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Hamza H, Ghosh M, Löffler MW, Rammensee HG, Planz O. Identification and relative abundance of naturally presented and cross-reactive influenza A virus MHC class I-restricted T cell epitopes. Emerg Microbes Infect 2024; 13:2306959. [PMID: 38240239 PMCID: PMC10854457 DOI: 10.1080/22221751.2024.2306959] [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: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Cytotoxic T lymphocytes are key for controlling viral infection. Unravelling CD8+ T cell-mediated immunity to distinct influenza virus strains and subtypes across prominent HLA types is relevant for combating seasonal infections and emerging new variants. Using an immunopeptidomics approach, naturally presented influenza A virus-derived ligands restricted to HLA-A*24:02, HLA-A*68:01, HLA-B*07:02, and HLA-B*51:01 molecules were identified. Functional characterization revealed multifunctional memory CD8+ T cell responses for nine out of sixteen peptides. Peptide presentation kinetics was optimal around 12 h post infection and presentation of immunodominant epitopes shortly after infection was not always persistent. Assessment of immunogenic epitopes revealed that they are highly conserved across the major zoonotic reservoirs and may contain a single substitution in the vicinity of the anchor residues. These findings demonstrate how the identified epitopes promote T cell pools, possibly cross-protective in individuals and can be potential targets for vaccination.
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Affiliation(s)
- Hazem Hamza
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Michael Ghosh
- Institute for Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty of Tübingen, Tübingen, Germany
- Centre for Clinical Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence CMFI (EXC2124) "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Oliver Planz
- Institute for Immunology, University of Tübingen, Tübingen, Germany
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2
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Schiffner T, Phung I, Ray R, Irimia A, Tian M, Swanson O, Lee JH, Lee CCD, Marina-Zárate E, Cho SY, Huang J, Ozorowski G, Skog PD, Serra AM, Rantalainen K, Allen JD, Baboo S, Rodriguez OL, Himansu S, Zhou J, Hurtado J, Flynn CT, McKenney K, Havenar-Daughton C, Saha S, Shields K, Schulze S, Smith ML, Liang CH, Toy L, Pecetta S, Lin YC, Willis JR, Sesterhenn F, Kulp DW, Hu X, Cottrell CA, Zhou X, Ruiz J, Wang X, Nair U, Kirsch KH, Cheng HL, Davis J, Kalyuzhniy O, Liguori A, Diedrich JK, Ngo JT, Lewis V, Phelps N, Tingle RD, Spencer S, Georgeson E, Adachi Y, Kubitz M, Eskandarzadeh S, Elsliger MA, Amara RR, Landais E, Briney B, Burton DR, Carnathan DG, Silvestri G, Watson CT, Yates JR, Paulson JC, Crispin M, Grigoryan G, Ward AB, Sok D, Alt FW, Wilson IA, Batista FD, Crotty S, Schief WR. Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Nat Immunol 2024; 25:1073-1082. [PMID: 38816615 PMCID: PMC11147780 DOI: 10.1038/s41590-024-01833-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/04/2024] [Indexed: 06/01/2024]
Abstract
A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.
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Affiliation(s)
- Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
| | - Ivy Phung
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Rashmi Ray
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Adriana Irimia
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Olivia Swanson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Chang-Chun D Lee
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ester Marina-Zárate
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - So Yeon Cho
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jiachen Huang
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Patrick D Skog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Andreia M Serra
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | | | - Jianfu Zhou
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Claudia T Flynn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Katherine McKenney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Steven Schulze
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Chi-Hui Liang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Toy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Simone Pecetta
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ying-Cing Lin
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Fabian Sesterhenn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaoya Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jennifer Ruiz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Hwei-Ling Cheng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jillian Davis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia T Ngo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Vanessa Lewis
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan D Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Skye Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Marc A Elsliger
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rama R Amara
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, USA
- San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Diane G Carnathan
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
- Generate Biomedicines, Inc., Somerville, MA, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Moderna, Inc., Cambridge, MA, USA.
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3
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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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4
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Bliss CM, Nachbagauer R, Mariottini C, Cuevas F, Feser J, Naficy A, Bernstein DI, Guptill J, Walter EB, Berlanda-Scorza F, Innis BL, García-Sastre A, Palese P, Krammer F, Coughlan L. A chimeric haemagglutinin-based universal influenza virus vaccine boosts human cellular immune responses directed towards the conserved haemagglutinin stalk domain and the viral nucleoprotein. EBioMedicine 2024; 104:105153. [PMID: 38805853 PMCID: PMC11154122 DOI: 10.1016/j.ebiom.2024.105153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The development of a universal influenza virus vaccine, to protect against both seasonal and pandemic influenza A viruses, is a long-standing public health goal. The conserved stalk domain of haemagglutinin (HA) is a promising vaccine target. However, the stalk is immunosubdominant. As such, innovative approaches are required to elicit robust immunity against this domain. In a previously reported observer-blind, randomised placebo-controlled phase I trial (NCT03300050), immunisation regimens using chimeric HA (cHA)-based immunogens formulated as inactivated influenza vaccines (IIV) -/+ AS03 adjuvant, or live attenuated influenza vaccines (LAIV), elicited durable HA stalk-specific antibodies with broad reactivity. In this study, we sought to determine if these vaccines could also boost T cell responses against HA stalk, and nucleoprotein (NP). METHODS We measured interferon-γ (IFN-γ) responses by Enzyme-Linked ImmunoSpot (ELISpot) assay at baseline, seven days post-prime, pre-boost and seven days post-boost following heterologous prime:boost regimens of LAIV and/or adjuvanted/unadjuvanted IIV-cHA vaccines. FINDINGS Our findings demonstrate that immunisation with adjuvanted cHA-based IIVs boost HA stalk-specific and NP-specific T cell responses in humans. To date, it has been unclear if HA stalk-specific T cells can be boosted in humans by HA-stalk focused universal vaccines. Therefore, our study will provide valuable insights for the design of future studies to determine the precise role of HA stalk-specific T cells in broad protection. INTERPRETATION Considering that cHA-based vaccines also elicit stalk-specific antibodies, these data support the further clinical advancement of cHA-based universal influenza vaccine candidates. FUNDING This study was funded in part by the Bill and Melinda Gates Foundation (BMGF).
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Affiliation(s)
- Carly M Bliss
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Cancer & Genetics and Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Mariottini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frans Cuevas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jodi Feser
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Abdi Naficy
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - David I Bernstein
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jeffrey Guptill
- Duke Early Phase Clinical Research Unit, Duke Clinical Research Institute, Durham, NC, USA
| | - Emmanuel B Walter
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Bruce L Innis
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; University of Maryland School of Medicine, Department of Microbiology and Immunology, Baltimore, MD 21201, USA; University of Maryland School of Medicine, Center for Vaccine Development and Global Health (CVD), Baltimore, MD 21201, USA.
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5
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Ray R, Nait Mohamed FA, Maurer DP, Huang J, Alpay BA, Ronsard L, Xie Z, Han J, Fernandez-Quintero M, Phan QA, Ursin RL, Vu M, Kirsch KH, Prum T, Rosado VC, Bracamonte-Moreno T, Okonkwo V, Bals J, McCarthy C, Nair U, Kanekiyo M, Ward AB, Schmidt AG, Batista FD, Lingwood D. Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. Immunity 2024; 57:1141-1159.e11. [PMID: 38670113 PMCID: PMC11096021 DOI: 10.1016/j.immuni.2024.03.022] [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: 12/12/2023] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
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Affiliation(s)
- Rashmi Ray
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
| | - Daniel P Maurer
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Jiachen Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Berk A Alpay
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Zhenfei Xie
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Monica Fernandez-Quintero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020 Innsbruck, Austria
| | - Quynh Anh Phan
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Rebecca L Ursin
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mya Vu
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Victoria C Rosado
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte-Moreno
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julia Bals
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron G Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Biology, The Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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6
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Petersen BM, Kirby MB, Chrispens KM, Irvin OM, Strawn IK, Haas CM, Walker AM, Baumer ZT, Ulmer SA, Ayala E, Rhodes ER, Guthmiller JJ, Steiner PJ, Whitehead TA. An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries. Nat Commun 2024; 15:3974. [PMID: 38730230 PMCID: PMC11087541 DOI: 10.1038/s41467-024-48072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of nine different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
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Affiliation(s)
- Brian M Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Monica B Kirby
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Karson M Chrispens
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Olivia M Irvin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Isabell K Strawn
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Cyrus M Haas
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Alexis M Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Zachary T Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sophia A Ulmer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Edgardo Ayala
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emily R Rhodes
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Jenna J Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
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7
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Li Y, Huo S, Yin Z, Tian Z, Huang F, Liu P, Liu Y, Yu F. Retracted and republished from: "The current state of research on influenza antiviral drug development: drugs in clinical trial and licensed drugs". mBio 2024; 15:e0017524. [PMID: 38551343 PMCID: PMC11077966 DOI: 10.1128/mbio.00175-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024] Open
Abstract
Influenza viruses (IVs) threaten global human health due to the high morbidity, infection, and mortality rates. Currently, the influenza drugs recommended by the Food and Drug Administration are oseltamivir, zanamivir, peramivir, and baloxavir marboxil. These recommended antivirals are currently effective for major subtypes of IVs as the compounds target conserved domains in neuraminidase or polymerase acidic (PA) protein. However, this trend may gradually change due to the selection of antiviral drugs and the natural evolution of IVs. Therefore, there is an urgent need to develop drugs related to the treatment of influenza to deal with the next pandemic. Here, we summarized the cutting-edge research in mechanism of action, inhibitory activity, and clinical efficacy of drugs that have been approved and drugs that are still in clinical trials for influenza treatment. We hope this review will provide up-to-date and comprehensive information on influenza antivirals and generate hypotheses for screens and development of new broad-spectrum influenza drugs in the near future.
