Characterization of human CMV-specific CD8+ T cells using multi-layer single-cell omics

Authors:

• Gemünd, Ioanna
• Bonaguro, Lorenzo
• Becker, Matthias
• Müller, Sophie
• Joos, Clemens
• De Domenico, Elena
• Aschenbrenner, Anna C.
• Schultze, Joachim L.
• Moosmann, Andreas
• Beyer, Marc D.

Details:

Cell Reports Methods, Volume 5, Issue 7, 2025-07-21

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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.