Integrative genomics to map risk genes and pathways in autism and epilepsy

整合基因组学绘制自闭症和癫痫的风险基因和途径

• 批准号: 9158894
• 负责人: Dalila Pinto
• 金额: $ 84.62万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-01 至 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9158894
• 关键词: 3' Untranslated Regions; Address; Affect; Alternative Splicing; Autistic Disorder; Behavioral; Binding; Binding Sites; Biological; Biological Assay; Brain; Brain imaging; Candidate Disease Gene; Cataloging; Catalogs; Cell Line; Cellular biology; Centers for Disease Control and Prevention (U.S.); Child; Childhood; Chromatin; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Cognitive; Copy Number Polymorphism; DNA; DNA Binding; Data; Data Set; Development; Diagnostic; Disease; Enhancers; Epigenetic Process; Epilepsy; Event; Exons; Family; Gender; Gene Expression; Gene Expression Regulation; General Population; Genes; Genetic; Genetic Transcription; Genomics; Hereditary Disease; Heterogeneity; Human; In Vitro; Individual; Inherited; Intervention; Knowledge; Link; Magnetic Resonance Imaging; Maps; MicroRNAs; Molecular; Molecular Profiling; Morphology; Mutate; Mutation; National Institute of Mental Health; Network-based; Neurodevelopmental Disability; Neurodevelopmental Disorder; Neurons; Nucleic Acid Regulatory Sequences; Nucleotides; Outcome; Pathway interactions; Phenotype; Population; Prosencephalon; Proteins; Publishing; RNA Splicing; RNA-Binding Proteins; Regulation; Regulatory Element; Risk; Role; Site; Societies; Source; Stem cells; Susceptibility Gene; Synapses; Syndrome; Variant; Whole Blood; autism spectrum disorder; clinical phenotype; cohort; disorder risk; exome; genetic variant; genome editing; high risk; induced pluripotent stem cell; insertion/deletion mutation; insight; molecular subtypes; multi-electrode arrays; mutant; nerve stem cell; next generation sequencing; novel; patient population; preference; promoter; risk variant; screening; synaptic function; tool; transcriptome sequencing

PROJECT SUMMARY Autism spectrum disorders (ASDs) affect 1% of the general population, and epilepsy (EPI) is observed in at least one-third of ASD individuals. ASDs with epilepsy (ASD-EPI) are typically more severe and treatment delay has a negative impact on outcome. The frequent association between epileptic and autistic phenotypes suggests that they share predisposing genes. Indeed, in recent years it has become clear that genes implicated in ASD and EPI, as well as other neurodevelopmental disorders, are interconnected in functional networks. Strikingly, there is a considerable overlap in the networks affected in each disorder, raising questions on how disruptions of these common networks can give rise to such phenotypical diversity. Despite ongoing large-scale efforts to identify risk genes for ASD, and to a lesser extent for pediatric EPI, the diagnostic yield remains low and most causal genes and risk variants are yet to be identified. New cohorts are also needed to discover additional variants in previously identified candidate genes and elevate them to the status of ASD-EPI risk genes. Our study differs from previous efforts by focusing on a set of 550 families with a specific ASD-EPI sub-phenotype that will result in less phenotypic heterogeneity to increase power to find variants in this specific subtype. For each family we will sequence the complete exome, as well as noncoding regulatory regions near genes with strong prior evidence for association with ASD and/or EPI. We will perform burden analysis of rare de novo and inherited gene-disruptive events in ASD-EPI, and correlate with clinical phenotype variables (early vs late-onset epilepsy, gender, IQ, and MRI abnormalities), and incorporate this into existing ASD/EPI datasets for gene-set and network analyses, as well as integrating SNVs and CNVs in a common framework (Aim 1). We will also identify risk variants in noncoding regulatory elements, including cis- regulatory elements near implicated, high confidence, and/or candidate genes for ASD and EPI (ASD/EPI- relevant genes), intronic RBFOX binding targets, and miRNA binding targets, using a new statistical framework followed by burden analyses (Aim 2). Finally, we will functionally characterize 8 high-impact variants, which will be introduced by CRISPR genome editing into isogenic human induced pluripotent stem cells (iPSCs) and further differentiated into forebrain neuronal progenitor cells (NPCs) and neurons. Functional assays will include RNA-Seq, neuronal connectivity and morphology, as well as activity using Multi-Electrode Arrays (Aim 3). The identification and functional characterization of additional mutations will help prioritize genes and reveal novel components of the pathways underlying ASD-EPI, and provide mechanistic insight into how they relate to each other. Our systematic approach also provides the opportunity to classify molecular subtypes of ASD/EPI and to distinguish how the genetic subnetworks underlying ASD-EPI differ from the framework of pathways associated with each disorder, as necessary steps toward tailored intervention and treatment. Our proposal will set a standard for rapid and large-scale screening for ASD and related neurodevelopmental disorders.

项目摘要 自闭症谱系障碍（ASD）影响1%的普通人群，癫痫（EPI）在10%的人群中被观察到。 三分之一的ASD患者。ASD伴癫痫（ASD-EPI）通常更严重， 拖延会对结果产生负面影响。癫痫和自闭症表型之间的频繁关联 表明他们有共同的易感基因事实上，近年来，基因 与ASD和EPI以及其他神经发育障碍有关的神经元在功能上相互关联， 网络.引人注目的是，在每种疾病中，受影响的网络都有相当大的重叠，这引发了一些问题。 这些共同网络的中断如何导致这种表型多样性。 尽管正在进行大规模的努力来确定ASD的风险基因，并在较小程度上确定儿科EPI的风险基因， 诊断率仍然很低，大多数致病基因和风险变异尚待确定。新的群体是 还需要在先前确定的候选基因中发现其他变异，并将其提升到 ASD-EPI风险基因的状态。我们的研究与以前的研究不同，我们关注的是一组550个家庭， 特异性ASD-EPI亚表型，这将导致表型异质性减少，从而增加发现的能力 在这个特定的子类型的变体。对于每个家庭，我们将测序完整的外显子组，以及非编码 与ASD和/或EPI相关的强有力的先前证据的基因附近的调节区域。我们将执行 ASD-EPI中罕见的新发和遗传性基因破坏事件的负担分析，以及与临床 表型变量（早发性与迟发性癫痫、性别、智商和MRI异常），并将其纳入 现有的ASD/EPI数据集用于基因集和网络分析，以及将SNV和CNV整合到一个 共同框架（目标1）。我们还将识别非编码调控元件中的风险变体，包括顺式- 调节元件，其与ASD和EPI（ASD/EPI-1）的相关、高置信度和/或候选基因接近。 相关基因），内含子RBFOX结合靶点和miRNA结合靶点，使用新的统计框架 然后进行负担分析（目标2）。最后，我们将在功能上描述8个高影响力的变体， 通过CRISPR基因组编辑引入到同基因的人诱导多能干细胞（iPSC）中， 进一步分化为前脑神经元祖细胞（NPC）和神经元。功能试验将包括 RNA-Seq、神经元连接和形态以及使用多电极阵列的活性（目的3）。的 对其他突变鉴定和功能表征将有助于区分基因的优先次序，并揭示新的 组成部分的途径基础ASD-EPI，并提供机械的洞察，他们如何与每个 其他.我们的系统方法还提供了对ASD/EPI的分子亚型进行分类的机会， 区分ASD-EPI的遗传子网络与通路框架的不同 与每种疾病相关，作为定制干预和治疗的必要步骤。我们的建议将 为ASD和相关神经发育障碍的快速和大规模筛查设定了标准。