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Voss WN, Hou YJ, Johnson NV, Delidakis G, Kim JE, Javanmardi K, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Chou CW, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye JM, Herbert AS, Finkelstein IJ, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science 2021; 372:1108-1112. [PMID: 33947773 PMCID: PMC8224265 DOI: 10.1126/science.abg5268] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.
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MESH Headings
- Animals
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/immunology
- COVID-19/prevention & control
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/immunology
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Mutation
- Protein Domains
- Proteomics
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Delidakis
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jin Eyun Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chelsea J Paresi
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Shawn A Abbasi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Whitney Pickens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Katia George
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, 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
| | | | - Daniel Billick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lori Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Tulane National Primate Research Center Department of Microbiology 18703 Three Rivers Road Covington, LA, USA
| | - Dhwani Batra
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Justin Lee
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shivaprakash Gangappa
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michelle Gadush
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Maria D Person
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Brent L Iverson
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- 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.
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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Voss WN, Hou YJ, Johnson NV, Kim JE, Delidakis G, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye J, Herbert A, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma. bioRxiv 2020. [PMID: 33398269 DOI: 10.1101/2020.12.20.423708] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq 1 ) to the spike ectodomain (S-ECD 2 ) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro , we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å 2 ). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning 3,4 our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.
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Barros M, Houlihan WJ, Paresi CJ, Brendel M, Rynearson KD, Lee CW, Prikhodko O, Cregger C, Chang G, Wagner SL, Gilchrist ML, Li YM. γ-Secretase Partitioning into Lipid Bilayers Remodels Membrane Microdomains after Direct Insertion. Langmuir 2020; 36:6569-6579. [PMID: 32432881 PMCID: PMC7887708 DOI: 10.1021/acs.langmuir.0c01178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
γ-Secretase is a multisubunit complex that catalyzes intramembranous cleavage of transmembrane proteins. The lipid environment forms membrane microdomains that serve as spatio-temporal platforms for proteins to function properly. Despite substantial advances in the regulation of γ-secretase, the effect of the local membrane lipid microenvironment on the regulation of γ-secretase is poorly understood. Here, we characterized and quantified the partitioning of γ-secretase and its substrates, the amyloid precursor protein (APP) and Notch, into lipid bilayers using solid-supported model membranes. Notch substrate is preferentially localized in the liquid-disordered (Ld) lipid domains, whereas APP and γ-secretase partition as single or higher complex in both phases but highly favor the ordered phase, especially after recruiting lipids from the ordered phase, indicating that the activity and specificity of γ-secretase against these two substrates are modulated by membrane lateral organization. Moreover, time-elapse measurements reveal that γ-secretase can recruit specific membrane components from the cholesterol-rich Lo phase and thus creates a favorable lipid environment for substrate recognition and therefore activity. This work offers insight into how γ-secretase and lipid modulate each other and control its activity and specificity.
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Affiliation(s)
- Marilia Barros
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - William J Houlihan
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Chelsea J Paresi
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
| | - Matthew Brendel
- Molecular Cytology Core, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Kevin D Rynearson
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Olga Prikhodko
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | - Cristina Cregger
- Department of Neurosciences, University of California, San Diego, California 92093, United States
| | | | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, California 92093, United States
- Research Biologist, VA San Diego Healthcare System, La Jolla, California 92161, United States
| | - M Lane Gilchrist
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
- Pharmacology Graduate Program, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
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Paresi CJ, Liu Q, Li YM. Benzimidazole covalent probes and the gastric H(+)/K(+)-ATPase as a model system for protein labeling in a copper-free setting. Mol Biosyst 2017; 12:1772-80. [PMID: 26952080 DOI: 10.1039/c6mb00024j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Affinity probes are useful tools for determining molecular targets and elucidating mechanism of action for novel, bioactive compounds. In the case of covalent inhibitors, activity based probes are particularly valuable for ensuring acceptable selectivity margins. However, there is a variety of bioorthogonal chemistry reactions available for modifying compounds of interest with clickable tags. Here, we describe a direct comparison of tetrazine ligation and strain promoted azide-alkyne cycloaddition using benzimidazole based probes to bind their known target, the gastric proton pump, ATP4A. This study validates the use of chemical probes for target identification and illustrates the superior efficiency of tetrazine ligation for copper-free click systems. In addition, we have identified several novel binding partners of benzimidazole probes: Isoform 2 of deleted in malignant brain tumors 1 protein (DMBT1) and three uncharacterized proteins.
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Affiliation(s)
- Chelsea J Paresi
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. and Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Qi Liu
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. and Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
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