DNA base modifications are key epigenetic markers that regulate gene expression. Among these modifications, 5-methylcytosine (5mC) in gene promoter regions is a crucial regulator of expression for certain genes. In high-grade serous ovarian carcinoma (HGSOC), BRCA1 gene silencing due to promoter methylation is observed in approximately 7-17% of cases. The resulting BRCA1 deficiency is associated with response to PARP inhibitors (PARPi), an important class of targeted therapies for ovarian cancer. However, loss of BRCA1 methylation under therapeutic pressure can reactivate BRCA1 expression, contributing to PARPi resistance.
Despite its clinical relevance, BRCA1 methylation is not thoroughly characterised in HGSOC, largely due to the lack of suitable models and the limitations of conventional methods, such as bisulfite sequencing, which requires DNA bisulfite conversion and does not differentiate between 5mC and 5-Hydroxymethylcytosine (5hmC), the second most prevalent DNA base modification. Recent advances in Nanopore sequencing offer a promising solution by enabling comprehensive profiling of multiple types of base modifications while simultaneously capturing DNA sequence alterations.
Here, we used Nanopore’s long-read direct DNA whole-genome sequencing to investigate five cell line models and eight xenograft models with varying levels of BRCA1 promoter methylation and PARPi resistance. We profiled these models for additional, less abundant DNA base modifications, including 5hmC, N6-Methyladenine (6mA) and 4-Methylcathinone (4mC). Our analysis did not identify consistent global base modification patterns associated with BRCA1 methylation loss. However, by integrating DNA sequence information with base modification data, we identified in-cis DNA sequence alterations that may be linked to methylation loss.
Our findings provide insights into the heterogeneous mechanisms underlying BRCA1 methylation loss in HGSOC. Future studies should focus on validating the relationship between the identified DNA sequence alterations and BRCA1 methylation loss to further understand their role in acquired PARPi resistance.