Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma

Gilchuk, Pavlo; Guthals, Adrian; Bonissone, Stefano R.; Shaw, Jared B.; Ilinykh, Philipp A.; Huang, Kai; Bombardi, Robin G.; Liang, Jenny; Grinyo, Ariadna; Davidson, Edgar; Chen, Elaine C.; Gunn, Bronwyn M.; Alter, Galit; Saphire, Erica Ollmann; Doranz, Benjamin J.; Bukreyev, Alexander; Zeitlin, Larry; Castellana, Natalie; Crowe, James E.

doi:10.3389/fimmu.2021.706757

Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma

Journal Article · Fri Jul 16 00:00:00 EDT 2021 · Frontiers in Immunology

DOI:https://doi.org/10.3389/fimmu.2021.706757· OSTI ID:1815687

Gilchuk, Pavlo ^[1]; Guthals, Adrian ^[2]; Bonissone, Stefano R. ^[3]; Shaw, Jared B. ^[4]; Ilinykh, Philipp A. ^[5]; Huang, Kai ^[5]; Bombardi, Robin G. ^[6]; Liang, Jenny ^[7]; Grinyo, Ariadna ^[7]; Davidson, Edgar ^[7]; Chen, Elaine C. ^[8]; Gunn, Bronwyn M. ^[9]; Alter, Galit ^[9]; Saphire, Erica Ollmann ^[10]; Doranz, Benjamin J. ^[7]; Bukreyev, Alexander ^[11]; Zeitlin, Larry ^[2]; Castellana, Natalie ^[3]; Crowe, James E. ^[12]

Vanderbilt Univ., Nashville, TN (United States). Univ. Medical Center. The Vanderbilt Vaccine Center; OSTI
Mapp Biopharmaceutical, Inc. San Diego, CA (United States)
Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab.
Univ. of Texas Medical Branch, Galveston, TX (United States). Dept. of Pathology; Univ. of Texas Medical Branch, Galveston, TX (United States). Galveston national Lab.
Vanderbilt Univ., Nashville, TN (United States). Univ. Medical Center. The Vanderbilt Vaccine Center
Integral Molecular, Inc., Philadelphia, PA (United States)
Vanderbilt Univ. Medical Center, Nashville, TN (United States). Dept. of Pathology, Microbiology, and Immunology
Massachusetts Inst. of Technology (MIT), and Harvard Univ., Cambridge, MA (United States). Ragon Inst. of MGH
La Jolla Inst. for Immunology, La Jolla, CA (United States). Center for Infectious Disease and Vaccine Research
Univ. of Texas Medical Branch, Galveston, TX (United States). Dept. of Pathology; Univ. of Texas Medical Branch, Galveston, TX (United States). Galveston national Lab.; Univ. of Texas Medical Branch, Galveston, TX (United States). Dept. of Microbiology and Immunology
Vanderbilt Univ., Nashville, TN (United States). Univ. Medical Center. The Vanderbilt Vaccine Center; Vanderbilt Univ. Medical Center, Nashville, TN (United States). Dept. of Pathology, Microbiology, and Immunology; Vanderbilt Univ., Nashville, TN (United States). Univ. Medical Center. Dept. of Pediatrics

