Mechanisms and dynamics of survival in the treatment of ovarian cancer

High-grade serous ovarian cancer (HGSOC) accounts for up to 80% of deaths from ovarian cancer, and overall survival has not improved much in decades. This is largely due to vast genome instability and genetic heterogeneity in HGSOC which contribute to chemoresistance. This substantial heterogeneity has been shown to result in the presence of rare pre-existing resistant clones in the tumor and the development of acquired resistance. Alongside paclitaxel, mutagenic platinum-based drugs remain the treatment mainstay for HGSOC. While cytotoxic, platinum-based drugs also increase genome instability, heterogeneity and chemoresistance. Such extensive heterogeneity promotes unique evolutionary trajectories that warrant detailed characterizations. In a multi-scale analysis, this dissertation leverages approaches from two disciplines to better understand the mechanisms and dynamics of survival in the treatment of ovarian cancer. The cisplatin-1,2-d(GpG) (Pt-GG) intrastrand cross-link is the major lesion produced by cisplatin and carboplatin and contributes to a predominant C:A mutation signature through the misincorporation of dATP opposite Pt-GG by polymerases such as DNA polymerase β (polβ). Using X-ray crystallography, we report the first structures of polβ misincorporating dATP opposite Pt-GG and demonstrate Pt-GG behaves like an abasic site to promote the misinsertion of dATP in a non-instructional manner, elucidating a molecular mechanism contributing to platinum-induced mutagenesis. We also conduct a systems level study of the clonal dynamics and mechanisms underlying HGSOC survival to chemotherapy using a multi-functional lineage tracing approach, ClonMapper, which combines clonal tracking with single-cell RNA sequencing and clonal isolation for further characterizations. We demonstrate that pre-existing features drive survival of clones, enabling a shift to a treatment-induced cell state characterized by cell growth (mTORC1, TNF-α signaling via NF-κB, Hedgehog signaling, androgen response), stress response (EMT, hypoxia, mitotic spindle, interferon response), and metabolism (glycolysis, oxidative phosphorylation). Genetic features underlie a rapid transition to this cell state in rare clones of one cell line. We also demonstrate successful isolation of a rare pre-existing resistant clone from pre-treatment for genomic and epigenetic characterizations. By harnessing two separate approaches, we gain a more holistic understanding of the mechanisms and dynamics underlying HGSOC survival to chemotherapy and provide insights into improving drug design and therapeutic strategies.Biochemistr