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Affiliation(s)
- Yanbai Li
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shanshan Huo
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhe Yin
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zuguang Tian
- Department of High-Tech Development, Baoding City Science and Technology Bureau, Baoding, China
| | - Fang Huang
- Epidemic Prevention Laboratory, Tongzhou District Center For Animal Disease Control and Prevention, Beijing, China
| | - Peng Liu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yue Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Fei Yu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
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8
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Luczo JM, Spackman E. Epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift. FEMS Microbiol Rev 2024; 48:fuae014. [PMID: 38734891 PMCID: PMC11149724 DOI: 10.1093/femsre/fuae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/23/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Avian influenza viruses evolve antigenically to evade host immunity. Two influenza A virus surface glycoproteins, the haemagglutinin and neuraminidase, are the major targets of host immunity and undergo antigenic drift in response to host pre-existing humoral and cellular immune responses. Specific sites have been identified as important epitopes in prominent subtypes such as H5 and H7, which are of animal and public health significance due to their panzootic and pandemic potential. The haemagglutinin is the immunodominant immunogen, it has been extensively studied, and the antigenic reactivity is closely monitored to ensure candidate vaccine viruses are protective. More recently, the neuraminidase has received increasing attention for its role as a protective immunogen. The neuraminidase is expressed at a lower abundance than the haemagglutinin on the virus surface but does elicit a robust antibody response. This review aims to compile the current information on haemagglutinin and neuraminidase epitopes and immune escape mutants of H5 and H7 highly pathogenic avian influenza viruses. Understanding the evolution of immune escape mutants and the location of epitopes is critical for identification of vaccine strains and development of broadly reactive vaccines that can be utilized in humans and animals.
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Affiliation(s)
- Jasmina M Luczo
- Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, East Geelong, Victoria 3219, Australia
| | - Erica Spackman
- Exotic & Emerging Avian Viral Diseases Research, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, United States
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9
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Zareein A, Mahmoudi M, Jadhav SS, Wilmore J, Wu Y. Biomaterial engineering strategies for B cell immunity modulations. Biomater Sci 2024; 12:1981-2006. [PMID: 38456305 PMCID: PMC11019864 DOI: 10.1039/d3bm01841e] [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: 11/11/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
B cell immunity has a penetrating effect on human health and diseases. Therapeutics aiming to modulate B cell immunity have achieved remarkable success in combating infections, autoimmunity, and malignancies. However, current treatments still face significant limitations in generating effective long-lasting therapeutic B cell responses for many conditions. As the understanding of B cell biology has deepened in recent years, clearer regulation networks for B cell differentiation and antibody production have emerged, presenting opportunities to overcome current difficulties and realize the full therapeutic potential of B cell immunity. Biomaterial platforms have been developed to leverage these emerging concepts to augment therapeutic humoral immunity by facilitating immunogenic reagent trafficking, regulating T cell responses, and modulating the immune microenvironment. Moreover, biomaterial engineering tools have also advanced our understanding of B cell biology, further expediting the development of novel therapeutics. In this review, we will introduce the general concept of B cell immunobiology and highlight key biomaterial engineering strategies in the areas including B cell targeted antigen delivery, sustained B cell antigen delivery, antigen engineering, T cell help optimization, and B cell suppression. We will also discuss our perspective on future biomaterial engineering opportunities to leverage humoral immunity for therapeutics.
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Affiliation(s)
- Ali Zareein
- Department of Biomedical Engineering, Syracuse University, Syracuse, NY, USA.
- The BioInspired Institute for Material and Living Systems, Syracuse University, Syracuse, NY, USA
| | - Mina Mahmoudi
- Department of Biomedical Engineering, Syracuse University, Syracuse, NY, USA.
- The BioInspired Institute for Material and Living Systems, Syracuse University, Syracuse, NY, USA
| | - Shruti Sunil Jadhav
- Department of Biomedical Engineering, Syracuse University, Syracuse, NY, USA.
| | - Joel Wilmore
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Yaoying Wu
- Department of Biomedical Engineering, Syracuse University, Syracuse, NY, USA.
- The BioInspired Institute for Material and Living Systems, Syracuse University, Syracuse, NY, USA
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
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10
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Del Moral-Sánchez I, Wee EG, Xian Y, Lee WH, Allen JD, Torrents de la Peña A, Fróes Rocha R, Ferguson J, León AN, Koekkoek S, Schermer EE, Burger JA, Kumar S, Zwolsman R, Brinkkemper M, Aartse A, Eggink D, Han J, Yuan M, Crispin M, Ozorowski G, Ward AB, Wilson IA, Hanke T, Sliepen K, Sanders RW. Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines. NPJ Vaccines 2024; 9:74. [PMID: 38582771 PMCID: PMC10998906 DOI: 10.1038/s41541-024-00862-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/14/2024] [Indexed: 04/08/2024] Open
Abstract
Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.
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Affiliation(s)
- Iván Del Moral-Sánchez
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Edmund G Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yuejiao Xian
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebeca Fróes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - James Ferguson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - André N León
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Edith E Schermer
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Judith A Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Sanjeev Kumar
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Robby Zwolsman
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Mitch Brinkkemper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Aafke Aartse
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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11
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Reperant L, Russell CA, Osterhaus A. Scientific highlights of the 9th ESWI Influenza Conference. ONE HEALTH OUTLOOK 2024; 6:5. [PMID: 38561784 PMCID: PMC10986029 DOI: 10.1186/s42522-024-00099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The European Scientific Working Group on Influenza (ESWI) held the 9th ESWI Influenza Conference in Valencia from 17-20 September 2023. Here we provide a summary of twelve key presentations, covering major topics on influenza virus, respiratory syncytial virus (RSV) and SARS coronavirus 2 (SARS-CoV-2) including: infection processes beyond acute respiratory disease, long COVID, vaccines against influenza and RSV, the implications of the potential extinction of influenza B virus Yamagata lineage, and the threats posed by zoonotic highly pathogenic avian influenza viruses.
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Affiliation(s)
| | - Colin A Russell
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Albert Osterhaus
- Center of Infection Medicine and Zoonosis Research and the University of Veterinary Medicine Hannover, Hannover, Germany.
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12
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Townsend DR, Towers DM, Lavinder JJ, Ippolito GC. Innovations and trends in antibody repertoire analysis. Curr Opin Biotechnol 2024; 86:103082. [PMID: 38428225 DOI: 10.1016/j.copbio.2024.103082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/07/2023] [Accepted: 01/28/2024] [Indexed: 03/03/2024]
Abstract
Monoclonal antibodies have revolutionized the treatment of human diseases, which has made them the fastest-growing class of therapeutics, with global sales expected to reach $346.6 billion USD by 2028. Advances in antibody engineering and development have led to the creation of increasingly sophisticated antibody-based therapeutics (e.g. bispecific antibodies and chimeric antigen receptor T cells). However, approaches for antibody discovery have remained comparatively grounded in conventional yet reliable in vitro assays. Breakthrough developments in high-throughput single B-cell sequencing and immunoglobulin proteomic serology, however, have enabled the identification of high-affinity antibodies directly from endogenous B cells or circulating immunoglobulin produced in vivo. Moreover, advances in artificial intelligence offer vast potential for antibody discovery and design with large-scale repertoire datasets positioned as the optimal source of training data for such applications. We highlight advances and recent trends in how these technologies are being applied to antibody repertoire analysis.
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Affiliation(s)
- Douglas R Townsend
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Dalton M Towers
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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13
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Fischer AL, Tichy A, Kokot J, Hoerschinger VJ, Wild RF, Riccabona JR, Loeffler JR, Waibl F, Quoika PK, Gschwandtner P, Forli S, Ward AB, Liedl KR, Zacharias M, Fernández-Quintero ML. The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics. J Chem Theory Comput 2024; 20:2321-2333. [PMID: 38373307 PMCID: PMC10938642 DOI: 10.1021/acs.jctc.3c01106] [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: 10/06/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.
