Dataset related to article "Transcriptomic profile of TNFhigh MAIT cells is linked to B cell response following SARS-CoV-2 vaccination"

This record contains raw data related to article “<em>Transcriptomic profile of TNF^high MAIT cells is linked to B cell response following SARS-CoV-2 vaccination"</em> <strong>ABSTRACT</strong> <strong>Introduction:</strong> Higher frequencies of Mucosal-associated invariant T (MAIT) cells were associated with an increased adaptive response to mRNA <em>BNT162b2</em> SARS-CoV-2 vaccine, however, the mechanistic insights into this relationship are unknown. Here, we hypothesized that the TNF response of MAIT cells supports B cell activation following SARS-CoV-2 immunization. <strong>Methods:</strong> To investigate the effects of repeated SARS-CoV-2 vaccinations on the peripheral blood mononuclear cells (PBMCs), we performed a longitudinal single cell (sc)RNA-seq and scTCR-seq analysis of SARS-CoV-2 vaccinated healthy adults with two doses of the Pfizer-BioNTech <em>BNT162b2 </em>mRNA vaccine. Collection of PBMCs was performed 1 day before, 3- and 17-days after prime vaccination, and 3-days and 3-months following vaccine-boost. Based on scRNA/TCR-seq data related to regulatory signals induced by the vaccine, we used computational approaches for the functional pathway enrichment analysis (Reactome), dynamics of the effector cell-polarization (RNA Velocity and CellRank) and cell-cell communication (NicheNet). <strong>Results:</strong> We identified MAIT cells as an important source of TNF across circulating lymphocytes in response to repeated SARS-CoV-2 <em>BNT162b2</em> vaccination. The <em>TNF^high</em> signature of MAIT cells was induced by the second administration of the vaccine. Notably, the increased <em>TNF</em> expression was associated with MAIT cell proliferation and efficient anti-SARS-CoV-2 antibody production. Finally, by decoding the ligand-receptor interactions and incorporating intracellular signaling, we predicted <em>TNF^high</em> MAIT cell interplay with different B cell subsets. In specific, predicted <em>TNF</em>-mediated activation was selectively directed to conventional switched memory B cells, which are deputed to high-affinity long-term memory. <strong>Discussion:</strong> Overall, our results indicate that SARS-CoV-2 <em>BNT162b2</em> vaccination influences MAIT cell frequencies and their transcriptional effector profile with the potential to promote B cell activation. This work also provides a blueprint for the promising use of MAIT cells as cellular adjuvants in mRNA-based vaccines.