Single-cell Epigenome Analysis of the Alzheimer's Disease Brain

Title: Single-cell Epigenome Analysis of the Alzheimer’s Disease Brain (PI: Hartl)Alzheimer’s disease (AD) affects more than 6 million American but no cures and few effective treatments are available. Genome-wide association studies (GWAS) have uncovered thousands of segregating mutations that significantly increase AD risk. Most of these variants alter non-protein-coding sequence and lack clear functional annotation, hindering efforts to translate risk-conferring mutations into curative or preventative therapies. Heritability partitioning suggests that these variants likely perturb gene expression in glial cells (especially microglia), ultimately leading to AD pathology. Linking these variants – and their downstream effects – to specific regulatory networks and pathways has been hindered by a lack of cis-regulatory element maps for these major glial cell classes and their subtypes. The proposed study addresses this critical knowledge gap by applying a cutting-edge single cell multi-omic technology to postmortem human brain samples from phenotypically normal donors and AD patients. Specifically, the chromatin accessibility or histone modifications will be interrogated jointly with gene expression at single cell resolution in dorsolateral prefrontal cortex (DLPFC) from multiple donors, to identify and characterize the cell-type-specific gene regulatory elements that drive aberrant cell states and disease-relevant cellular responses in human AD brains. The single cell chromatin state and gene expression atlases from phenotypically normal individuals will be compared to those from AD subjects to determine the brain cell types, genes and regulatory elements that exhibit significant changes in pathological conditions. Finally, the newly generated cell-type resolved epigenome maps will be integrated with public genomic resources to provide functional annotation of the AD risk variants, identify disease-relevant cell types, prioritize genes, transcription factors, and molecular pathways for future mechanistic investigation. Results of the proposed study will provide a much-needed tool for study of AD pathogenesis and development of improved AD therapies.