Multi-omics integration reveals the role of N6-methyladenosine in epilepsy, ischemic stroke, and vascular dementia

N6-methyladenosine (m6A) methylation is an essential epigenetic modification that regulates mRNA stability, splicing, and translation. Its role in neurological diseases, including epilepsy, ischemic stroke, and vascular dementia (VaD), remains poorly understood.

We integrated multi-omics data, including GWAS, m6A quantitative trait loci (QTL), expression QTL (eQTL), and protein QTL (pQTL), and using FUSION to assess the association of m6A with these diseases. Transcriptome-wide association studies (TWAS) and Mendelian Randomization (MR) were performed to identify causal relationships between m6A sites, gene expression, and disease. Differentially expressed genes (DEGs) were analyzed via RNA sequencing and enriched for biological pathways. Protein-protein interaction (PPI) networks and m6A-related gene-disease associations were constructed to reveal regulatory mechanisms.

We identified 218 m6A sites significantly associated with the three diseases, highlighting 3,430 associations between m6A sites and gene expression. Functional enrichment analysis revealed key pathways, including base excision repair and chemokine-mediated signaling. MR analysis identified causal relationships, such as NBL1 in epilepsy, TPGS2 in ischemic stroke, and SERINC2 in VaD. PPI analysis revealed interactions involving critical proteins like PARP1, MCL1, and CD40, underscoring their role in neuroinflammation and apoptosis.

Our findings elucidate the genetic and epigenetic roles of m6A in epilepsy, ischemic stroke, and VaD, uncovering potential mechanisms by which m6A modulates gene and protein expression to influence disease outcomes. These insights highlight m6A as a promising biomarker and therapeutic target for neurological diseases.