Bioinformatics analysis of the CDK2 functions in neuroblastoma

The present study aimed to elucidate the potential mechanism of cyclin-dependent kinase 2 (CDK2) in neuroblastoma progression and to identify the candidate genes associated with neuroblastoma with CDK2 silencing. The microarray data of GSE16480 were obtained from the gene expression omnibus database. This dataset contained 15 samples: Neuroblastoma cell line IMR32 transfected with CDK2 shRNA at 0, 8, 24, 48 and 72 h (n=3 per group; total=15). Significant clusters associated with differentially expressed genes (DEGs) were identified using fuzzy C-Means algorithm in the Mfuzz package. Gene ontology and pathway enrichment analysis of DEGs in each cluster were performed, and a protein-protein interaction (PPI) network was constructed. Additionally, functional annotation of DEGs in clusters was performed for the detection of transcription factors and tumor-associated genes. A total of 4 clusters with significant change tendency and 1,683 DEGs were identified. The hub nodes of the PPI network constructed by DEGs in Cluster 1, Cluster 2, Cluster 3 and Cluster 4 were MDM2 oncogene, E3 ubiquitin protein ligase (MDM2), cyclin-dependent kinase 1 (CDK1), proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 (PSMD14) and translocator protein (18 kDa) (TSPO) respectively. These genes were significantly enriched in the p53 signaling pathway, cell cycle, proteasome and systemic lupus erythematosus pathways. MDM2, CDK1, PSMD14 and TSPO may be key target genes of CDK2. CDK2 may have key functions in neuroblastoma progression by regulating the expression of these genes.