Three clinically relevant ebolaviruses – Ebola (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) viruses, are responsible for severe disease and occasional deadly outbreaks in Africa. The largest Ebola virus disease (EVD) epidemic to date in 2013-2016 in West Africa highlighted the urgent need for countermeasures, leading to the development and FDA approval of the Ebola virus vaccine rVSV-ZEBOV (Ervebo^®) in 2020 and two monoclonal antibody (mAb)-based therapeutics (Inmazeb^®[atoltivimab, maftivimab, and odesivimab-ebgn] and Ebanga^®(ansuvimab-zykl) in 2020. The humoral response plays an indispensable role in ebolavirus immunity, based on studies of mAbs isolated from the antibody genes in peripheral blood circulating ebolavirus-specific human memory B cells. However, antibodies in the body are not secreted by circulating memory B cells in the blood but rather principally by plasma cells in the bone marrow. Little is known about the protective polyclonal antibody responses in convalescent plasma. Here we exploited both single-cell antibody gene sequencing and proteomic sequencing approaches to assess the composition of the ebolavirus glycoprotein (GP)-reactive antibody repertoire in the plasma of an EVD survivor. We first identified 1,512 GP-specific mAb variable gene sequences from single cells in the memory B cell compartment. Using mass spectrometric analysis of the corresponding GP-specific plasma IgG, we found that only a portion of the large B cell antibody repertoire was represented in the plasma. Molecular and functional analysis of proteomics-identified mAbs revealed recognition of epitopes in three major antigenic sites - the GP head domain, the glycan cap, and the base region, with a high prevalence of neutralizing and protective mAb specificities that targeted the base and glycan cap regions on the GP. Polyclonal plasma antibodies from the survivor reacted broadly to EBOV, BDBV, and SUDV GP, while reactivity of the potently neutralizing mAbs we identified was limited mostly to the homologous EBOV GP. Together these results reveal a restricted diversity of neutralizing humoral response in which mAbs targeting two antigenic sites on GP – glycan cap and base – play a principal role in plasma-antibody-mediated protective immunity against EVD.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1815687

Journal Information:: Frontiers in Immunology, Journal Name: Frontiers in Immunology Vol. 12; ISSN 1664-3224

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (52)

