Microarray screening for key genes and prognosis factors in interferon regulatory factor 1-silenced ovarian cancer SKOV-3 cells

Abstract

Background: Ovarian cancer is a gynecological neoplastic disease with high mortality rate. Its early detection is difficult because of the lack of specific clinical symptoms. This study aimed to identify key genes and prognosis factors associated with ovarian cancer to provide new information and thus better understanding of ovarian cancer. Methods: Microarray data from the Gene Expression Omnibus (GEO) database (accession number GSE38551) were used for analysis. Differentially expressed genes (DEGs) were screened, and functional enrichment and protein-protein interaction (PPI) network analyses for DEGs were performed. A subnetwork was constructed to gain further information regarding DEGs scored in the PPI network. Finally, we performed survival analysis. Results: In total, 427 DEGs were obtained in interferon regulatory factor 1 ( IRF-1 )-silenced ovarian cancer SKOV-3 cell line samples compared to SKOV-3 samples without IRF-1 silencing. DEGs were mainly enriched in metabolic pathways and systemic lupus erythematosus. Tumor necrosis factor ( TNF ) and cadherin 1 ( CDH1 ; type 1, E-cadherin) were present in had higher degrees than others in both the PPI network and the subnetwork. The subnetwork results presented that CDH1 was enriched in the epithelium morphogenesis and cancer pathways, and TNF was enriched in response to lipids. The Mir-30 family served as a tumor suppressor in ovarian cancer. Survival analysis revealed that CDH1 was associated with ovarian cancer prognosis. Conclusions: TNF and CDH1 play important roles in ovarian cancer: CDH1 is an important prognosis factor for ovarian cancer and may be involved mainly via epithelial morphogenesis and cancer pathways. TNF may be involved via response to lipids.