M6A modification suppresses ocular melanoma through modulating HINT2 mRNA translation

Ruobing Jia,Xianqun Fan,Yangfan Xu,Shanzheng Wang,Baofa Sun,Shengfang Ge,Yun-Gui Yang,Renbing Jia,Peiwei Chai,Ying Yang

doi:10.1186/s12943-019-1088-x

Abstract

BackgroundDynamic N6-methyladenosine (m6A) RNA modification generated and erased by N6-methyltransferases and demethylases regulates gene expression, alternative splicing and cell fate. Ocular melanoma, comprising uveal melanoma (UM) and conjunctival melanoma (CM), is the most common primary eye tumor in adults and the 2nd most common melanoma. However, the functional role of m6A modification in ocular melanoma remains unclear.Methodsm6A assays and survival analysis were used to explore decreased global m6A levels, indicating a late stage of ocular melanoma and a poor prognosis. Multiomic analysis of miCLIP-seq, RNA-seq and Label-free MS data revealed that m6A RNA modification posttranscriptionally promoted HINT2 expression. RNA immunoprecipitation (RIP)-qPCR and dual luciferase assays revealed that HINT2 mRNA specifically interacted with YTHDF1. Furthermore, polysome profiling analysis indicated a greater amount of HINT2 mRNA in the translation pool in ocular melanoma cells with higher m6A methylation.ResultsHere, we show that RNA methylation significantly inhibits the progression of UM and CM. Ocular melanoma samples showed decreased m6A levels, indicating a poor prognosis. Changes in global m6A modification were highly associated with tumor progression in vitro and in vivo. Mechanistically, YTHDF1 promoted the translation of methylated HINT2 mRNA, a tumor suppressor in ocular melanoma.ConclusionsOur work uncovers a critical function for m6A methylation in ocular melanoma and provides additional insight into the understanding of m6A modification.

Highlights

Dynamic N6-methyladenosine (m6A) RNA modification generated and erased by N6methyltransferases and demethylases regulates gene expression, alternative splicing and cell fate
The expression of the known m6A “writer” methyltransferase-like 3 (METTL3) was decreased in ocular melanoma tissue compared to normal melanocyte tissue (p < 0.05) (Fig. 1b; Additional file 2: Table S2; Additional file 3: Table S3), while the opposite trend was observed for m6A “eraser” alkB homolog 5 (ALKBH5) (p < 0.01) (Fig. 1c; Additional file 2: Table S2; Additional file 3: Table S3)
M6A methylation inhibits ocular melanoma To evaluate whether the global m6A level is related to tumorigenesis in ocular melanoma, we first inhibited the expression of methyltransferase METTL3 in normal pigmented cells and ocular melanoma cells

Summary

Introduction

Dynamic N6-methyladenosine (m6A) RNA modification generated and erased by N6methyltransferases and demethylases regulates gene expression, alternative splicing and cell fate. N6-Methyladenosine (m6A), the most prevalent modification in mRNA [1, 2], is a dynamic RNA modification installed by “writer” methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14) and Wilms tumor associated protein (WTAP) [3,4,5]; erased by “eraser” fat-mass and obesity-associated protein (FTO) and α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) [6, 7]; and recognized by “readers”. Decreased METTL3 expression or METTL14 mutation in endometrial cancer reduces the m6A modification of AKT pathway-related genes, resulting in the activation of the AKT signaling pathway and contributing to tumorigenesis [10]. FTO erases m6A modification of tumor suppressor genes MYC/CEBPA, which contributes to the tumor formation of leukemia. Exploration of the novel m6A RNA methylation drivers of tumorigenesis is potentially interesting

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Conclusion