Characterization of human CMV-specific CD8+ T cells using multi-layer single-cell omics
Ioanna Gemünd1, Lorenzo Bonaguro2, Matthias Becker3
1Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia; Institute of Virology, Technical University of Munich School of Medicine/Helmholtz Munich, Munich, Germany.
Abstract:
In this study, we established a comprehensive workflow to collect multi-omics single-cell data using a commercially available micro-well-based platform. This included whole transcriptome, cell surface markers (targeted sequencing-based cell surface proteomics), T cell specificities, adaptive immune receptor repertoire (AIRR) profiles, and sample multiplexing. With this technique, we identified paired T cell receptor sequences for three prominent human CMV epitopes. In addition, we assessed the ability of dCODE dextramers to detect antigen-specific T cells at low frequencies by estimating sensitivities and specificities when used as reagents for single-cell multi-omics.
