Comprehensive Analysis of Aberrant m6A RNA Modifications Identifies Prognostic Biomarkers in Non-Small Cell Lung Cancer

<b>Background:</b> Dysregulation of N6-methyladenosine (m6A) RNA modification plays a critical role in the development and progression of non-small cell lung cancer (NSCLC). <b>Methods:</b> To explore the m6A modification landscape in NSCLC, we utilized direct RNA nanopore sequencing (dRNA-seq) to compare m6A patterns between NSCLC and adjacent normal tissues. <b>Results:</b> Our analysis revealed distinct m6A modification differences, with tumor tissues showing reduced m6A density compared to normal tissues. Aberrantly modified genes, such as <i>SOX2</i> and <i>TOP2A</i>, exhibited hypomethylated m6A modifications and were upregulated in NSCLC tissues. We identified 14,419 differentially methylated m6A sites, with 49.5% hypermethylated and 50.5% hypomethylated. Functional enrichment analysis showed that hypermethylated genes were involved in DNA replication and transcription regulation, while hypomethylated genes were linked to cell migration and MAPK signaling. The expression patterns of m6A regulators, including <i>METTL3</i>, <i>METTL16</i>, <i>CBLL1</i>, <i>FTO</i>, <i>ALKBH5</i>, and <i>ELAVL1</i>, were consistent across NSCLC subtypes. Furthermore, correlation with clinical data from the TCGA database revealed that m6A-associated DEGs, such as <i>HMGA1</i>, <i>ERO1A</i>, <i>LRFN4</i>, <i>SNTN</i>, <i>SLC2A1</i>, <i>DNASE2B</i>, and <i>VSIG2</i>, were prognostically significant in NSCLC. <b>Conclusions:</b> This study underscores the pivotal role of m6A modifications in NSCLC and highlights the potential of dRNA-seq for identifying RNA epigenetic changes that may serve as novel therapeutic targets.