VIM-AS1, regulated by CpG methylation, cooperates with IGF2BP1 to inhibit tumor aggressiveness via EPHA3 degradation in hepatocellular carcinoma

Background Early tumor recurrence observed in hepatocellular carcinoma (HCC) remains challenging, as the mechanisms involved have not been completely elucidated. Microvascular invasion is associated with early recurrence; however, well-established biomarkers for diagnosis and predicting prognosis are lacking. In this study, we aimed to identify DNA methylation sites predicting liver cancer patient prognosis and validate HCC aggressiveness molecular mechanisms. Methods DNA methylome data from HCC patient samples (CGRC and TCGA) were analyzed to identify hypermethylated CpG sites. RNA-sequencing was performed on HCC cells with modulated expression of VIM-AS1 , a long non-coding RNA regulated by CpG methylation. In vitro and in vivo studies investigated the intracellular molecular mechanism of action of VIM-AS1 , and the CRISPR-dCas9 system was used for validating the potential of targeted DNA methylation as a therapeutic target. Results We observed that cg02746869, significantly associated with HCC patient prognosis, acted as a pivotal regulatory site for VIM-AS1 . Suppression of VIM-AS1 due to methylation profoundly influenced the HCC cellular dynamics, specifically impairing the motility and invasiveness of cancer cells. This effect involved modulating EPHA3 expression and its subsequent interaction with the m6A-associated protein, IGF2BP1. Additionally, we observed that modifications in the methylation state of cg02746869 directly affected the invasive properties of HCC cells, underscoring the critical role of this methylation site in the oncogenic behavior of HCC. Conclusions Our results highlighted the significant role of DNA methylation in controlling lncRNA expression and its impact on HCC pathophysiology. Thus, cg02746869 is an emergent biomarker for prognostic evaluation and therapeutic intervention in HCC.