The Effect of m6A Methylation Regulatory Factors on the Malignant Progression and Clinical Prognosis of Hepatocellular Carcinoma.

Zhongwei Zhao,Jingjing Song,Lili Yang,Shiji Fang,Minjiang Chen,Liyun Zheng,Weiqian Chen,Fazong Wu,Jiansong Ji

doi:10.3389/fonc.2020.01435

Abstract

The modification level of the transcript N6-methyladenosine (m6A), dynamically regulated by methyltransferases, binding proteins and demethylases, is closely related to the occurrence, and progression of tumors. Here, 13 differentially expressed m6A methylation regulators were confirmed in 374 hepatocellular carcinoma (HCC) patients, among which RBM15, YTHDC1, YTHDF1, and YTHDF2 were significantly variant in different stages and grades. Further consensus clustering analysis identified two HCC subtypes (cluster1/2) in this cohort, finding an active role of the m6A methylation regulators in the malignant progression of HCC. Furthermore, GESA enrichment analysis showed that PPAR signaling pathway, and the pathways involved in retinol metabolism and peroxisome were related to tumor progression. Additionally, a 4-gene risk model (ROC = 0.729) that can be used as a prognostic marker and a predictor for clinicopathological characteristics of HCC was constructed via univariate and multivariate Cox regression analyses. Analysis on overall survival and disease-free survival demonstrated that METTL3 and YTHDF1 out of the four genes in the model could serve as independent prognostic factors for HCC. Overall, this study systematically investigated the effect of m6A methylation regulators on the malignant progression of HCC and proposed a 4-gene risk prediction model, laying a theoretical foundation for the further research on HCC prognosis.

Highlights

More than 160 kinds of RNA modification have been found in organisms as a kind of post-transcriptional regulation [1]
We analyzed the relationship between the expression of the 13 widely reported methylation regulatory factors (METTL3, METTL14, FTO, ZC3H13, YTHDC1, YTHDC2, ALKBH5, WTAP, KIAA1429, RBM15, YTHDF1, YTHDF2, HNRNPC) and the clinicopathologic features systematically
We further analyzed the correlation between the expression of methylation regulatory factors and the clinicopathological features, and discovered that four genes (RBM15, YTHDC1, YTHDF1, and YTHDF2) showed significant differential expression in different stages and grades, and their expression levels gradually increased with the progression of the disease (Figures 1C–F)

Summary

Introduction

More than 160 kinds of RNA modification have been found in organisms as a kind of post-transcriptional regulation [1]. The modification level of the transcript m6A is dynamically regulated by “writers” (methyltransferases), “readers” (binding proteins), and “erasers” (demethylases). The core components of m6A methyltransferase complex include METTL3, METTL14, and WTAP, among which METTL3 acts as a core catalyst, METTL14 functions as a structural support for METTL3, and WTAP stabilizes core complex [8,9,10,11,12]. The currently identified m6A RNA “erasers” include FTO and ALKBH5, both of which belong to the ALKB dioxygenase family proteins and have catalytic function depending on cofactor Fe2+/αKetoglutaric acid. FTO is the earliest discovered m6A RNA demethylase, which first reveals the reversibility of RNA chemical modification [15]. “Readers” can decode m6A methylation and generate functional signals, including the YTH family members (YTHDC1, YTHDF2, YTHDF1, THDF3, YTHDC2, and Mrb, etc.), ELAVL1, FMR1, LRPPRC, and IGF2BP, etc. [17,18,19,20]

Methods

Results

Conclusion