Integrative bioinformatics analysis for identification of hub genes and pathways responsible for early pathogenesis of retinoblastoma

Abstract Background Retinoblastoma (Rb) is the most common childhood malignancy in which intra-ocular tumors developed at a very young age. It is very crucial to detect Rb at an earlier stage and start appropriate therapy to prevent further metastasis. With the recent advancement of multi-omics analysis of microarray data and sophisticated bioinformatics tools, we could possibly identify potential early diagnostic biomarkers and novel therapeutic targets for retinoblastoma. Methods Microarray datasets (DNA methylation-GSE57362, miRNA-GSE7072, & mRNA-GSE110811) were utilized from NCBI-GEO. The GEO2R were employed to discover Differentially Expressed Genes (DEGs) in Retinoblastoma. Further, an integrated analysis of these genes was performed and a co-expression network was formed to identify hub genes. GEPIA server was used to validate these genes which are responsible for the progression of retinoblastoma. Results Differentially expressed genes were identified on the basis of P-value ≤ 0.05 and log2fc ≥ 2. In GSE57362 a total no of 267 genes methylated status, in GSE7072 a total no. of 265 gene targets of miRNAs and in GSE110811 a total no. of 770 genes were shown to be differentially expressed. Further, 10 hub genes, 5 bottleneck genes, and 3 common genes were identified by constructing the co-expression network. Survival analysis was done to validate the identified candidate genes using the GEPIA web server. Pathway enrichment analysis and gene ontology demonstrated that these genes were mostly enriched in biological processes such as regulation of cell proliferation and involved in multiple pathways like p53 pathway, cell cycle, and apoptosis. Conclusion This study suggested that these hub genes possibly will play vital roles in the onset and progression of retinoblastoma and could be serve as potential biomarkers to facilitate the diagnosis and treatment of this disease in the future.