Abstract B039: APEX2 is a synthetic lethal target for RNASEH2B-deleted or BRCA-mutant tumors

Abstract The genomic regions surrounding tumor suppressor genes are often lost as collateral damage during tumorigenesis, providing novel therapeutic vulnerabilities. To systematically identify synthetic lethal pairs of genes within DNA damage repair (DDR) pathways, we conducted a combinatorial genome-wide CRISPR screen. We found that RNASEH2B, a gene frequently co-deleted with RB1 in prostate cancers, emerged as a top vulnerability with knockout of APEX2, which is a nuclease involved in DNA repair. This interaction was validated in RNASEH2B isogenic cell line pairs using whole-genome CRISPR screens and further confirmed across multiple cancer lineages using a focused mini-pool sgRNA library. Single gene knockouts demonstrated that loss of APEX2, specifically its catalytic activity, is sufficient to eliminate RNASEH2B mutant cells both in vitro and in vivo. Importantly, loss of RB1 did not impact the synthetic lethal interaction between RNASEH2B and APEX2. Consistent with prior reports, APEX2 knockout also impairs growth of BRCA1 mutant cells and enhances sensitivity to PARP inhibitors. Overall, these findings position APEX2 as a compelling synthetic lethal target in tumors with RNASEH2B deletion or BRCA1 mutations and support the development of APEX2 inhibitors as a potential monotherapy to improve patient outcome. Citation Format: Antoine Simoneau, Steve Lombardo, Ruthie Swain, Serge Gueroussov, Binzhang Shen, Shangtao Liu, Samuel R. Meier, Gwen Cusing, Ashley H. Choi, Tenzing Khendu, Hannah Stowe, Hsin-Jung Wu, Hongxiang Zhang, Douglas A. Whittington, Yi Yu, Jannik N. Andersen, Teng Teng. APEX2 is a synthetic lethal target for RNASEH2B-deleted or BRCA-mutant tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr B039.