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Affiliation(s)
- Anna-Lena
M. Fischer
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Anna Tichy
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Robert F. Wild
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Patrick K. Quoika
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | | | - Stefano Forli
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Andrew B. Ward
- Department
of Integrative Structural and Computational Biology, Scripps Research Institute, La
Jolla, California 92037, United States
| | - Klaus R. Liedl
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
| | - Martin Zacharias
- Center
for Protein Assemblies (CPA), Physics Department, Chair of Theoretical
Biophysics, Technical University of Munich, D-80333 Munich, Germany
| | - Monica L. Fernández-Quintero
- Institute
for General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, A-6020 Innsbruck, Austria
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14
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Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [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: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
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Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
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15
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do Nascimento GM, de Oliveira PSB, Butt SL, Diel DG. Immunogenicity of chimeric hemagglutinins delivered by an orf virus vector platform against swine influenza virus. Front Immunol 2024; 15:1322879. [PMID: 38482020 PMCID: PMC10933025 DOI: 10.3389/fimmu.2024.1322879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/22/2024] [Indexed: 04/05/2024] Open
Abstract
Orf virus (ORFV) is a large DNA virus that can harbor and efficiently deliver viral antigens in swine. Here we used ORFV as a vector platform to deliver chimeric hemagglutinins (HA) of Influenza A virus of swine (IAV-S). Vaccine development against IAV-S faces limitations posed by strain-specific immunity and the antigenic diversity of the IAV-S strains circulating in the field. A promising alternative aiming at re-directing immune responses on conserved epitopes of the stalk segment of the hemagglutinin (HA2) has recently emerged. Sequential immunization with chimeric HAs comprising the same stalk but distinct exotic head domains can potentially induce cross-reactive immune responses against conserved epitopes of the HA2 while breaking the immunodominance of the head domain (HA1). Here, we generated two recombinant ORFVs expressing chimeric HAs encoding the stalk region of a contemporary H1N1 IAV-S strain and exotic heads derived from either H6 or H8 subtypes, ORFVΔ121cH6/1 and ORFVΔ121cH8/1, respectively. The resulting recombinant viruses were able to express the heterologous protein in vitro. Further, the immunogenicity and cross-protection of these vaccine candidates were assessed in swine after sequential intramuscular immunization with OV-cH6/1 and OV-cH8/1, and subsequent challenge with divergent IAV-S strains. Humoral responses showed that vaccinated piglets presented increasing IgG responses in sera. Additionally, cross-reactive IgG and IgA antibody responses elicited by immunization were detected in sera and bronchoalveolar lavage (BAL), respectively, by ELISA against different viral clades and a diverse range of contemporary H1N1 IAV-S strains, indicating induction of humoral and mucosal immunity in vaccinated animals. Importantly, viral shedding was reduced in nasal swabs from vaccinated piglets after intranasal challenge with either Oh07 (gamma clade) or Ca09 (npdm clade) IAV-S strains. These results demonstrated the efficiency of ORFV-based vectors in delivering chimeric IAV-S HA-based vaccine candidates and underline the potential use of chimeric-HAs for prevention and control of influenza in swine.
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Affiliation(s)
- Gabriela Mansano do Nascimento
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Pablo Sebastian Britto de Oliveira
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Salman Latif Butt
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
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16
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He Y, Guo Z, Subiaur S, Benegal A, Vahey MD. Antibody inhibition of influenza A virus assembly and release. J Virol 2024; 98:e0139823. [PMID: 38179944 PMCID: PMC10878280 DOI: 10.1128/jvi.01398-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Antibodies are frontline defenders against influenza virus infection, providing protection through multiple complementary mechanisms. Although a subset of monoclonal antibodies (mAbs) has 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 1-20-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.IMPORTANCEAntibodies against influenza A virus provide multifaceted protection against infection. Although sensitive and quantitative assays are widely used to measure inhibition of viral attachment and entry, the ability of diverse antibodies to inhibit viral egress is less clear. We address this challenge by developing an imaging-based approach to measure antibody inhibition of virus release across a panel of monoclonal antibodies targeting the influenza A virus surface proteins. Using this approach, we find that inhibition of viral egress is common and can have similar potency to the ability of an antibody to inhibit viral entry. Insights into this understudied aspect of antibody function may help guide the development of improved countermeasures.
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Affiliation(s)
- Yuanyuan He
- 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
| | - Zijian Guo
- 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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17
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Hinke DM, Anderson AM, Katta K, Laursen MF, Tesfaye DY, Werninghaus IC, Angeletti D, Grødeland G, Bogen B, Braathen R. Applying valency-based immuno-selection to generate broadly cross-reactive antibodies against influenza hemagglutinins. Nat Commun 2024; 15:850. [PMID: 38346952 PMCID: PMC10861589 DOI: 10.1038/s41467-024-44889-w] [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: 10/26/2022] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
Conserved epitopes shared between virus subtypes are often subdominant, making it difficult to induce broadly reactive antibodies by immunization. Here, we generate a plasmid DNA mix vaccine that encodes protein heterodimers with sixteen different influenza A virus hemagglutinins (HA) representing all HA subtypes except H1 (group 1) and H7 (group 2). Each single heterodimer expresses two different HA subtypes and is targeted to MHC class II on antigen presenting cells (APC). Female mice immunized with the plasmid mix produce antibodies not only against the 16 HA subtypes, but also against non-included H1 and H7. We demonstrate that individual antibody molecules cross-react between different HAs. Furthermore, the mix vaccine induces T cell responses to conserved HA epitopes. Immunized mice are partially protected against H1 viruses. The results show that application of valency-based immuno-selection to diversified antigens can be used to direct antibody responses towards conserved (subdominant) epitopes on viral antigens.
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Affiliation(s)
- Daniëla Maria Hinke
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ane Marie Anderson
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kirankumar Katta
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Demo Yemane Tesfaye
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Gunnveig Grødeland
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bjarne Bogen
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway.
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Ranveig Braathen
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway.
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway.
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18
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Chen X, Huang Y, Gao P, Wu F, Han Y, Zhang C, Hu Z, Zhao F, Shcherbakov DN, Pan W, Niu X, Li X, Liu S, Xu W. Engineering of novel hemagglutinin biosensors for rapid detection and drug screening of Influenza A H7N9 virus. Int J Biol Macromol 2024; 258:129126. [PMID: 38163504 DOI: 10.1016/j.ijbiomac.2023.129126] [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: 08/15/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
New pathogenic influenza virus strains are constantly emerging, posing a serious risk to both human health and economic growth. To effectively control the spread of this virus, there is an urgent need for early, rapid, sensitive, simple, and cost-effective detection technologies, as well as new and effective antiviral drugs. In this study, we have successfully achieved a significant milestone by successfully fusing the H7N9 influenza virus hemagglutinin (HA) protein with the nano-luciferase component, resulting in the development of a novel set of biosensors. This remarkable achievement marks the first instance of utilizing this biosensor technology for influenza antibody detection. Our biosensor technology also has the potential to facilitate the development of antiviral drugs targeting specific epitopes of the HA protein, providing a promising avenue for the treatment of H7N9 influenza virus infections. Furthermore, our biosensors have broad applications beyond H7N9 influenza virus detection, as they can be expanded for the detection of other pathogens and drug screening applications in the future. By providing a novel and effective solution to the detection and treatment of influenza viruses, our biosensors have the potential to revolutionize the field of infectious disease control.
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Affiliation(s)
- Xin Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yuan Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Peixuan Gao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fang Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yongyue Han
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chuwen Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zhuowen Hu
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510070, China
| | - Fang Zhao
- National Clinical Research Centre for Infectious Diseases, the Third People's Hospital of Shenzhen and the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Dmitry N Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo 630559, Russia; Department of Physical-Chemistry Biology and Biotechnology, Altai State University, Barnaul 656049, Russia
| | - Weiqi Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Xiaoyan Li
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510070, China.
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Southern Medical University, Guangzhou 510515, China.
| | - Wei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, Guangdong 510515, China.
