Tanaka, Shiho and Olson, C. Anders and Barnes, Christopher O. and Higashide, Wendy and Gonzales, Marcos and Taft, Justin and Richardson, Ashley and Martin-Fernandez, Marta and Bogunovic, Dusan and Gnanapragasam, Priyanthi N. P. and Bjorkman, Pamela J. and Spilman, Patricia and Niazi, Kayvan and Rabizadeh, Shahrooz and Soon-Shiong, Patrick (2022) Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Cell Reports, 38 (6). Art. No. 110348. ISSN 2211-1247. PMCID PMC8769934; PMC8452091. doi:10.1016/j.celrep.2022.110348. https://resolver.caltech.edu/CaltechAUTHORS:20210915-214123136
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Abstract
The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identify a set of antibodies against SARS-CoV-2 spike (S) proteins and characterize the structures of nAbs that recognize epitopes in the S1 subunit of the S glycoprotein. These structural studies reveal distinct binding modes for several antibodies, including the targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interact with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is an approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.
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| Additional Information: | © 2022 The author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received 17 September 2021, Revised 6 December 2021, Accepted 14 January 2022, Available online 20 January 2022, Version of Record 8 February 2022. We thank J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance and K. Huey-Tubman for assistance with soluble spike purification. Electron microscopy was performed in the Caltech Cryo-EM Center with assistance from S. Chen and A. Malyutin. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory. We thank J. Kaiser, director of the Molecular Observatory at Caltech, and beamline staff C. Smith and S. Russi at SSRL for data collection assistance. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. This work was supported by NIH (P01-AI138938-S1 to P.J.B.), the Caltech Merkin Institute for Translational Research (P.J.B.), and a George Mason University Fast Grant (P.J.B.). C.O.B was supported by the Hanna Gray Fellowship Program from the Howard Hughes Medical Institute and the Postdoctoral Enrichment Program from the Burroughs Wellcome Fund. This work was also supported by ImmunityBio, Inc. Author contributions: Experimental designs, C.A.O., S.T., C.O.B., K.N., S.R., and P.S.-S.; mRNA library display, C.A.O.; cloning, C.A.O. and W.H.; protein expression and purification, C.A.O., S.T., and M.G.; kinetic analysis, ACE2 blocking assay, epitope binning, and convalescent plasma blocking assay, S.T.; developability assays M.G. and S.T.; cryo-EM and X-ray crystallography, C.O.B. and P.J.B.; Vero E6 live virus neutralization assay, J.T., A.R., M.M.-F., and D.B.; pseudovirus neutralization assay, P.G.; manuscript preparation, S.T., C.O.B., C.A.O., and P.S. Declaration of interests: C.A.O., S.T., W.H., K.N., and P.S.-S. are inventors for an international patent application with this work (US 11,015,188 B2). M.G. and P.S. are employees of ImmunityBio, Inc., and S.R. was a former employee and is a current shareholder of ImmunityBio, Inc. | ||||||||||||||||||||||
| Group: | COVID-19, Richard N. Merkin Institute for Translational Research | ||||||||||||||||||||||
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| Issue or Number: | 6 | ||||||||||||||||||||||
| PubMed Central ID: | PMC8769934; PMC8452091 | ||||||||||||||||||||||
| DOI: | 10.1016/j.celrep.2022.110348 | ||||||||||||||||||||||
| Record Number: | CaltechAUTHORS:20210915-214123136 | ||||||||||||||||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20210915-214123136 | ||||||||||||||||||||||
| Official Citation: | Shiho Tanaka, C. Anders Olson, Christopher O. Barnes, Wendy Higashide, Marcos Gonzalez, Justin Taft, Ashley Richardson, Marta Martin-Fernandez, Dusan Bogunovic, Priyanthi N.P. Gnanapragasam, Pamela J. Bjorkman, Patricia Spilman, Kayvan Niazi, Shahrooz Rabizadeh, Patrick Soon-Shiong, Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display, Cell Reports, Volume 38, Issue 6, 2022, 110348, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2022.110348. | ||||||||||||||||||||||
| Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | ||||||||||||||||||||||
| ID Code: | 110909 | ||||||||||||||||||||||
| Collection: | CaltechAUTHORS | ||||||||||||||||||||||
| Deposited By: | Tony Diaz | ||||||||||||||||||||||
| Deposited On: | 15 Sep 2021 22:15 | ||||||||||||||||||||||
| Last Modified: | 10 May 2022 18:34 |
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