Extended Data Fig. 8: Peripheral blood T cell responses to PTCV are primarily driven by clonal expansion of T cell effector memory cells clusters.

a, Uniform Manifold Approximation and Projection (UMAP) of single-cell transcriptomes of 39,435 T cells from peripheral blood samples (n = 4) obtained at 12 weeks post-vaccination from 3 patients (#6, #7, and #8), colored by cluster. b, Barplot showing the number of cells occupying each cluster. c, Dotplot showing gene expression CD3E, CD3G, CD8A, CD8B, CCL5, IDO1, CD69, NKG7, LCK, IFNG, CXCR6, CD27, PDCD1, and TIGIT. Size of the dot indicates the percent expression among cells assigned to each cluster and the color represents the average expression across all cells within the cluster. d, Heatmaps showing scaled expression of the top 5 marker genes identified for each subset. e, UMAP indicating areas of clonal expansion within the 31,842 cells identified as having a TCR by paired single-cell TCR-sequencing. Colors indicate the degree of clonal expansion of each TCR clonotype. f, UMAPs indicating single cells with a TCRβ identified as clonally expanded after vaccination by bulk TCRβ sequencing of pre- and post-treatment peripheral blood, by patient. g, Transcriptional phenotype of cells with a TCRβ identified as clonally expanded by bulk TCR sequencing of pre- and post-treatment peripheral blood, represented as a percentage of total number of single cells per patient.