2/3 Integrative Genomic Analysis of Human Brain Development and Autism

摘要 遗传和基因组研究已经取得了重要的发现，关于基因对主要的 精神疾病，说明了显著的病因学异质性，以及跨障碍重叠。它有 了解这种基因变异是如何导致大脑发育和 作为精神疾病病理生理学基础的功能将得到极大的进步 人类大脑皮层跨关键发育窗口的转录和表观遗传图景。 在这里，我们建议通过一个高度协作的调查小组，每个调查小组都有不同的专业领域和 研究重点，为理解ASD的病理生理学和精神病学创建基因组数据的支架 更广泛的障碍。这里提出的工作代表了一个雄心勃勃的多PI项目(耶鲁大学、加州大学洛杉矶分校和 加州大学旧金山分校)，汇集了三名主要调查人员和合作者，他们有着良好的发表记录和 使用最先进和新颖的方法进行这项工作所需的所有方法方面的专业知识。我们 将对对照和ASD大脑进行时间、区域和细胞类型特定的分子图谱(目标1)， 包括基于RNA-SEQ的转录组学，通过CHIP-SEQ识别顺式调控元件，并使用Hi-C来 确定作为转录调控基础的3D染色质结构和物理关系 涉及神经精神疾病的三个主要区域(额叶、颞叶皮质和纹状体) 代表人类大脑发育中与疾病相关的五个主要阶段。这将包括 对对照和匹配的ASD脑进行互补基因组分析以确定基因 ASD大脑中潜在的过程机制发生了变化。我们将通过以下方式解决细胞异构性 荧光激活的核分选(FANS)，以分离神经元和非神经细胞，这 将补充整个组织分析。我们将分析和整合这些数据集，以确定区域、 开发和与ASD相关的流程，以深入了解潜在机制，协调这些 多组数据与其他心理编码研究，以及其他大规模数据集，如BrainSpan， Encode、GTEx和路线图表观基因组学项目(目标2)。我们将进行种系的综合分析 在Simons Simplex收集的1000多个家系中发现ASD变异以表征原因 丰富的发育周期，大脑区域和细胞类型，以更好地表征机制，通过 在健康和疾病中，人类的哪些基因变异改变了大脑的发育和功能(目标3)。 完成这些目标将导致在人类大脑皮层和大脑中的主要时期有一个良好的整合资源 纹状体发育，将允许产生ASD机制的具体可测试假说，以及 告知我们对其他相关神经精神疾病的病理生理学理解。

ABSTRACT Genetic and genomic investigations have yielded important findings as to the genetic contributions to major psychiatric illnesses, illustrating significant etiological heterogeneity, as well as cross-disorder overlap. It has also become clear that understanding how this genetic variation leads to alterations in brain development and function that underlies psychiatric disease pathophysiology will be greatly advanced by a roadmap of the transcriptomic and epigenetic landscape of the human cerebral cortex across key developmental windows. Here, we propose, via a highly collaborative group of investigators, each with distinct areas of expertise and research focus, to create a scaffold of genomic data for understanding ASD pathophysiology, and psychiatric disorders more broadly. The work proposed here represents an ambitious multi-PI project (Yale, UCLA, and UCSF) that brings together three principal investigators and collaborators with strong publication records and expertise in all approaches necessary to perform this work using state-of-the-art and novel methodologies. We will perform time-, region-, and cell type-specific molecular profiling of control and ASD brains (Aim 1), including RNA-seq based transcriptomics, identifying cis-regulatory elements via ChIP-seq, and use Hi-C to determine the 3D chromatin architecture and physical relationships that underlie transcriptional regulation in three major regions implicated in neuropsychiatric disease (frontal and temporal cortex and striatum) across five major epochs representing disease-relevant stages in human brain development. This will include complementary genomic analyses in controls and matched post mortem ASD brain to identify genetic mechanisms underlying processes altered in ASD brain. We will address cellular heterogeneity via fluorescence-activated nuclear sorting (FANS) so as to profile neurons and non-neural cells separately, which will complement the whole tissue analyses. We will analyze and integrate these datasets to identify regional, developmental, and ASD-related processes to gain insight into underlying mechanisms, harmonizing these multi-omic data with other psychENCODE studies, as well as other large scale data sets, such as BrainSpan, ENCODE, GTEx and Roadmap Epigenomics Project (Aim 2). We will perform integrated analysis of germ-line ASD variations identified in more than 1000 families from the Simons Simplex Collection to characterize causal enrichments in developmental periods, brain regions, and cell types to better characterize the mechanisms by which genetic variation in humans alters brain development and function in health and disease (Aim 3). Completion of these aims will lead to a well-integrated resource across major periods in human cortical and striatal development that will permit generation of concrete testable hypotheses of ASD mechanisms, and inform our pathophysiological understanding of other related neuropsychiatric disorders.