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19
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Petersen BM, Kirby MB, Chrispens KM, Irvin OM, Strawn IK, Haas CM, Walker AM, Baumer ZT, Ulmer SA, Ayala E, Rhodes ER, Guthmiller JJ, Steiner PJ, Whitehead TA. An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575852. [PMID: 38293170 PMCID: PMC10827193 DOI: 10.1101/2024.01.16.575852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of ten different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
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Affiliation(s)
- Brian M. Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Monica B. Kirby
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Karson M. Chrispens
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Olivia M. Irvin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Isabell K. Strawn
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Cyrus M. Haas
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Alexis M. Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Zachary T. Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Sophia A. Ulmer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Edgardo Ayala
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily R. Rhodes
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Paul J. Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
| | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80305, USA
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20
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Wang M, Hao MC, Huangfu Y, Yang KZ, Zhang XQ, Zhang Y, Chen J, Zhang ZL. A Universal Aptamer for Influenza A Viruses: Selection, Recognition, and Infection Inhibition. ACS Pharmacol Transl Sci 2024; 7:249-258. [PMID: 38230279 PMCID: PMC10789145 DOI: 10.1021/acsptsci.3c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
It is crucial to develop universal inhibitors for viral inhibition due to the rapid mutation of viruses. Herein, a universal aptamer inhibitor was developed that enabled a single DNA molecule to recognize several hemeagglutinin (HA) protein subtypes, inducing broad neutralization against influenza A viruses (IAVs). Through a multi-channel enrichment (MCE) strategy, a high-affinity aptamer named UHA-2 was obtained, with its dissociation constants (Kd) for three different HA proteins being 1.5 ± 0.2 nM (H5N1), 3.7 ± 0.4 nM (H7N9), and 10.1 ± 1.1 nM (H9N2). The UHA-2 aptamer had a universal inhibition effect, by which it could broadly neutralize influenza A H5N1, H7N9, H9N2, H1N1, and H3N2 viruses. Universal aptamer inhibitors have the advantages of acquisition in vitro, stability, simple structure, small size, etc. This study not only develops a novel universal aptamer to achieve a broad inhibition effect on various IAVs, but also opens up an efficient strategy for the development of universal inhibitors against viruses.
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Affiliation(s)
- Meng Wang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
| | - Meng-Chan Hao
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueyue Huangfu
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
| | - Ke-Zhu Yang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
| | - Xiao-Qing Zhang
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Zhang
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianjun Chen
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Ling Zhang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
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21
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Finney J, Moseman AP, Kong S, Watanabe A, Song S, Walsh RM, Kuraoka M, Kotaki R, Moseman EA, McCarthy KR, Liao D, Liang X, Nie X, Lavidor O, Abbott R, Harrison SC, Kelsoe G. Protective human antibodies against a conserved epitope in pre- and postfusion influenza hemagglutinin. Proc Natl Acad Sci U S A 2024; 121:e2316964120. [PMID: 38147556 PMCID: PMC10769852 DOI: 10.1073/pnas.2316964120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both IAV and IBV hemagglutinins (HAs) could protect against disease by diverse virus subtypes. Only one reported HA Ab, isolated from a combinatorial display library, protects against both IAV and IBV. Thus, there has been so far no information on the likelihood of finding naturally occurring human Abs that bind HAs of diverse IAV subtypes and IBV lineages. We have now recovered from several unrelated human donors five clonal Abs that bind a conserved epitope preferentially exposed in the postfusion conformation of IAV and IVB HA2. These Abs lack neutralizing activity in vitro but in mice provide strong, IgG subtype-dependent protection against lethal IAV and IBV infections. Strategies to elicit similar Abs routinely might contribute to more effective influenza vaccines.
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Affiliation(s)
- Joel Finney
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA02115
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Annie Park Moseman
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Susan Kong
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA02115
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Shengli Song
- Department of Surgery, Duke University, Durham, NC27710
| | - Richard M. Walsh
- The Harvard Cryo-Electron Microscopy (Cryo-EM) Center for Structural Biology, Harvard Medical School, Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Ryutaro Kotaki
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA15261
| | - Dongmei Liao
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Xiaoe Liang
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Xiaoyan Nie
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
| | - Olivia Lavidor
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA02115
| | - Richard Abbott
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA02115
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA02115
- HHMI, Boston, MA02115
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, NC27710
- Department of Surgery, Duke University, Durham, NC27710
- Duke Human Vaccine Institute, Duke University, Durham, NC27710
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22
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Sun X, Ma H, Wang X, Bao Z, Tang S, Yi C, Sun B. Broadly neutralizing antibodies to combat influenza virus infection. Antiviral Res 2024; 221:105785. [PMID: 38145757 DOI: 10.1016/j.antiviral.2023.105785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
The diversified classification and continuous alteration of influenza viruses underscore for antivirals and vaccines that can counter a broad range of influenza subtypes. Hemagglutinin (HA) and neuraminidase (NA) are two principle viral surface targets for broadly neutralizing antibodies. A series of monoclonal antibodies, targeting HA and NA, have been discovered and characterized with a wide range of neutralizing activity against influenza viruses. Clinical studies have demonstrated the safety and efficacy of some HA stem-targeting antibodies against influenza viruses. Broadly neutralizing antibodies (bnAbs) can serve as both prophylactic and therapeutic agents, as well as play a critical role in identifying antigens and epitopes for the development of universal vaccines. In this review, we described and summarized the latest discoveries and advancements of bnAbs against influenza viruses in both pre- and clinical development. Additionally, we assess whether bnAbs can serve as a viable alternative to vaccination against influenza. Finally, we discussed the rationale behind reverse vaccinology, a structure-guided universal vaccine design strategy that efficiently identifies candidate antigens and conserved epitopes that can be targeted by antibodies.
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Affiliation(s)
- Xiaoyu Sun
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Hanwen Ma
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xuanjia Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhiheng Bao
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shubing Tang
- Department of Investigational New Drug, Shanghai Reinovax Biologics Co., Ltd, Shanghai, 200135, China
| | - Chunyan Yi
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Bing Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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23
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Park J, Champion JA. Development of Self-Assembled Protein Nanocage Spatially Functionalized with HA Stalk as a Broadly Cross-Reactive Influenza Vaccine Platform. ACS NANO 2023; 17:25045-25060. [PMID: 38084728 PMCID: PMC10753887 DOI: 10.1021/acsnano.3c07669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
There remains a need for the development of a universal influenza vaccine, as current seasonal influenza vaccines exhibit limited protection against mismatched, mutated, or pandemic influenza viruses. A desirable approach to developing an effective universal influenza vaccine is the incorporation of highly conserved antigens in a multivalent scaffold that enhances their immunogenicity. Here, we develop a broadly cross-reactive influenza vaccine by functionalizing self-assembled protein nanocages (SAPNs) with multiple copies of the hemagglutinin stalk on the outer surface and matrix protein 2 ectodomain on the inner surface. SAPNs were generated by engineering short coiled coils, and the design was simulated by MD GROMACS. Due to the short sequences, off-target immune responses against empty SAPN scaffolds were not seen in immunized mice. Vaccination with the multivalent SAPNs induces high levels of broadly cross-reactive antibodies of only external antigens, demonstrating tight spatial control over the designed antigen placement. This work demonstrates the use of SAPNs as a potential influenza vaccine.
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Affiliation(s)
- Jaeyoung Park
- School of Chemical and Biomolecular
Engineering, Georgia Institute of Technology, 950 Atlantic Dr. NW, Atlanta, Georgia 30332-2000, United States
| | - Julie A. Champion
- School of Chemical and Biomolecular
Engineering, Georgia Institute of Technology, 950 Atlantic Dr. NW, Atlanta, Georgia 30332-2000, United States
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24
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Dosey A, Ellis D, Boyoglu-Barnum S, Syeda H, Saunders M, Watson MJ, Kraft JC, Pham MN, Guttman M, Lee KK, Kanekiyo M, King NP. Combinatorial immune refocusing within the influenza hemagglutinin RBD improves cross-neutralizing antibody responses. Cell Rep 2023; 42:113553. [PMID: 38096052 PMCID: PMC10801708 DOI: 10.1016/j.celrep.2023.113553] [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
The receptor-binding domain (RBD) of influenza virus hemagglutinin (HA) elicits potently neutralizing yet mostly strain-specific antibodies. Here, we evaluate the ability of several immunofocusing techniques to enhance the functional breadth of vaccine-elicited immune responses against the HA RBD. We present a series of "trihead" nanoparticle immunogens that display native-like closed trimeric RBDs from the HAs of several H1N1 influenza viruses. The series includes hyperglycosylated and hypervariable variants that incorporate natural and designed sequence diversity at key positions in the receptor-binding site periphery. Nanoparticle immunogens displaying triheads or hyperglycosylated triheads elicit higher hemagglutination inhibition (HAI) and neutralizing activity than the corresponding immunogens lacking either trimer-stabilizing mutations or hyperglycosylation. By contrast, mosaic nanoparticle display and antigen hypervariation do not significantly alter the magnitude or breadth of vaccine-elicited antibodies. Our results yield important insights into antibody responses against the RBD and the ability of several structure-based immunofocusing techniques to influence vaccine-elicited antibody responses.
