Mapping cell-type-specific regulatory genomic variation in Alzheimer's disease pathology.

Alzheimer's disease (AD) is a chronic neurodegenerative disorder affecting >26 million people worldwide, with no disease-modifying treatments available. Despite major advances in identifying genetic risk factors for AD, there remains uncertainty about the specific causal genes involved and how their function is dysregulated during the progression of neuropathology.

Sequencing the genome was only the first step in our quest to understand how genes are expressed and regulated. Increased understanding about the functional complexity of the genome has led to recognition about the role of regulatory variation in health and disease. Sitting above the DNA sequence is a second layer of information (the 'epigenome') that mediates the regulation of when and where genes are functionally transcribed. These mechanisms play a critical role in determining cell-type-specific patterns of gene transcription in the human brain.

Previous genomic analyses of AD brain have been limited by their use of 'bulk' tissue, comprising a mix of different neural cell-types. Because AD is characterised by changes in specific cell-types (for example it involves the extensive loss of neurons and the proliferation of glial cells) it is critical to consider cellular differences in gene regulation. Our study will, for the first time, systematically examine the role of regulatory genomic processes in specific cell types in AD pathology.

Our innovative proposal leverages the unprecedented brain-banking efforts currently taking place in the UK, specifically within the Brains for Dementia Research (BDR) cohort. We propose an integrative-genomics approach, profiling purified populations of cortical nuclei from donors with low and high levels of AD pathology. Our project has the following key aims

First, we will profile markers of epigenomic regulation in purified nuclei from three different cell types (neurons, oligodendrocytes and microglia) isolated from cortex tissue from donors with low and high levels of AD pathology.

Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets.

Third, we will examine how AD-associated genetic variation influences gene regulation in specific cortical cell-types.

Our team is uniquely placed to undertake this ambitious project given our pioneering work assessing epigenomic variation in AD brain and our role in developing novel methods for regulatory genomic profiling across distinct neural cell-types.

Finally, we are passionate advocates for Open Science, and we will make all data and methods freely available to the wider research community. In conjunction with the extensive clinical and neuropathological data being collected on each donor included in the study, we will generate an unrivalled data resource that will stimulate dementia research and enable a step-change in understanding of the mechanistic pathways involved in AD.

We propose the most comprehensive analysis of regulatory genomic variation associated with Alzheimer's disease (AD). The project builds on our previous work assessing the role of epigenomic variation in AD and success in developing methods for regulatory genomic profiling across distinct neural cell-types.

First, we will profile multiple markers of genomic regulation (DNA methylation, DNA hydroxymethylation, lysine H3K27 acetylation (H3K27ac) and chromatin accessibility) in purified nuclei populations from the dorsolateral prefrontal cortex (DLPFC) from 200 donors with low and high AD neuropathology. We will use a fluorescence-activated nuclei sorting (FANS) protocol developed by our group to simultaneously purify nuclei from neurons, oligodendrocytes and microglia prior to genomic profiling.

Second, we will validate regulatory regions associated with AD pathology in additional samples and datasets. We will use cell-type-specific epigenomic data to develop and validate cellular deconvolution algorithms, enabling us to leverage large existing AD genomic datasets generated by us and our collaborators for replication. We will also integrate our cell-type-specific epigenomic data with single nuclei transcriptomic data from the Multi-Omics Atlas Project (MAP) funded by the UK Dementia Research Institute (DRI). Finally, we will explore overlap with cortical genomic changes identified in our ongoing analyses of transgenic mouse models of tau and amyloid pathology.

Finally, we will integrate cell-type-specific genomic annotations with AD genetic data, exploring the extent to which AD-associated variants are enriched for regulatory quantitative trait loci (QTLs). We will extend our use of co-localization approaches and Summary data-based Mendelian Randomization (SMR) analyses to identify variants that are pleiotropically associated with both AD and regulatory variation in specific cortical cell-types.