Exploring multiple biomarkers and constructing ferroptosis-associated competing endogenous RNA networks as dual...

This study investigated the potential role of ferroptosis-associated competing endogenous RNA (ceRNA) networks in retinoblastoma (RB). In total, two independent RB gene expression datasets (GSE97508 and GSE208143) and a microRNA (miRNA) expression dataset (GSE208677) were retrieved from the Gene Expression Omnibus database. Differential expression analysis was conducted to identify ferroptosis-related (FR) differentially expressed genes (DEGs) in RB. A protein-protein interaction network for FR-DEGs was constructed using the STRING database, whereas hub genes were determined using the CytoHubba plugin. Reverse transcription-quantitative PCR (RT-qPCR) was used to verify the expression of IDH2 and CDKN2A. Immune cell infiltration in RB was assessed using the CIBERSORT algorithm. Additionally, miRNA-targeting hub genes were predicted, where an FR miRNA-mRNA regulatory network was constructed. Finally, a ceRNA network and a drug-gene interaction network were constructed. A total of 584 FR-DEGs were identified from the GSE97508 dataset, revealing 135 upregulated and 449 downregulated genes. The intersection of FR-DEGs with FerrDb-extracted FRGs yielded 23 genes that were defined as core FR-DEGs for subsequent analysis. Functional and pathway enrichment analyses highlighted their involvement in iron and transition metal ion homeostasis, response to hypoxic and ischemic conditions and apoptotic processes. Hub genes (CAV1, CDKN2A, EPAS1, IDH2, RB1 and SLC2A3) were identified and validated in an independent dataset, with RT-qPCR confirming IDH2 and CDKN2A upregulation. Immune cell infiltration analysis indicated altered immune cell populations in RB, where an association analysis revealed associations between hub genes and immune cells. A comprehensive FR miRNA-mRNA regulatory network and a ceRNA network were established, shedding light on additional layers of regulatory mechanisms in RB. Furthermore, the drug-gene interaction network consisted of 20 potential candidate drugs. In conclusion, the present integrated analysis offers a comprehensive understanding of the potential role in RB, providing valuable insights into the molecular mechanisms and potential therapeutic targets for this childhood ocular tumor.