CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target Cleavage and Polyadenylation Specificity Factor 3 (CPSF3), the 3' endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of non-transformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional read-through in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC. Overall design: For the knockdown experiment, Panc1 cells were infected with lentivirus harboring pLKO.1-shNTC (non-targeting control) and pLKO.1-shCPSF3 at 40% confluency. Polybrene was used to increase the efficacy of infection. After 72 hours, cells were selected with 2.5µg/ml puromycin. Cells were then collected for RNAseq.For drug treatment, Panc1 cells were treated with DMSO control or 10uM of JTE-607 for 24 hours then cells were collected for RNAseq.3 biological replicates were used for each condition.