UCLA

The widespread adoption of genome-wide association studies (GWAS) has revolutionized the detection of genetic loci associated with complex traits. However, the majority of common susceptibility loci reside in poorly annotated noncoding genomic regions and are composed of many correlated polymorphisms due to linkage disequilibrium, obscuring identification of the causal variants and mechanisms underlying trait association. Thus, the functional annotation of noncoding variation is a major impediment to interpretation of genetic risk. Massively Parallel Reporter Assays (MPRA) are a novel experimental approach for the high-throughput functional characterization of noncoding genetic variation, yet remain to be systematically applied to any neurologic disorder. In this dissertation, I utilize MPRA to characterize variation associated with two neurodegenerative disorders that share tau-protein neuropathology, Alzheimer’s disease and Progressive Supranuclear Palsy. First, I describe the design and implementation of an MPRA to screen 5,706 noncoding variants derived from three GWAS for AD and PSP, identifying 320 regulatory polymorphisms comprising 27 of 34 tested loci. These results enable subsequent identification of novel putative risk genes including PLEKHM1 and APOC1 distributed across the complex 17q21.31 and 19q13.32 regions. In Chapter 3, I show that functional predictions from four popular computational algorithms for variant prioritization are discordant both with MPRA results and each other. In Chapter 4, I find that MPRA-defined functional variants preferentially disrupt predicted transcription factor binding sites that converge on enhancers with differential cell-type specific activity in PSP and AD, implicating a neuronal SP1-driven regulatory network in PSP pathogenesis. These analyses support a novel mechanism underlying noncoding genetic risk, whereby common genetic variants drive disease risk via their aggregate activity on specific transcriptional programs. In Chapter 5, I perform genome editing to validate four causal loci, identifying C4 as a novel genetic risk factor for AD. Finally, in Chapter 6, I interrogate technical parameters relevant to assay performance, aiding future studies. Taken together, this work represents a comprehensive characterization of common genetic risk associated with AD and PSP and implicates variants, genes, and transcriptional regulatory networks that represent novel risk factors for neurodegenerative tauopathies.