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具有高度遗传性，影响约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至关重要。然而，已经清楚的是，数百个基因可能参与ASD的发病机制，因此需要以深入，公正的方式评估人类基因组比以往任何时候都更大。通过生物信息学工具，如共表达网络分析，可以有效地解释和测试来自全基因组信息的假设，共表达网络分析通过跨生物条件的RNA转录本表达的共享模式识别基因组，称为模块。在这个项目中，我的目标是通过整合转录因子（TF），microRNA（miRNA）及其对靶基因转录的影响，使用共表达网络和调控分子结合位点信息，显着扩展我们目前对人类大脑区域转录调控和失调的认识。为了实现这一点，我将使用死后大脑中RNA测序的数据，这使得蛋白质编码RNA和非编码RNA水平的准确定量成为可能。我将应用共表达网络分析，将成千上万的遗传变化总结为可管理数量的基因组或模块，我将表征与脑区域，细胞类型和细胞内细胞器相关的表达模式。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过程中的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，我将在该网络的模块中应用TF和miRNA结合位点富集分析，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节因子。在目标2中，我将应用共表达网络分析来自ASD和对照个体死后大脑中五个ASD相关脑区的RNA-seq数据。我将描述目标1中的模块，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富集来鉴定参与失调途径的TF和miRNA。我将评估这些失调的通路是否映射到产前和早期大脑发育的重要通路。我还将评估是否失调的途径富集了ASD基因组研究中涉及的常见和罕见遗传变异。在目标3中，作为原则的关键证明，我将验证候选监管机构 以及它们在体外正常人神经祖细胞分化过程中通过敲低优先的TF和miRNA对靶途径的影响。该项目整合了神经科学，遗传学和生物信息学，系统地识别和验证大脑中编码和非编码RNA转录调控的新型ASD相关破坏。经验证的TF和miRNA可能是脑发育的重要转录调节因子，并可能是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.