Comprehensive analysis and validation reveal potential MYCN regulatory biomarkers associated with neuroblastoma prognosis

Abstract

Neuroblastoma (NB) is an embryonic malignant tumor that occurs in the sympathetic nervous system. The treatment results of patients in the high-risk group are poor, and relapse and treatment failure can occur even with multiple combination treatments. The proto-oncogene MYCN is a BHLH Transcription Factor used as an independent prognostic factor for NB. The proportion of MYCN amplification in tumor tissues of high-risk patients reaches 40–50%. Hence, exploring new MYCN target genes is a meaningful approach in developing treatment for high-risk NB patients. The microarray datasets were obtained from Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and miRPathDB were used for enrichment analysis. STRING and Cytoscape were used to construct a protein-protein interaction (PPI) network and for modular analysis. The miRNet and NetworkAnalyst databases were used to predict and construct gene-miRNA and gene-TFs networks. The R2 database was used for expression, correlation, and prognostic analyses. The diagnostic value of the biomarkers was predicted by ROC analysis, and RT-qPCR was used to validate the identified hub genes. Finally, using specific MYCN siRNA and overexpressing plasmids, the correlation between the identified hub genes and MYCN was investigated. Our results showed that FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 are novel biomarkers that affect the prognosis of the NB patients. In addition, FBXO9, RNF19B, and TRIM36 were preliminarily confirmed as potential target genes of MYCN. Overall, FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 are expected to become novel biomarkers for the treatment of high-risk NB patients. Communicated by Ramaswamy H. Sarma