Fig. 4

RCT increases the abundance of CD16_NK cells with cytotoxic features, while T-cell subclusters show decreased cytotoxic features. a UMAP visualization of 12 lymphocyte subclusters in all (left panel), pre-RCT (middle panel), and post-RCT (right panel) samples. b Bar plot showing the relative abundance of 12 subclusters in all lymphocytes in pre/post-RCT samples. c Box plot showing the fold change in the abundance of CD16_NK and CD56_NK cells post-RCT. The p values correspond to the paired Wilcoxon tests. d Representative images of IHC staining of CD16 in paired pre-RCT and post-RCT FFPE tissues. Scale bar, 50 μm. e Box plot showing the fraction of CD16⁺ NK cells in paired pre-RCT and post-RCT samples based on IHC results in d. The p value corresponds to the paired t test. f Box plot showing gene expression of CD16 in pre-RCT and post-RCT bulk RNA-seq data. The p value corresponds to the paired t test. g Volcano plots showing the gene expression changes in NK cells pre- and post-RCT. The colored dots represent the top most variable genes. h GO term analysis of NK cells in pre-RCT versus post-RCT samples. i Heatmap showing the relative changes in cytotoxic and inhibitory signature gene expression in all NK cells and individual NK cell subclusters between pre- and post-RCT groups. The intensity of the color indicates the extent of upregulation in post-RCT (red) or pre-RCT (blue) samples. j Kaplan-Meier analysis of overall survival in 295 TCGA bulk RNA-seq data of patients with CC, separated by high and low expression of cytotoxic genes. The p values correspond to the log-rank tests. k Bar plots showing the fold change in the abundance of 10 T cell subclusters in pre/post-RCT samples. The colors of dots and squares represent patients and sample groups, respectively. The p values correspond to the paired Wilcoxon tests. l Heatmap showing the changes in the expression level of cytotoxic and inhibitory signature genes in all T cells and T cell subclusters between pre- and post-RCT groups. The intensity of the color indicates the extent of upregulation in post-RCT (red) or pre-RCT (blue) samples