Abstract B093: Investigating mechanisms of PARP inhibitor resistance in homologous recombination deficient PDAC using patient-derived organoid models

Abstract PARP inhibitors (PARPi) offer clinical benefit in pancreatic ductal adenocarcinoma (PDAC) with BRCA1/2 mutations (BR-PDAC), but patient responses vary widely, and resistance mechanisms remain undefined in most cases using standard clinical assays. Patient-derived organoids (PDOs) offer a powerful system to study PARPi resistance, as they can be generated from tumors after progression on therapy and enable functional in vitro interrogation of underlying mechanisms. Here, we investigate PARPi resistance in BR-PDAC organoid lines lacking evidence of reversion mutations from clinical sequencing studies. Whole genome sequencing identified large deletions overlapping BRCA2 splice regions in several PARPi-resistant organoid lines. These variants have not been reported in prior BRCA2 reversion studies and were missed by commercial clinical assays in these cases likely due to challenges in detecting structural variants from panel-based next generation sequencing of patient samples with varying tumor cellularity. Long read sequencing confirmed the presence of these variants in the organoid lines, while RNA-seq demonstrated novel splice isoforms created by the deletion variants that restored the open reading frame of BRCA2, albeit with loss of substantial portions of the gene. To test whether these deletions conferred resistance, we used CRISPR interference to deplete BRCA2, which significantly increased PARPi sensitivity, suggesting at least partial restoration of BRCA2 function by these atypical reversion events. RAD51 foci assays demonstrated varying effects of the deletions on homologous recombination repair (HRR), indicating that HRR is not always required for PARPi resistance in BR-PDAC. Future work will include studying the effect of the atypical reversion events on replication fork stability, the other main role attributed to BRCA2 outside of HRR. These findings underscore the value of PDOs in dissecting resistance mechanisms in BR-PDAC and expand our understanding of clinically relevant genetic variants contributing to PARPi resistance. Citation Format: Austin L. Good, Sean O'Connor, Timour Baslan, Kim Reiss Binder, Ben Z. Stanger. Investigating mechanisms of PARP inhibitor resistance in homologous recombination deficient PDAC using patient-derived organoid models abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85 (18Suppl₃): Abstract nr B093.