Identification of potential oncogenic miRNA clusters with a special focus on miR-106b/25 cluster-regulated networks and their clinical utility in hepatocellular carcinoma

The lack of reliable early markers specific to hepatocellular carcinoma (HCC) limits its effective management. While the genetic factors defining this disease are largely understood, the epigenetic mechanisms that cause HCC remain elusive. MicroRNAs (miRNAs) operate as polycistronic clusters rather than individual genes and are critical to the development and progression of multiple cancers, including HCC. In this study, we identified several miRNA clusters, including the miR-106b/25 cluster (miR-106b-5p, miR-25-3p, and miR-93-5p), that are overexpressed in HCC cells, suggesting their oncogenic function. We then performed whole-transcriptomic sequencing and identified gene targets of this cluster, namely, CAV1, DNAJB4, PTPRD, MFSD2A, TCF4, KLF6, MCC, CYB5A, ESR2, NR4A3, PRKCB, RASSF2, TXNIP, and SOD2, to be downregulated in the HCC spheroids and clinical datasets. Further, gene enrichment analysis revealed associations with critical pathways, such as Wnt signaling, TGF-beta signaling, VEGFA-VEGFR2 signaling, and EGF/R signaling pathways. Furthermore, survival analysis revealed that miR-93-5p (HR = 0.72, p = 0.0246), HCC stage (HR = 2.43, p = 0.0000113), TCF4 (HR = 0.66, p = 0.0106), DNAJB4 (HR = 1.29, p = 0.0214), MCC (HR = 1.35, p = 0.0268), and CYB5A (HR = 0.77, p = 0.0423) affect overall survival (OS). Finally, a combined prognostic model for the miRNA cluster and its target genes via the random forest approach revealed that the miR-106b/25 cluster and its interactome are significantly associated with OS (p < 0.0001), thereby providing a comprehensive understanding of the cluster and its targets in the development and progression of HCC and its use as a potential marker for HCC.