Abstract 4004: Identification of predictive biomarkers of USP1 inhibitor sensitivity using ovarian cancer organoid models
Authors: Ozge Somuncu, Nicholas Ashton, Alexandre A. B. A. da Costa, Sirisha Mukkavalli, Ramya Ravindranathan, Benjamin Lamarre, Huy Nguyen, Lisa Moreau, Joyce Liu, Geoffrey I. Shapiro, Kalindi Parmar, Alan D. D’Andrea
Journal: Cancer Research (2025)

Abstract BRCA1-deficient tumors are unable to efficiently perform DNA repair by homologous recombination (HR) and are dependent on alternative DNA damage response pathways. PARP inhibitors have improved the progression-free survival of HR-deficient ovarian cancer patients in clinical settings. However, PARP inhibitor (PARPi) resistance often develops, and new therapies are required for these patients. USP1 is a deubiquitinating enzyme that controls DNA repair pathways through the deubiquitination of PCNA-Ub and the activation of Translesion DNA Synthesis (TLS). Inhibitors of USP1 result in a strong upregulation of PCNA-Ub levels and a dysregulation of TLS repair. Importantly, USP1 is synthetically lethal in BRCA1-deficient tumors (Lim et al., Mol Cell, 2018), and USP1 inhibitors (USP1is) are currently undergoing clinical development for the treatment of these cancers as monotherapy or in combination with a PARPi. USP1is kill BRCA1-mutated patient-derived ovarian cancer organoids (PDOs) and overcome PARPi resistance in BRCA1-WT PDOs (da Costa et al, Cancer Research, 2024). Sensitivity to USP1i strongly correlates with the accumulation of single strand DNA (ssDNA) gaps in both PARPi-sensitive and PARPi-resistant PDOs. Moreover, knockdown of RAD18, the E3 ubiquitin ligase required for PCNA ubiquitination, results in a reduction in PCNA-Ub levels and a corresponding reduction in ssDNA gaps, and in USP1i resistance. These findings suggest that ssDNA gaps and RAD18 levels in the tumors can predict the sensitivity to USP1 inhibitors. As BRCA1-mutated tumors express high levels of USP1 mRNA, we also investigated the relevance of this biomarker in predicting the sensitivity to USP1 inhibitors. Interestingly, the USP1i sensitivity correlated with increased USP1 mRNA expression, at baseline, in ovarian cancer PDO and patient-derived xenograft-derived organoid (PDXO) models. Similar results were obtained in BRCA1-deficient breast cancer cell line models with acquired PARPi resistance. USP1i sensitive ovarian cancer organoid models retained high USP1 mRNA levels upon PARPi treatment. The specific organoid models that were resistant to PARPi or USP1i monotherapy exhibited up to 40-fold increase in expression of USP1 mRNA and they were sensitive to a combination of USP1i plus PARPi. Taken together, in addition to the accumulation of ssDNA gaps and RAD18 levels, the relative expression of USP1 mRNA is a useful prognostic biomarker for patients who may respond to USP1 inhibitors, either as monotherapy or in combination with PARP inhibitors. These predictive biomarkers will be useful in monitoring the response of ovarian cancer patients enrolled in USP1i plus PARPi clinical trials. Citation Format: Ozge Somuncu, Nicholas Ashton, Alexandre A. B. A. da Costa, Sirisha Mukkavalli, Ramya Ravindranathan, Benjamin Lamarre, Huy Nguyen, Lisa Moreau, Joyce Liu, Geoffrey I. Shapiro, Kalindi Parmar, Alan D. D’Andrea. Identification of predictive biomarkers of USP1 inhibitor sensitivity using ovarian cancer organoid models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4004.