INTRODUCTION:

DNA methylation may help mediate interactions between genetic and environmental risk factors in Alzheimer’s disease (AD). However, previous large-scale AD epigenome-wide association studies (EWASs) have largely relied on Illumina 450K methylation arrays and have not comprehensively assessed the impact of APOE genotype on methylation in the human brain.

We performed three coordinated EWAS meta-analyses using Illumina 450K and higher-density EPIC array data from post-mortem prefrontal cortex (PFC):

1. APOE ε4risk allele1 EWAS meta-analysis (N = 1334)
2. APOE ε2protective allele2 EWAS meta-analysis (N = 1334)
3. AD Braak stage EWAS meta-analysis – the largest of its kind in post-mortem PFC to date (N = 1978)

 

APOE ε4 META ANALYSIS

Five Bonferroni-significant differentially methylated positions (DMPs) found, all in the broad APOE region. Three have been previously reported. Two additional FDR-significant DMPs were detected: a hypomethylated exonic site in FEM1C (chr5:114,880,330), a gene involved in ubiquitin-dependent protein degradation, and a hypermethylated exonic site in ARMC1 (chr8:66,546,317), a gene encoding a protein involved in mitochondrial distribution.

 

APOE ε2 META ANALYSIS

Two hypermethylated Bonferroni-significant DMPs were identified: one intergenic site between APOE and APOC1, and one in the HOMER1 promoter, a gene implicated in glutamatergic signalling, synaptic plasticity and AD brain expression changes.

DMR analysis (seed p ≤ 1×10⁻⁴; region Šidák-adjusted p ≤ 0.05) identified a ε2-associated hypermethylated promoter CpG island at the CAT locus, a key peroxisomal antioxidant gene. Catalase plays a central role in hydrogen peroxide detoxification and oxidative stress regulation, processes implicated in AD pathophysiology.

 

BRAAK STAGE META ANALYSIS

287 Bonferroni-significant Braak stage-associated DMPs were identified, including known AD methylation loci such as SPG7, ANK1, MYO1C, CSF1R, CDH23 & SLC44A2. The top DMP was a hypermethylated site in the gene body of SPG7.

 

CONCLUSION

This comprehensive meta-analysis links APOE genotype and Braak stage to APOE-proximal and widespread AD-associated methylation changes using 450K and EPIC-array data.