Association analysis of CPSF4/PRKDC co-expression with poor prognosis, immune microenvironment characteristics, and sorafenib sensitivity in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide with a poor prognosis largely due to late diagnosis and treatment resistance. This study investigates the cooperative roles of cleavage and polyadenylation-specific factor 4 (CPSF4) and DNA-activated protein kinase catalytic polypeptide (PRKDC) in HCC progression and sorafenib sensitivity. We analyzed expression levels and clinical outcomes using datasets. Prognostic risk score models were constructed based on gene expression profiles. Immunohistochemistry assessed protein expression in tumor samples. In vitro experiments employed various HCC cell lines (HepG2 and HCCLM3) to evaluate the effects of CPSF4 and PRKDC knockdown on cell proliferation, migration, invasion, and apoptosis, using colony formation, transwell migration/invasion assays, and flow cytometry. Additionally, xenograft models were established in BALB/c nude mice to evaluate the impact of combined CPSF4 and PRKDC silencing on tumor growth under sorafenib treatment. An analysis of the TCGA cohort revealed a significant positive correlation between the expression levels of CPSF4 and PRKDC in HCC (r = 0.31, p < 0.001). Patients exhibiting high expression levels of both genes demonstrated notably reduced overall survival (HR = 2.202, p = 0.002). The risk score model, constructed based on these two genes, yielded area under the curve values of 0.703, 0.631, and 0.611 at 1, 2, and 3 years, respectively, in the TCGA training dataset and 0.684, 0.736, and 0.757 in the ICGC validation dataset. Further analysis indicated a strong association between elevated expression of both genes and the characteristics of an immunosuppressive tumor microenvironment. Functional experiments confirmed that the simultaneous knockdown of CPSF4 and PRKDC synergistically inhibited malignant phenotypes in HCC cells, significantly reducing their proliferation, migration, and invasion capabilities while enhancing sensitivity to sorafenib. Notably, tumor xenograft models demonstrated that their simultaneous knockdown synergistically reduced tumor growth in vivo. Mechanistically, CPSF4 and PRKDC were found to be associated with the c-Myc and YAP/TAZ pathways. Our findings elucidate the synergistic roles of CPSF4 and PRKDC in HCC malignancy and resistance to sorafenib, suggesting their potential as therapeutic targets to improve patient outcomes. Targeted interventions aimed at disrupting their synergistic effects may enhance the efficacy of current treatment strategies for HCC.