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Affiliation(s)
- Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, 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
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mason Saunders
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael J Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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25
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Brouwer PJ, Perrett HR, Beaumont T, Nijhuis H, Kruijer S, Burger JA, Lee WH, Müller-Kraüter H, Sanders RW, Strecker T, van Gils MJ, Ward AB. Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572918. [PMID: 38187682 PMCID: PMC10769344 DOI: 10.1101/2023.12.21.572918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Lassa fever continues to be a major public health burden in endemic countries in West Africa, yet effective therapies or vaccines are lacking. The isolation of potent and protective neutralizing antibodies against the Lassa virus glycoprotein complex (GPC) justifies the development of vaccines that can elicit strong neutralizing antibody responses. However, Lassa vaccines candidates have generally been unsuccessful in doing so and the associated antibody responses to these vaccines remain poorly characterized. Here, we establish an electron-microscopy based epitope mapping pipeline that enables high-resolution structural characterization of polyclonal antibodies to GPC. By applying this method to rabbits vaccinated with a recombinant GPC vaccine and a GPC-derived virus-like particle, we reveal determinants of neutralization which involve epitopes of the GPC-C, GPC-A, and GP1-A competition clusters. Furthermore, by identifying previously undescribed immunogenic off-target epitopes, we expose challenges that recombinant GPC vaccines face. By enabling detailed polyclonal antibody characterization, our work ushers in a next generation of more rational Lassa vaccine design.
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Affiliation(s)
- Philip J.M. Brouwer
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Hailee R. Perrett
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Tim Beaumont
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Haye Nijhuis
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Sabine Kruijer
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Judith A. Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | | | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam 1105 AZ, the Netherlands
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
- Lead contact
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26
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Simmons HC, Finney J, Kotaki R, Adachi Y, Moseman AP, Watanabe A, Song S, Robinson-McCarthy LR, Sage VL, Kuraoka M, Moseman EA, Kelsoe G, Takahashi Y, McCarthy KR. A broad antibody class engages the influenza virus hemagglutinin head at its stem interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571543. [PMID: 38168412 PMCID: PMC10760138 DOI: 10.1101/2023.12.13.571543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Influenza infection and vaccination impart strain-specific immunity that fails to protect against both seasonal antigenic variants and the next pandemic. However, antibodies directed to conserved sites can confer broad protection. We identify and characterize a class of human antibodies that engage a previously undescribed, conserved, epitope on the influenza hemagglutinin protein (HA). Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal infection in mice. Their breadth of binding extends across most influenza A serotypes and seasonal human variants. Antibodies to the head-stem interface epitope are present at low frequency in the memory B cell populations of multiple donors. The immunogenicity of the epitope warrants its consideration for inclusion in improved or "universal" influenza vaccines.
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Affiliation(s)
- Holly C. Simmons
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joel Finney
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Ryutaro Kotaki
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yu Adachi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Annie Park Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Shengli Song
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Lindsey R. Robinson-McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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27
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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28
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Kastenschmidt JM, Sureshchandra S, Wagar LE. Leveraging human immune organoids for rational vaccine design. Trends Immunol 2023; 44:938-944. [PMID: 37940395 DOI: 10.1016/j.it.2023.10.008] [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: 10/03/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Current influenza A and B virus (IABV) vaccines provide suboptimal protection and efforts are underway to develop a universal IABV vaccine. Blood neutralizing antibodies are the current gold standard for protection, but many processes that regulate human IABV-specific immunity occur in mucosal and lymphoid tissues. We need an improved mechanistic understanding of how immune cells respond within these tissues to advance our current (slow and expensive) vaccine testing model. We posit that advanced in vitro models of human adaptive immunity can bridge some of the gaps between vaccine design, animal models, and human clinical trials. Here, we highlight how they can be integrated into current practices and play a role in reverse translating the defined features of protective vaccines to rationally design new candidates.
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Affiliation(s)
- Jenna M Kastenschmidt
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA, 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA, 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA, 92617, USA
| | - Suhas Sureshchandra
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA, 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA, 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA, 92617, USA
| | - Lisa E Wagar
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA, 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA, 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA, 92617, USA.
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29
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Lázaro-Gorines R, Pérez P, Heras-Murillo I, Adán-Barrientos I, Albericio G, Astorgano D, Flores S, Luczkowiak J, Labiod N, Harwood SL, Segura-Tudela A, Rubio-Pérez L, Nugraha Y, Shang X, Li Y, Alfonso C, Adipietro KA, Abeyawardhane DL, Navarro R, Compte M, Yu W, MacKerell AD, Sanz L, Weber DJ, Blanco FJ, Esteban M, Pozharski E, Godoy-Ruiz R, Muñoz IG, Delgado R, Sancho D, García-Arriaza J, Álvarez-Vallina L. Dendritic Cell-Mediated Cross-Priming by a Bispecific Neutralizing Antibody Boosts Cytotoxic T Cell Responses and Protects Mice against SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304818. [PMID: 37863812 DOI: 10.1002/advs.202304818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/24/2023] [Indexed: 10/22/2023]
Abstract
Administration of neutralizing antibodies (nAbs) has proved to be effective by providing immediate protection against SARS-CoV-2. However, dual strategies combining virus neutralization and immune response stimulation to enhance specific cytotoxic T cell responses, such as dendritic cell (DC) cross-priming, represent a promising field but have not yet been explored. Here, a broadly nAb, TNT , are first generated by grafting an anti-RBD biparatopic tandem nanobody onto a trimerbody scaffold. Cryo-EM data show that the TNT structure allows simultaneous binding to all six RBD epitopes, demonstrating a high-avidity neutralizing interaction. Then, by C-terminal fusion of an anti-DNGR-1 scFv to TNT , the bispecific trimerbody TNT DNGR-1 is generated to target neutralized virions to type 1 conventional DCs (cDC1s) and promote T cell cross-priming. Therapeutic administration of TNT DNGR-1, but not TNT , protects K18-hACE2 mice from a lethal SARS-CoV-2 infection, boosting virus-specific humoral responses and CD8+ T cell responses. These results further strengthen the central role of interactions with immune cells in the virus-neutralizing antibody activity and demonstrate the therapeutic potential of the Fc-free strategy that can be used advantageously to provide both immediate and long-term protection against SARS-CoV-2 and other viral infections.
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Affiliation(s)
- Rodrigo Lázaro-Gorines
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, 28041, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Patricia Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, 28029, Spain
| | - Ignacio Heras-Murillo
- Immunobiology lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Irene Adán-Barrientos
- Immunobiology lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Guillermo Albericio
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - David Astorgano
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Sara Flores
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Joanna Luczkowiak
- Virology and HIV/AIDS Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Nuria Labiod
- Virology and HIV/AIDS Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
| | - Seandean L Harwood
- Department of Molecular Biology and Genetics - Protein Science, Aarhus University, Aarhus, 80000, Denmark
| | - Alejandro Segura-Tudela
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, 28041, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Laura Rubio-Pérez
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, 28041, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
- Chair for Immunology UFV/Merck, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Yudhi Nugraha
- Protein Crystallography Unit, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Xiaoran Shang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- The Center for Biomolecular Therapeutics, Rockville, MD, 20850, USA
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28040, Spain
| | - Kaylin A Adipietro
- The Center for Biomolecular Therapeutics, Rockville, MD, 20850, USA
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Dinendra L Abeyawardhane
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- The Center for Biomolecular Therapeutics, Rockville, MD, 20850, USA
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rocío Navarro
- Department of Antibody Engineering, Leadartis SL, Tres Cantos, Madrid, 28002, Spain
| | - Marta Compte
- Department of Antibody Engineering, Leadartis SL, Tres Cantos, Madrid, 28002, Spain
| | - Wenbo Yu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
| | - Alexander D MacKerell
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
- Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Laura Sanz
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro Majadahonda, Majadahonda, Madrid, 28220, Spain
| | - David J Weber
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- The Center for Biomolecular Therapeutics, Rockville, MD, 20850, USA
| | - Francisco J Blanco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28040, Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Edwin Pozharski
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- The Center for Biomolecular Therapeutics, Rockville, MD, 20850, USA
| | - Raquel Godoy-Ruiz
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA
- The Center for Biomolecular Therapeutics, Rockville, MD, 20850, USA
| | - Inés G Muñoz
- Protein Crystallography Unit, Structural Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
| | - Rafael Delgado
- Virology and HIV/AIDS Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, 28041, Spain
- Department of Medicine, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - David Sancho
- Immunobiology lab, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, 28029, Spain
| | - Luis Álvarez-Vallina
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, 28041, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, 28041, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, 28029, Spain
- Chair for Immunology UFV/Merck, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, Madrid, 28223, Spain
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Tan K, Chen J, Kaku Y, Wang Y, Donius L, Khan RA, Li X, Richter H, Seaman MS, Walz T, Hwang W, Reinherz EL, Kim M. Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility. Nat Commun 2023; 14:7218. [PMID: 37940661 PMCID: PMC10632514 DOI: 10.1038/s41467-023-42097-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023] Open
Abstract
Broadly neutralizing antibodies (bnAbs) against HIV-1 target conserved envelope (Env) epitopes to block viral replication. Here, using structural analyses, we provide evidence to explain why a vaccine targeting the membrane-proximal external region (MPER) of HIV-1 elicits antibodies with human bnAb-like paratopes paradoxically unable to bind HIV-1. Unlike in natural infection, vaccination with MPER/liposomes lacks a necessary structure-based constraint to select for antibodies with an adequate approach angle. Consequently, the resulting Abs cannot physically access the MPER crawlspace on the virion surface. By studying naturally arising Abs, we further reveal that flexibility of the human IgG3 hinge mitigates the epitope inaccessibility and additionally facilitates Env spike protein crosslinking. Our results suggest that generation of IgG3 subtype class-switched B cells is a strategy for anti-MPER bnAb induction. Moreover, the findings illustrate the need to incorporate topological features of the target epitope in immunogen design.
