Cell-type Specific Interrogation of Variant Function in Alzheimer's Disease

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Abstract Alzheimer’s Disease (AD) affects over 26 million people worldwide, yet the treatment options are limited. This is in large part due to the unclear molecular mechanisms underlying AD. Genome-wide association studies (GWAS) have identified genomic regions that are associated with AD, but determining the exact causal variants and genes remains a major challenge. Recent developments in high throughput genomic technologies have incredible potential to functionally characterize these causal features, but must be applied to the correct cell types. Neurons, astrocytes, and microglia are all thought to play key roles in the etiology of AD but obtaining viable primary human brain cells for these experiments is understandably very difficult. Therefore, recent protocols to rapidly differentiate human induced pluripotent stem cells into various brain cell types offer great promise as tools to decipher the genetic basis of AD and guide future therapeutic efforts. The goal of this project is to identify which AD risk variants alter transcriptional regulatory capacity in human brain cells and to map them to the genes they regulate. To understand which variants are functional in microglia, astrocytes, and neurons, I will perform massively parallel reporter assays in human induced pluripotent stem cells (hiPSCs) differentiated into each cell type (Aim 1). To identify AD risk genes, I will use publicly available Hi-C, ATAC-seq, and RNA-seq in hiPSC-derived microglia, astrocytes, and neurons to link variants to genes (Aim 2A). I will functionally validate a selection of putative variant-gene pairs with CRISPR inhibition (Aim 2B). The results of this work will identify cell-type specific causal variants, and the genes that they regulate. This will have a positive impact because understanding exactly which genes are involved in which cell types in AD will elucidate the molecular mechanisms of the disease etiology. The genes identified in this study can act as targets for future studies and candidates for therapeutic design.