Rapid characterization of spike variants via mammalian cell surface display

Kamyab Javanmardi; Chia Wei Chou; Cynthia I. Terrace; Ankur Annapareddy; Tamer S. Kaoud; Qingqing Guo; Josh Lutgens; Hayley Zorkic; Andrew P. Horton; Elizabeth C. Gardner; Giaochau Nguyen; Daniel R. Boutz; Jule Goike; William N. Voss; Hung Che Kuo; Kevin N. Dalby; Jimmy D. Gollihar; Ilya J. Finkelstein

doi:10.1016/j.molcel.2021.11.024

Rapid characterization of spike variants via mammalian cell surface display

Kamyab Javanmardi, Chia Wei Chou, Cynthia I. Terrace, Ankur Annapareddy, Tamer S. Kaoud, Qingqing Guo, Josh Lutgens, Hayley Zorkic, Andrew P. Horton, Elizabeth C. Gardner, Giaochau Nguyen, Daniel R. Boutz, Jule Goike, William N. Voss, Hung Che Kuo, Kevin N. Dalby, Jimmy D. Gollihar, Ilya J. Finkelstein

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Abstract

The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.

Original language	English (US)
Pages (from-to)	5099-5111.e8
Journal	Molecular Cell
Volume	81
Issue number	24
DOIs	https://doi.org/10.1016/j.molcel.2021.11.024
State	Published - Dec 16 2021

Keywords

COVID-19
N-terminal domain
cell display
receptor-binding domain
variants
Protein Binding/genetics
Cell Line
Mammals/immunology
SARS-CoV-2/genetics
Humans
COVID-19/immunology
Spike Glycoprotein, Coronavirus/genetics
Animals
Antibodies, Monoclonal/immunology
Epitopes/genetics
HEK293 Cells
Antibodies, Neutralizing/immunology

ASJC Scopus subject areas

Molecular Biology
Cell Biology

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10.1016/j.molcel.2021.11.024

Cite this

Javanmardi, K., Chou, C. W., Terrace, C. I., Annapareddy, A., Kaoud, T. S., Guo, Q., Lutgens, J., Zorkic, H., Horton, A. P., Gardner, E. C., Nguyen, G., Boutz, D. R., Goike, J., Voss, W. N., Kuo, H. C., Dalby, K. N., Gollihar, J. D., & Finkelstein, I. J. (2021). Rapid characterization of spike variants via mammalian cell surface display. Molecular Cell, 81(24), 5099-5111.e8. https://doi.org/10.1016/j.molcel.2021.11.024

Javanmardi, K, Chou, CW, Terrace, CI, Annapareddy, A, Kaoud, TS, Guo, Q, Lutgens, J, Zorkic, H, Horton, AP, Gardner, EC, Nguyen, G, Boutz, DR, Goike, J, Voss, WN, Kuo, HC, Dalby, KN, Gollihar, JD & Finkelstein, IJ 2021, 'Rapid characterization of spike variants via mammalian cell surface display', Molecular Cell, vol. 81, no. 24, pp. 5099-5111.e8. https://doi.org/10.1016/j.molcel.2021.11.024

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title = "Rapid characterization of spike variants via mammalian cell surface display",

abstract = "The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.",

keywords = "COVID-19, N-terminal domain, cell display, receptor-binding domain, variants, Protein Binding/genetics, Cell Line, Mammals/immunology, SARS-CoV-2/genetics, Humans, COVID-19/immunology, Spike Glycoprotein, Coronavirus/genetics, Animals, Antibodies, Monoclonal/immunology, Epitopes/genetics, HEK293 Cells, Antibodies, Neutralizing/immunology",

