Abstract 1803: Dynamic copy number changes and de novo generation of extrachromosomal DNA modulate therapy resistance.

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Abstract Extrachromosomal DNA (ecDNA) is increasingly recognized as a driver of cellular plasticity, yet its role in therapy adaptation in pancreatic ductal adenocarcinoma (PDAC) remains poorly defined. In patient-derived PDAC models, we identify extrachromosomal ABCB1 amplification as a mechanism of resistance to paclitaxel and KRAS inhibitors and show that ABCB1 copy number dynamically adjusts to selective pressure. Notably, paclitaxel-resistant cells remain primed for rapid de novo ecDNA generation: after eliminating pre-existing ABCB1 ecDNA through single-cell cloning, new and structurally distinct ABCB1 ecDNA rapidly emerges, indicating treatment-induced molecular changes that prime these cells for ecDNA formation. In metastatic breast cancer, taxane-associated ABCB1 amplification is likewise observed and can be tracked in cell-free DNA (cfDNA), underscoring clinical relevance beyond PDAC. Finally, gemcitabine co-treatment suppresses ABCB1 ecDNA generation, suggesting potential strategies to counteract ecDNA-mediated resistance. Together, these findings demonstrate that dynamic ecDNA modulation and inducible ecDNA biogenesis enable rapid, reversible drug resistance, providing a rationale for ecDNA-targeted combination therapies and longitudinal monitoring. Citation Format: Tim Vorberg, Manuel Reitberger, Bernardo Rodriguez Martin, Maja Starostecka, Dominique Schulz, Arlou K. Angeles, Kate I. Glennon, Tasneem Cheytan, Roberto Würth, Vera Thiel, Paul Schwerd-Kleine, Verena Thewes, Laura Michel, Ewgenija Gutjahr, Simon J. Ogrodnik, Heike Conrad, Steffi O. Mehlhorn, Vanessa Vogel, Corinna Klein, Albrecht Stenzinger, Peter Lichter, Andreas Schneeweiss, Martin Granzow, Marc Zapatka, Anna Jauch, Holger Sültmann, Jan Korbel, Andreas Trumpp, Martin R. Sprick. Dynamic copy number changes and de novo generation of extrachromosomal DNA modulate therapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1803.

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