Dementias, neurodegenerative cognitive disorders that include Alzheimer's disease (AD) and frontotemporal dementia (FTD), are slated to become a global epidemic due to a rapidly aging population. Disease etiology remains poorly understood and there are no effective treatments. Therefore, elucidating molecular mechanisms underlying the pathogenesis of neurodegeneration and identifying novel therapeutic targets is critically important. Progressive supranuclear palsy (PSP) is a neurodegenerative disease that has significant clinical, pathological, and genetic overlap with several dementias including AD, FTD, and Parkinson's disease. In contrast to these disorders, PSP has a relatively homogenous clinical and neuropathological phenotype, which motivates the study of PSP as a tractable yet generalizable model of neurodegenerative disease. One method that has proven useful for identifying casual disease mechanisms underlying PSP and neurodegeneration more broadly is genetic analysis. However, the majority of human variation is in non- coding regions of the genome and is difficult to functionally interpret. This includes rare and structural variants from whole genome sequencing (WGS) efforts and common susceptibility loci identified by genome-wide association studies (GWAS). Therefore, functional annotation of non-coding variation remains a major impediment to the elucidation of neurodegenerative disease. Massively Parallel Reporter Assays (MPRA) are a powerful approach for experimentally characterizing the regulatory effects of non-coding variation in a high- throughput manner, but have yet to be widely applied to neurologic disorders. The purpose of this study is to utilize MPRA to functionally characterize non-coding common and rare variation associated with PSP and identify causal genetic risk. To accomplish this, the experiments proposed in Aim 1 will first establish a novel protocol for implementing MPRA within differentiated human neural progenitor cells (hNPCs) ? an in vitro model system germane to the study of neurological disease. A critical innovation will be to deliver the MPRA library into hNPCs using adeno-associated viruses (AAV).
Aim 2 will use this approach to 1) identify causal variants underlying 9 PSP susceptibility loci identified by GWAS, and 2) model select functional variants in vitro using CRISPR-Cas9. This includes a systematic characterization of 17q21.31, an important risk locus associated with PSP, AD, and PD that has remained difficult to study.
In Aim 3, variation from the largest PSP WGS study to date (1293 cases and 2000 controls) will be prioritized using multiple functional genomics datasets and characterized using MPRA, representing the first systematic analysis of PSP non-coding rare variation (allele frequency < 1%). Taken together, this work will elucidate the regulatory genetic architecture of PSP and provide mechanistic insights into variation underlying disease risk. More broadly, it will provide generalizable understanding of the genetics and fundamental biology of neurodegenerative disease and serve as a model for future studies seeking to comprehensively characterize non-coding variation in complex traits.
Progressive supranuclear palsy (PSP) is an important yet poorly understood neurodegenerative disorder that shares clinical, pathological, and genetic features with dementias including Alzheimer's disease, Frontotemporal dementia, and Parkinson's disease. We propose developing high-throughput experimental approaches to identify and characterize functional genetic variation underlying PSP risk. Ultimately, this work may yield mechanistic insights into the pathogenesis of neurodegeneration and provide novel therapeutic targets, while serving as a model for future studies of neurological disease.