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Affiliation(s)
- Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Junjian Chen
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Laboratory of Immunology, Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu Kaku
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yi Wang
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- NeoCura Bio-Medical Technology Co., Ltd., Beijing, China
| | - Luke Donius
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- AbbVie Bioresearch Center, AbbVie Inc., Worcester, MA, USA
| | - Rafiq Ahmad Khan
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xiaolong Li
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Hannah Richter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
- Department of Physics & Astronomy, Texas A&M University, College Station, TX, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Mikyung Kim
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Dermatology, Harvard Medical School, Boston, MA, USA.
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31
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Li Y, Huo S, Yin Z, Tian Z, Huang F, Liu P, Liu Y, Yu F. The current state of research on influenza antiviral drug development: drugs in clinical trial and licensed drugs. mBio 2023; 14:e0127323. [PMID: 37610204 PMCID: PMC10653855 DOI: 10.1128/mbio.01273-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
Influenza viruses (IVs) threaten global human health due to the high morbidity, infection, and mortality rates. Currently, the influenza drugs recommended by the FDA are oseltamivir, zanamivir, peramivir, and baloxavir marboxil. Notably, owing to the high variability of IVs, no drug exists that can effectively treat all types and subtypes of IVs. Moreover, the current trend of drug resistance is likely to continue as the viral genome is constantly mutating. Therefore, there is an urgent need to develop drugs related to the treatment of influenza to deal with the next pandemic. Here, we summarized the cutting-edge research in mechanism of action, inhibitory activity, and clinical efficacy of drugs that have been approved and drugs that are still in clinical trials for influenza treatment. We hope this review will provide up-to-date and comprehensive information on influenza antivirals and generate hypotheses for screens and development of new broad-spectrum influenza drugs in the near future.
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Affiliation(s)
- Yanbai Li
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shanshan Huo
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhe Yin
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zuguang Tian
- Baoding City Science and Technology Bureau, Baoding, China
| | - Fang Huang
- Tongzhou District Center For Animal Disease Control and Prevention, Beijing, China
| | - Peng Liu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yue Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Fei Yu
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Hebei Wild Animal Health Center, College of Life Sciences, Hebei Agricultural University, Baoding, China
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Fernández-Quintero ML, Pomarici ND, Fischer ALM, Hoerschinger VJ, Kroell KB, Riccabona JR, Kamenik AS, Loeffler JR, Ferguson JA, Perrett HR, Liedl KR, Han J, Ward AB. Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines. Antibodies (Basel) 2023; 12:67. [PMID: 37873864 PMCID: PMC10594513 DOI: 10.3390/antib12040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nancy D. Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna-Lena M. Fischer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Valentin J. Hoerschinger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Katharina B. Kroell
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Jakob R. Riccabona
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Johannes R. Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James A. Ferguson
- 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
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
There are at least 21 families of enveloped viruses that infect mammals, and many contain members of high concern for global human health. All enveloped viruses have a dedicated fusion protein or fusion complex that enacts the critical genome-releasing membrane fusion event that is essential before viral replication within the host cell interior can begin. Because all enveloped viruses enter cells by fusion, it behooves us to know how viral fusion proteins function. Viral fusion proteins are also major targets of neutralizing antibodies, and hence they serve as key vaccine immunogens. Here we review current concepts about viral membrane fusion proteins focusing on how they are triggered, structural intermediates between pre- and postfusion forms, and their interplay with the lipid bilayers they engage. We also discuss cellular and therapeutic interventions that thwart virus-cell membrane fusion.
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Affiliation(s)
- Judith M White
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA;
| | - Amanda E Ward
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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Wang Y, Lv H, Lei R, Yeung YH, Shen IR, Choi D, Teo QW, Tan TJ, Gopal AB, Chen X, Graham CS, Wu NC. An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557288. [PMID: 37745338 PMCID: PMC10515799 DOI: 10.1101/2023.09.11.557288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite decades of antibody research, it remains challenging to predict the specificity of an antibody solely based on its sequence. Two major obstacles are the lack of appropriate models and inaccessibility of datasets for model training. In this study, we curated a dataset of >5,000 influenza hemagglutinin (HA) antibodies by mining research publications and patents, which revealed many distinct sequence features between antibodies to HA head and stem domains. We then leveraged this dataset to develop a lightweight memory B cell language model (mBLM) for sequence-based antibody specificity prediction. Model explainability analysis showed that mBLM captured key sequence motifs of HA stem antibodies. Additionally, by applying mBLM to HA antibodies with unknown epitopes, we discovered and experimentally validated many HA stem antibodies. Overall, this study not only advances our molecular understanding of antibody response to influenza virus, but also provides an invaluable resource for applying deep learning to antibody research.
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Affiliation(s)
- 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
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuen-Hei Yeung
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ivana R. Shen
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Danbi Choi
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - 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
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Akshita B. Gopal
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire S. Graham
- 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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Saravanakumar S, Chatterjee J. The Use of In Silico Methods to Identify and Assess Antigenic Regions Suitable for the Development of Peptide-based Pan-viral Vaccines. Altern Lab Anim 2023; 51:313-322. [PMID: 37548284 DOI: 10.1177/02611929231193416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The constant evolution of pathogenic viral variants and the emergence of new viruses have reinforced the need for broad-spectrum vaccines to combat such threats. The spread of new viral variants leading to epidemic and pandemic infection can be effectively contained, if broad-spectrum vaccines effective against the newer viral variants are readily available. The development of broad-spectrum, pan-neutralising antibodies against viruses which, in general terms, are very antigenically different - such as HIV, influenza virus and paramyxoviruses - has been reported in the literature. The amino acid sequences used to generate a range of approved recombinant anti-viral vaccines were analysed by using in silico methods, with the aim of identifying highly antigenic peptide regions that may be suitable for the development of broad-spectrum peptide-based anti-viral vaccines. This was achieved through the use of open-source data, an algorithm-driven probability matrix, and published in silico prediction tools (SVMTriP, IEDB-AR, VaxiJen 2.0, AllergenFP v. 1.0, AllerTOP v. 2.0, ToxinPred and ProtParam) to evaluate antigenicity, MHC-I and MHC-II binding potential, immunogenicity, allergenicity, toxicity and physicochemical properties. We report a pan-antigenic peptide region with strong affinity for MHC-I and MHC-II, and good immunogenic potential. According to the output from the relevant in silico tools, the peptide was predicted to be non-toxic, non-allergic and to possess the desired physicochemical properties for potentially successful vaccine production. With further investigation and optimisation, this peptide could be considered for use in the development of a broad-spectrum anti-viral vaccine that may protect against emerging new viruses. Our approach of using in silico methods to identify candidate antigenic peptides with the desired physicochemical properties could potentially circumvent the use of some animal studies for peptide vaccine candidate evaluation.
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Partlow EA, Jaeggi-Wong A, Planitzer SD, Berg N, Li Z, Ivanovic T. Influenza A Virus Infections Sense Host Membrane Tension to Dynamically Tune Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555166. [PMID: 37693449 PMCID: PMC10491151 DOI: 10.1101/2023.08.28.555166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Enveloped viruses often exhibit a pleomorphic morphology, ranging in size from 100nm spheres to tens-of-micron long filaments. For influenza A virus (IAV), spheres enable rapid replication and minimize metabolic cost, while filaments resist effects of antibodies or other cell-entry pressures. The current paradigm is that virion shape changes require genetic adaptation; however, a virus evolved to alter its shape phenotypically would outperform one that relies on genetic selection. Using a novel quantitative flow virometry assay to characterize virion shape dynamics we find that IAV rapidly tunes its shape distribution to favor spheres under optimal, and filaments under attenuating conditions including the presence of antibodies. We identify membrane tension as a key cue sensed by IAV determining shape distributions. This phenotypic shift outpaces genetic change and serves to enable additional life cycles under pressure. Our work expands knowledge of the complex host-virus interplay to include viral responses to the local environment by optimizing its structure to maximize replication and ultimately host-host transmission.
