1/3 Integrative Genomic Analysis of Human Brain Development and Autism

摘要 遗传学和基因组学的研究已经取得了重要的发现，基因的贡献，以主要的 精神疾病，说明显着的病因异质性，以及交叉障碍重叠。它有 也变得清楚，了解这种遗传变异如何导致大脑发育的改变， 作为精神疾病病理生理学基础的功能将通过一个路线图得到极大的推进， 人类大脑皮层在关键发育窗口的转录组学和表观遗传学景观。 在这里，我们建议，通过一个高度合作的调查小组，每个人都有不同的专业领域， 研究重点，为理解ASD病理生理学和精神病学创建基因组数据支架 更广泛的疾病。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， UCSF），汇集了三个主要研究者和合作者，具有强大的出版记录， 专业知识，在所有必要的方法来执行这项工作，使用国家的最先进的和新的方法。我们 将对对照组和ASD脑进行时间、区域和细胞类型特异性分子分析（目标1）， 包括基于RNA-seq的转录组学，通过ChIP-seq鉴定顺式调控元件，并使用Hi-C 确定3D染色质结构和物理关系，这些结构和物理关系是转录调控的基础， 涉及神经精神疾病的三个主要区域（额叶和颞叶皮层以及纹状体）， 代表人类大脑发育中疾病相关阶段的五个主要时期。这将包括 在对照组和匹配的死后ASD脑中进行互补基因组分析，以确定遗传 ASD大脑中改变的潜在过程机制。我们将通过以下方式解决细胞异质性问题： 荧光激活核分选（FANS），以便分别对神经元和非神经细胞进行分析， 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， 发展和ASD相关的过程，以深入了解潜在的机制，协调这些 多组学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Roadmap表观基因组学项目（Aim 2）。我们将进行生殖系的综合分析， 在Simons Simplex Collection的1000多个家庭中鉴定出ASD变异，以表征因果关系 丰富的发育时期，大脑区域和细胞类型，以更好地表征机制， 人类的遗传变异会改变健康和疾病时的大脑发育和功能（目标3）。 这些目标的完成将导致在人类皮层和大脑皮层的主要时期有一个很好的整合资源， 纹状体发育，这将允许产生ASD机制的具体可检验假设，以及 告知我们对其他相关神经精神障碍的病理生理学理解。

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.