METTL3-mediated m6A modification of pri-miR-93 promotes hepatocellular carcinoma progression via CDKN1A suppression

Abstract

N6-methyladenosine (m⁶A) is the most common RNA modification in eukaryotic transcriptomes and plays a key role in various biological processes. However, its function in disease, particularly in microRNA regulation, remains unclear. Hepatocellular carcinoma (HCC) is a major global health challenge, with high morbidity and mortality rates. Investigating the role of m⁶A modification in HCC may provide valuable insights into its molecular mechanisms.

This study found that METTL3, an m⁶A methyltransferase, is significantly upregulated in HCC and is associated with poor prognosis. Bioinformatics analysis of the GSE37001 dataset showed that silencing METTL3 in HepG2 cells suppressed cell cycle-related pathways. Among several candidate miRNAs potentially regulated by METTL3 in an m⁶A-dependent manner, miR-93–5p was selected for further study. Experimental results demonstrated that METTL3-mediated m⁶A modification promotes miR-93–5p expression by facilitating pri-miR-93 processing. Functional assays confirmed that miR-93–5p directly targets CDKN1A and downregulates its expression. Moreover, METTL3 overexpression rescued the effects of METTL3 knockdown on pri-miR-93 m⁶A levels and miR-93–5p expression. Rescue experiments further showed that METTL3 promotes HCC cell proliferation and cell cycle progression while inhibiting apoptosis via the miR-93–5p/CDKN1A axis.

In summary, METTL3 is highly expressed in HCC and contributes to tumor progression by promoting miR-93–5p expression through m⁶A modification, thereby suppressing CDKN1A. These findings highlight a potential regulatory mechanism in HCC and suggest that targeting the METTL3/miR-93–5p/CDKN1A axis could be a novel therapeutic strategy.