Exploring novel blood-based DNA methylation biomarkers for alzheimer’s disease via targeted sequencing of highly variable CpG sites

Dementia, particularly Alzheimer’s disease (AD), continues to be a major public health concern due to population aging, yet minimally invasive biomarkers for early diagnosis have not been established. DNA methylation (DNAm) has recently attracted considerable attention as a promising biomarker. This study aimed to identify blood-based DNAm biomarkers for early detection of AD. We analysed blood-derived DNA from 48 patients with AD (from Biobank Japan) and 48 age- and sex-matched controls (from the Tohoku Medical Megabank Biobank) using Apolipoprotein ε type 4 (APOE)-associated genotype analysis and targeted-bisulfite sequencing. High-risk APOE genotypes were more frequent in AD patients (23/48, [47.9%]) than in controls (6/48, [12.5%]). A typical case-control and APOE genotype-stratified epigenome-wide association study (EWAS) did not identify any genome-wide significant CpG sites. Although the primary findings were negative, some top CpG sites appeared in both analyses, including loci on the Cell Adhesion Molecule 1 (CADM1), Tubulin alpha 1b (TUBA1B), and Exocyst complex component 2 (EXOC2) genes, which have previously been linked to AD-related pathways. The relatively early clinical stage and uncertainty of disease onset might have limited detection sensitivity. Longitudinal studies with refined staging and multi-omics integration might clarify the biomarker potential of blood DNAm in AD.