Abstract

High grade serous ovarian carcinoma (HGSOC) is an aggressive, highly lethal subtype of ovarian cancer. These cancers are typically diagnosed in later stages and are associated with poor patient prognosis. Additionally, HGSOC is characterized by numerous markers of genomic instability and defects in DNA repair pathways, vulnerabilities which have been exploited by the advancement of chemotherapy. Despite these clinical advancements, HGSOC remains a significant therapeutic challenge due to emergence of chemoresistance and limited targeted treatment options. Taken together, these factors highlight an ongoing need to study the development of HGSOC and its progression to identify more effective treatment opportunities. We aimed to investigate how replication stress and genome instability contribute to ovarian cancer through three distinct but interconnected approaches. First, we aimed to understand how to enhance sensitivity to a targeted therapy in a subset of breast and ovarian cancers that have mutations in BReast CAncer genes 1/2 (BRCA1/2). Specifically, we investigated the mechanism by which the loss of the chromatin remodeler, Amplified in Liver Cancer 1 (ALC1), can modulate hypersensitivity to a common targeted therapy, poly (ADP-ribose) polymerase inhibitors (PARPi), in BRCA-mutant cancers. We showed that without ALC1, the endonuclease APE1 cannot access and process abasic sites buried in the chromatin, hindering repair. These unrepaired abasic lesions accumulate until DNA replication opens the chromatin, allowing for APE1 endonuclease activity. Cleavage of these sites results in fork breakage and upon PARPi treatment, PARP1/2 enzymes are trapped at these lesions, which results in hypersensitivity. We showed that this replication-associated damage can be exploited to improve PARPi response in ALC1-deficient BRCA-mutant cancers. Next, we examined a different subset of HGSOC, which are the cyclin E1-high cancers. Since cyclin E1 is expressed very early on in the development of HGSOC, we engineered a physiologically relevant model of cyclin E1-high precursor cells to examine the initiating replication-associated events that drive early disease progression. Utilizing DNA fiber and immunofluorescence microscopy assays, we characterized replication-associated defects and markers of genomic instability. Consistent with previous literature, we examined an increase in replication origin firing in cyclin E1-high cells. Notably, we identified a role for the histone methyltransferase, SETD2, in this phenotype. We observed that increased replication origin firing was rescued upon the loss of the histone methyltransferase, SETD2, specifically in cyclin E1-high contexts. Our findings point to a potential hypothesis identifying SETD2-mediated histone marks that support E2F-regulated transcription of origin firing genes. Through this work, we uncovered a novel role of SETD2 and provided a potential target to treat cyclin E1-high cancers. Finally, we observed that in these early contexts, cyclin E1-high cells display a highly deleterious phenotype termed endoreduplication, a process by which cells bypass mitosis and continue to replicate with double the amount of DNA. In contrast to previous reports however, we examined that our physiologically relevant precursor cell line displayed this phenotype even with the loss of the tumor suppressor protein, p53. We aimed to determine the mechanism of this p53-independent process, uncovering a pathway that can be further examined to prevent tumorigenesis of this deadly disease.

Committee Chair

Priyanka Verma

Committee Members

Amber Stratman; Gabor Egervari; George Souroullas; Katherine Weilbaecher; Priyanka Verma

Degree

Doctor of Philosophy (PhD)

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

6-11-2026

Language

English (en)

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