High-resolution comparative genomics of RB1 mutations in gastric and hepatocellular carcinoma: Functional insights through the TP53 co-mutational landscape

Abstract

Retinoblastoma protein (pRb) is a critical tumor suppressor that regulates the cell cycle and maintains genetic stability. While mutations in the retinoblastoma 1(RB1) gene are well-documented in gastric adenocarcinoma (GAC) and hepatocellular carcinoma (HCC), the genomic landscape in Middle Eastern populations remains largely unknown. Thus, this study aimed to systematically characterize the entire spectrum of RB1 mutations in a large cohort of Iraqi patients with GAC and HCC. In a cohort of 885 patients (487 GAC and 398 HCC), genomic analysis was conducted. The study incorporated CRISPR-Cas9 knockout models, protein-protein interaction assays, pathway enrichment analysis, and machine learning for predictive modeling. Results showed higher rates of RB1 mutations in GAC (28.3%) and HCC (35.6%) compared to global averages (GAC: 12.1%; HCC: 8.7%) in the TCGA registry. Notably, GAC mutations predominantly affected the B-pocket domain (60.9%), while HCC mutations favored the A-pocket (62.7%). Dual RB1/p53 mutations were present in 71.2% of GAC and 38.9% of HCC patients. Functional studies revealed a significant activation of the DNA damage response in GAC (ATM/Chk2: 3.4-fold increase, p=1.2×10⁻⁸) and upregulation of the Wnt/β-catenin pathway in HCC (2.8-fold increase, p=3.7×10⁻⁶). Patient survival was notably lower in dual-mutant groups (GAC: HR = 2.67, 95% CI: 1.89–3.78; HCC: HR = 2.14, 95% CI: 1.52–3.01). The machine learning model accurately predicted therapeutic responses (89.3% accuracy), identifying heightened sensitivity to PARP inhibitors in RB1-mutant GAC (IC_50: 2.3 vs. 8.7 μM) and to CDK4/6 inhibitors in RB1-mutant HCC (IC_50: 3.1 vs. 12.4 μM). In conclusion, this study elucidates the RB1 mutational landscape in different cancers and highlights the therapeutic implications of these mutations in Iraqi patients, suggesting a synergistic role of RB1 and p53 mutations in gastric carcinoma, which indicates strategies for precision oncology tailored to Middle Eastern populations.