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Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease

ABSTRACT: Genome-wide association studies (GWAS) have identified thousands of variants associated with disease phenotypes. However, the majority of these variants do not alter coding sequences, making it difficult to assign their function. To this end, we present a multi-omic epigenetic atlas of the adult human brain through profiling of the chromatin accessibility landscapes and three-dimensional chromatin interactions of seven brain regions across a cohort of 39 cognitively healthy individuals. Single-cell chromatin accessibility profiling of 70,631 cells from six of these brain regions identifies 24 distinct cell clusters and 359,022 cell type-specific regulatory elements, capturing the regulatory diversity of the adult brain. We develop a machine learning classifier to integrate this multi-omic framework and predict dozens of functional single nucleotide polymorphisms (SNPs), nominating gene and cellular targets for previously orphaned GWAS loci. These predictions both inform well-studied disease-relevant genes, such as BIN1 in microglia for Alzheimer’s disease (AD) and reveal novel gene-disease associations, such as STAB1 in microglia and MAL in oligodendrocytes for Parkinson’s disease (PD). Moreover, we dissect the complex inverted haplotype of the MAPT (encoding tau) PD risk locus, identifying ectopic enhancer-gene contacts in neurons that increase MAPT expression and may mediate this disease association. This work greatly expands our understanding of inherited variation in AD and PD and provides a roadmap for the epigenomic dissection of noncoding regulatory variation in disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE147672 | GEO | 2020/07/26

REPOSITORIES: GEO

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Project description:Public transcriptomics studies have shown that several genes display pronounced gender differences in their expression in the human brain, and these differences may influence the clinical manifestations and risk for neuronal disorders. While disease relevant implications have already been proposed for gender differences in hormone levels, life style and genetic diversity, a systems level analysis of brain gene expression disparities between the genders in the context of brain disorders like Alzheimer’s disease (AD) has not yet been conducted. Here we apply a transcriptome-wide analysis to discover genes with gender-specific expression and significant alterations in public post mortem brain tissue from AD patients compared to unaffected controls. We identify the sex-linked ubiquitin specific peptidase 9 (USP9) as an outstanding candidate gene with one of the largest ratios of male to female median expression levels during adulthood and a highly significant underexpression of the Y-chromosomal form of the gene (USP9Y) in male AD patients compared to controls. Previous studies have shown that USP9 can modulate the phosphorylation of the microtubule-associated protein tau (MAPT), whose dysregulation in AD is thought to play a key role in disease. Here, after observing a high positive correlation between USP9Y and MAPT expression in public transcriptomics data from AD case/control studies, we show that USP9 knockdown results in significantly decreased MAPT expression in the in vitro DU145 cell culture model. From the analysis of transcriptomics data for the knockdown in DU145 cells and prior knowledge from the literature, we derive a model for a USP9-dependent regulatory mechanism modulating MAPT expression via BACH1 and SMAD4. Overall, the combined transcriptomics analyses and identified functional links between USP9 and MAPT suggest USP9 may partially account for gender differences observed in tauopathies and could provide a new target for intervention strategies to modulate MAPT expression and phosphorylation.

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Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease

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