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：
10689799
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/10689799
关键词：
3-Dimensional ATAC-seq Affect Alzheimer&apos s Disease 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 Research Personnel Role Techniques Technology Testing Therapeutic Trisomy Untranslated RNA Work 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各种人类疾病的基础。其中最突出的范式是唐氏综合症（DS），是由21（HSA21）的Homo Sapiens染色体额外副本引起的。作为人类认知障碍最常见的遗传疾病，DS影响了750名活出生的婴儿中约1个美国及其将患者预见到肌肉性肌张力低下，营养不良特征，先天性心脏缺陷和早期发作阿尔茨海默氏病。尽管有很多进展，但我们对病理的概念理解到目前为止，这种染色体异常的基础在很大程度上仅限于“基因剂量假设” 但是，无法解释在特定细胞类型中整个基因组中发生的广泛基因失调。出乎意料的是，3D基因组折叠是否可能在DS和其他中扮演未实现的角色非整倍性。在这里，我们组建了一个强大的团队，以检验一个总体假设，即三体术的存在21 取消结合3D基因组作为完整的，并改变DS细胞中的基因表达，尤其是通过形成异常的染色体相互作用（ICIS）。我们有两个具体的目标。在AIM-1中，有多对等基因IPSC细胞及其衍生的神经元/胶质细胞，其中包含病毒与三体性HSA21，我们将进行系统的测定，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Hisstone修改芯片seq）。综合分析将剖析异常染色质相互作用，尤其是这些在三体中发生了改变的这些染色体相互作用细胞核，并在特定发育阶段或细胞类型（神经元，星形胶质细胞或小胶质细胞）。我们将使用基于长读取测序的领先新技术来进一步表征异常的染色体相互作用，并将使用DNA和/或RNA鱼类来验证它们。在 AIM-2，我们专注于在功能上剖析基因异常间相互作用的作用放松管制。这将首先通过化学和表观遗传扰动在两个培养的原发性中进行研究神经祖细胞和脑皮质器官中。然后，我们将使用新颖的光遗传学工具来建模与疾病相关的ICI形成，以推断出其在基因放松管制中的潜在因果作用。预期该提案的结果不仅对我们对4D基因组的理解至关重要，而且对人类也很重要大脑发育障碍。这里产生的知识将阐明多种形式的非整倍性，除了“基因剂量效应”以外，还提供了一个新的概念框架，以了解基因放松管制，并通过恢复3D基因组体系结构来启发策略来改善这些疾病。