PMC6700248 DOI: 10.3389/fimmu.2019.01851] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/23/2019] [Indexed: 12/21/2022] Open
Abstract
Antibodies serve as the primary correlate of protection following most clinically approved vaccines and are thought to confer protection in part through their ability to block (neutralize) infection. Increasingly, studies have shown that beyond their blocking activities, the ability of antibodies to leverage the innate immune response may serve a vital role in protection from infection. Specifically, antibodies can drive phagocytosis, complement activation, and cellular cytotoxicity by interacting with Fc-receptors found on all innate immune cells. Measuring the capacity of antibodies to induce these functions has become critical for the identification of correlates of protection in large-scale vaccine trials. Therefore, there is a growing need to develop robust, high throughput assays able to interrogate the functional capacity of innate immune recruiting antibodies. However, in many instances, only small sample volumes are available. Nevertheless, profiling antibody functions across many pathogen-associated antigens or across global intra-pathogen variants is in high demand, making sample sparing approaches to perform this antibody evaluation critical. Here we describe the development of an approach to interrogate the functional activity of antibodies in serum against up to 5 antigen targets simultaneously. A single bead-based cellular assay was adapted to accommodate 5 different fluorescently colored beads, allowing for the concurrent investigation of antibody responses directed against multiple antigens in a single well. The multiplexed assay was as sensitive, specific, and accurate as the single antigen assay and robustly able to assess functional differences mediated by antibodies across different samples. These findings show multiplexing allows for accurate and more efficient analysis of antibody-mediated effector profiles.
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Affiliation(s)
| | | | - Galit Alter
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
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44
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Antibody responses to viral infections: a structural perspective across three different enveloped viruses. Nat Microbiol 2019; 4:734-747. [PMID: 30886356 PMCID: PMC6818971 DOI: 10.1038/s41564-019-0392-y] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
Antibodies serve as critical barriers to viral infection. Humoral immunity to a virus is achieved through the dual role of antibodies in communicating the presence of invading pathogens in infected cells to effector cells and interfering with processes essential to the viral lifecycle, chiefly entry into the host cell. For individuals that successfully control infection, virus-elicited antibodies can provide lifelong surveillance and protection from future insults. One approach to understand the nature of a successful immune response has been to utilize structural biology to uncover the molecular details of the antibodies derived from vaccines or natural infection and how they interact with their cognate microbial antigens. The ability to isolate antigen specific B-cells and rapidly solve structures of functional, monoclonal antibodies in complex with viral glycoprotein surface antigens has greatly expanded our knowledge of the sites of vulnerability on viruses. In this review, we compare the adaptive humoral immune responses to HIV, influenza, and filoviruses, with a particular focus on neutralizing antibodies. The pathogenesis of each of these viruses is quite different, providing an opportunity for comparison of immune responses: HIV causes a persistent, chronic infection; influenza an acute infection with multiple exposures during a lifetime and annual vaccination; and filoviruses, a virulent, acute infection. Neutralizing antibodies that develop under these different constraints are therefore sentinels that can provide insight into the underlying humoral immune responses and important lessons to guide future development of vaccines and immunotherapeutics.
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45
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V H1-69 antiviral broadly neutralizing antibodies: genetics, structures, and relevance to rational vaccine design. Curr Opin Virol 2019; 34:149-159. [PMID: 30884330 DOI: 10.1016/j.coviro.2019.02.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) are potential therapeutic molecules and valuable tools for studying conserved viral targets for vaccine and drug design. Interestingly, antibody responses to conserved epitopes can be highly convergent at the molecular level. Human antibodies targeting a number of viral antigens have often been found to utilize a restricted set of immunoglobulin germline genes in different individuals. Here we review recent knowledge on VH1-69-encoded antibodies in antiviral responses to influenza virus, HCV, and HIV-1. These antibodies share common genetic and structural features, and often develop neutralizing activity against a broad spectrum of viral strains. Understanding the genetic and structural characteristics of such antibodies and the target epitopes should help advance novel strategies to elicit bnAbs through vaccination.
