Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination

Kocher K, Drost F, Schülein C, Spriewald B, Schubert B, Schober K (2026)

Publication Type: Journal article

Publication year: 2026

Journal

iScience Elsevier

Book Volume: 29

Article Number: 116175

Journal Issue: 6

DOI: 10.1016/j.isci.2026.116175

Abstract

Understanding antigen reactivity is crucial for characterizing CD4+ T helper (Th) cell fate, yet conventional peptide restimulation assays introduce phenotypic bias by activating cells ex vivo. By combining single-cell RNA and T cell receptor (TCR) sequencing on antigen-stimulated and unstimulated samples, clonotypes can be tracked across conditions to identify antigen-reactive CD4+ T cells while assessing their phenotypes in the unperturbed state. Using this “reverse phenotyping” strategy, complemented by DNA-barcoded peptide-HLA class II multimers and TCR similarity metrics, we tracked SARS-CoV-2 spike-reactive CD4+ T cells longitudinally after repeated mRNA vaccination. Without stimulation, reactive clones showed more Th-neutral features and less activated Th1-like states than after restimulation. Furthermore, transgenic TCR re-expression further separated antigen-specific from bystander-activated clones. These results demonstrate the complementary value of different methods to identify and characterize antigen-reactive CD4+ T cells, and highlight that cell state classification can differ when defined by phenotype versus function.

Authors with CRIS profile

Katharina Kocher Institute of Microbiology – Clinical Microbiology, Immunology and Hygiene Bernd Spriewald Department of Medicine 5 – Haematology and Oncology Kilian Schober Institute of Microbiology – Clinical Microbiology, Immunology and Hygiene

Involved external institutions

Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE)

How to cite

APA:

Kocher, K., Drost, F., Schülein, C., Spriewald, B., Schubert, B., & Schober, K. (2026). Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination. iScience, 29(6). https://doi.org/10.1016/j.isci.2026.116175

MLA:

Kocher, Katharina, et al. "Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination." iScience 29.6 (2026).

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