Post-transcriptional upregulation of GPC3 via CSTF2-driven 3'UTR remodeling promotes hepatocellular carcinoma progression

Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that generates mRNA isoforms with variable 3′ untranslated regions (3′UTRs), influencing transcript stability and translation. Aberrant 3′UTR shortening frequently occurs in cancer, allowing oncogenic transcripts to evade microRNA (miRNA)-mediated repression. However, the global landscape and functional impact of APA alterations in hepatocellular carcinoma (HCC) remain incompletely defined. We performed transcriptome-wide APA profiling across a multistage human liver cancer cohort to identify genes exhibiting significant 3′UTR alterations during hepatocarcinogenesis. Differential Poly(A) Site Usage Index (ΔPDUI) analysis was applied to detect APA-driven isoform shifts. Candidate genes were validated using independent HCC datasets and correlated with clinical outcomes. Functional assays-including RNA interference, overexpression, and proliferation/apoptosis measurements-were conducted in HCC cell lines to define mechanistic and phenotypic consequences. Approximately 77% of APA-affected mRNAs displayed 3′UTR shortening in HCC compared to normal liver tissue. Among these, Glypican-3 (GPC3) emerged as one of the most prominently upregulated transcripts, with high expression levels strongly associated with poor patient prognosis. Manipulation of GPC3 expression confirmed its oncogenic role, as silencing GPC3 suppressed proliferation and enhanced apoptosis, whereas ectopic expression promoted growth. Among core APA regulators, Cleavage Stimulation Factor 2 (CSTF2) was markedly upregulated in HCC and positively correlated with both GPC3 expression and poor clinical outcomes. CSTF2 overexpression induced 3′UTR shortening of GPC3 and elevated its protein levels, while CSTF2 knockdown lengthened the GPC3 3′UTR and decreased expression. Mechanistically, truncation of the GPC3 3′UTR eliminated binding sites for miR-96-5p and miR-140-5p, relieving translational repression and sustaining oncogenic GPC3 expression. Our findings reveal that CSTF2-driven APA remodeling serves as a key post-transcriptional mechanism promoting GPC3 activation in HCC. CSTF2 overexpression shortens the GPC3 3′UTR, abrogating miRNA-mediated repression and enhancing tumorigenic potential. This CSTF2-GPC3 axis underscores APA dysregulation as a pivotal driver of hepatocarcinogenesis and highlights CSTF2 as a promising therapeutic target for liver malignancies.