Abstract 2012: Extrachromosomal DNA promotes drug resistance in pancreatic ductal adenocarcinoma cells
Authors: Vorberg Tim , Reitberger Manuel , Rodriguez-Martin Bernardo , Starostecka Maja , Kossi Ornella , Vogel Vanessa , Korbel Jan , Trumpp Andreas , Sprick Martin 
Published: March 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related deaths in Western Countries and has been predicted to become the second leading cause of cancer-related deaths by 2030. Difficulties in early detection as well as strong chemoresistance of the disease prevent the successful treatment of PDAC patients. Although we have previously identified CYP3A5 as a mediator of paclitaxel resistance, further targets remain elusive. Thus, we set out to identify these CYP3A5-independent mechanisms which could lead to the identification of novel biomarkers and drug targets to improve PDAC treatment. For this project, pancreatic cancer cell lines were derived from treatment-naive PDAC samples and exposed to increasing paclitaxel concentrations to induce resistance. The cells were characterized on a genomic and transcriptomic level using short-read sequencing as well as optical mapping to characterize potential candidate genes in vitro. In our results, multi-drug resistance protein 1 (ABCB1) was highly upregulated in our differential gene expression analysis and confirmed as a CYP3A5-independent mediator of acquired paclitaxel resistance. Its overexpression was mediated by extrachromosomal DNA (ecDNA) amplifications upon drug treatment. These circular DNAs were characterized by short-read sequencing as well as long-read optical mapping, which revealed the structures of the most abundant molecules. Furthermore, we investigated the biogenesis of the ecDNA. Current models propose different events such as chromothripsis or breakage-fusion-bridge cycles to initiate ecDNA formation, however, knowledge about the underlying mechanisms remains limited. To study the ecDNA dynamics, we generated ecDNA-negative cell clones from a paclitaxel resistant PDAC cell line. Interestingly, our clonal cell population appears to show the capacity for ecDNA de novo generation and quickly adapts to changing selective pressure such as therapy. This finding might unveil new insights into the triggers of ecDNA formation and its dynamic regulation. In conclusion, our results suggest the clinical relevance of ABCB1 as a mediator of paclitaxel resistance in PDAC and we currently validate our findings in patient samples. However, ABCB1 inhibition is associated with severe side effects. Instead, the regulatory pathways associated with enhanced ABCB1 expression and the formation of ecDNAs might provide therapeutic potential. Additionally, the characterization of ecDNA de novo generation might unveil new insights into how cancer cells adapt to changing selective pressures.
Citation Format: Tim Vorberg, Manuel Reitberger, Bernardo Rodriguez-Martin, Maja Starostecka, Ornella Kossi, Vanessa Vogel, Jan Korbel, Andreas Trumpp, Martin Sprick. Extrachromosomal DNA promotes drug resistance in pancreatic ductal adenocarcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2012.