Gene signatures linked to the cell biological phenotypes of familial PD

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化机制下的遗传相互作用的新假说。我们预计，需要生物相关通路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氏病研究工具的有效性。来自明确定义的帕金森氏病家族病例的细胞虽然罕见，但为此类分析提供了一个很好的起点。我们和其他人已经证明，携带LRRK2或PINK1突变的帕金森氏症患者的细胞显示出线粒体缺陷。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尚不清楚。使用一种创新的方法来解释神经元转录组，我们的目标是产生关于LRRK2或PINK1相关线粒体缺陷的分子机制的新假说。我们将把我们观察到的携带帕金森氏病相关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。通过结合高通量转录组测序和新的定量PCR阵列，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签名，这些基因标志着患者来源神经元的线粒体缺陷。多个年龄匹配、兄弟姐妹和同基因对照的IPSCs克隆将被用来将跨神经元样本的基因组差异的影响降至最低。在迈向我们目标的第一步中，对携带LRRK2和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)来源神经元的RNA分子进行了测序。对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，功能性线粒体缺陷与线粒体DNA编码转录本的异常处理有关。这些来自人类神经元的数据可以用来建立一个合理和连贯的细胞生物学反应框架，以解释患者的转录组。我们的结果将对未来有效分析人类细胞生物学表型与散发性帕金森氏病的多种潜在遗传相互作用的尝试具有指导意义和关键意义。

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.