Abstract 2904: Synthetic lethal relationship between pharmacologic PARP inhibition and loss of LIG1 in chordoma

Abstract Impaired homologous recombination (HR) repair of DNA double-strand breaks (DSB) renders cancer cells sensitive to poly(ADP-ribose) polymerase inhibitors (PARPi). This synthetic lethal relationship is used to treat several epithelial cancers. However, the efficacy of PARPi is often limited by primary or acquired resistance, which might be overcome by rational combination therapies. We previously observed that most patients with advanced chordoma, a spinal neoplasm with no standard treatments, show genomic imprints of HR deficiency without mutations in HR-related genes such as BRCA1/2 or PALB2. Notably, a patient with HR-deficient, refractory chordoma responded to the PARPi olaparib for 10 months before developing resistance through a secondary PARP1 mutation (PMID: 30967556). To identify genes whose depletion increases the sensitivity of chordoma cells to olaparib, we conducted a genome-wide CRISPR/Cas9 screen in a patient-derived chordoma cell line (UM-Chor1). We identified several strong synthetic lethal interactors whose depletion conferred higher sensitivity to olaparib than knockout of BRCA1. These included LIG1, encoding an ATP-dependent DNA ligase involved in Okazaki fragment maturation and base excision repair, and PRDX1, encoding an enzyme that mitigates oxidative stress by neutralizing reactive oxygen species (ROS). Functional validation showed that LIG1 knockout alone had only a minor effect on chordoma cell lines. In contrast, its combination with olaparib induced significant toxicity, associated with increased DSB, as determined by γH2AX staining, G2/M cell cycle arrest, and apoptosis. Furthermore, the screening results could be recapitulated with the second-generation PARPi talazoparib. Proteome analysis of LIG1-depleted, olaparib-treated chordoma cells revealed significant downregulation of proteins involved in DNA repair and oxidative phosphorylation. Concomitant phosphoproteome profiling identified increased kinase activity in pathways responsive to ROS, DNA damage, and apoptosis. Proteomic analysis of nuclear fractions revealed that olaparib treatment of LIG1-depleted cells upregulated the E3 ligase TRIM4, which collaborates with PRDX1 to mediate cell death caused by oxidative stress. Consistent with this, we observed significant ROS induction in LIG1-depleted, olaparib-treated cells. In summary, our integrated genomic and proteomic analysis revealed that LIG1 loss enhances the effect of PARPi in chordoma cells, suggesting a potential strategy for combination therapies. Further investigation is required to determine if LIG1 is a viable therapeutic target and to unravel the mechanisms underlying olaparib-induced cell death in LIG1-deficient chordoma cells. This process may be influenced by the collaborative roles of TRIM4 and PRDX1, offering avenues for future research. Citation Format: Kwang Seok Lee, Tatjana Walther, Stefanie Reinhart, Lena Wickenhäuser, Christina Schniederjohann, Maria Frolova, Dominic Helm, Schneider Martin, Mikolaj Slabicki, Claudia Scholl, Stefan Fröhling. Synthetic lethal relationship between pharmacologic PARP inhibition and loss of LIG1 in chordoma [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 2904.