Genomic and epigenomic effects of large CNV in neurons from iPSC

iPSC 神经元中大 CNV 的基因组和表观基因组效应

基本信息

批准号：
8357036
负责人：
Alexander Eckehart Urban
金额：
$ 235.5万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-30 至 2017-06-30
项目状态：
已结题

项目摘要

DESCRIPTION (Provided by the applicant) Abstract: I propose to study through which molecular mechanisms of genetic control it is that large genomic Copy Number Variants (CNVs) exert their effects on gene regulation, dynamically over cellular differentiation and cellular functioning. We aim to establish a novel research program and paradigm in our laboratory that combines the use of induced Pluripotent Stem Cells (iPSC) and multi-level, comprehensive and integrated analysis of genomic and epigenomic layers of control and activity. In the process we will be testing several novel hypotheses on the molecular mechanisms through which CNVs affect gene regulation and thus cellular and eventually organismal phenotypes. This will also serve as a model for smaller CNVs and their potentially subtle and cumulative or combinatorial yet potentially substantive effects on phenotype in health and disease. Copy Number Variation (CNV) is common in the genome of healthy humans and is associated with phenotypic variation. CNV is also frequently and strongly associated with major disease phenotypes, especially in neuropsychiatric diseases that involve an aberrant development of the brain such as schizophrenia and autism. There are now several prominent examples for CNVs that are strongly associated with neuropsychiatric disorders such as schizophrenia, autism, mental retardation and epilepsy (22q11.2 deletions, 1q21.1 deletions and duplications, 15q13.3 deletions, 16p11.2 deletions and duplications, 3q29 microduplications). CNVs (and sometimes the same CNVs as mentioned above) are also strongly associated with malformation diseases of the heart as well as in phenotypes that involve the functioning of the immune system. CNVs are therefore an important phenomenon to study both in its own right as a strong predisposing factor for disease as well as an enticing point of entry for the better understanding of the molecular etiology of complex diseases with a strong and complex genetic and genomic component. A major barrier to a better understanding of how the molecular mechanisms through which CNV affect phenotype is the lack of access to relevant human tissues that carry a given disease associated CNV, for example neuronal tissue cultures with a large genomic deletion that is strongly associated with schizophrenia or autism. The use of iPSC lines from probands with a given CNV promises to overcome this barrier and will allow us to observe the effects of CNVs on a molecular level in the relevant tissue as it progresses along a developmental trajectory and then settles into the neuronal phenotype. The complete and multilevel high-resolution genomics and epigenomics analyses based on massively parallel DNA next-generation-sequencing will include comprehensive transcriptome analyses by RNA-Seq, meDNA- Seq to study DNA methylation patterns and ChIP-Seq to map regulatory histone modifications and transcription factor networks. Public Health Relevance: Neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism spectrum disorders are a major public health concern. Copy Number Variations are amongst the candidate loci with the strongest association with such diseases but they typically affect multiple genes and only very little basic knowledge about their molecular mechanisms of action exists. Our project will create a new research paradigm into the effects of CNV during neuronal development by combining iPSC techniques with comprehensive nextgeneration genomics analyses.

描述（由申请人提供）摘要：我建议研究大基因组拷贝数变异 (CNV) 通过哪些遗传控制的分子机制对基因调控、动态地影响细胞分化和细胞功能发挥作用。我们的目标是在我们的实验室建立一个新颖的研究计划和范例，将诱导多能干细胞 (iPSC) 的使用与基因组和表观基因组控制和活性层的多层次、全面和综合分析相结合。在此过程中，我们将测试关于 CNV 影响基因调控以及细胞和最终有机体表型的分子机制的几个新假设。这也将作为较小 CNV 及其对健康和疾病表型潜在微妙、累积或组合但潜在实质性影响的模型。拷贝数变异 (CNV) 在健康人类的基因组中很常见，并且与表型变异相关。 CNV 也经常与主要疾病表型密切相关，尤其是涉及大脑异常发育的神经精神疾病，如精神分裂症和自闭症。现在有几个突出的 CNV 例子与精神分裂症、自闭症、智力低下和癫痫等神经精神疾病密切相关（22q11.2 缺失、1q21.1 缺失和重复、15q13.3 缺失、16p11.2 缺失和重复、 3q29 微重复）。 CNV（有时是与上述相同的 CNV）也与心脏畸形疾病以及涉及免疫系统功能的表型密切相关。因此，CNV 是一种重要的研究现象，它本身是一种强烈的疾病诱发因素，也是更好地了解具有强大而复杂的遗传和基因组成分的复杂疾病的分子病因学的一个诱人的切入点。更好地理解 CNV 如何影响表型的分子机制的一个主要障碍是缺乏携带特定疾病相关 CNV 的相关人体组织，例如与精神分裂症密切相关的具有大基因组缺失的神经元组织培养物或自闭症。使用来自具有给定 CNV 的先证者的 iPSC 系有望克服这一障碍，并使我们能够在相关组织沿着发育轨迹前进并随后进入神经元表型时观察 CNV 对分子水平的影响。基于大规模并行 DNA 下一代测序的完整、多层次的高分辨率基因组学和表观基因组学分析将包括通过 RNA-Seq、meDNA-Seq 进行全面的转录组分析，以研究 DNA 甲基化模式，以及通过 ChIP-Seq 来绘制调控组蛋白修饰和转录图谱因素网络。公共卫生相关性：精神分裂症和自闭症谱系障碍等神经发育、神经精神疾病是主要的公共卫生问题。拷贝数变异是与此类疾病关联性最强的候选基因座之一，但它们通常影响多个基因，并且对其分子作用机制的基本了解很少。我们的项目将通过将 iPSC 技术与全面的下一代基因组学分析相结合，创建一个新的研究范式，研究 CNV 在神经元发育过程中的影响。

项目成果

期刊论文数量（2）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders.

DOI：
10.1016/j.cels.2015.11.002
发表时间：
2015-11-25
期刊：
Cell systems
影响因子：
9.3
作者：
Li J;Ma Z;Shi M;Malty RH;Aoki H;Minic Z;Phanse S;Jin K;Wall DP;Zhang Z;Urban AE;Hallmayer J;Babu M;Snyder M
通讯作者：
Snyder M

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.