Extended Data Fig. 6: Clonal analysis of T cells in T-VEC-treated basal cell carcinomas.
a, Box plots for eight T cell subclusters and one natural killer (NK) cell cluster (cp. Fig. 4) according to pathological and clinical response. Brackets and numbers indicate the p-value of each cell population (two-sided Wilcoxon rank-sum test; statistical significance determined with p < 0.05) (n = 12). b, Paired scRNA-seq and single-cell T cell receptor sequencing (scTCR-seq) are presented by UMAP showing the density of hyper-expanded, large, medium, and small T cell clones. c, Box plots illustrate the absolute number, the number of unique clones, relative percent of unique clonotypes, and repertoire clonality of T cell clones according to patients with a pathological complete response (pCR) and pathological non-complete response (non-pCR) (n = 12). Data are presented as mean values +/- SEM, p-values are included in individual plots (two-sided, Wilcoxon signed sum rank test; statistical significance determined with p < 0.05). Each box extends from the 25th (Q1, lower bound of box) to the 75th (Q3, upper bound of box) percentile, the horizontal line in the center of the box represents the median value (Q2). The whiskers extend to the 5th (min, lower bound) and the 95th percentile (max, upper bound). Dots outside the whiskers indicate outliers. d, Bar plots indicating the relative abundance of T cells by clonality in each paired single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) dataset, split by pathological response. UMAP shows the distribution of cells by clonality. e, Bubble plot indicating the average expression of differentially expressed (DE) genes of T cell clones.
