Epitope-specific T cell responses after SARS-CoV-2 vaccination [scRNA-dextramer_s2]

Clonal expansion is a hallmark of adaptive immunity, and appears to be driven by high antigen-specific receptor avidity as shown by research using murine in vivo models. In humans, however, the functionality of antigen-specific T cell clonotypes that are recruited into primary and recall immune responses remains surprisingly elusive. In this regard, the vaccination program during the SARS-CoV-2 pandemic represented a unique research opportunity by provision of highly standardized cohorts of healthy human individuals receiving immunizations against a previously unseen antigen. Here, we analyzed 30 HLA-typed individuals before, short-term and long-term after three mRNA vaccinations against SARS-CoV-2. We performed an in-depth characterization of the magnitude, phenotype, clonal composition and functionality of antigen-specific CD8 T cell responses by ELISPOT, flow cytometry and single-cell RNA sequencing, including CITE seq of 130 surface antigens and 16 T cell epitope specificities. 89 T cell receptors (TCRs) covering three complete epitope-specific repertoires were re-expressed by CRISPR/Cas9-mediated orthotopic TCR replacement and tested for their avidity. TCR repertoires underwent continuous tailoring, with high TCR avidity being linked to both clonal persistence and expansion. However, epitope-specific repertoires also maintained diversity by concomitant contraction and new emergence of functional T cell clones over time. These data on the phenotype and clonal selection within human antigen-specific T cell responses instruct our understanding of human T cell biology and may guide the development of enhanced or novel vaccines. Overall design: Antigen-specific T cells (as well as unspecific T cells as a control) were identified by DNA-baroded pMHC multimers (Dextramers) including the SARS-CoV-2 spike specificity LTD as well as 15 additional SARS-CoV-2 spike epitopes. Dextramer+ and - cells were sorted by FACS and subjected to 5' scRNAseq on a 10x Genomics platform including CITEseq for Dextramers and TotalSeq-C anti-human hashtag antibodies; different samples from different donors were labelled with hasthag antibodies