Use of DNA-alkylating pyrrole-imidazole polyamides for anti-cancer drug sensitivity screening in PDAC

Activating mutations of the KRAS gene are found in >90% of pancreatic ductal adenocarcinoma (PDAC) cases. However, direct pharmacological targeting of the activated KRAS protein has been challenging. We previously reported that KR12, a DNA-alkylating pyrrole-imidazole polyamide designed to recognize the KRAS G12D/V mutation, showed an anti-tumor effect in colorectal cancer. In this study, we evaluated the anti-tumor effect of KR12 in PDAC. We found that KR12 inhibited tumor growth in a spontaneous PDAC mouse model, although the anti-tumor activity appeared to be limited in a human PDAC xenograft model. We developed a pyrrole-imidazole polyamide screening process based on the hypothesis that genetic elements otherwise unaffected by KR12 could exert attenuating effects on KRAS-suppression-resistant PDAC. We identified RAD51 as a potential therapeutic target in human PDAC cells. A RAD51 inhibitor showed an inhibitory effect on cell growth and affected the cytotoxic activity of KR12 in PDAC cells. These data suggested that the simultaneous inhibition of RAD51 and mutant KRAS blockage would be an important therapeutic strategy for PDAC. KP-4 cells were plated overnight prior to the administration of polyamide (100 nM) for 12 h. DMSO (0.01%) was used as control. According to the instructions provided by the manufacturer, cells were lysed for RNA extraction using the RNeasy Plus Mini Kit (Qiagen), and sample replicates were labeled with the RNA Spike-In Kit to be analyzed by SurePrint G3 Human GE 8x60K V2 expression microarrays (Agilent). Differential expression analyses were performed with our previously developed custom R workflow (Lin et al PLoS ONE 14:e0215247, 2019).