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46
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Soto C, Bombardi RG, Branchizio A, Kose N, Matta P, Sevy AM, Sinkovits RS, Gilchuk P, Finn JA, Crowe JE. High frequency of shared clonotypes in human B cell receptor repertoires. Nature 2019; 566:398-402. [PMID: 30760926 DOI: 10.1038/s41586-019-0934-8] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/14/2019] [Indexed: 12/18/2022]
Abstract
The human genome contains approximately 20 thousand protein-coding genes1, but the size of the collection of antigen receptors of the adaptive immune system that is generated by the recombination of gene segments with non-templated junctional additions (on B cells) is unknown-although it is certainly orders of magnitude larger. It has not been established whether individuals possess unique (or private) repertoires or substantial components of shared (or public) repertoires. Here we sequence recombined and expressed B cell receptor genes in several individuals to determine the size of their B cell receptor repertoires, and the extent to which these are shared between individuals. Our experiments revealed that the circulating repertoire of each individual contained between 9 and 17 million B cell clonotypes. The three individuals that we studied shared many clonotypes, including between 1 and 6% of B cell heavy-chain clonotypes shared between two subjects (0.3% of clonotypes shared by all three) and 20 to 34% of λ or κ light chains shared between two subjects (16 or 22% of λ or κ light chains, respectively, were shared by all three). Some of the B cell clonotypes had thousands of clones, or somatic variants, within the clonotype lineage. Although some of these shared lineages might be driven by exposure to common antigens, previous exposure to foreign antigens was not the only force that shaped the shared repertoires, as we also identified shared clonotypes in umbilical cord blood samples and all adult repertoires. The unexpectedly high prevalence of shared clonotypes in B cell repertoires, and identification of the sequences of these shared clonotypes, should enable better understanding of the role of B cell immune repertoires in health and disease.
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Affiliation(s)
- Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin G Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andre Branchizio
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pranathi Matta
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexander M Sevy
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA
| | - Robert S Sinkovits
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA, USA
| | - Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica A Finn
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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47
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Turner HL, Pallesen J, Lang S, Bangaru S, Urata S, Li S, Cottrell CA, Bowman CA, Crowe JE, Wilson IA, Ward AB. Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor-binding head domains. PLoS Biol 2019; 17:e3000139. [PMID: 30716060 PMCID: PMC6375650 DOI: 10.1371/journal.pbio.3000139] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/14/2019] [Accepted: 01/18/2019] [Indexed: 01/02/2023] Open
Abstract
Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy (cryoEM) to decipher the mechanism of action of a potent HA head-directed monoclonal antibody (mAb) bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, prefusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the prefusion conformation. The "breathing" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/metabolism
- Antibody Specificity
- Baculoviridae/genetics
- Baculoviridae/metabolism
- Binding Sites
- Cloning, Molecular
- Cryoelectron Microscopy
- Gene Expression
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hydrogen Bonding
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/metabolism
- Influenza A virus/chemistry
- Influenza A virus/genetics
- Influenza A virus/immunology
- Molecular Docking Simulation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sf9 Cells
- Spodoptera
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Affiliation(s)
- Hannah L. Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Shanshan Lang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sandhya Bangaru
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Sarah Urata
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Charles A. Bowman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - James E. Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
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48
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Li H, Li M, Xu R, Wang S, Zhang Y, Zhang L, Zhou D, Xiao S. Synthesis, structure activity relationship and in vitro anti-influenza virus activity of novel polyphenol-pentacyclic triterpene conjugates. Eur J Med Chem 2019; 163:560-568. [DOI: 10.1016/j.ejmech.2018.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 01/11/2023]
