The vulnerabilities of chemotherapy resistant pancreatic cancer revealed by organoids of pre- and post-neoadjuvant therapy.

Pancreatic ductal adenocarcinoma (PDAC) remains highly lethal due to intrinsic and acquired chemotherapy resistance, particularly after neoadjuvant therapy (NAT). To uncover therapy-induced vulnerabilities, we established matched patient-derived organoids from PDAC tissues obtained before and after NAT, creating a unique platform to track treatment-driven evolution. Comparative analysis of these organoids revealed negligible variation in key driver gene mutations but identified a transition from classical to basal-like subtype in one patient after neoadjuvant therapy. Notably, albumin-bound paclitaxel and gemcitabine (AG) treatment induced the resistance to paclitaxel, accompanied by elevated KRAS and MAPK signaling, which was confirmed by transcriptomic comparison of PDAC patient samples with (30 cases) and without (60 cases) AG treatment. Single-cell RNA sequencing of the organoid-derived xenografts revealed AG treatment promoted the emergence of resistant cell clusters characterized by KRAS and MAPK signaling activation. Importantly, EGFR/KRAS/BRAF signaling inhibitors effectively suppressed the growth of AG-resistant PDAC organoids. In a validation cohort of 29 organoids, pan-KRAS inhibitors exhibited superior efficacy against the residual organoids after AG treatment. These results provided insights into molecular changes in PDAC during treatment process and demonstrate that AG chemotherapy can activate the KRAS and MAPK signaling, presenting a potential target for therapeutic intervention.