Construction and experimental validation of ferroptosis-related competing endogenous RNA networks in hepatocellular carcinoma based on WGCNA

Abstract The ferroptosis-related competing endogenous RNAs (ceRNA) network in hepatocellular carcinoma (HCC) has not been fully explored. In this study, RNA sequence data of HCC and clinic data were downloaded from The Cancer Genome Atlas (TCGA) database. Through the pre-set three gene sets of autophagy, pyroptosis, and ferroptosis, each sample was scored by single-sample Gene Set Enrichment Analysis (ssGSEA), and ferroptosis was associated with overall survival. We used Weighted Gene Co-Expression Network Analysis (WGCNA) analysis to modularize long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA). The most ferroptosis related modules were identified by correlation analysis. Enrichment analysis showed the genes were significantly enriched in ferroptosis-related functions and pathways. The ceRNA network was constructed by the prediction from online tools. We randomly selected one axis for laboratory verification, the DNAJC27-AS1/miR-23b-3p/PPIF axis. Functionally, DNAJC27-AS1 and PPIF could negatively regulate the level of ferroptosis in HCC cells, while miR-23b-3p played positively. Mechanistically, miR-23b-3p can directly bind to DNAJC27-AS1 and PPIF, respectively. DNAJC27-AS1 and PPIF can regulate mutually through sponging miR-23b-3p and act as potential ferroptosis regulators. Taken together, we provided a reliable ferroptosis-related ceRNA network and preliminarily verified it. This study may offer new insights for future research on ferroptosis in HCC.