Journal Article

DZNE-2025-00891

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Characterization of human CMV-specific CD8+ T cells using multi-layer single-cell omics.

Gemünd, I. (First author)DZNE* ; Bonaguro, L.DZNE* ; Becker, M.DZNE* ; Müller, S.DZNE* ; Joos, C. ; De Domenico, E.DZNE* ; Aschenbrenner, A. C.DZNE* ; Schultze, J. L.DZNE* ; Moosmann, A. ; Beyer, M. D. (Last author)DZNE*

2025
Cell Press Cambridge, MA

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Please use a persistent id in citations: doi:10.1016/j.crmeth.2025.101085

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.

Keyword(s): Humans (MeSH) ; Cytomegalovirus: immunology (MeSH) ; Single-Cell Analysis: methods (MeSH) ; CD8-Positive T-Lymphocytes: immunology (MeSH) ; CD8-Positive T-Lymphocytes: metabolism (MeSH) ; Proteomics: methods (MeSH) ; Transcriptome (MeSH) ; Receptors, Antigen, T-Cell: metabolism (MeSH) ; Cytomegalovirus Infections: immunology (MeSH) ; BD Rhapsody ; CD8(+) T cells ; CMV ; CP: immunology ; TCR sequencing ; antigen-specific T cells ; dCODE dextramers ; single-cell multi-omics ; systems immunology ; Receptors, Antigen, T-Cell

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Contributing Institute(s):

1. Immunogenomics and Neurodegeneration (AG Beyer)
2. Clinical Single Cell Omics (CSCO) / Systems Medicine (AG Schultze)
3. Molecular and Translational Immunaging (AG Bonaguro)
4. Modular High Performance Computing and Artificial Intelligence (AG Becker)
5. Aging and Immunity (AG Aschenbrenner)
6. Platform for Single Cell Genomics and Epigenomics (PRECISE)

Research Program(s):

1. 351 - Brain Function (POF4-351) (POF4-351)
2. 354 - Disease Prevention and Healthy Aging (POF4-354) (POF4-354)
3. 352 - Disease Mechanisms (POF4-352) (POF4-352)

Experiment(s):

1. Platform for Single Cell Genomics and Epigenomics at DZNE University of Bonn

Appears in the scientific report 2025

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Database coverage:
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