Background <p>Dysregulated ribosome biogenesis (RB) is strongly linked to tumorigenesis and progression, but the prognostic role of RB-related genes in hepatocellular carcinoma (HCC) remains incompletely understood. This study aimed to systematically analyze the prognostic value of RB-related genes in HCC, establish a robust risk prediction model, and identify novel biomarkers for HCC.</p> Methods <p>HCC sample data were obtained from the TCGA and GEO databases. Differential expression analysis detected differentially expressed genes (DEGs), and weighted gene co-expression network analysis (WGCNA) uncovered modules related to RB score. Prognostic genes were screened by LASSO regression, stepwise multivariate Cox regression, and univariate Cox regression to establish a risk scoring model, which was independently validated in a validation cohort. Further analyses, including ssGSEA, GSVA, immune infiltration profiling, mutant-allele tumor heterogeneity (MATH) score assessment, and drug sensitivity prediction, were carried out to elucidate the model’s biological implications. Finally, the mRNA expression differences of key genes were detected in HCC cell line Hep3B and normal cell line THLE-2 by using qRT-PCR. The CGREF1 gene was knocked down by siRNA technology, and its effects on cell proliferation, migration, and drug sensitivity were evaluated through CCK-8 and Transwell assays.</p> Results <p>A risk prognostic model incorporating seven signature genes was constructed, demonstrating robust forecasting efficacy across the training and validation cohorts. The high-risk group displayed a tumor microenvironment (TME) with significantly enhanced immunosuppression, characterized by elevated infiltration of regulatory T cells (Tregs), neutrophils, and myeloid-derived suppressor cells (MDSCs). Furthermore, the high-risk group demonstrated higher sensitivity to predicted chemotherapeutic agents (Docetaxel, Paclitaxel, Bortezomib, Staurosporine, Vinblastine, and Vinorelbine). qRT-PCR validation demonstrated that genes such as CGREF1 and SLC7A11 were significantly upregulated in Hep3B cells, while TMEM45A exhibited higher expression in normal liver tissue. Moreover, high expression of CGREF1 was significantly associated with shortened overall survival in HCC patients. Functional experiments confirmed that knockdown of CGREF1 effectively reduced the expression of ribosomal protein genes (RPL7/8/30) and significantly inhibited cell proliferation, migration, and invasion. Additionally, co-knockdown of CGREF1 with gefitinib treatment exhibited a synergistic enhancement effect in suppressing cell proliferation and migration.</p> Conclusion <p>A novel prediction model was constructed based on seven RB-related signature genes for prognostic prediction in HCC patients. Targeted inhibition of CGREF1 may represent a potential strategy to improve therapeutic outcomes in HCC.</p>