Fig. 3
Post-treatment enrichment of resistance markers. The non-luminal A subtype (A), HRD-H cluster (B), and proliferative cluster (C) were enriched in PD compared to baseline (Fisher’s exact test: p = 0.0084 for subtype; p = 0.054 for HRD cluster; p = 0.035 for proliferative cluster). Comparing the changes in HRD index, proliferative index, and S13 mutation signature at BL vs. PD among all samples (D) and longitudinally paired samples (E). The non-luminal A subtype (A), HRD-H cluster (B), and proliferative cluster (C) were enriched in PD compared to baseline (Fisher’s exact test: p = 0.0084 for subtype; p = 0.00314 for HRD cluster; p = 0.06351 for proliferative cluster). Comparing the changes in HRD index, proliferative index, and S13 mutation signature at BL vs. PD among all samples (D) and longitudinally paired samples (E). F Sankey diagram showing the switching of subtypes from luminal A at BL into HER2E or luminal B subtypes at PD. Comparing the changes in E2F targets signature (G), estrogen response early signature (H), and S13 mutation signature (I) between paired BL and PD tumors among the three groups of patients. To-HER2E: subtypes switched to HER2E at PD. To-LumB: subtypes switched to luminal B at PD. No-Switch: subtypes remained the same between BL and PD. GSVA: signature scored calculated by gene set variation analysis