Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation Article Swipe

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Kocher, Katharina , Drost, Felix , Schülein, Christine , Spriewald Bernd , Schubert, Benjamin , Schober, Kilian ·

YOU? · · 2026 · Open Access · · DOI: https://doi.org/10.5281/zenodo.17091561

Understanding T cell fate requires precise knowledge of antigen reactivity. For CD4+ T cells, conventional identification of antigen reactivity by peptide restimulation relies on cellular activation, but thereby also introduces a phenotypic bias. However, by performing single-cell RNA and TCR sequencing on both antigen-stimulated and unstimulated samples, clonotypes can be tracked across conditions to identify antigen-reactive CD4+ T cells and simultaneously assess their phenotypes in the unperturbed state. Using this “reverse phenotyping” strategy, complemented by DNA-barcoded peptide–HLA class II multimers, we here investigated the longitudinal phenotypic evolution of SARS-CoV-2 spike–reactive CD4+ T cells after repeated mRNA vaccination. Without stimulation, reactive clones showed more Th-neutral features and less of an activated Th1-like state than would be assessed after antigen restimulation, yet retained a distinct transcriptional state into the memory phase. These results uncover durable imprints in antigen-reactive CD4+ T cells and highlight that cell state classification can differ fundamentally when judged by phenotype versus function.

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Computational Biology

Vaccination

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Phenotype Biology Antigen T cell Identification (biology) Genetics Immunology Gene T-cell receptor Cell T lymphocyte Immune system Antigen processing Cytotoxic T cell Messenger RNA Cell biology Molecular biology RNA Cd4 t cell Antigen-presenting cell Antigen presentation Gene expression Computational biology Cell type Negative selection Vaccination

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Landing Page: https://doi.org/10.5281/zenodo.17091561
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OpenAlex ID: https://openalex.org/W7106160140

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DOI: https://doi.org/10.5281/zenodo.17091561

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Title: Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation

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Publication year: 2026

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Publication date: 2026-09-10

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Authors: Kocher, Katharina, Drost, Felix, Schülein, Christine, Spriewald Bernd, Schubert, Benjamin, Schober, Kilian

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Landing page: https://doi.org/10.5281/zenodo.17091561

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Concepts: Phenotype, Biology, Antigen, T cell, Identification (biology), Genetics, Immunology, Gene, T-cell receptor, Cell, T lymphocyte, Immune system, Antigen processing, Cytotoxic T cell, Messenger RNA, Cell biology, Molecular biology, RNA, Cd4 t cell, Antigen-presenting cell, Antigen presentation, Gene expression, Computational biology, Cell type, Negative selection, Vaccination

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