Abstract B129: Tracking genome evolution and chemoresistance in pancreatic cancer

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is projected to become the second leading cause of cancer-related death within the next decade. Population-scale genomic analyses of PDAC tumors have revealed extensive chromosomal instability (CIN), indicating high levels of genomic diversification that may influence therapy response. However, the mechanisms driving CIN during PDAC progression and its role in treatment response remain poorly understood. We hypothesize that specific patterns of genomic rearrangements emerging during PDAC evolution can inform two key aspects of tumor biology: (i) the underlying processes driving CIN, which may be therapeutically targetable, and (ii) subclonal CIN signatures that predispose tumors to develop chemoresistance. Methods: To investigate the dynamics of CIN and chemoresistance, we employed an in-house single-cell clonal outgrowth assay integrated with single-cell whole-genome sequencing (sc-WGS) and mathematical modelling of clonal growth. Experiments were performed in PDX-derived primary cultures and patient-derived 3D organoids. We tracked clonal outgrowth under both untreated conditions and following exposure to chemotherapeutic agents relevant to PDAC treatment. Comparative analyses of single-cell copy number profiles between parental populations and drug-exposed clones allow us to identify any de novo genomic alterations acquired during treatment, as well as pre-existing events enriched by drug selection. Results: We observed ongoing CIN in PDAC cells, leading to continuous generation of new CNAs and enhanced cell-to-cell genomic diversity. Our data demonstrate pronounced heterogeneity in copy number states and growth dynamics among individual clones from the same cell line. This intrinsic heterogeneity provides a reservoir for evolutionary selection and may promote the emergence of drug-resistant phenotypes. We were able to analyse which clones carried pre-existing alterations and/or which generated new ones under the pressure of chemotherapy, allowing us to understand the diversity of responses and general principles of CNA changes in response to therapy. These findings underscore the innate adaptability of PDAC cells under therapeutic pressure. Conclusion: Our study highlights the dynamic nature of CIN in PDAC and its critical role in promoting chemoresistance. The identification of specific genomic alterations enriched in resistant subclones could offer potential biomarkers predictive of therapy response. This approach provides new insights into the interplay between CIN, cell-to-cell heterogeneity, and therapeutic adaptation, with potential future implications for guiding personalized treatment strategies in PDAC. Citation Format: Audrey Lumeau, Molly Anne. Guscott, Nathaniel Mon Pere, Isabel Nichols, Benjamin Werner, Nelson Dusetti, Sarah E. McClelland. Tracking genome evolution and chemoresistance in pancreatic cancer 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 B129.