Epitranscriptome Mapping of m ⁶ A RNA Modifications in Glioma Tumor Tissue

Glioma represents the most common primary central nervous system (CNS) neoplasm in adults. IDH1 mutation is recognized as a hallmark alteration with important diagnostic and prognostic implications. There is considerable evidence for global DNA hypermethylation induced secondary to IDH mutation. However, there is limited understanding of the RNA methylation patterns and its role in glioma biology. In this study, we performed transcriptome wide profiling of N6-methyladenosine (m ⁶ A) modifications across IDH mutant (n = 8) and wild-type (n = 7) gliomas using Oxford Nanopore Technologies’ direct RNA sequencing platform. Our approach enabled high-depth coverage of native transcripts, revealing nearly twice as many full-length transcripts in IDH mutant gliomas compared to wild-type. Notable differences in alternative splicing were observed across glioma subtypes, with truncated and non-coding isoforms more prevalent in glioblastoma (GBM). We further identified significant changes in isoform usage within key metabolic (NAMPT, PKM) and immune (CD63, CD151, CD81) pathways. Chromosomal distribution of m ⁶ A sites showed a higher prevalence of m ⁶ A modifications in IDH mutant gliomas, with the most pronounced differences on chromosomes 19 and 16. Further stratification by TERT, MGMT, and TP53 mutations revealed similar patterns of increased m6A site numbers in mutant groups, highlighting the importance of integrating epigenomic and epitranscriptomic data in glioma research. These findings highlight the role of m ⁶ A modifications in the metabolic reprogramming unique to IDH mutant gliomas, providing insights into potential mechanisms of tumorigenesis and therapeutic resistance.