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37
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Azulay A, Cohen-Lavi L, Friedman LM, McGargill MA, Hertz T. Mapping antibody footprints using binding profiles. CELL REPORTS METHODS 2023; 3:100566. [PMID: 37671022 PMCID: PMC10475849 DOI: 10.1016/j.crmeth.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The increasing use of monoclonal antibodies (mAbs) in biology and medicine necessitates efficient methods for characterizing their binding epitopes. Here, we developed a high-throughput antibody footprinting method based on binding profiles. We used an antigen microarray to profile 23 human anti-influenza hemagglutinin (HA) mAbs using HA proteins of 43 human influenza strains isolated between 1918 and 2018. We showed that the mAb's binding profile can be used to characterize its influenza subtype specificity, binding region, and binding site. We present mAb-Patch-an epitope prediction method that is based on a mAb's binding profile and the 3D structure of its antigen. mAb-Patch was evaluated using four mAbs with known solved mAb-HA structures. mAb-Patch identifies over 67% of the true epitope when considering only 50-60 positions along the antigen. Our work provides proof of concept for utilizing antibody binding profiles to screen large panels of mAbs and to down-select antibodies for further functional studies.
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Affiliation(s)
- Asaf Azulay
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Liel Cohen-Lavi
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M. Friedman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tomer Hertz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, USA
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38
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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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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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40
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Kastenschmidt JM, Sureshchandra S, Jain A, Hernandez-Davies JE, de Assis R, Wagoner ZW, Sorn AM, Mitul MT, Benchorin AI, Levendosky E, Ahuja G, Zhong Q, Trask D, Boeckmann J, Nakajima R, Jasinskas A, Saligrama N, Davies DH, Wagar LE. Influenza vaccine format mediates distinct cellular and antibody responses in human immune organoids. Immunity 2023; 56:1910-1926.e7. [PMID: 37478854 PMCID: PMC10433940 DOI: 10.1016/j.immuni.2023.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
Highly effective vaccines elicit specific, robust, and durable adaptive immune responses. To advance informed vaccine design, it is critical that we understand the cellular dynamics underlying responses to different antigen formats. Here, we sought to understand how antigen-specific B and T cells were activated and participated in adaptive immune responses within the mucosal site. Using a human tonsil organoid model, we tracked the differentiation and kinetics of the adaptive immune response to influenza vaccine and virus modalities. Each antigen format elicited distinct B and T cell responses, including differences in their magnitude, diversity, phenotype, function, and breadth. These differences culminated in substantial changes in the corresponding antibody response. A major source of antigen format-related variability was the ability to recruit naive vs. memory B and T cells to the response. These findings have important implications for vaccine design and the generation of protective immune responses in the upper respiratory tract.
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Affiliation(s)
- Jenna M Kastenschmidt
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Suhas Sureshchandra
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Aarti Jain
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Jenny E Hernandez-Davies
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Rafael de Assis
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Zachary W Wagoner
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Andrew M Sorn
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Mahina Tabassum Mitul
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Aviv I Benchorin
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Elizabeth Levendosky
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - Gurpreet Ahuja
- Department of Pediatric Otolaryngology, Children's Hospital of Orange County, Orange, CA 92868, USA; Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Qiu Zhong
- Department of Pediatric Otolaryngology, Children's Hospital of Orange County, Orange, CA 92868, USA; Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Douglas Trask
- Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Jacob Boeckmann
- Department of Otolaryngology-Head and Neck Surgery, University of California Irvine, Orange, CA 92868, USA
| | - Rie Nakajima
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Algimantas Jasinskas
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA; Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA; Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - D Huw Davies
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA
| | - Lisa E Wagar
- Department of Physiology & Biophysics, University of California Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California Irvine, Irvine, CA 92617, USA; Center for Virus Research, University of California Irvine, Irvine, CA 92617, USA; Vaccine R&D Center, University of California Irvine, Irvine, CA 92617, USA.
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41
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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42
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Tonouchi K, Adachi Y, Suzuki T, Kuroda D, Nishiyama A, Yumoto K, Takeyama H, Suzuki T, Hashiguchi T, Takahashi Y. Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope. PLoS Pathog 2023; 19:e1011554. [PMID: 37556494 PMCID: PMC10411744 DOI: 10.1371/journal.ppat.1011554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
Plasticity of influenza virus hemagglutinin (HA) conformation increases an opportunity to generate conserved non-native epitopes with unknown functionality. Here, we have performed an in-depth analysis of human monoclonal antibodies against a stem-helix region that is occluded in native prefusion yet exposed in postfusion HA. A stem-helix antibody, LAH31, provided IgG Fc-dependent cross-group protection by targeting a stem-helix kinked loop epitope, with a unique structure emerging in the postfusion state. The structural analysis and molecular modeling revealed key contact sites responsible for the epitope specificity and cross-group breadth that relies on somatically mutated light chain. LAH31 was inaccessible to the native prefusion HA expressed on cell surface; however, it bound to the HA structure present on infected cells with functional linkage to the Fc-mediated clearance. Our study uncovers a novel non-native epitope that emerges in the postfusion HA state, highlighting the utility of this epitope for a broadly protective antigen design.
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Affiliation(s)
- Keisuke Tonouchi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku, Tokyo, Japan
| | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Ayae Nishiyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics research, National Institutes of Biomedical Innovation, Health and Nutrition; Saito-Asagi, Ibaraki City, Osaka, Japan
| | - Kohei Yumoto
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Shinjuku, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Shinjuku, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
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43
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Vieira MC, Palm AKE, Stamper CT, Tepora ME, Nguyen KD, Pham TD, Boyd SD, Wilson PC, Cobey S. Germline-encoded specificities and the predictability of the B cell response. PLoS Pathog 2023; 19:e1011603. [PMID: 37624867 PMCID: PMC10484431 DOI: 10.1371/journal.ppat.1011603] [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: 02/01/2023] [Revised: 09/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Antibodies result from the competition of B cell lineages evolving under selection for improved antigen recognition, a process known as affinity maturation. High-affinity antibodies to pathogens such as HIV, influenza, and SARS-CoV-2 are frequently reported to arise from B cells whose receptors, the precursors to antibodies, are encoded by particular immunoglobulin alleles. This raises the possibility that the presence of particular germline alleles in the B cell repertoire is a major determinant of the quality of the antibody response. Alternatively, initial differences in germline alleles' propensities to form high-affinity receptors might be overcome by chance events during affinity maturation. We first investigate these scenarios in simulations: when germline-encoded fitness differences are large relative to the rate and effect size variation of somatic mutations, the same germline alleles persistently dominate the response of different individuals. In contrast, if germline-encoded advantages can be easily overcome by subsequent mutations, allele usage becomes increasingly divergent over time, a pattern we then observe in mice experimentally infected with influenza virus. We investigated whether affinity maturation might nonetheless strongly select for particular amino acid motifs across diverse genetic backgrounds, but we found no evidence of convergence to similar CDR3 sequences or amino acid substitutions. These results suggest that although germline-encoded specificities can lead to similar immune responses between individuals, diverse evolutionary routes to high affinity limit the genetic predictability of responses to infection and vaccination.
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Affiliation(s)
- Marcos C. Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, United States of America
| | - Anna-Karin E. Palm
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States of America
| | - Christopher T. Stamper
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Committee on Immunology, University of Chicago, Chicago, United States of America
| | - Micah E. Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States of America
| | - Khoa D. Nguyen
- Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
| | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
| | - Patrick C. Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States of America
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine, New York City, United States of America
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, United States of America
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44
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Tan K, Chen J, Kaku Y, Wang Y, Donius L, Khan RA, Li X, Richter H, Seaman MS, Walz T, Hwang W, Reinherz EL, Kim M. Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546734. [PMID: 37425731 PMCID: PMC10327024 DOI: 10.1101/2023.06.27.546734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Broadly neutralizing antibodies (bnAbs) against HIV-1 target conserved epitopes, thereby inhibiting viral entry. Yet surprisingly, those recognizing linear epitopes in the HIV-1 gp41 membrane proximal external region (MPER) are elicited neither by peptide nor protein scaffold vaccines. Here, we observe that while Abs generated by MPER/liposome vaccines may exhibit human bnAb-like paratopes, B-cell programming without constraints imposed by the gp160 ectodomain selects Abs unable to access the MPER within its native "crawlspace". During natural infection, the flexible hinge of IgG3 partially mitigates steric occlusion of less pliable IgG1 subclass Abs with identical MPER specificity, until affinity maturation refines entry mechanisms. The IgG3 subclass maintains B-cell competitiveness, exploiting bivalent ligation resulting from greater intramolecular Fab arm length, offsetting weak antibody affinity. These findings suggest future immunization strategies.
