m⁶A modification suppresses ocular melanoma through modulating HINT2 mRNA translation

Dynamic 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.

m⁶A 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.

Here, 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.

Our work uncovers a critical function for m⁶A methylation in ocular melanoma and provides additional insight into the understanding of m⁶A modification.