Modeling the impact of regulatory and splicing variants on cellular function in Alzheimer's disease

Alzheimer's disease (AD) is an age-related neurodegenerative disease characterized by progressive cognitive decline and dementia. Despite more than fifty years of research, no cures exist and the standard of treatment remains unsatisfactory. Genome wide association studies (GWAS) indicate that AD risk reflects both highly penetrant rare variants as well as common single nucleotide polymorphisms with small effect sizes. By overlapping GWAS and post-mortem and myeloid cell expression analyses, we have identified common variants with expression and splicing quantitative trait loci that may contribute to altered gene expression or alternative splicing; however, demonstrating which risk loci are the causal contributors to disease risk remains an intractable problem. Here, we will apply statistical approaches to prioritize putative causal variants in AD-associated loci by incorporating expanded AD GWAS functional annotations, single cell chromatin profiles and histone modification and microglia gene expression datasets. We will then apply a human induced pluripotent stem cell (hiPSC)-based approach to manipulate the genotype of prioritized putative causal AD risk variants that alter gene expression or alternative splicing of mRNAs, focusing largely on genes implicated in phagocytosis and lysosomal-autophagy function. Through isogenic comparisons of neurons, microglia, and astrocytes, we propose to examine the molecular and functional effects of perturbing five putative causal SNPs separately testing their cell autonomous and non-cell autonomous impact on cellular function. Our hope is that this work may identify novel therapeutic points of intervention in order to prevent or slow disease course in individuals with AD. This project will have a large overall impact by providing a mechanistic interpretation of genetic variants associated with AD susceptibility.