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45
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Qerqez AN, Silva RP, Maynard JA. Outsmarting Pathogens with Antibody Engineering. Annu Rev Chem Biomol Eng 2023; 14:217-241. [PMID: 36917814 PMCID: PMC10330301 DOI: 10.1146/annurev-chembioeng-101121-084508] [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] [Indexed: 03/16/2023]
Abstract
There is growing interest in identifying antibodies that protect against infectious diseases, especially for high-risk individuals and pathogens for which no vaccine is yet available. However, pathogens that manifest as opportunistic or latent infections express complex arrays of virulence-associated proteins and are adept at avoiding immune responses. Some pathogens have developed strategies to selectively destroy antibodies, whereas others create decoy epitopes that trick the host immune system into generating antibodies that are at best nonprotective and at worst enhance pathogenesis. Antibody engineering strategies can thwart these efforts by accessing conserved neutralizing epitopes, generating Fc domains that resist capture or degradation and even accessing pathogens hidden inside cells. Design of pathogen-resistant antibodies can enhance protection and guide development of vaccine immunogens against these complex pathogens. Here, we discuss general strategies for design of antibodies resistant to specific pathogen defense mechanisms.
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Affiliation(s)
- Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas, Austin, Texas, USA;
| | - Rui P Silva
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas, Austin, Texas, USA;
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46
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Dosey A, Ellis D, Boyoglu-Barnum S, Syeda H, Saunders M, Watson M, Kraft JC, Pham MN, Guttman M, Lee KK, Kanekiyo M, King NP. Combinatorial immune refocusing within the influenza hemagglutinin head elicits cross-neutralizing antibody responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541996. [PMID: 37292967 PMCID: PMC10245820 DOI: 10.1101/2023.05.23.541996] [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
The head domain of influenza hemagglutinin (HA) elicits potently neutralizing yet mostly strain-specific antibodies during infection and vaccination. Here we evaluated a series of immunogens that combined several immunofocusing techniques for their ability to enhance the functional breadth of vaccine-elicited immune responses. We designed a series of "trihead" nanoparticle immunogens that display native-like closed trimeric heads from the HAs of several H1N1 influenza viruses, including hyperglycosylated variants and hypervariable variants that incorporate natural and designed sequence diversity at key positions in the periphery of the receptor binding site (RBS). Nanoparticle immunogens displaying triheads or hyperglycosylated triheads elicited higher HAI and neutralizing activity against vaccine-matched and -mismatched H1 viruses than corresponding immunogens lacking either trimer-stabilizing mutations or hyperglycosylation, indicating that both of these engineering strategies contributed to improved immunogenicity. By contrast, mosaic nanoparticle display and antigen hypervariation did not significantly alter the magnitude or breadth of vaccine-elicited antibodies. Serum competition assays and electron microscopy polyclonal epitope mapping revealed that the trihead immunogens, especially when hyperglycosylated, elicited a high proportion of antibodies targeting the RBS, as well as cross-reactive antibodies targeting a conserved epitope on the side of the head. Our results yield important insights into antibody responses against the HA head and the ability of several structure-based immunofocusing techniques to influence vaccine-elicited antibody responses.
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Affiliation(s)
- Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, 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
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mason Saunders
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - John C. Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N. Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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47
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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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48
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Andrews SF, Cominsky LY, Shimberg GD, Gillespie RA, Gorman J, Raab JE, Brand J, Creanga A, Gajjala SR, Narpala S, Cheung CSF, Harris DR, Zhou T, Gordon I, Holman L, Mendoza F, Houser KV, Chen GL, Mascola JR, Graham BS, Kwong PD, Widge A, Dropulic LK, Ledgerwood JE, Kanekiyo M, McDermott AB. An influenza H1 hemagglutinin stem-only immunogen elicits a broadly cross-reactive B cell response in humans. Sci Transl Med 2023; 15:eade4976. [PMID: 37075126 DOI: 10.1126/scitranslmed.ade4976] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Current yearly seasonal influenza vaccines primarily induce an antibody response directed against the immunodominant but continually diversifying hemagglutinin (HA) head region. These antibody responses provide protection against the vaccinating strain but little cross-protection against other influenza strains or subtypes. To focus the immune response on subdominant but more conserved epitopes on the HA stem that might protect against a broad range of influenza strains, we developed a stabilized H1 stem immunogen lacking the immunodominant head displayed on a ferritin nanoparticle (H1ssF). Here, we evaluated the B cell response to H1ssF in healthy adults ages 18 to 70 in a phase 1 clinical trial (NCT03814720). We observed both a strong plasmablast response and sustained elicitation of cross-reactive HA stem-specific memory B cells after vaccination with H1ssF in individuals of all ages. The B cell response was focused on two conserved epitopes on the H1 stem, with a highly restricted immunoglobulin repertoire unique to each epitope. On average, two-thirds of the B cell and serological antibody response recognized a central epitope on the H1 stem and exhibited broad neutralization across group 1 influenza virus subtypes. The remaining third recognized an epitope near the viral membrane anchor and was largely limited to H1 strains. Together, we demonstrate that an H1 HA immunogen lacking the immunodominant HA head produces a robust and broadly neutralizing HA stem-directed B cell response.
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Affiliation(s)
- Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lauren Y Cominsky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Geoffrey D Shimberg
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Joshua Brand
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Suprabhath R Gajjala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Crystal S F Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Ingelise Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - LaSonji Holman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Floreliz Mendoza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Katherine V Houser
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Alicia Widge
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Lesia K Dropulic
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Julie E Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20902, USA
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49
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Cable J, Sun J, Cheon IS, Vaughan AE, Castro IA, Stein SR, López CB, Gostic KM, Openshaw PJM, Ellebedy AH, Wack A, Hutchinson E, Thomas MM, Langlois RA, Lingwood D, Baker SF, Folkins M, Foxman EF, Ward AB, Schwemmle M, Russell AB, Chiu C, Ganti K, Subbarao K, Sheahan TP, Penaloza-MacMaster P, Eddens T. Respiratory viruses: New frontiers-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1522:60-73. [PMID: 36722473 PMCID: PMC10580159 DOI: 10.1111/nyas.14958] [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] [Indexed: 02/02/2023]
Abstract
Respiratory viruses are a common cause of morbidity and mortality around the world. Viruses like influenza, RSV, and most recently SARS-CoV-2 can rapidly spread through a population, causing acute infection and, in vulnerable populations, severe or chronic disease. Developing effective treatment and prevention strategies often becomes a race against ever-evolving viruses that develop resistance, leaving therapy efficacy either short-lived or relevant for specific viral strains. On June 29 to July 2, 2022, researchers met for the Keystone symposium "Respiratory Viruses: New Frontiers." Researchers presented new insights into viral biology and virus-host interactions to understand the mechanisms of disease and identify novel treatment and prevention approaches that are effective, durable, and broad.
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Affiliation(s)
| | - Jie Sun
- Division of Pulmonary and Critical Medicine, Department of Medicine; Department of Immunology; and Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Carter Immunology Center and Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - In Su Cheon
- Division of Pulmonary and Critical Medicine, Department of Medicine; Department of Immunology; and Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Carter Immunology Center and Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Andrew E Vaughan
- University of Pennsylvania School of Veterinary Medicine, Biomedical Sciences, Philadelphia, Pennsylvania, USA
| | - Italo A Castro
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo - USP, São Paulo, Brazil
| | - Sydney R Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center and Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine, St Louis, Missouri, USA
| | - Katelyn M Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | | | - Ali H Ellebedy
- Department of Pathology and Immunology; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs; and Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, Missouri, USA
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, UK
| | | | | | - Ryan A Langlois
- Center for Immunology and Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
| | - Steven F Baker
- Lovelace Biomedical Research Institute, Albuquerque, New Mexico, USA
| | - Melanie Folkins
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Ellen F Foxman
- Department of Laboratory Medicine and Department of Immunology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Martin Schwemmle
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alistair B Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kanta Subbarao
- Department of Microbiology and Immunology, WHO Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute for Infection and Immunity, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pablo Penaloza-MacMaster
- Department of Microbiology-Immunology, School of Medicine, Northwestern University Feinberg, Chicago, Illinois, USA
| | - Taylor Eddens
- Pediatric Scientist Development Program, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
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50
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McGrath JJC, Wilson PC. Fate-mapping antibodies to study sinful immune dynamics. Nat Immunol 2023; 24:570-572. [PMID: 36959294 DOI: 10.1038/s41590-023-01467-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- Joshua J C McGrath
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
| | - Patrick C Wilson
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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