Regulation of ABCB1 expression is a potential therapeutic target in drug resistant pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive and lethal disease with a miserable prognosis. Chemotherapeutic regimens, like FOLFIRINOX or gemcitabine plus nab-paclitaxel remain the standard treatment of care in patients diagnosed with PDAC while only achieving a modest increase in overall survival. Transcriptional subtyping of PDAC discerns tumors into two broad lineages which provides the opportunity to improve patient stratification and treatment, but has not been translated into clinical practice yet. Meanwhile, resistance to chemotherapy continues to be the limiting factor that prevents a patient’s cure from cancer and finding improved therapeutic options could overcome resistance of PDAC to current treatment regimens. With our previously established culturing model for patient-derived PDAC cells, we could investigate the development of resistance to paclitaxel and/or gemcitabine in the different subtypes. We developed a long-term treatment regime that enabled the generation of drug-resistant cells which were analyzed in a multi-omics approach. ATP-binding cassette (ABC) transporter B1 (ABCB1), a membrane-bound glycoprotein that is predominantly expressed in excretory tissue and a common resistance mechanism against paclitaxel in various tumor entities, was found to be overexpressed in all paclitaxel-resistant cells. CRISPR/Cas9-guided knockout and pharmacological inhibition re-sensitized these drug resistant cancer cells to paclitaxel. We found ABCB1 to be heterogeneously expressed in the paclitaxel resistant cell population and expression was lost after prolonged absence of paclitaxel treatment. Short-term drug treatment dynamically increased the proportion of ABCB1-expressing cells in former paclitaxel resistant cell population, re-acquiring paclitaxel-resistance. In of the paclitaxel resistant cell lines, expression of ABCB1 was further enhanced by de novo generation of extrachromosomal DNA (ecDNA), carrying the ABCB1 gene. Similar to ABCB1 gene expression, number ecDNA inside paclitaxel resistant cells was dynamically increased upon paclitaxel treatment. These findings describe a dual mechanism for acquired ABCB1 expression that is dependent on paclitaxel treatment and leads to the induction of ABCB1 expression and amplification of ABCB1-carrying ecDNA