Synergistic targeting of DNA repair pathways to decipher PARP-inhibitor resistance in ATM-deficient pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is todays 4th leading cause of cancer-associated death in the Western World with an increasing tendency. Ataxia-Telangiectasia Mutated (ATM) is the most frequently mutated DNA-damage repair gene and missense mutations can be found in both sporadic and familiar pancreatic cancer. We previously showed that ATM levels inversely correlate with patient's prognosis and the deletion of ATM in a mouse model of pancreatic cancer (AKC) accelerates tumorigenesis, metastasis and leads to genomically instable tumours. The latter characteristic opens vulnerability for a synthetic lethal attack using Parp inhibitors. However, we faced early resistance and tumour control required additional chemotherapy. In the current study, we systematically performed combinational screening for synergistic routes based on actionable perturbations in the DNA damage response to present an ATM null tailored targeted therapy at low dosage. Synergistic tumour impact was found upon simultaneous inhibition of Parp-, Atr-, and DNA-Pkc-signaling (termed PAD) leading to synthetic lethality in AKC cell lines in vivo and in vitro. Mechanistically, PAD lead to cytokinesis failure, replication folk stalling, Parp trapping, reversal of Atm-induced track lengthening finally leading to p53-mediated apoptosis. Chemical and genetic targeting of ATM together with PAD in human PDAC lines and organoid cultures substantiated these data. Additionally, we elaborated consequences of Parp1 inhibitor resistance within the AKC background. Arising cell clones were aneuploid, highly genomically unstable and underwent epithelial-mesenchymal transition to boost an intrinsically program present in Atm-deficient PDAC. These features were associated with the acquisition of a multi-drug resistant phenotype caused by up-regulation of drug-transporters and de-toxification enzymes. Finally, exome-sequencing identified Drg1 loss as an additional crucial mediator in resistant cells. Thus, we provide coherent understanding of the molecular mechanism occurring upon Atm deletion in PDAC to precisely interfere with tumor characteristic for therapeutic success in mice and men.