Panel A shows an experimental timeline schematic for inoculation, co housing, and sorting nasal cavity IV negative SenNP positive CD8 positive T cells for single cell RNA sequencing; Panel B shows a UMAP plot of six Seurat cell clusters numbered 0 through 5; Panel C shows a stacked bar graph of cell proportions across Seurat clusters at D35, D35 plus 3, and D35 plus 6; Panel D shows a bubble plot of gene expression across clusters for Xcl1, Ifng, Gzmb, Tnf, Nr4a1, Fas, and Mki67; Panel E shows a UMAP plot highlighting Itgae positive Cd69 positive cells; Panel F shows a UMAP plot distinguishing Itgae positive Cd69 positive from Itgae negative and or Cd69 negative cells with trajectory arrows; Panel G shows a UMAP plot displaying D35, D35 plus 3, and D35 plus 6 cells with trajectory arrows.
URT-resident memory CD8 T cells initiate antiviral effector transcriptional programs during respiratory virus transmission. (A) Experimental schematic where PR8-SenNP i.n. immunized contact mice were co-housed with a Sendai-Luc–infected index mouse, and SenNP+ CD8+ T cells from the nasal cavity were sorted for single-cell RNA sequencing at D35 + 0, D35 + 3, and D35 + 6. (B) UMAP projection of nasal cavity SenNP+ IV− CD8+ T cells from contact mice during Sendai-Luc transmission. (C) Composition of UMAP Seurat clusters by day post co-housing. (D) Bubble plot with expression of effector function genes for each cluster. (E) Itgae+ Cd69+ cells overlaid on UMAP. (F) RNA velocity analysis with streamlines in the direction of cellular trajectory and Itgae and Cd69 expression status overlaid. (G) RNA velocity with time point post co-housing overlaid. Data are representative of two independent experimental replicates.