Gene signatures linked to the cell biological phenotypes of familial PD

与家族性 PD 细胞生物学表型相关的基因特征

• 批准号: 8670043
• 负责人: OLE ISACSON
• 金额: $ 19.55万
• 依托单位: MCLEAN HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-07-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8670043
• 关键词: Age; Binding; Biogenesis; Bioinformatics; Biological; Biomedical Research; Candidate Disease Gene; Cell Line; Cells; Cellular biology; DNA; DNA Damage; DNA Repair; DNA Sequence; Data; Databases; Future; Gene Expression; Gene Expression Profile; Gene Mutation; Genes; Genetic; Genome; Genomics; Goals; High-Throughput Nucleotide Sequencing; Human; Individual; Informatics; LRRK2 gene; Link; Methods; Mitochondria; Mitochondrial DNA; Molecular; Movement; Mutation; Nerve Degeneration; Neurodegenerative Disorders; Neurons; Nuclear; Nucleotides; PINK1 gene; Parkinson Disease; Pathway interactions; Patients; Pattern; Phenotype; Principal Component Analysis; Process; RNA; RNA Sequences; Reactive Oxygen Species; Resolution; Sampling; Siblings; Solutions; Testing; Transcript; Variant; genome-wide; human data; induced pluripotent stem cell; innovation; mitochondrial dysfunction; novel strategies; public health relevance; research study; response; tool; transcriptome sequencing; transcriptomics

DESCRIPTION (provided by applicant): High throughput sequencing of the genome-wide transcriptome will generate many new hypotheses regarding the genetic interactions underlying neurodegenerative mechanisms. We expect that marker genes of biologically relevant pathways are needed to efficiently interrogate the large sets of raw data produced by the experiments. The goal of this new R21 proposal is to help validate the neuronal transcriptome as a tool for the study of Parkinson's disease. Cells from well-defined familial cases of Parkinson's disease, although rare, provide an excellent starting point for such analyses. We and others have shown that cells from Parkinson's disease patients carrying LRRK2 or PINK1 mutations demonstrate mitochondrial deficits. Importantly, the molecular mechanisms that connect LRRK2 or PINK1 mutations to the mitochondrial deficits remain unclear. Using an innovative approach to interpreting the neuronal transcriptome, we aim to generate new hypotheses regarding the molecular mechanisms of LRRK2 or PINK1 associated mitochondrial deficits. We will link the functional mitochondrial deficits of human neurons carrying Parkinson's disease associated LRRK2 and PINK1 mutations that we have observed to the RNA sequences expressed by the neurons. By combining high- throughput transcriptome sequencing with new quantitative PCR arrays, we propose to determine the expression level and sequence signatures of mitochondrial DNA (SA1) and nuclear DNA (SA2) encoded genes that mark the mitochondrial deficits of patient-derived neurons. Multiple clones of age-matched, sibling and isogenic control iPSCs will be used to minimize the influence of genomic variation across neuronal samples. In a first step towards our goal, RNA molecules from induced pluripotent stem cell (iPSC)-derived neurons carrying LRRK2, PINK1 mutations and showing mitochondrial deficits or healthy subjects were sequenced. Preliminary analyses of the RNAseq data confirmed the presence of the LRRK2 and PINK1 mutations in the neuronal transcriptome. Furthermore, our analysis suggests that the functional mitochondrial deficits are associated with aberrant processing of mitochondrial DNA-encoded transcripts. These data from human neurons can be used to establish a reasonable and coherent framework of cell biological responses to interpret a patient's transcriptome. Our results will be instructive and critical to future attempts to effectively analyze human cell biological phenotypes with the multiple underlying genetic interactions of sporadic forms of Parkinson's disease.

描述（由申请人提供）：全基因组转录组的高通量测序将产生许多关于神经退行性机制背后的遗传相互作用的新假设。我们预计需要生物学相关途径的标记基因来有效地询问实验产生的大量原始数据。这项新的 R21 提案的目标是帮助验证神经元转录组作为帕金森病研究的工具。来自明确的帕金森病家族病例的细胞虽然很少见，但却为此类分析提供了一个极好的起点。我们和其他人已经证明，携带 LRRK2 或 PINK1 突变的帕金森病患者的细胞表现出线粒体缺陷。重要的是，将 LRRK2 或 PINK1 突变与线粒体缺陷联系起来的分子机制仍不清楚。使用创新方法解释神经元转录组，我们的目标是提出关于 LRRK2 或 PINK1 相关线粒体缺陷的分子机制的新假设。我们将观察到携带帕金森病相关 LRRK2 和 PINK1 突变的人类神经元的功能性线粒体缺陷与神经元表达的 RNA 序列联系起来。通过将高通量转录组测序与新的定量 PCR 阵列相结合，我们建议确定线粒体 DNA (SA1) 和核 DNA (SA2) 编码基因的表达水平和序列特征，这些基因标记患者源性神经元的线粒体缺陷。年龄匹配、同级和同基因对照 iPSC 的多个克隆将用于最大限度地减少神经元样本中基因组变异的影响。在实现我们目标的第一步中，对来自携带 LRRK2、PINK1 突变并显示线粒体缺陷或健康受试者的诱导多能干细胞 (iPSC) 衍生神经元的 RNA 分子进行了测序。 RNAseq 数据的初步分析证实神经元转录组中存在 LRRK2 和 PINK1 突变。此外，我们的分析表明，线粒体功能缺陷与线粒体 DNA 编码转录本的异常加工有关。来自人类神经元的这些数据可用于建立合理且连贯的细胞生物反应框架，以解释患者的转录组。我们的结果对于未来有效分析人类细胞生物表型与散发性帕金森病的多种潜在遗传相互作用的尝试具有指导意义和关键性。