Fig. 4: Treatment induced transcriptomic changes.

A Alterations in PAM50 subtypes throughout treatment. B Unique and shared, upregulated and downregulated, DEGs (adj. P-value < 0.05 and log twofold change > 1 or < −1) across C1D15 versus baseline timepoints in Resistant and Sensitive patients. C Notable cell cycle genes significantly downregulated at C1D15 versus baseline in Sensitive but not Resistant samples. Left panels represent all samples at each timepoint with two-tailed Mann–Whitney U test; n = 13 baseline S, 19 C1D15 S 7 baseline R, 9 C1D15 R. Dashed line denoting mean expression. Right panels represent paired samples throughout treatment with Wilcoxon match-pairs signed rank test; n = 12 S and 4 R. D Hallmark GSEA analysis of C1D15 versus Baseline samples in Sensitive and Resistant tumors. E Density plot of genes in pathways of interest. Z-scores were calculated for each gene across Sensitive and Resistant tumors at Baseline and C1D15 timepoints followed by plotting of mean group expression of each gene.