An iPSC based platform for functionally assessing genetic and environmental risk

基于 iPSC 的平台，用于功能性评估遗传和环境风险

• 批准号: 8764379
• 负责人: RUDOLF JAENISCH
• 金额: $ 102.7万
• 依托单位: WHITEHEAD INSTITUTE FOR BIOMEDICAL RES
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-23 至 2019-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8764379
• 关键词: Affect; Age; Alleles; Binding; Biological; Biological Assay; Brain; Cell Nucleus; Cells; Chromosomes; Chronic; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Deoxyribonucleases; Development; Disease; Distal; Elements; Enhancers; Environmental Risk Factor; Functional RNA; Gene Expression; Gene Targeting; Generations; Genes; Genetic; Genetic Determinism; Genetic Enhancer Element; Genetic Predisposition to Disease; Genetic Risk; Genome; Genomics; Genotype; Goals; Health; Human; In Vitro; Individual; Link; Maps; Mediating; Messenger RNA; Microsatellite Repeats; Midbrain structure; Mitochondria; Molecular; Molecular Conformation; Mutation; Neurodegenerative Disorders; Neurons; Parkinson Disease; Pathogenesis; Patients; Phenotype; Population; Predisposition; Prevalence; Printing; RNA; Regulatory Element; Risk; Role; SNCA gene; Single Nucleotide Polymorphism; Site; Somatic Cell; Sorting - Cell Movement; Specificity; Stress; System; Testing; Therapeutic; Time; Toxin; Validation; Variant; aging population; alpha synuclein; base; candidate selection; disorder risk; dopaminergic neuron; foot; genetic variant; genome wide association study; global health; human embryonic stem cell; induced pluripotent stem cell; insight; novel; research study; response; risk variant; single molecule; stem cell technology; transcription factor; transcriptome sequencing

DESCRIPTION (provided by applicant): Parkinson's disease (PD) is the second most common chronic progressive neurodegenerative disease worldwide, with a prevalence of more than 1% in the population over the age of 60, thus constituting a major global health problem of the aging population. The disease is primarily characterized by a major loss of nigrostriatal dopaminergic neurons but the genetic etiology leading to the neuronal cell loss has largely remained unknown. Numerous genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) that point to more than 50 genomic loci containing "risk variants" for sporadic PD. However the identified risk variants predominantly map to poorly understood non-coding regions of the genome, which has impeded functional and molecular understanding of how these genetic variants contribute to the increased risk for PD. Importantly, it has been established that PD GWAS associated loci are typically non-coding and mediate allele-specific effects on distal gene expression, consistent with a central role for disruption on enhancer element function in PD pathogenesis Human induced pluripotent stem cell (hiPSC) technology offers for the first time the unique opportunity to study sporadic diseases whose genetic components are poorly understood, by allowing for the generation of human patient-derived somatic cells such as midbrain dopaminergic neurons which carry all the genetic alterations that contributed to the development of the disease. The overall goal of this project is to establish a transformational paradigm, which overcomes the substantial technical limitations of the iPS system and creates a genetically defined experimental in vitro system for studying the molecular and biological mechanisms of sporadic PD in the dish. To achieve this, we will establish a novel experimental framework to link "descriptive" GWAS PD hits to genomic regulatory enhancer elements and establish functional assays for connecting PD risk alleles to the expression of disease relevant effector genes. Our aim is to gain molecular understanding of the complex interactions between multiple genetic risk alleles and to identify key genes of which the expression level affects the PD specific cellular phenotype. To identify functional relevant candidate risk variants (PD-eQLTs) we will link PD associated risk alleles to genomic regulatory (enhancer) elements that are relevant for gene activity in neurons by establishing an enhancer map in cultured homogenous dopaminergic neurons as well as in sorted neuronal nuclei from human brain. Insights into these interactions will facilitate devising rational therapeutic strategies. This experimental in vitro platform will be used to define the interactions of environmental risk factors with the genetic determinants that have been predicted from GWA studies to predispose to PD (GxE).

描述（由申请人提供）：帕金森病（PD）是全球第二大最常见的慢性进行性神经退行性疾病，在60岁以上人群中患病率超过1%，构成了全球人口老龄化的主要健康问题。该疾病的主要特征是黑质纹状体多巴胺能神经元的大量丢失，但导致神经元细胞丢失的遗传病因在很大程度上仍然未知。许多全基因组关联研究（GWAS）已经确定了单核苷酸多态性（snp），指出50多个基因组位点包含散发性帕金森病的“风险变异”。然而，已确定的风险变异主要映射到基因组的非编码区域，这阻碍了对这些遗传变异如何导致PD风险增加的功能和分子理解。重要的是，已经确定PD - GWAS相关位点通常是非编码的，并且介导远端基因表达的等位基因特异性作用，这与破坏PD - GWAS的核心作用一致