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

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options. This potentiates the importance of uncovering novel drug targets. We have discovered global dysregulation of the gene regulatory process alternative polyadenylation (APA) in PDAC. APA is a pre-mRNA processing mechanism that generates mRNAs with distinct 3’ ends, impacting gene expression and protein function. We revealed that APA dysregulation in PDAC drives oncogenic signatures and predicts poor patient outcome. As APA directs widespread gene expression dysregulation across the PDAC patient population, we hypothesized that inhibition of APA has therapeutic potential. APA is controlled by a complex of proteins, including cleavage and polyadenylation specificity factor 3 (CPSF3). CPSF3 is the endonuclease catalyzing mRNA cleavage, and a potentially druggable target. We now find that CPSF3 is highly expressed and associated with poor prognosis in PDAC patients. CPSF3 knockdown decreases PDAC proliferation and clonogenicity in vitro and tumor growth in vivo. We demonstrate that CPSF3 knockdown induces widespread APA alterations of oncogenes and tumor suppressors, and determine the contribution of one of these events to CPSF3-induced cell proliferation phenotype. Furthermore, we find that PDAC, but not non-transformed pancreatic cells, are sensitive to the CPSF3 small molecule inhibitor JTE-607. Mechanistically, JTE-607 impairs replication-dependent histone processing, disrupting nucleosome assembly and destabilizing chromatin structure. Finally, we determine that JTE-607 attenuates cell proliferation by arresting cells in early S-phase of the cell cycle. Altogether, we identify CPSF3 as a druggable target in PDAC and reveal novel mechanisms by which CPSF3 controls cancer cell growth.SignificanceThis work identifies CPSF3 as a potential drug target in pancreatic ductal adenocarcinoma and reveals new mechanisms by which CPSF3 inhibition attenuates PDAC cell proliferation through modulating alternative polyadenylation and histone processing.

Elevated pre-mRNA 3′ end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation

“…CPSF-73 is also responsible for 3′ end processing of replicationdependent histone pre-mRNAs, whose mature forms do not have the poly(A) tail 57 . In fact, a recent study of pancreatic cancers showed drastic downregulation of these histone proteins after JTE-607 treatment 41 . Therefore, JTE-607-mediated inhibition of histone transcripts could further exacerbate S phase crisis, adding another layer of its function in suppressing proliferative cells.…”

“…While CPSF-73 inhibitors have been used in multiple parasitic protozoans 37,38 , JTE-607 is the first known CPAi compound in human cells. JTE-607 has also been shown to suppress certain cancer cells, including those from acute myeloid leukemia 39 , Ewing's sarcoma 36 , some lung and hepatocellular carcinoma 36 , breast cancer 40 and pancreatic cancer 41 . However, some cancer cells appear quite tolerant of the compound 36 , raising the question as to what cellular features are deterministic for cell survival upon JTE-607 treatment.…”

3′-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression

“…Another compound that targets CPSF73, JTE-607, prevents inflammation and also inhibits growth of Ewing's sarcoma, acute myeloid leukemia, and pancreatic ductal adenocarcinoma cell lines (109,113). JTE-607 induces global read-through transcription and R-loop formation in cancer cells (109).…”

“…JTE-607 induces global read-through transcription and R-loop formation in cancer cells (109). Many types of cancers overexpress CPSF73 (113,114). The elevated transcriptional activity of cancer cells may make their survival more dependent on pre-mRNA processing than that of nontransformed tissues, providing a therapeutic window where cancer cells are more susceptible to inhibition of CPSF73.…”