Systematic Characterization of Tauopathy-Associated Genetic Variation using Multiplexed Reporter Assays

使用多重报告基因检测系统表征 Tau 病相关遗传变异

基本信息

批准号：
10463634
负责人：
Yonatan Cooper
金额：
$ 5.18万
依托单位：
UNIVERSITY OF CALIFORNIA LOS ANGELES
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-30 至 2023-09-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10463634
关键词：
17q21 ATAC-seq Affect Alzheimer&apos s Disease Biological Assay Biological Models Biology Brain CRISPR/Cas technology Cells ChIP-seq Chromatin Clinical Cognition Disorders Complex Data Dementia Dependovirus Disease Disease model Disease susceptibility Epidemic Etiology Follow-Up Studies Frontotemporal Dementia Future Gene Expression Gene Frequency Genes Genetic Genetic Risk Genetic Variation Genetic study Genome Heritability Hi-C Human In Vitro Individual Libraries Linkage Disequilibrium Methods Modality Modeling Molecular Molecular Conformation Nerve Degeneration Neurodegenerative Disorders Neuroglia Neurons Nuclear Pore Complex Nucleic Acid Regulatory Sequences Parkinson Disease Pathogenesis Pathologic Performance Phenotype Polygenic Traits Progressive Supranuclear Palsy Protocols documentation Reporter Risk Role Serotyping Single Nucleotide Polymorphism Susceptibility Gene System Tauopathies Testing Tissues Transfection Untranslated RNA Variant Viral Virus Diseases Work aging population causal variant cell type cohort disorder risk effective therapy experimental study functional genomics gene network genetic analysis genetic architecture genome sequencing genome wide association study genome-wide genomic data improved in vitro Model in vivo innovation insight mortality nerve stem cell nervous system disorder neurodegenerative dementia new therapeutic target novel rare variant risk variant tau Proteins tau aggregation trait whole genome

项目摘要

PROJECT SUMMARY/ABSTRACT 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.

项目摘要/摘要痴呆症，神经退行性认知障碍，包括阿尔茨海默氏病（AD）和额颞由于人口迅速老龄化，痴呆症（FTD）被计划成为全球流行病。疾病病因仍然很了解，没有有效的治疗方法。因此，阐明分子神经退行性发病机理和识别新型治疗靶标的机制是至关重要。进行性上腹部麻痹（PSP）是一种神经退行性疾病，具有显着的临床，病理和遗传与多种痴呆症重叠，包括AD，FTD和帕金森氏病。与这些疾病相反，PSP具有相对同质的临床和神经病理表型，这动机将PSP作为神经退行性疾病的可传输但可推广的模型。一事实证明，方法可用于识别PSP的偶然疾病机制和神经变性更广泛的是遗传分析。但是，大多数人的变异是非 - 基因组的编码区域，很难在功能上解释。这包括稀有和结构性变体从整个基因组测序（WGS）工作和全基因组定位的常见敏感性协会研究（GWAS）。因此，非编码变化的功能注释仍然是主要的阐明神经退行性疾病的障碍。大规模平行的记者测定（MPRA）是强大的方法，以实验表征非编码变化的调节作用吞吐量方式，但尚未广泛应用于神经系统疾病。这项研究的目的是利用MPRA在功能上表征与PSP和PSP相关的非编码常见和罕见变化确定因果遗传风险。为此，AIM 1中提出的实验将首先建立新颖在分化的人类祖细胞（HNPC）中实施MPRA的方案 - 体外模型系统与神经系统疾病的研究。关键的创新将是交付MPRA 使用腺相关病毒（AAV）库中的HNPC库。 AIM 2将使用此方法1）确定因果关系由GWAS定位的9个PSP敏感性的基础的变体和2）模型选择功能变体使用CRISPR-CAS9的体外。这包括17q21.31的系统表征，一个重要的风险基因座与PSP，AD和PD相关的研究仍然很难研究。在AIM 3中，最大的PSP的变化迄今为止，WGS研究（1293例和2000个对照）将使用多个功能基因组优先考虑数据集并使用MPRA进行表征，代表PSP非编码罕见的第一个系统分析变异（等位基因频率<1％）。综上所述，这项工作将阐明 PSP并提供有关疾病风险差异的机械见解。更广泛地，它将提供对神经退行性疾病的遗传学和基本生物学的普遍理解，并作为未来研究的模型，旨在全面地表征复杂特征的非编码变化。