Fine‐mapping and replication of EWAS loci harboring putative epigenetic alterations associated with AD neuropathology in a large collection of human brain tissue samples

Abstract

Introduction Our previous epigenome‐wide association study (EWAS) of Alzheimer's disease (AD) in human brain identified 71 CpGs associated with AD pathology. However, due to low coverage of the Illumina platform, many important CpGs might have been missed. Methods In a large collection of human brain tissue samples (N = 864), we fine‐mapped previous EWAS loci by targeted bisulfite sequencing and examined their associations with AD neuropathology. DNA methylation was also linked to gene expression of the same brain cortex. Results Our targeted sequencing captured 130 CpGs (∼1.2 kb), 93 of which are novel. Of the 130 CpGs, 57 sites (only 17 included in previous EWAS) and 12 gene regions (e.g., ANK1, BIN1, RHBDF2, SPG7, PODXL) were significantly associated with amyloid load. DNA methylation in some regions was associated with expression of nearby genes. Discussion Targeted methylation sequencing can validate previous EWAS loci and discover novel CpGs associated with AD pathology.

Identification of a specific APOE transcript and functional elements associated with Alzheimer’s disease

“…APOE acts in conjunction with other genetic and environmental factors to confer AD risk. DNA methylation and chromatin status are associated with genetic and environmental factors, and previous studies have identified associations with AD and neuropathological hallmarks of AD in large collections of human brain tissue samples 36,37 . However, DNA methylation at the APOE locus has not been well studied.…”