Transcriptional Regulators in Normal Human Brain Development and Autism

描述(申请人提供)：自闭症谱系障碍(ASD)是一种具有复杂遗传学的异质性神经发育障碍。ASD是高度可遗传的，影响大约1%的人口。为了更好地了解ASD并开发临床治疗方法，了解其病因的遗传成分是至关重要的。然而，很明显，数百个基因可能参与了ASD的发病机制，因此，深入、公正地评估人类基因组的必要性比以往任何时候都更加迫切。通过生物信息学工具，如共表达网络分析，可以从全基因组信息中有效地解释和测试假说，共表达网络分析通过生物条件下RNA转录表达的共享模式来识别被称为模块的基因组。在这个项目中，我的目标是通过转录因子(TF)、microRNAs(MiRNAs)的整合，以及它们利用共表达网络和调控分子结合位点信息对靶基因转录的影响，显著扩展我们目前关于转录调控和大脑区域调控失调的知识。为了做到这一点，我将使用死后大脑的RNA测序数据，这使得蛋白质编码RNA和非编码RNA水平的准确量化成为可能。我将应用共表达网络分析，将数以万计的遗传变化总结为可管理数量的基因组或模块，我将根据与大脑区域、细胞类型和细胞内细胞器相关的表达模式来表征这些基因组或模块。在目标1中，我将定义一个转录网络中的模块，该网络来自正常衰老的16个大脑区域，以表征正常大脑发育和功能的转录结构。然后，我将在这个网络的模块中应用Tf和miRNA结合位点丰富分析，以预测、表征和优先考虑影响正常大脑发育和功能所必需的基因的转录调控因子。在目标2中，我将应用共表达网络分析来自ASD死后大脑中与ASD相关的五个脑区的RNA-seq数据，并在不同的样本组中控制个体。我将像在目标1中一样描述模块的特征，但也通过与ASD的表达模式关联来描述。然后，我将在ASD相关模块中应用调节分子结合位点浓缩，以确定参与异常调控途径的转录因子和miRNAs。我将评估这些失调的通路是否与产前和早期大脑发育中重要的通路相对应。我还将评估ASD基因组研究中常见和罕见的遗传变异是否丰富了失调的途径。在目标3中，作为原则的关键证明，我将验证候选监管者 以及在正常人类神经前体细胞体外分化过程中，它们通过敲除优先排列的转录因子和miRNAs对靶通路的影响。该项目整合了神经科学、遗传学和生物信息学，以系统地识别和验证与ASD相关的新的大脑编码和非编码RNA转录调控的中断。有效的转录因子和miRNAs可能是脑发育的重要转录调节因子，并可能成为ASD的潜在治疗靶点。

DESCRIPTION (provided by applicant): Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with complex genetics. ASD is highly heritable and affects around 1% of the population. To better understand ASD and develop clinical treatments, it is essential to understand the genetic component of its etiology. However, it has become clear that hundreds of genes are likely involved in ASD pathogenesis, so the need to evaluate the human genome in a deep, unbiased manner is greater than ever. Effectively interpreting and testing hypotheses from genome- wide information is made possible by bioinformatic tools such as co-expression network analysis, which identifies groups of genes, known as modules, by their shared patterns of RNA transcript expression across biological conditions. In this project, my goal is to significantly extend our current knowledge of transcriptional regulation and dysregulation across human brain regions through the integration of transcription factors (TFs), microRNAs (miRNAs), and their effect on the transcription of target genes using co-expression networks and regulatory molecule binding site information. To accomplish this, I will use data from RNA sequencing in post- mortem brain, which enables accurate quantification of protein coding RNA and noncoding RNA levels. I will apply co-expression network analysis to summarize tens of thousands of genetic changes into a manageable number of gene groups or modules, which I will characterize for expression patterns related to brain region, cell-type, and intracellular organelle. In Aim 1, I will define modules in a transcriptional network from sixteen brain regions across normal aging to characterize the transcriptional architecture of normal brain development and function. I will then apply TF and miRNA binding site enrichment analysis in modules from this network to predict, characterize, and prioritize transcriptional regulators affecting genes essential to normal brain development and function. In Aim 2, I will apply co-expression network analysis to RNA-seq data from five ASD-related brain regions in post-mortem brains from ASD and control individuals in a different sample set. I will characterize modules as in Aim 1, but also by expression pattern association to ASD. I will then apply regulatory molecule binding site enrichment in ASD-associated modules to identify TFs and miRNAs involved in dysregulated pathways. I will assess whether these dysregulated pathways map to pathways important in prenatal and early brain development. I will also assess if dysregulated pathways are enriched for common and rare genetic variants implicated in genomic studies of ASD. In Aim 3, as a key proof of principle, I will validate candidate regulators and their effect on target pathways by knockdown of prioritized TFs and miRNAs during the differentiation of normal human neural progenitor cells in vitro. This project integrates neuroscience, genetics, and bioinformatics to systematically identify and validate novel ASD-associated disruption in transcriptional regulation of coding and noncoding RNA in brain. Validated TFs and miRNAs are likely to be essential transcriptional regulators for brain development and may be potential therapeutic targets in ASD.