a, Change in Ki67 positivity (by immunohistochemistry) comparing paired on- versus pre-treatment biopsies in Es (n = 8) versus NEs (n = 19). Box, median ± interquartile range; whiskers, minimum and maximum. b-c, Differences in pathway activities scored per cell by GSVA pre-treatment in Es versus NEs (b) and on- versus pre-treatment in Es (c). Shown are the top 35 pathways based on absolute t-values obtained by a linear model. d, Violin plots showing GSVA scores for the indicated pathways. Stripes indicate median values. ***P < 0.001 (Benjamini-Hochberg adjusted) and absolute t-value>10 by a linear model. e-f, GSEA of DEGs upregulated on-treatment in cancer cells of Es using hypeR on GO (e) and hallmark gene sets (f). Genes driving enrichment included CD74, HLA-DQA1 (antigen presentation), IDO1 (antigen-dependent T-cell activation), A2M (tumour migration and growth), CXCL10 and CXCL14 (chemoattractant of immune cells), CHI3L1 (IFN production).