Fig. 6

Endogenous T cells show transcriptional changes with enhanced cytotoxic function and more memory-like phenotype in response to intranasal vaccine. a Timeline of the experiment to isolate the endogenous T cells for single-cell RNA sequencing. Mice received LNP without RNA (mock, n = 3) or SIINFEKL-RFP-coding circRNA vaccine group (vac., n = 3) for two doses. Cells from lung tissues were mixed for staining and sorting in the same group. Sorted cells were sent for single-cell RNA sequencing. b UMAP plot of CD3 + T cells colored by clusters. c Dot plots showing differential expression of marker genes in endogenous CD3 + T cells. d UMAP plot of the T cells with cytotoxic function in mock group (mock) and vaccine group (vac.). e Statistical analysis of the cytotoxic gene expression in different clusters. Data were analyzed through the Wilcoxon signed-rank test. f UMPA plot of CD4 + T cells in two groups. g Statistical analysis of the CD4+ cell number of various clusters compared to their naïve cells in mock and vac group. h UMAP plot of CD8 + T cells in two groups. i Statistical analysis of the CD8+ cell number of various clusters compared to their naïve cells in mock and vac group. j Statistical analysis of Gzma and Gzmb expression in effector CD8 clusters. Data were analyzed through the Wilcoxon signed-rank test. k, l GO enrichment analysis showing the enriched terms of vac. group compared with mock group in effector CD4 (k) and effector CD8 (l) clusters