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Published December 28, 2021 | Supplemental Material + Published
Journal Article Open

HLA-A∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses


Cross-reactivity and direct killing of target cells remain underexplored for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific CD8⁺ T cells. Isolation of T cell receptors (TCRs) and overexpression in allogeneic cells allows for extensive T cell reactivity profiling. We identify SARS-CoV-2 RNA-dependent RNA polymerase (RdRp/NSP12) as highly conserved, likely due to its critical role in the virus life cycle. We perform single-cell TCRαβ sequencing in human leukocyte antigen (HLA)-A∗02:01-restricted, RdRp-specific T cells from SARS-CoV-2-unexposed individuals. Human T cells expressing these TCRαβ constructs kill target cell lines engineered to express full-length RdRp. Three TCR constructs recognize homologous epitopes from common cold coronaviruses, indicating CD8⁺ T cells can recognize evolutionarily diverse coronaviruses. Analysis of individual TCR clones may help define vaccine epitopes that can induce long-term immunity against SARS-CoV-2 and other coronaviruses.

Additional Information

© 2021 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Received 11 August 2021, Revised 15 October 2021, Accepted 2 December 2021, Available online 10 December 2021. We thank Michael T. Bethune for providing advice throughout this project, as well as providing the Jurkat-CD8 cells while at the laboratory of David Baltimore (Caltech). The NFAT reporter was a gift from Christopher S. Seet (UCLA) and the laboratory of David Baltimore (Caltech). We thank Caius Radu and Ting-Ting Wu (UCLA) for critical reading of the manuscript. The UCLA Technology Center for Genomics and Bioinformatics constructed single-cell human TCR libraries and performed TCR sequencing. Funding: National Cancer Institute grants U01 CA233074 (O.N.W.) and U24 CA248265 (P.C.B.); Parker Institute for Cancer Immunotherapy grant (O.N.W. and J.R.H.); UCLA Broad Stem Cell Research Center (O.N.W.); USHHS Ruth L. Kirschstein Institutional National Research Service Award T32 CA009056 (P.A.N.); Broad Stem Cell Research Center (BSCRC) predoctoral fellowship (Z.M.); The Jeff and Liesl Wilke Foundation (J.R.H.); The Washington State Andy Hill CARE Fund (J.R.H.); The Biomedical Advanced Research and Development Authority HHSO10201600031C (J.R.H.); UCLA W. M. Keck Foundation COVID-19 Research Award Program (O.N.W.). Data and code availability: Reactive TCR alpha/beta nucleotide sequences are provided in this paper. We have not created any original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. Author contributions: Conceptualization, P.A.N. and O.N.W.; supervision, P.A.N., O.N.W., J.M., J.T.K., J.R.H., P.C.B., and J.W.P.; methodology, M.T.B., P.A.N., P.C.B., J.R.H., W.C., Y.S., L.Y., Z.M., N.J.B., Y.L., D.L., and J.T.K.; investigation, G.B.S., J.M., P.A.N., J.X., R.N., B.L.T., D.C., C.C., and M.N.; funding acquisition, J.W.P., P.C.B., and O.N.W.; software, M.B.O., B.L.T., R.N., and D.Z.; resources, J.X., W.C., and Y.L.; visualization, M.B.O., P.A.N., B.L.T., D.Z., and R.N.; project administration, P.A.N., J.M., and O.N.W.; writing – original draft, review & editing, P.A.N., O.N.W., and J.W.P. Declaration of interests: O.N.W., J.M., and P.A.N. are inventors of a patent application in progress that will be filed prior to manuscript publication. J.R.H. is a board member of PACT Pharma and Isoplexis. O.N.W. currently has consulting, equity, and/or board relationships with Trethera Corporation, Kronos Biosciences, Sofie Biosciences, Breakthrough Properties, Vida Ventures, Nammi Therapeutics, Two River, Iconovir, Appia BioSciences, Neogene Therapeutics, and Allogene Therapeutics. None of these companies contributed to or directed any of the research reported in this article.

Attached Files

Published - 1-s2.0-S2211124721016673-main.pdf

Supplemental Material - 1-s2.0-S2211124721016673-mmc1.pdf

Supplemental Material - 1-s2.0-S2211124721016673-mmc2.xlsx

Supplemental Material - 1-s2.0-S2211124721016673-mmc3.xlsx

Supplemental Material - 1-s2.0-S2211124721016673-mmc4.csv

Supplemental Material - 1-s2.0-S2211124721016673-mmc5.csv


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August 22, 2023
October 23, 2023