DNA hydroxymethylation and AD

This project was funded by NIA (7RF1AG052476, 6/15/2016-8/31/2021, PI: Jinying Zhao). The goal of this project is to identify causative 5hmC alterations associated with quantitative neuropathological measures for early features of AD pathology (e.g., amyloid plaques, neurofibrillary tangles). To achieve this, we propose four specific aims: (1) Identify differentially hydroxymethylated regions associated with AD pathology by genome-wide profiling of 5hmC in 740 postmortem brains collected by two large, community-based population studies of aging and dementia: the Religious Order Study (discovery sample) and the Rush Memory and Aging Project (replication sample). As traditional methods cannot discriminate between 5mC and 5hmC, we will perform 5hmC-capture sequencing, followed by TET-assisted bisulfite sequencing using novel techniques developed by our group and collaborators. (2) Conduct targeted methylation sequencing to identify additional AD-associated 5mC alterations that may have been missed by our previous EWAS as a result of the limited resolution and genome coverage of the Illumina platform. (3) Functionally validate the putative genes identified in Aims 1 and 2 using existing RNA-seq data from the same brain cortex and a fly model for AD. (4) Perform integrative `omics’ analyses to test the joint and interactive effects of multi-layer `omics’ markers on AD pathology.