Comprehensive analysis of the transcriptome-wide m⁶A methylome in invasive malignant pleomorphic adenoma

Invasive malignant pleomorphic adenoma (IMPA) is a highly invasive parotid gland tumor and lacks effective therapy. N6-Methyladenosine (m⁶A) is the most prevalent post-transcriptional modification of mRNAs in eukaryotes and plays an important role in the pathogenesis of multiple tumors. However, the significance of m⁶A-modified mRNAs in IMPA has not been elucidated to date. Hence, in this study, we attempted to profile the effect of IMPA in terms of m⁶A methylation in mRNA.

Methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were utilized to acquire the first transcriptome-wide profiling of the m⁶A methylome map in IMPA followed by bioinformatics analysis.

In this study, we obtained m⁶A methylation maps of IMPA samples and normal adjacent tissues through MeRIP-seq. In total, 25,490 m⁶A peaks associated with 13,735 genes were detected in the IMPA group, whereas 33,930 m⁶A peaks associated with 18,063 genes were detected in the control group. Peaks were primarily enriched within coding regions and near stop codons with AAACC and GGAC motifs. Moreover, functional enrichment analysis demonstrated that m⁶A-containing genes were significantly enriched in cancer and metabolism relevant pathways. Furthermore, we identified a relationship between the m⁶A methylome and the RNA transcriptome, indicating a mechanism by which m⁶A modulates gene expression.

Our study is the first to provide comprehensive and transcriptome-wide profiles to determine the potential roles played by m⁶A methylation in IMPA. These results may open new avenues for in-depth research elucidating the m⁶A topology of IMPA and the molecular mechanisms governing the formation and progression of IMPA.