Efficacy and effectiveness of an rVSV-vectored vaccine in preventing Ebola virus disease: final results from the Guinea ring vaccination, open-label, cluster-randomised trial (Ebola Ça Suffit!) Henao-Restrepo, Ana Maria; Camacho, Anton; Longini, Ira M. The Lancet, Vol. 389, Issue 10068 https://doi.org/10.1016/S0140-6736(16)32621-6	journal	February 2017
Determinants of antibody persistence across doses and continents after single-dose rVSV-ZEBOV vaccination for Ebola virus disease: an observational cohort study Huttner, Angela; Agnandji, Selidji Todagbe; Combescure, Christophe The Lancet Infectious Diseases, Vol. 18, Issue 7 https://doi.org/10.1016/S1473-3099(18)30165-8	journal	July 2018
Mechanism of Human Antibody-Mediated Neutralization of Marburg Virus Flyak, Andrew I.; Ilinykh, Philipp A.; Murin, Charles D. Cell, Vol. 160, Issue 5 https://doi.org/10.1016/j.cell.2015.01.031	journal	February 2015
Cross-Reactive and Potent Neutralizing Antibody Responses in Human Survivors of Natural Ebolavirus Infection Flyak, Andrew I.; Shen, Xiaoli; Murin, Charles D. Cell, Vol. 164, Issue 3 https://doi.org/10.1016/j.cell.2015.12.022	journal	January 2016
Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses Wec, Anna Z.; Herbert, Andrew S.; Murin, Charles D. Cell, Vol. 169, Issue 5 https://doi.org/10.1016/j.cell.2017.04.037	journal	May 2017
Immunization-Elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability Zhao, Xuelian; Howell, Katie A.; He, Shihua Cell, Vol. 169, Issue 5 https://doi.org/10.1016/j.cell.2017.04.038	journal	May 2017
Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection Saphire, Erica Ollmann; Schendel, Sharon L.; Fusco, Marnie L. Cell, Vol. 174, Issue 4 https://doi.org/10.1016/j.cell.2018.07.033	journal	August 2018
Longitudinal Analysis of the Human B Cell Response to Ebola Virus Infection Davis, Carl W.; Jackson, Katherine J. L.; McElroy, Anita K. Cell, Vol. 177, Issue 6 https://doi.org/10.1016/j.cell.2019.04.036	journal	May 2019
Cooperativity Enables Non-neutralizing Antibodies to Neutralize Ebolavirus Howell, Katie A.; Brannan, Jennifer M.; Bryan, Christopher Cell Reports, Vol. 19, Issue 2 https://doi.org/10.1016/j.celrep.2017.03.049	journal	April 2017
Therapeutic Monoclonal Antibodies for Ebola Virus Infection Derived from Vaccinated Humans Rijal, Pramila; Elias, Sean C.; Machado, Samara Rosendo Cell Reports, Vol. 27, Issue 1 https://doi.org/10.1016/j.celrep.2019.03.020	journal	April 2019
Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies Murin, Charles D.; Gilchuk, Pavlo; Ilinykh, Philipp A. Cell Reports, Vol. 35, Issue 2 https://doi.org/10.1016/j.celrep.2021.108984	journal	April 2021
A Role for Fc Function in Therapeutic Monoclonal Antibody-Mediated Protection against Ebola Virus Gunn, Bronwyn M.; Yu, Wen-Han; Karim, Marcus M. Cell Host & Microbe, Vol. 24, Issue 2 https://doi.org/10.1016/j.chom.2018.07.009	journal	August 2018
A Two-Antibody Pan-Ebolavirus Cocktail Confers Broad Therapeutic Protection in Ferrets and Nonhuman Primates Bornholdt, Zachary A.; Herbert, Andrew S.; Mire, Chad E. Cell Host & Microbe, Vol. 25, Issue 1 https://doi.org/10.1016/j.chom.2018.12.005	journal	January 2019
Persistent Antibody Clonotypes Dominate the Serum Response to Influenza over Multiple Years and Repeated Vaccinations Lee, Jiwon; Paparoditis, Philipp; Horton, Andrew P. Cell Host & Microbe, Vol. 25, Issue 3 https://doi.org/10.1016/j.chom.2019.01.010	journal	March 2019
Structural Basis for a Convergent Immune Response against Ebola Virus Cohen-Dvashi, Hadas; Zehner, Matthias; Ehrhardt, Stefanie Cell Host & Microbe, Vol. 27, Issue 3 https://doi.org/10.1016/j.chom.2020.01.007	journal	March 2020
The structural basis for filovirus neutralization by monoclonal antibodies King, Liam B.; West, Brandyn R.; Schendel, Sharon L. Current Opinion in Immunology, Vol. 53 https://doi.org/10.1016/j.coi.2018.05.001	journal	August 2018
Multifunctional Pan-ebolavirus Antibody Recognizes a Site of Broad Vulnerability on the Ebolavirus Glycoprotein Gilchuk, Pavlo; Kuzmina, Natalia; Ilinykh, Philipp A. Immunity, Vol. 49, Issue 2 https://doi.org/10.1016/j.immuni.2018.06.018	journal	August 2018
Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination Lindesmith, Lisa C.; McDaniel, Jonathan R.; Changela, Anita Immunity, Vol. 50, Issue 6 https://doi.org/10.1016/j.immuni.2019.05.007	journal	June 2019
Analysis of a Therapeutic Antibody Cocktail Reveals Determinants for Cooperative and Broad Ebolavirus Neutralization Gilchuk, Pavlo; Murin, Charles D.; Milligan, Jacob C. Immunity, Vol. 52, Issue 2 https://doi.org/10.1016/j.immuni.2020.01.001	journal	February 2020
A Fc engineering approach to define functional humoral correlates of immunity against Ebola virus Gunn, Bronwyn M.; Lu, Richard; Slein, Matthew D. Immunity, Vol. 54, Issue 4 https://doi.org/10.1016/j.immuni.2021.03.009	journal	April 2021
Neutralizing ebolavirus: structural insights into the envelope glycoprotein and antibodies targeted against it Lee, Jeffrey E.; Saphire, Erica Ollmann Current Opinion in Structural Biology, Vol. 19, Issue 4 https://doi.org/10.1016/j.sbi.2009.05.004	journal	August 2009
Generation of eGFP expressing recombinant Zaire ebolavirus for analysis of early pathogenesis events and high-throughput antiviral drug screening Towner, Jonathan S.; Paragas, Jason; Dover, Jason E. Virology, Vol. 332, Issue 1 https://doi.org/10.1016/j.virol.2004.10.048	journal	February 2005
Human and murine immunoglobulin expression vector cassettes McLean, Gary R.; Nakouzi, Antonio; Casadevall, Arturo Molecular Immunology, Vol. 37, Issue 14 https://doi.org/10.1016/s0161-5890(00)00101-2	journal	October 2000
Sequencing Grade Tandem Mass Spectrometry for Top–Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer Shaw, Jared B.; Malhan, Neha; Vasil’ev, Yury V. Analytical Chemistry, Vol. 90, Issue 18 https://doi.org/10.1021/acs.analchem.8b01901	journal	August 2018
Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor Lee, Jeffrey E.; Fusco, Marnie L.; Hessell, Ann J. Nature, Vol. 454, Issue 7201 https://doi.org/10.1038/nature07082	journal	July 2008
Ebola virus entry requires the cholesterol transporter Niemann–Pick C1 Carette, Jan E.; Raaben, Matthijs; Wong, Anthony C. Nature, Vol. 477, Issue 7364 https://doi.org/10.1038/nature10348	journal	August 2011
Small molecule inhibitors reveal Niemann–Pick C1 is essential for Ebola virus infection Côté, Marceline; Misasi, John; Ren, Tao Nature, Vol. 477, Issue 7364 https://doi.org/10.1038/nature10380	journal	August 2011
Reversion of advanced Ebola virus disease in nonhuman primates with ZMapp Qiu, Xiangguo; Wong, Gary; Audet, Jonathan Nature, Vol. 514, Issue 7520 https://doi.org/10.1038/nature13777	journal	August 2014
A proteomics approach for the identification and cloning of monoclonal antibodies from serum Cheung, Wan Cheung; Beausoleil, Sean A.; Zhang, Xiaowu Nature Biotechnology, Vol. 30, Issue 5 https://doi.org/10.1038/nbt.2167	journal	March 2012
Proteomics-directed cloning of circulating antiviral human monoclonal antibodies Sato, Shuji; Beausoleil, Sean A.; Popova, Lana Nature Biotechnology, Vol. 30, Issue 11 https://doi.org/10.1038/nbt.2406	journal	November 2012
Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination Lee, Jiwon; Boutz, Daniel R.; Chromikova, Veronika Nature Medicine, Vol. 22, Issue 12 https://doi.org/10.1038/nm.4224	journal	November 2016
Integrated pipeline for the accelerated discovery of antiviral antibody therapeutics Gilchuk, Pavlo; Bombardi, Robin G.; Erasmus, Jesse H. Nature Biomedical Engineering, Vol. 4, Issue 11 https://doi.org/10.1038/s41551-020-0594-x	journal	August 2020
The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses Goldstein, Tracey; Anthony, Simon J.; Gbakima, Aiah Nature Microbiology, Vol. 3, Issue 10 https://doi.org/10.1038/s41564-018-0227-2	journal	August 2018
B cell memory: building two walls of protection against pathogens Akkaya, Munir; Kwak, Kihyuck; Pierce, Susan K. Nature Reviews Immunology, Vol. 20, Issue 4 https://doi.org/10.1038/s41577-019-0244-2	journal	December 2019
Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV Ehrhardt, Stefanie A.; Zehner, Matthias; Krähling, Verena Nature Medicine, Vol. 25, Issue 10 https://doi.org/10.1038/s41591-019-0602-4	journal	October 2019
Monoclonal Antibody Therapy for Ebola Virus Disease Levine, Myron M. New England Journal of Medicine, Vol. 381, Issue 24 https://doi.org/10.1056/NEJMe1915350	journal	December 2019
Ebola Feldmann, Heinz; Sprecher, Armand; Geisbert, Thomas W. New England Journal of Medicine, Vol. 382, Issue 19 https://doi.org/10.1056/NEJMra1901594	journal	May 2020
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response Wine, Y.; Boutz, D. R.; Lavinder, J. J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 8 https://doi.org/10.1073/pnas.1213737110	journal	February 2013
A Mouse Model for Evaluation of Prophylaxis and Therapy of Ebola Hemorrhagic Fever Bray, Mike; Davis, Kelly; Geisbert, Tom The Journal of Infectious Diseases, Vol. 178, Issue 3 https://doi.org/10.1086/515386	journal	September 1998
Development of Clinical-Stage Human Monoclonal Antibodies That Treat Advanced Ebola Virus Disease in Nonhuman Primates Pascal, Kristen E.; Dudgeon, Drew; Trefry, John C. The Journal of Infectious Diseases, Vol. 218, Issue suppl_5 https://doi.org/10.1093/infdis/jiy285	journal	May 2018
IMGT/JunctionAnalysis: IMGT Standardized Analysis of the V-J and V-D-J Junctions of the Rearranged Immunoglobulins (IG) and T Cell Receptors (TR) Giudicelli, V.; Lefranc, M. -P. Cold Spring Harbor Protocols, Vol. 2011, Issue 6 https://doi.org/10.1101/pdb.prot5634	journal	June 2011
Endosomal Proteolysis of the Ebola Virus Glycoprotein Is Necessary for Infection Chandran, K. Science, Vol. 308, Issue 5728 https://doi.org/10.1126/science.1110656	journal	June 2005
Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers Fibriansah, Guntur; Ibarra, Kristie D.; Ng, Thiam-Seng Science, Vol. 349, Issue 6243 https://doi.org/10.1126/science.aaa8651	journal	July 2015
Protective monotherapy against lethal Ebola virus infection by a potently neutralizing antibody Corti, D.; Misasi, J.; Mulangu, S. Science, Vol. 351, Issue 6279 https://doi.org/10.1126/science.aad5224	journal	February 2016
Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak Bornholdt, Z. A.; Turner, H. L.; Murin, C. D. Science, Vol. 351, Issue 6277 https://doi.org/10.1126/science.aad5788	journal	February 2016
Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes Voss, William N.; Hou, Yixuan J.; Johnson, Nicole V. Science, Vol. 372, Issue 6546 https://doi.org/10.1126/science.abg5268	journal	June 2021
Chimeric Filoviruses for Identification and Characterization of Monoclonal Antibodies Ilinykh, Philipp A.; Shen, Xiaoli; Flyak, Andrew I. Journal of Virology, Vol. 90, Issue 8 https://doi.org/10.1128/JVI.00101-16	journal	January 2016
Early Human B Cell Response to Ebola Virus in Four U.S. Survivors of Infection Williamson, Lauren E.; Flyak, Andrew I.; Kose, Nurgun Journal of Virology, Vol. 93, Issue 8 https://doi.org/10.1128/JVI.01439-18	journal	February 2019
Mechanism of Binding to Ebola Virus Glycoprotein by the ZMapp, ZMAb, and MB-003 Cocktail Antibodies Davidson, Edgar; Bryan, Christopher; Fong, Rachel H. Journal of Virology, Vol. 89, Issue 21 https://doi.org/10.1128/JVI.01490-15	journal	August 2015
Properties of Replication-Competent Vesicular Stomatitis Virus Vectors Expressing Glycoproteins of Filoviruses and Arenaviruses Garbutt, Michael; Liebscher, Ryan; Wahl-Jensen, Victoria Journal of Virology, Vol. 78, Issue 10 https://doi.org/10.1128/jvi.78.10.5458-5465.2004	journal	May 2004
Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies Bornholdt, Zachary A.; Ndungo, Esther; Fusco, Marnie L. mBio, Vol. 7, Issue 1 https://doi.org/10.1128/mBio.02154-15	journal	February 2016
Ebola GP-Specific Monoclonal Antibodies Protect Mice and Guinea Pigs from Lethal Ebola Virus Infection Qiu, Xiangguo; Fernando, Lisa; Melito, P. Leno PLoS Neglected Tropical Diseases, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pntd.0001575	journal	March 2012

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