Identification of HSP90AB1 as a key R-loop-related gene in hepatocellular carcinoma

An R-loop is a triple-stranded structure that plays a crucial role in tumorigenesis and development; however, the relevant genes in hepatocellular carcinoma (HCC) remain poorly characterized. This study aimed to identify key R-loop-related genes in HCC. Based on microarray data, potential R-loop-related differentially expressed genes (RDEGs) were screened by intersecting HCC-related DEGs, module genes (WGCNA), and R-loop genes. RDEGs with diagnostic value for HCC were refined by four machine learning algorithms, including Maximal Clique Centrality, Maximal Neighborhood Component, Degree, and Edge Percolated Component, and validated by ROC analysis. Subsequently, functional enrichment (GSEA), immune infiltration (ssGSEA), candidate small molecules prediction, and molecular docking were performed on the isolated 4 RDEGs. For verification, HSP90AB1 was selected as a key RDEG, and its function was validated in HCC cells using siRNA-mediated silencing and RNase H1 rescue assays. NCAPG , HSP90AB1 , CCT5 , and HSPA4 were isolated as key RDEGs in HCC, which had a promising diagnostic performance for HCC, with AUC > 0.898 for individual genes and AUC > 0.978 for the nomogram. These RDEGs were enriched in R-loop-related pathways and correlated with immune cells. Geldanamycin, Vorinostat, and Troglitazone were candidate candidate small molecules with moderate binding affinity to these RDEGs. Of note, HSP90AB1 was determined as a key RDEG that was up-regulated in HCC cells. Silencing of HSP90AB1 inhibited cell viability, migration, and invasion, and promoted R-loop accumulation in HCC cells. The up-regulation of RNase H1 partially reversed the anti-tumor effects of HSP90AB1 silencing in HCC cells. NCAPG , HSP90AB1 , CCT5 and HSPA4 were key RDEGs in HCC. Silencing of HSP90AB1 might inhibit the progression of HCC by promoting R-loop accumulation.