Biology subjects

Kocher, K.

Publications and source records attributed to Kocher, K..

3 recordsLinked to original sources

bioRxiv2025

Antigen-reactive CD4+ T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation bias

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. However, by performing single-cell RNA and T cell receptor (TCR) sequencing on both antigen-stimulated and unstimulated samples, clonotypes can be tracked across conditions to identify antigen-reactive CD4+ T cells and simultaneously be assessed for their phenotypes in the unperturbed state. Using this reverse phenotyping strategy, complemented by DNA-barcoded peptide-HLA (pHLA) class II multimers, we here 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 of an activated Th1-like state than would be assessed after antigen restimulation. Furthermore, transgenic TCR re-expression guided separation of antigen-specific from bystander-activated clones. These results uncover unbiased phenotypes of antigen-reactive CD4+ T cells and highlight that cell state classification can differ fundamentally when judged by phenotype versus function.

immunology↗

bioRxiv2024

Benchmarking of T-Cell Receptor - Epitope Predictors with ePytope-TCR

Understanding the recognition of disease-derived epitopes through T-cell receptors (TCRs) has the potential to serve as a stepping stone for the development of efficient immunotherapies and vaccines. While a plethora of sequence-based prediction methods for TCR-epitope binding exists, their available pre-trained models have not been comparatively evaluated on standardized datasets and evaluation settings. Furthermore, technical problems such as non-standardized input and output formats of these prediction tools hinder interoperability and broad usage in applied research. To alleviate these shortcomings, we introduce ePytope-TCR, an extension of the vaccine design and immuno-prediction framework ePytope. We integrated 18 TCR-epitope prediction methods into this common framework offering interoperable interfaces with standard TCR repertoire data formats. We showcase the applicability of ePytope-TCR by evaluating the performance of the prediction methods on two challenging datasets for annotating single-cell repertoires and predicting TCR cross-reactivity towards mutated epitopes. While novel predictors successfully predicted binding to frequently observed epitopes, all methods failed for less observed epitopes. Further, we detected a strong bias in the prediction scores between different epitope classes. We envision this benchmark to guide researchers in their choice of a predictor for a given setting. Further, we aspire to accelerate the development of novel prediction models by allowing fast benchmarking against existing approaches through common interfaces and defining standardized evaluation settings.

bioinformatics↗

bioRxiv2024

Quality of vaccination-induced T cell responses is conveyed by polyclonality and high, but not maximum, antigen receptor avidity

While the quantity of vaccination-induced T cells represents a routine immunogenicity parameter, the quality of such responses is poorly understood. Here, we report on a clinical cohort of 29 human healthy individuals who received three mRNA vaccinations against SARS-CoV-2 before any breakthrough infection. We characterized the magnitude, phenotype and clonal composition of CD8 T cell responses against 16 epitope specificities by ELISpot, flow cytometry as well as single-cell RNA, TCR and surface protein sequencing. To test the functionality of identified clonotypes, 106 T cell receptors (TCR) from five epitope-specific repertoires were re-expressed and tested for peptide sensitivity. While recruited repertoires were overall enriched for high-avidity TCRs, differential clonal expansion was not linked to fine avidity differences. Instead, maintenance of polyclonality ensured robustness in counteracting mutational escape of epitopes. Our findings on the induction and maintenance of high-functionality polyclonal T cell repertoires shed light on T cell quality as a neglected criterion in the assessment of vaccine immunogenicity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/620795v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@f48079org.highwire.dtl.DTLVardef@1eaa46org.highwire.dtl.DTLVardef@13cfb93org.highwire.dtl.DTLVardef@a8a6e5_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