Beyond Gene Dosage: Understanding Down Syndrome via 4D Genome Organization

超越基因剂量：通过 4D 基因组组织了解唐氏综合症

• 批准号: 10264939
• 负责人: Wenbo Li
• 金额: $ 62.42万
• 依托单位: UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-18 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10264939
• 关键词: 3-Dimensional; ATAC-seq; Affect; Alzheimer' s Disease; Amines; Amyloid; Aneuploidy; Architecture; Area; Astrocytes; Biological Assay; Brain; Bromodomain; CRISPR interference; Cell Differentiation process; Cell Nucleus; Cells; ChIP-seq; Chemicals; Chromatin; Chromosome 21; Chromosome abnormality; Chromosomes; Congenital Heart Defects; DNA; Data; Development; Disease; Disease model; Down Syndrome; Enhancers; Epigenetic Process; Etiology; Gene Dosage; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Diseases; Genetic Transcription; Genome; Goals; Hematopoietic; Hi-C; Histones; Homo sapiens; Human; Human Chromosomes; Human Development; Human Genetics; Impaired cognition; In Situ; Individual; Infant; Interphase Chromosome; Knowledge; Left; Light; Malignant Neoplasms; Mediating; Methods; Microglia; Modeling; Molecular; Muscle hypotonia; Neurodevelopmental Disorder; Neuroglia; Neurons; Nuclear Pore Complex; Oncogene Deregulation; Organoids; Pathologic; Patients; Phase; Play; Presenile Alzheimer Dementia; Proteins; RNA; Reader; Regulation; Research Personnel; Role; Techniques; Technology; Testing; Therapeutic; Trisomy; Untranslated RNA; Work; base; brain cell; cell type; congenital heart disorder; developmental disease; disease phenotype; epigenetic drug; epigenome; experimental study; genome-wide; histone modification; human disease; induced pluripotent stem cell; inhibitor/antagonist; insight; nanopore; nerve stem cell; novel; novel therapeutic intervention; optogenetics; programs; success; tool; transcriptome

ABSTRACT Chromosomal aneuploidy underlies a variety of human diseases. The most prominent paradigm among these is Down syndrome (DS) that is caused by an extra copy of homo sapiens chromosome 21 (HSA21). As the most common genetic disease of human cognitive impairment, DS affects about 1 in 750 live-born infants in the US, and it pre-disposes patients to muscle hypotonia, dysmorphic features, congenital heart defects and early onset Alzheimer's disease. Despite many progress, our conceptual understanding of the pathological basis of such chromosomal abnormality is so far largely limited to the “gene dosage hypothesis”, which however cannot explain broad gene deregulation that takes place throughout the genome in specific cell types. It has been unexplored that whether 3D genome mal-folding may play yet unrealized roles in DS and other aneuploidies. Here, we assembled a strong team to test an overall hypothesis that the presence of trisomy 21 deregulates 3D genome as an entirety and changes gene expression in DS cells, particularly via forming aberrant inter-chromosomal interactions (ICIs). We have two specific aims. In Aim-1, in multiple pairs of isogenic iPSC cells and their derived neuron/glia cells that contain disomic versus trisomy HSA21, we will conduct assays to systematically characterize their 3D genome (in situ Hi-C and PLAC-Seq), transcriptome and 1D epigenome (PRO-Seq, ATAC-Seq, and histone modification ChIP-Seq). Integrative analyses will dissect the aberrant chromatin interactomes, particularly these interchromosomal interactions altered in trisomy nucleus, and correlate those with gene deregulation in specific developmental stages or cell types (neurons, astrocytes or microglia). We will use leading-edge new techniques based on long reads sequencing to further characterize aberrant inter-chromosomal interactions, and will validate them using DNA and/or RNA FISH. In Aim-2, we focus on functionally dissecting the roles of aberrant inter-chromosomal interactions in gene deregulation. This will be first investigated by chemical and epigenetic perturbation in both cultured primary neural progenitor cells and in brain cortical organoids. We will then use novel optogenetic tools to model disease-relevant formation of ICIs to deduce their potential causal roles in gene deregulation. The expected results from this proposal are significant not only to our understanding of the 4D genome, but also to human brain developmental disorders. The knowledge generated here will shed light on many forms of aneuploidy, providing a new conceptual framework beyond “gene dosage effects” to understand gene deregulation, and inspire strategies to ameliorate these diseases via restoring 3D genome architecture.

摘要 染色体非整倍性是多种人类疾病的基础。其中最突出的范例是 唐氏综合症是由人类21号染色体（HSA 21）的额外拷贝引起的。为 DS是人类认知障碍的最常见遗传疾病，在美国，每750名活产婴儿中就有1名患有DS。 它使患者容易出现肌肉张力减退、畸形特征、先天性心脏缺陷和 早发性阿尔茨海默病尽管取得了许多进展，但我们对病理学的概念性理解 迄今为止，这种染色体异常的基础主要限于“基因剂量假说”， 然而，不能解释在特定细胞类型的整个基因组中发生的广泛的基因失调。 3D基因组错误折叠是否可能在DS和其他疾病中发挥尚未实现的作用， 非整倍性在这里，我们组建了一个强大的团队来测试一个总体假设，即21三体的存在 作为一个整体，3D基因组失调，并改变DS细胞中的基因表达，特别是通过形成 异常染色体间相互作用（ICI）。我们有两个具体目标。在Aim-1中，在多对 等基因iPSC细胞和它们衍生的神经元/神经胶质细胞含有二体与三体HSA 21，我们将 进行分析以系统地表征其3D基因组（原位Hi-C和PLAC-Seq）、转录组 和1D表观基因组（PRO-Seq、ATAC-Seq和组蛋白修饰ChIP-Seq）。综合分析将 解剖异常的染色质相互作用，特别是在三体中改变的这些染色体间相互作用 核，并将其与特定发育阶段或细胞类型中的基因失调相关（神经元， 星形胶质细胞或小胶质细胞）。我们将使用基于长读段测序的前沿新技术， 研究人员将对异常的染色体间相互作用进行表征，并将使用DNA和/或RNA FISH对其进行验证。在 目的-2：从功能上剖析异常染色体间相互作用在基因表达调控中的作用， 放松管制。这将首先通过化学和表观遗传扰动在两个培养的原代 神经祖细胞和脑皮质类器官中。然后，我们将使用新颖的光遗传学工具来建模 疾病相关的ICI形成，以推断其在基因失调中的潜在因果作用。预期 这一建议的结果不仅对我们理解4D基因组，而且对人类 大脑发育障碍这里产生的知识将揭示许多形式的非整倍体， 提供一个新的概念框架，超越“基因剂量效应”，以了解基因失调，和 启发通过恢复3D基因组结构来改善这些疾病的策略。