PARP inhibitor resistance induces massive genome alterations responsible of the acquisition of multidrug resistance in DNA damage repair-deficient pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is the 4th leading cause of cancer-related death in the Western World. Recent sequencing studies found ATM serine/threonine kinase(ATM)as the most frequently mutated DNA damage repair gene, involved in homologous recombination (HR), in PDAC. We previously showed that ATM loss promotes EMT and genomic instability. In line with the altered genomic integrity of ATM-mutated PDAC, we demonstrated the efficacy of strategies like PARP and ATR inhibition. Moreover, synergy was found upon inhibition of PARP, ATR, and DNA-PK leading to synthetic lethality in ATM-deficient PDAC. Unfortunately, long-term maintenance monotherapy with PARP inhibitor(PARPi) might promote resistance acquisition. We then explored PARPi resistance within the ATM-null background. Several PARPi-resistant AKC(Atm^fl/fl; Kras^G12D;p48^Cre ) cell lines were generatedand characterized. Interestingly, resistance persisted even after olaparib removal. PARPi-resistant AKC (R-AKC) cells exhibited impaired proliferation and increased genomic instability. These observations together with persisting PARPi resistance beyond drug release suggest permanent genome alterations. Thus, we performed a whole exome sequencing (WES) on parental and R-AKCcells. Interestingly, it revealed a higher number of single-nucleotide variants as well as copy number alterations in the resistant ATM-deficient counterparts. Intriguingly, we observed a structural aberration pattern with an amplification of a particular locus called Abcb1amplicon in R-AKC. Numerous genes located at this locus were previously associated with tumorigenesis and multidrug resistance (MDR). RNA-sequencing followed by qPCR validation confirmed that structural amplification patterns in R-AKCcells directly translate into a transcriptional regulation of upregulated MDR genes e.g. Mdr1. WES alsoprovided evidence of clonal evolution during acquired resistance, suggesting that massive genomic instability in the context of HR-deficiency can lead to massive genetic rearrangements favoring PDAC drug resistance and aggressivity.Hence, PARPimonotherapy needs to be monitored with caution, particularly in case of remission as instead of preventing relapse it can trigger a MDR rendering subsequent strategies inefficient.

Publication History

Article published online:
08 September 2020