The current strategy for identifying HGSC precursors in the fallopian tube relies on morphological assessment of the fimbria, which is limited as it examines only a small fraction of the tubal epithelium, potentially missing critical lesions. We propose that brushing epithelium from surgically removed fallopian tubes and assessing aneuploidy and DNA methylation will provide more comprehensive sampling than routine pathology.

A key question is whether all STIC lesions are equivalent or if some can regress, akin to early cervical neoplasms. Our studies will use novel models to investigate if certain amplified genes (e.g., CCNE1, RSF-1, MYC) drive more aggressive tumor biology and can serve as biomarkers for tumors that might benefit from alternative therapies explored in other SPORE projects.

High-grade serous carcinomas (HGSCs) exhibit significant molecular heterogeneity, with CCNE1 amplification being common and linked to platinum resistance and poor survival. The PIs of this SPORE have shown that CCNE1 amplification is an early event in HGSC precursors. Thus, CCNE1-amplified HGSCs pose a major clinical challenge, and this proposal aims to develop treatment strategies for this patient subset.

ZN-c3, a next-generation WEE1 kinase inhibitor, has shown less heme toxicity in Phase I trials than its predecessor, adavosertib. It is now progressing to a Phase II clinical trial for HGSC, led by Dr. Simpkins. Our hypothesis is that WEE1 inhibitors (WEE1i) will be effective against CCNE1-overexpressing HGSCs and that additional molecular alterations will enhance responsiveness. We will evaluate CCNE1 as a biomarker for WEE1i response using clinical trial samples, assessing whether CCNE1 gene copy number or protein levels are more reliable predictors.

Additionally, we will explore if circulating tumor DNA (ctDNA) can measure tumor CCNE1 copy number and identify sensitivity biomarkers using whole genome cfDNA analysis (DELFI), whole exome, and RNA sequencing. Although WEE1i monotherapy is expected to be effective, we hypothesize that resistance will emerge, and that combining WEE1i with ATR inhibitors (ATRi) will overcome this resistance in CCNE1-amplified HGSCs. We will test the WEE1i-ATRi combination using annotated PDX and organoid models.

Furthermore, we expect DNA repair factors recruited to replication forks following WEE1i and ATRi treatment to impact drug responsiveness and serve as potential biomarkers. These factors will be identified using iPOND2-QMS in CCNE1-amplified WEE1i-resistant cells. These studies aim to uncover mechanisms of drug resistance and identify high-priority biomarkers for future clinical trials.

While less common than high-grade serous carcinoma, advanced ovarian clear cell and endometrioid carcinomas have the poorest 5-year survival rates for advanced-stage disease among all subtypes. Chemotherapy response rates for these patients are below 10%, and approximately 1% in recurrent cases, highlighting a dire unmet medical need.

ARID1A mutations are common in ovarian clear cell carcinoma and are linked to chemotherapy resistance. Our recent studies show that these mutations impair DNA double-strand break repair. Although ARID1A mutant ovarian clear cell carcinomas are not typically sensitive to PARP inhibitors (PARPi), we identified that alkylating agents like temozolomide (TMZ) exhibit synergistic anti-tumor activity with PARPi. TMZ-induced methylated DNA lesions are repaired by DNA base excision repair (BER), and our data indicate that ARID1A-deficient cells struggle to resolve these lesions, leading to enhanced replication fork stalling and collapse when combined with PARPi.

We hypothesize that in ARID1A mutant cells, TMZ-induced methylated DNA lesions and single-stranded DNA breaks increase reliance on PARP1. We will test this using isogenic ARID1A mutant and knockout cells, examining replication perturbations from TMZ/PARPi treatment. Additionally, we will investigate if BER inhibitors sensitize ARID1A wild-type tumors to PARPi combined with TMZ.

Finally, we will evaluate the clinical efficacy of the TMZ and PARPi (senaparib) combination in a Phase II trial for ARID1A mutant ovarian clear cell and endometrioid carcinomas. This will be the first study to focus on this combination in tumors with ARID1A mutations.

The Career Enhancement Program provides funding and support to promising young investigators to help facilitate their early career development and build a firm foundation for their future leadership in the translational ovarian cancer research field. Secondarily, the program will also support established investigators who want to redirect their research efforts to translational ovarian cancer research.

The Developmental Research Program provides funding for pilot studies with potential for development into large-scale translational research projects, collaborations, and new methodologies that may be integrated into other existing projects. This program is a major focus of the SPORE because it encourages the flow of innovative ideas and new research efforts that may emerge within the context of SPORE research.