Fig. 2: Changes in mutation and DNA methylation at secondary resistance.

A Overview of mutated cancer genes (according to OncoKB) and recurrently mutated genes gained or lost at secondary resistance compared with baseline for each patient. Acquisition of AC03 signature (BRCAness) is indicated in the upper row. VAF, variant allele frequency. B Comparative heatmap displaying methylated CpG sites for each patient at treatment start (t1) and resistance (t2). Group-wise differential analysis to show methylation changes between baseline (t1) and resistance (t2). The x-axis represents individual patients, and the y-axis corresponds to CpG sites showing hypomethylation. Patients are grouped by treatment (as indicated). C Genomic distribution of differentially methylated CpGs. Hypomethylated sites were annotated based on their genomic context and assessed for their enrichment relative to the overall distribution of these regions in the EPIC array. Enrichment of hypomethylated CpGs of the intergenic region can be seen, as well as depletion of hypomethylation in the TSS200 promoter regions. D Identification of shared hypomethylated CpGs across patients. Significant non-random overlap of hypomethylated CpGs (p value 7.03E-09). Blue lines are random CpGs from the EPIC array, whereas the black lines are CpGs commonly hypomethylated across patients. Of overall 208, 248 hypomethylated CpGs, 21,235 were consistently hypomethylated in >50% of patients. ATRA all-trans retinoic acid, DEC decitabine, VPA valproic acid.