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

基本信息

批准号：
10487485
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
项目类别：
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/10487485
关键词：
3-Dimensional ATAC-seq Affect Alzheimer&apos s Disease Amines Amyloid Aneuploidy Architecture Area Astrocytes Biological Assay Black race 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 Early Onset Alzheimer Disease 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 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 insight nanopore nerve stem cell novel novel therapeutic intervention optogenetics programs success tool transcriptome

项目摘要

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.

抽象的染色体非整倍性是多种人类疾病的基础。唐氏综合症 (DS) 是由智人 21 号染色体 (HSA21) 的额外拷贝引起的。 DS 是人类认知障碍最常见的遗传病，大约每 750 名活产婴儿中就有 1 人受到 DS 的影响在美国，它使患者容易出现肌张力低下、畸形特征、先天性心脏病和尽管取得了许多进展，但我们对早发性阿尔茨海默病的病理学的概念性理解仍然有限。迄今为止，这种染色体异常的基础很大程度上仅限于“基因剂量假说”，即然而，无法解释特定细胞类型中整个基因组中发生的广泛基因失调。目前尚未探索 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。在这里，我们组建了一个强大的团队来测试 21 三体性的存在的总体假设。解除对 3D 基因组整体的管制并改变 DS 细胞中的基因表达，特别是通过形成在 Aim-1 中，我们有两个具体目标。含有二体性和三体性 HSA21 的同基因 iPSC 细胞及其衍生神经元/神经胶质细胞，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）、转录组和一维表观基因组（PRO-Seq、ATAC-Seq 和组蛋白修饰 ChIP-Seq 综合分析）。剖析异常染色质相互作用组，特别是三体性中的染色体间相互作用核，并将那些与特定发育阶段或细胞类型（神经元、我们将使用基于长读长测序的前沿新技术来进一步发展。表征异常的染色体间相互作用，并将使用 DNA 和/或 RNA FISH 对其进行验证。 Aim-2，我们专注于从功能上剖析异常染色体间相互作用在基因中的作用这将首先通过化学和表观遗传扰动在培养的原代细胞中进行研究。然后，我们将使用新型光遗传学工具来建模神经祖细胞和大脑皮质类器官。疾病相关的 ICI 形成，以推断它们在基因失调中的潜在因果作用。该提案的结果不仅对我们对 4D 基因组的理解具有重要意义，而且对人类也具有重要意义这里产生的知识将揭示许多形式的非整倍性，提供超越“基因剂量效应”的新概念框架来理解基因放松管制，以及通过恢复 3D 基因组结构来激发改善这些疾病的策略。