Chemosensitivity associated chromatin conformation changes and genomic cisplatin-DNA adduct distribution

Abstract

Epigenetic changes are associated with the emergence of resistance to DNA damaging, anti-cancer drugs, such as cisplatin; widely used in the treatment of ovarian cancer. However, how chromatin conformation changes during the acquisition of resistance and how this influences cisplatin-DNA adduct formation are poorly understood. We have investigated chromatin conformation in matched sensitive and resistant ovarian cell lines, including lines isolated from high-grade serous ovarian cancer patients before and after the in vivo acquisition of platinum-resistance. ATAC-seq analysis reveals differences in chromatin conformation, with resistant lines showing variation in accessibility at intergenic regions. Furthermore, the loss or gain of super-enhancer elements in the resistant lines corresponded with altered expression of nearby genes. Using a novel assay, Pt-exo-seq, we show genome wide distribution of platinum-DNA adducts distinguish sensitive from resistant lines, even when inducing equivalent levels of platinum-DNA adducts and is associated with chromatin conformation changes and levels of gene expression. Repressed chromatin states were particularly pronounced in the regions showing increased adduct formation in the resistant line, with these regions being frequently intergenic and repetitive. Modulation of chromatin conformation using the HDAC inhibitor Vorinostat causes a global increase in conformation change and an overall increase in platinum-DNA adducts, concomitant with increased sensitivity to cisplatin. These data raise the suggestion that high platinum damage in repressed regions in resistant lines is a mechanism of cell survival in the presence of DNA-damage by acting as a “sink” for platinum molecules. We speculate that cells may tolerate cisplatin-DNA adducts at these sites through mechanisms which may potentiate the structural variation that is a defining feature of ovarian cancer. In combination with the potential for the repair of cisplatin-DNA adducts to induce epigenetic changes, these data provide a link between altered epigenetic states as a driver of drug resistance, the effect of chromatin conformation on DNA adduct distribution, and the epigenetic and genetic consequences of DNA damage and repair. These findings highlight altered genome distribution of platinum-DNA adducts as a key feature of resistant tumour cells and suggest the chemo-sensitising activity of chromatin modifying agents are related to their effect on levels of initial DNA damage and adduct distribution.