The Cancer Genome Atlas (TCGA) based m ⁶ A methylation-related genes predict prognosis in hepatocellular carcinoma

Abstract

The current study aims to investigate the significance of <i>N</i>⁶-methyladenosine (m⁶A) methylation-related genes in the clinical prognosis of hepatocellular carcinoma (HCC) using bioinformatics analyses based on The Cancer Genome Atlas (TCGA) database. Transcriptome data and corresponding clinical data on m⁶A methylation-related genes (including 15 genes) were obtained from TCGA database. Differential expression of 15 genes was identified. Survival curves of subgroups based on m⁶A methylation-related gene expression levels were plotted. We selected potential predictive genes and analyzed their prognostic values using bioinformatics methods. Eleven genes (<i>METTL3, YTHDF1, YTHDF2, YTHDF3, YTHDC1, YTHDC2, FTO, KIAA1429, HNRNPC, HNRNPA2B1</i>, and <i>RBM15</i>) were found to be overexpressed in HCC. Of these, five genes had worse survival (P < 0.05). There was a significant difference in the survival rate between subgroups with different expression levels of m⁶A. We selected five potential predictors (<i>METTL3, KIAA1429, ZC3H13, YTHDF1</i>, and <i>YTHDF2</i>) that met the independent predictive value. ZC3H13 was upregulated in patients with high cancer risk, whereas <i>METTL3, KIAA1429, YTHDF1</i>, and <i>YTHDF2</i> were downregulated. In summary, we found that the expression levels of m⁶A methylation-related genes were different in patients with HCC and correlated with survival and prognosis. This implies that m⁶A methylation-related genes may be promising prognostic indicators or therapeutic targets for HCC.