Epigenome-wide DNA methylation profiling reveals risk genes for migraine and its subtypes

Migraine is a highly disabling neurovascular disorder, yet its underlying molecular mechanisms remain incompletely understood. Emerging evidence implicates epigenetic modifications, particularly DNA methylation, in migraine pathophysiology, but whether these changes play a causal role has not been established.

We integrated large-scale brain and blood methylation quantitative trait loci (mQTL) datasets with genome-wide association study (GWAS) data to investigate the causal role of DNA methylation in migraine and its subtypes. Two-sample Mendelian randomization (MR) was applied to evaluate the effects of cytosine-phosphate-guanine (CpG) methylation on migraine risk. Significant CpG sites were annotated to genes and refined through a multi-step prioritization framework incorporating colocalization, expression QTL (eQTL)-MR, two-step MR, and gene-based association analyses. Functional enrichment, protein-protein interaction, and drug-gene analyses were then performed to explore biological mechanisms and therapeutic potential.

We identified 169 CpG sites with causal effects on migraine, mapping to 68 genes. Subtype analyses revealed 10 additional genes associated with MA and MO, including three genes specific to MA and one to MO, expanding the total to 72 non-overlapping migraine risk genes. Integrative prioritization highlighted 12 high-confidence genes, among which CFDP1, ICA1L and SERPING1 was supported by all five analytical approaches. Functional characterization indicated significant enrichment in calcitonin-like ligand receptors, axon development and neurovascular regulation, while drug-gene interaction analyses suggested therapeutic potential for targets such as MAPT and CALCA.

Our findings provide robust evidence that DNA methylation contributes causally to migraine risk and its subtypes, identify genes of biological and therapeutic relevance, and offer novel insights into the epigenetic mechanisms underlying migraine pathophysiology.