N6 -methyladenosine-modified lncRNA ARHGAP5-AS1 stabilises CSDE1 and coordinates oncogenic RNA regulons in hepatocellular carcinoma

Background: Hepatocellular carcinoma (HCC) ranks fourth among the malignancies leading to cancer-related deaths all around the world. It is increasingly evident that long non-coding RNAs (lncRNAs) are a key mode of hepatocarcinogenesis. As the most prevalent mRNA modification form, N⁶ -methyladenosine (m⁶ A) regulates gene expression by impacting multiple aspects of mRNA metabolism. However, there are still no reports on genome-wide screening and functional annotation of m⁶ A-methylated lncRNAs in HCC.

Methods: The m⁶ A modification and biologic functions of ARHGAP5-AS1 in HCC were investigated through a series of biochemical assays. Clinical implications of ARHGAP5-AS1 were examined in tissues from HCC patients.

Results: After systematically analysing the m⁶ A-seq data of HCC cells, we identified 22 candidate lncRNAs with evidently dysregulated m⁶ A levels. Among these lncRNAs, we found that ARHGAP5-AS1 is the lncRNA with the highest levels of m⁶ A modification and significantly increased expression in HCC specimens. METTL14 acts as the m⁶ A writer of ARHGAP5-AS1 and IGF2BP2 stabilises the lncRNA as its m⁶ A reader. ARHGAP5-AS1 remarkably promotes malignant behaviours of HCC cells ex vivo and in vivo. We identified oncoprotein CSDE1 working as the interacting protein of the lncRNA and TRIM28 as the E3 ligase of CSDE1 in HCC. Interestingly, ARHGAP5-AS1 could attenuate interactions between CSDE1 and TRIM28, which prevents the degradation of CSDE1 via the ubiquitin-proteasome pathway. Elevated levels of CSDE1 coordinate oncogenic RNA regulons, promote translation of VIM and RAC1 and activate the ERK pathway, which contributes to HCC prognosis.

Conclusions: Our study reveals a new paradigm in m⁶ A-modified lncRNAs controlling CSDE1-mediated oncogenic RNA regulons and highlights lncRNAs as potential targets for future therapeutics against HCC.

ARHGAP5-AS1; CSDE1; N6-methyladenosine; hepatocellular carcinoma; lncRNA.