Targeting the Mesenchymal Lineage of Pancreatic Ductal Adenocarcinoma via PP2A Inhibition

Pancreatic ductal adenocarcinoma (PDAC) remains a therapeutic challenge, with the aggressive basal-like/mesenchymal subtype demonstrating pronounced resistance to current standard-of-care chemotherapy. Novel, targeted therapeutic strategies are urgently needed to improve outcomes for these patients. Leveraging CRISPR-Cas9 screens, we identified PP2A’s catalytic subunit, PPP2CA, as a relevant PDAC target. Pharmacological PP2A inhibition (PP2Ai) selectively impaired mesenchymal PDAC growth. To delineate the molecular mechanisms underlying PP2Ai sensitivity, we employed a dual-pronged strategy. Functional characterization of mesenchymal PDAC cells revealed metabolic reprogramming, marked by suppressed oxidative phosphorylation and heightened autophagy, coupled with endoplasmic reticulum stress and subsequent apoptosis induction upon blockade of PP2A. Genome-wide CRISPR screens identified key genetic modifiers of PP2Ai sensitivity, revealing critical roles for transcriptional regulators, mRNA processing, translation, and metabolic pathways. Guided by human expression data implicating PP2A in splicing and transcriptional regulation, we prioritized these interconnected processes for orthogonal validation. Mesenchymal PDAC cells exhibited significantly enhanced splicing following PP2Ai treatment, with skipped exons (SE) representing the most prominently altered splicing event. Notably, we identified enhanced transcriptional elongation upon PP2A inhibition, particularly of short genes, driven by CDK9. Our findings establish a reciprocal regulatory relationship between PP2A and CDK9 that controls the activation of ER stress response factors, particularly the key transcriptional regulator ATF4. Our findings establish PP2A as a promising therapeutic target in mesenchymal PDAC and reveal its critical role in regulating transcriptional elongation. These insights enable both the precise application of PP2A inhibitors and the development of rational combination therapies.