Identification of Driver Genes and Key Pathways of Ependymoma

AIM: To identify ependymoma (EPN) driver genes and key pathways, and also to illuminate the connection between prognosis of EPN patients and expression levels of driver genes. MATERIAL and METHODS: The gene expression profiles of GSE50161, GSE66354, GSE74195, and GSE86574 were analyzed to figure out the differentially expressed genes (DEGs) between tissue of EPN and normal brain samples. To harvest the enrichment functions, pathways and hub genes, the Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein -protein interaction (PPI) network analysis were made. Subsquently, survival analysis was performed in 325 patients to illuminate the connection between prognosis of EPN and expression levels of hub genes. RESULTS: 20 functions and 10 pathways which were up- or downregulated between the EPN and normal samples were revealed applying GO and KEGG analysis. Mutual hub genes were TP53, TOP2A, CDK1, PCNA, and ACTA2. The pathways of Hedgehog and notch signaling, mismatch repair (MMR), and retrograde endocannabinoid were significantly abnormally regulated in EPN tissue. Survival analysis revealed favorable progression -free (PFS) and overall (OS) survival in EPN patients with low expression of TOP2A, CDK1, PCNA, and ACTA2 (p<0.05). CONCLUSION: Patients with lower expression of TOP2A, CDK1, PCNA, and ACTA2 had a longer OS and PFS. The differential expressed genes identified and the key pathways selected in this research provided unprecedented and promising targets for diagnosis and treatment of EPN patients.