CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression

Abstract

Background Alternative polyadenylation (APA) is an important mechanism of gene expression regulation through generation of RNA isoforms with distinct 3′ termini. Increasing evidence has revealed that APA is actively involved in development and disease, including hepatocellular carcinoma (HCC). However, how APA functions in tumor formation and progression remains elusive. In this study, we investigated the role of cleavage factor I (CFIm) subunit CPSF6 in human hepatocellular carcinoma (HCC). Methods Expression levels of CPSF6 in clinical tissues and cell lines were determined by qRT-PCR and western blot. Functional assays, including the cell number, MTT, colony formation and transwell, were used to determine the oncogenic role of CPSF6 in HCC. Animal experiments were used to determine the role of CPSF6 in HCC tumorigenicity in vivo. Deep sequencing-based 3 T-seq was used to profile the transcriptome-wide APA sites in both HCC cells and CPSF6 knockdown HCC cells. The function of CPSF6-affected target NQO1 with distinct 3′UTRs was characterized by metabolism assays. Results We observed CPSF6 was upregulated in HCC and the high expression of CPSF6 was associated with poor prognosis in patients. Overexpression of CPSF6 promoted proliferation, migration and invasion of HCC cells in vitro and in vivo. Transcriptome-wide APA profiling analysis indicated that high expression of CPSF6 promoted the favorable usage of the proximal poly(A) site in the 3′UTR of NQO1. We demonstrated CPSF6-induced tumorigenic activities were mediated by the NQO1 isoform with short 3′UTR. Furthermore, we found that CPSF6 induced metabolic alterations in liver cells through NQO1. Conclusion CPSF6 plays a critical role in HCC progression by upregulating NQO1 expression through APA. These findings provide evidence to demonstrate that APA of NQO1 contributes to HCC progression and may have implications for developing new therapeutic strategy against this disease.

Deregulated expression and subcellular localization of CPSF6, a circRNA-binding protein, promote malignant development of esophageal squamous cell carcinoma

“…Previous studies have demonstrated that CPSF6 plays a pro-oncogenic role in several human cancers ( 13 , 18 , 19 ). Herein, we investigated the expression and functions of CPSF6 in ESCC.…”

“…For instance, CPSF6 is highly expressed in aggressive breast cancer and is a clinically relevant marker of poor patient outcomes ( 12 ). In hepatocellular carcinoma, overexpression of CPSF6 increases cell proliferation, migration and invasion both in vitro and in vivo ( 13 ). Whereas, there are no studies concerning the biological roles of CPSF6 in ESCC.…”

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

“…Here, we demonstrated their high expression levels in HCC cell lines, which were consistent in HCC samples through bioinformatics analyses. Several studies have shown that seven other miR-30 c target genes, including CPSF6 [ 37 ], KIAA1522 [ 38 ], XPO1 [ 39 ], SOX12 [ 40 ], PTBP3 [ 41 ], MYBL2 [ 42 ], and GALNT10 [ 43 ] had a pro-developmental effect on HCC.…”

Suppression of CPSF6 Enhances Apoptosis Through Alternative Polyadenylation-Mediated Shortening of the VHL 3′UTR in Gastric Cancer Cells

“…The lentiviral vector pLKO.1-puro-shRNA- CPSF6 was constructed for CPSF6 knockdown as described previously ( Tan et al, 2021 ). The lentiviral vectors pCDH-PGK- VHL -CDS-short 3′UTR-SV40-NeoR and pCDH-PGK- VHL -CDS-long 3′UTR-SV40-NeoR were constructed for VHL overexpression.…”