Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms (RNA-Seq)

Epigenetic control of enhancers alters neuron functions and may be involved in Alzheimer’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology (n=101). We identify 1,224 differentially methylated enhancer regions; most of which are hypomethylated at CpH sites in AD neurons. CpH methylation losses occur in normal aging neurons, but are accelerated in AD. Integration of epigenetic and transcriptomic data demonstrates a pro-apoptotic reactivation of the cell cycle in post-mitotic AD neurons. Furthermore, AD neurons have a large cluster of significantly hypomethylated enhancers in the DSCAML1 gene that targets BACE1. Hypomethylation of these enhancers in AD is associated with an upregulation of BACE1 transcripts and an increase in amyloid plaques, neurofibrillary tangles, and cognitive decline. In order to identify enhancers involved in AD, we comprehensively mapped DNA methylation at enhancers, genome-wide, in neurons isolated from the prefrontal cortex of 106 individuals with no/mild, moderate and severe AD pathology (Braak stage: I-II n=38, III-IV n=32, and V-VI n=36). We first isolated neuronal nuclei using an established antibody (NeuN+) and flow cytometry-based approach. We then fine-mapped DNA methylation at enhancer elements using a targeted bisulfite sequencing strategy, known as bisulfite padlock probe sequencing.