Abstract ND01: KSQ-4279: A first-in-class USP1 inhibitor for the treatment of cancers with homologous recombination deficiencies

Abstract

Tumors with BRCA1/2 mutations and other homologous repair deficiencies (HRD) are vulnerable to agents that target the remaining DNA repair pathways, including platinum-containing chemotherapy agents and molecules targeting poly (ADP-ribose) polymerase-1 (PARP1). Despite the clinical benefit achieved with these drugs, many patients achieve incomplete disease control and resistance often emerges. With the goal of addressing this clinical need, we applied our proprietary CRISPRomics technology to identify novel targets in cancer indications characterized by defects in DNA repair pathways. One of the top ranked targets was the deubiquitinating enzyme USP1. USP1 has established roles in DNA damage repair processes including Translesion Synthesis and the Fanconi Anemia pathway. We developed KSQ-4279, a potent, highly selective inhibitor of USP1. KSQ-4279 was active in cells, leading to the accumulation of mono-ubiquitinated substrates of USP1 and inhibited the proliferation of cancer cell lines with BRCA mutations or other HRD alterations. Studies investigating the effect of combining KSQ-4279 with PARP inhibitors revealed clear evidence of synergy in cell lines with partial or no sensitivity to each agent alone. To investigate how the distinct mechanisms of action of KSQ-4279 and PARP inhibitors would be reflected in their resistance profiles, we used our CRISPRomics technology to perform functional genomic resistance screens. The top scoring resistance genes for KSQ-4279 were distinct from those identified for PARP inhibitors, which raised the possibility that combining PARP and USP1 inhibitors may provide more durable disease control by reducing the emergence of resistance. Evaluation of KSQ-4279 in patient-derived ovarian and triple-negative breast cancer xenograft models demonstrated dose-dependent tumor growth inhibition as a single agent and in combination with PARP inhibitors. In xenograft models that were insensitive or only partially sensitive to PARP inhibitors, the combination of KSQ-4279 and Olaparib led to tumor regressions and durable tumor control. This data supports the ongoing clinical trial of KSQ-4279 in patients with tumors harboring BRCA1/2 or other HRD mutations, both as a single agent and in combination with PARP inhibitors. Citation Format: Louise Cadzow, Erica Tobin, Pamela Sullivan, Sol Shenker, Sumeet Nayak, Janid Ali, Hugh Gannon, Anne Dodson, Paula Grasberger, Alyssa Carlson, Michael McGuire, Jehrod Brenneman, Hanlan Liu, Andrew Olaharski, Kerstin Sinkevicius, Jeff Hixon, Elsa Krall, Mike Schlabach, Matt Goulet, Jeremy Wilt, Patricia Harris, Frank Stegmeier, Andrew Wylie. KSQ-4279: A first-in-class USP1 inhibitor for the treatment of cancers with homologous recombination deficiencies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr ND01.

USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress

“…This was confirmed using the S1 nuclease DNA fiber combing assay in HeLa-PRIMPOL OE cells (Figure 4E ). Finally, we validated these results using another USP1 small molecule inhibitor, namely KSQ-4279, which selectively inhibits USP1 activity ( 65–67 ). Treatment with KSQ-4279 also suppressed ssDNA gap accumulation in PRIMPOL-overexpressing HeLa cells upon both cisplatin and HU treatment as measured by the BrdU alkaline comet assay, in a dose-dependent manner ( Supplementary Figure S4A, B ).…”