Landscape of m6A mRNA Methylation and Expression Signatures in Human Glioma

Glioblastoma (GB) are highly aggressive and genetically complex brain tumors that infiltrate surrounding brain tissue, making them extremely difficult to treat effectively. Recent research has revealed that m6A modification is abnormally activated in glioma, underscoring its key role in various processes of glioma development. m6A modifications in mRNA of glioma stem cells NCH421k (GSCs) and in glioblastoma tumor tissues were investigated using methylation-based RNA immunoprecipitation (MeRIP) and direct Nanopore RNA sequencing (dRNA-seq). Data analysis amongst GSCs demonstrated 740 hypermethylated and 830 hypomethylated genes after MeRIP-seq. dRNA-seq data presented 4,340 RRACH motifs associated with hyper-methylated up-regulated genes and 9,106 motifs associated with hyper-methylated down-regulated genes across samples taken from glioma patients. We identified eight statistically significant RRACH motifs across seven genes — AAACA|2129|OS9, AGACA|1210|PAGR1, GGACA|2173|OS9, GGACT|2187|TOB1, AAACC|3283|PIK3R2, GAACC|3068|GP1BB, GGACA|3110|RETREG1, and GGACT|3122|LUC7L3 — to narrow down potential gene candidates. Findings indicated that m6A in target motifs is modified approximately 3.4-fold more in LGG than in GB, distinguishing patient samples by pathology. Next, we found that global m6A methylation score was significantly lower in GB cluster compared to LGG cluster (p=0.0002). Furthermore, lower m6A methylation scores were associated with shorter survival in glioma patients (p=0.016) while the expression levels did not differ among m6A-based clusters (p=0.08) or in a Kaplan-Meier survival analysis (p=0.79). In summary, m6A modifications in mRNA may emerge as future-defining biomarkers capable of reshaping gliomas biology.