Gene expression differences in those with AD neuropathology and either clinical
  
   Lead Investigator:    Anand Mattay
   Institution      :    Lieber Institute for Brain Development
   E-Mail           :    Anand.Mattay@libd.org
   Proposal ID      :    700



   Proposal Description:
   This study will investigate differential gene expression between subjects with Alzheimer's disease neuropathology (presence of amyloid plaques and neurofibrillary tangles) and clinical dementia versus subjects with Alzheimer's disease neuropathology and normal cognition. The goal of this study is to identify genetic mechanisms of resilience to Alzheimer's disease neuropathology. We will control for center related variability in brain collection and other factors, we plan on using center as a specific co-variate of no interest in our analysis along with any other factors that might be different between the two groups (except for pathology which we will be matching for). As an added quality control measure for potential variability in tissue composition across multiple centers, we plan on quantifying the relative proportions of neurons in each sample. This approach utilizes DNA methylation (DNAm) data as a surrogate for cell mixtures, leveraging the cell type-specificity of DNAm marks, and has previously been designed, applied, and validated with both blood and brain [1, 2] samples. We also plan on performing bisulfite pyrosequencing using two primer sets for each sample, which, when combined with neuronal and non-neuronal cell populations derived from FACS data [3], will result in estimation of the proportion of neurons in each sample. We also routinely perform the RNA Integrity Number (RIN) test on each case to ensure that our gene expression studies are not subject to confounds including tissue degradation or pH changes. These measures will ensure that all cases collected and processed from multiple centers will be normalized for center specific collection, processing and storage variability.