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49
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Smith SA, Burton SL, Kilembe W, Lakhi S, Karita E, Price M, Allen S, Derdeyn CA. VH1-69 Utilizing Antibodies Are Capable of Mediating Non-neutralizing Fc-Mediated Effector Functions Against the Transmitted/Founder gp120. Front Immunol 2019; 9:3163. [PMID: 30697215 PMCID: PMC6341001 DOI: 10.3389/fimmu.2018.03163] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/21/2018] [Indexed: 01/05/2023] Open
Abstract
Multiple antibody effector functions arise in HIV-1 infection that could be harnessed to protect against infection or clear the persistent reservoir. Here, we have investigated the genetic and functional memory B cell and antibody landscape present during early infection in six individuals infected with either subtype A, C, or an A/C recombinant HIV-1. These individuals demonstrated varying levels of plasma autologous neutralization (nAb) against the transmitted/founder envelope (T/F Env) pseudovirus and non-neutralizing Fc-mediated effector function (nnFc) antibody-dependent cell-mediated cytotoxicity (ADCC) against the T/F Env gp120 protein at ~7 months after infection. Genetic analysis of the immunoglobulin heavy (VH) and light (VL) chain variable domain gene segments from 352 autologous T/F Env gp120-specific single B cells recovered at this same 7-month time-point revealed an over-representation of the VH1-69 germline in five of six individuals. A defining feature of the VH1-69 utilizing gp120-specific antibodies was their significantly more hydrophobic complementarity-determining region-2 (CDRH2) regions compared to other VH CDRH2 sequences from each individual. While none of the VH1-69 antibodies possessed strong neutralizing activity against virions pseudotyped with the autologous T/F Env, almost a third were capable of mediating high ADCC activity, as assayed by intracellular granzyme B activity in CEM.NKr.CCR5 target cells coated with autologous T/F Env gp120. High ADCC mediating VH1-69 antibodies exhibited shorter complementarity-determining region-3 (CDRH3) lengths and a more neutral isoelectric point than antibodies lacking this function. In the individual that developed the highest autologous ADCC responses, the high granzyme B producing antibodies bound to surface expressed envelope in the absence of CD4 and were not enhanced by the addition of soluble CD4. Overall, VH1-69 utilizing antibodies are commonly induced against gp120 in diverse HIV-1 infections and a subset of these antibodies can mediate ADCC functions, serving as a bridge between the innate and adaptive immune response to HIV-1.
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Affiliation(s)
- S Abigail Smith
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Samantha L Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | | | - Shabir Lakhi
- Zambia Emory HIV Research Project, Lusaka, Zambia
| | | | - Matt Price
- International AIDS Vaccine Initiative, New York, NY, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Cynthia A Derdeyn
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
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50
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Yasuhara A, Yamayoshi S, Ito M, Kiso M, Yamada S, Kawaoka Y. Isolation and Characterization of Human Monoclonal Antibodies That Recognize the Influenza A(H1N1)pdm09 Virus Hemagglutinin Receptor-Binding Site and Rarely Yield Escape Mutant Viruses. Front Microbiol 2018; 9:2660. [PMID: 30443246 PMCID: PMC6222141 DOI: 10.3389/fmicb.2018.02660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/18/2018] [Indexed: 11/13/2022] Open
Abstract
The influenza A virus rapidly mutates to escape from antibodies. Here, we isolated and characterized three human monoclonal antibodies (mAbs) that neutralize A(H1N1)pdm09 viruses. Generation of escape mutant viruses suggested that these antibodies recognized conserved residues of the receptor-binding site (RBS) of hemagglutinin (HA) and that mutant viruses that escaped from these mAbs rarely appeared. Moreover, the escape mutant viruses grew significantly slower than wild-type virus, indicating their reduced fitness. These results indicate that these three human mAbs against the RBS of HA have the potential to be anti-influenza agents with a low propensity for the development of resistant viruses.
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Affiliation(s)
- Atsuhiro Yasuhara
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Mutsumi Ito
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Maki Kiso
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Shinya Yamada
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,ERATO Infection-Induced Host Responses Project, Japan Science and Technology Agency, Saitama, Japan
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