Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping'

David S. Fischer, Meshal Ansar, Karolin I. Wagner, Sebastian Jarosch, Yiqi Huang, Christoph H. Mayr, Maximilian Strunz, Niklas J. Lang, Elvira D’Ippolito , Monika Hammel, Laura Mateyka, Simone Weber, Lisa S. Wolff, Klaus Witter, Isis E. Fernandez, Gabriela Leuschner, Katrin Milger, Marion Frankenberger, Lorenz Nowak, Katharina Heinig-Menhard, Ina Koch, Mircea G. Stoleriu, Anne Hilgendorff, Jürgen Behr, Andreas Pichlmair, Benjamin Schubert, Fabian J. Theis, Dirk H. Busch, Herbert B. Schiller, Kilian Schober (2021) Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’. Nat Commun 12, 4515 (2021). https://doi.org/10.1038/s41467-021-24730-4 (Project B09)

Abstract cited from the publication:

The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for ‘reverse phenotyping’. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.