author = "Kamyab Javanmardi and Chou, {Chia Wei} and Terrace, {Cynthia I.} and Ankur Annapareddy and Kaoud, {Tamer S.} and Qingqing Guo and Josh Lutgens and Hayley Zorkic and Horton, {Andrew P.} and Gardner, {Elizabeth C.} and Giaochau Nguyen and Boutz, {Daniel R.} and Jule Goike and Voss, {William N.} and Kuo, {Hung Che} and Dalby, {Kevin N.} and Gollihar, {Jimmy D.} and Finkelstein, {Ilya J.}",

note = "Funding Information: We thank Drs. Ching-Lin Hseih, Jason S. McLellan, Jason Lavinder, and Gregory C. Ippolito for generously sharing ACE2, antibody expression constructs, and purified antibodies. We are grateful to members of the Finkelstein and Ippolito laboratories for carefully reading the manuscript. We also thank our Center for Biomedical Research Support for their continuous work and dedication throughout the pandemic. This work was supported by the Welch Foundation ( F-1808 to I.J.F.; F-1390 to K.N.D.), the Bill and Melinda Gates Foundation ( INV-017592 to I.J.F.), and a Cooperative Agreement between UT Austin and ARL ( W911NF-17-2-0091 to J.D.G.). Publisher Copyright: {\textcopyright} 2021 Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2021",

month = dec,

day = "16",

doi = "10.1016/j.molcel.2021.11.024",

language = "English (US)",

volume = "81",

pages = "5099--5111.e8",

journal = "Molecular Cell",

issn = "1097-2765",

publisher = "Cell Press",

number = "24",

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TY - JOUR

T1 - Rapid characterization of spike variants via mammalian cell surface display

AU - Javanmardi, Kamyab

AU - Chou, Chia Wei

AU - Terrace, Cynthia I.

AU - Annapareddy, Ankur

AU - Kaoud, Tamer S.

AU - Guo, Qingqing

AU - Lutgens, Josh

AU - Zorkic, Hayley

AU - Horton, Andrew P.

AU - Gardner, Elizabeth C.

AU - Nguyen, Giaochau

AU - Boutz, Daniel R.

AU - Goike, Jule

AU - Voss, William N.

AU - Kuo, Hung Che

AU - Dalby, Kevin N.

AU - Gollihar, Jimmy D.

AU - Finkelstein, Ilya J.

N1 - Funding Information: We thank Drs. Ching-Lin Hseih, Jason S. McLellan, Jason Lavinder, and Gregory C. Ippolito for generously sharing ACE2, antibody expression constructs, and purified antibodies. We are grateful to members of the Finkelstein and Ippolito laboratories for carefully reading the manuscript. We also thank our Center for Biomedical Research Support for their continuous work and dedication throughout the pandemic. This work was supported by the Welch Foundation ( F-1808 to I.J.F.; F-1390 to K.N.D.), the Bill and Melinda Gates Foundation ( INV-017592 to I.J.F.), and a Cooperative Agreement between UT Austin and ARL ( W911NF-17-2-0091 to J.D.G.). Publisher Copyright: © 2021 Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/12/16

Y1 - 2021/12/16

N2 - The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.

AB - The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.

KW - COVID-19

KW - N-terminal domain

KW - cell display

KW - receptor-binding domain

KW - variants

KW - Protein Binding/genetics

KW - Cell Line

KW - Mammals/immunology

KW - SARS-CoV-2/genetics

KW - Humans

KW - COVID-19/immunology

KW - Spike Glycoprotein, Coronavirus/genetics

KW - Animals

KW - Antibodies, Monoclonal/immunology

KW - Epitopes/genetics

KW - HEK293 Cells

KW - Antibodies, Neutralizing/immunology

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U2 - 10.1016/j.molcel.2021.11.024

DO - 10.1016/j.molcel.2021.11.024

M3 - Article

C2 - 34919820

AN - SCOPUS:85121137350

SN - 1097-2765

VL - 81

SP - 5099-5111.e8

JO - Molecular Cell

JF - Molecular Cell

IS - 24

ER -

Rapid characterization of spike variants via mammalian cell surface display

Abstract

Keywords

ASJC Scopus subject areas

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