Multi-Omics analysis and in vitro validation reveal diagnostic and therapeutic roles of novel hub genes in ovarian cancer.

Abstract

Ovarian cancer (OC) remains a highly lethal gynecologic malignancy due to late diagnosis and limited therapeutic options. In this study, we aimed to identify and functionally validate novel hub genes associated with OC progression. We integrated four GEO microarray datasets (GSE54388, GSE40595, GSE18521, and GSE12470) to identify differentially expressed genes (DEGs) between OC and healthy tissues using the limma package. A total of 22 common DEGs were identified, of which four-SNRPA1, LSM4, TMED10, and PROM2-emerged as hub genes based on PPI network centrality. Expression analyses using TCGA data and RT-qPCR confirmed the significant upregulation of these genes in OC samples. Promoter methylation analysis showed hypomethylation in tumors, while ROC analysis revealed high diagnostic accuracy (AUC = 1.0). Although these genes were not significantly associated with overall survival in meta-analysis, they were strongly involved in oncogenic pathways such as EMT, apoptosis, and DNA repair. Predicted miRNAs (e.g., hsa-miR-1178-5p and hsa-miR-31-5p) targeting hub genes were significantly downregulated in OC cell lines. Immune analysis indicated that hub gene expression was correlated with immune subtypes, checkpoint inhibitors, and reduced immune infiltration. Drug sensitivity analysis suggested that high expression of TMED10 and PROM2 may confer susceptibility to chemotherapeutic agents. Functional assays following siRNA-mediated knockdown of TMED10 and PROM2 in A2780 and OVCAR3 cells revealed significant reductions in proliferation, colony formation, and migration. These findings highlight SNRPA1, LSM4, TMED10, and PROM2 as potential diagnostic markers and therapeutic targets in OC, warranting further investigation for clinical translation.