Defining molecular and gene-regulatory dysregulation in Down Syndrome tissues and models

定义唐氏综合症组织和模型中的分子和基因调节失调

基本信息

批准号：
10433667
负责人：
Luis de la Torre-Ubieta
金额：
$ 19.44万
依托单位：
UNIVERSITY OF CALIFORNIA LOS ANGELES
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-03-10 至 2024-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10433667
关键词：
Affect Age Architecture Atlases Automobile Driving Autopsy Biological Brain Cell Line Cell Nucleus Cells Chromatin Chromatin Structure Chromosome 21 Cluster Analysis Cognitive deficits Collection Data Data Set Development Disease Disease Progression Disease model Distal Down Syndrome Embryo Enhancers Epigenetic Process Etiology Experimental Models Foundations Future Gene Dosage Gene Expression Gene Expression Profile Gene Expression Regulation Gene Mutation Genes Genomics Goals Human Impairment In Vitro Individual Joints Knowledge LGALS3BP gene Language Language Development Lead Learning Maps Memory Methylation Methyltransferase Modeling Molecular Molecular Profiling Morphogenesis Morphology Neocortex Neurodevelopmental Disorder Neuroglia Neurons Newborn Infant Pathogenesis Pathology Pathway interactions Patients Pregnancy Process Proteins Publishing Regulator Genes Regulatory Element Reporting Research Resolution Role Sampling Small Nuclear RNA Technology Testing Therapeutic Time TimeLine Tissue Model Tissue-Specific Gene Expression Tissues arm base brain cell brain tissue cell fate specification cell type epigenome epigenomics experimental study gene regulatory network human model in vitro Model in vivo mRNA Differential Displays multiple omics nerve stem cell neurodevelopment neurogenesis neuropathology novel progenitor sex stem cell biology stem cell model stem cells synaptogenesis therapy development transcription factor transcriptome transcriptome sequencing treatment strategy

项目摘要

PROJECT ABSTRACT Down syndrome (DS) is a neurodevelopmental disorder causing cognitive deficits including impaired learning and memory, and language development, affecting 1 in 750 newborns. DS is caused by triplication of chromosome 21 (T21), leading to altered gene dosage, and to changes in the proportion of brain cell types, and in neuronal morphology and maturation, suggesting a neurodevelopmental etiology. However, the underlying molecular mechanisms causing the observed neuropathology and functional deficits are still largely unknown. Progress has been hindered by the overall complexity of brain architecture, an incomplete knowledge of the cell types and molecular pathways dysregulated in DS during development, and limited human-relevant experimental models. Moreover, bulk transcriptome and epigenome profiling indicates that T21 not only alters gene dosage within the locus, but also leads to broad changes in gene expression and may lead to altered gene regulatory dynamics. Based on these data, we hypothesize that increased chr21 gene dosage alters global gene expression in neural progenitors, changing neural cell fate specification and differentiation. Here, we leverage novel genomic technologies including joint single-nucleus transcriptome (snRNAseq), single-nucleus chromatin accessibility (snATACseq) profiling, and single-cell joint chromatin interaction and methylation profiling (sc-m3C-seq), as well as primary human neural progenitors (phNPCs), a validated model of human corticogenesis, to test this hypothesis. We will first define cell-specific molecular and gene-regulatory dysregulation in DS by performing joint snRNAseq, snATACseq and sc-m3C-seq in a collection of control and DS developing neocortex, at a time period of peak neurogenesis. This comprehensive multi-omic profiling will uncover changes in cell composition and cell-specific gene expression signatures in DS neocortex as well as reveal perturbations in cellular lineage maps and specification. By integrating single-cell expression and epigenetic profiles we will define the proximal and distal gene regulatory elements, as well as the transcription factors driving DS disease mechanisms. Finally, we will leverage a unique collection of DS patient-derived and control phNPC lines to model disease in vitro in order to characterize neural progenitor proliferation and specification in DS, as well as changes in neuronal morphogenesis and synaptogenesis. We perform joint snRNAseq and snATACseq over a differentiation timeline that recapitulates embryonic to mid-gestation corticogenesis in order to interrogate cellular, molecular and gene regulatory dysregulation in DS and directly compare this model with in vivo DS mechanisms. Altogether, we present a comprehensive project providing an in-depth cell biological and molecular characterization of DS progression using in vivo tissues and a human-relevant model, and establishes this model for future mechanistic interrogation. The long-term goal of this research is to provide the foundational molecular knowledge that will ultimately contribute to the development of treatments for DS.

项目摘要唐氏综合症（DS）是一种神经发育障碍，导致认知缺陷，包括学习受损和记忆和语言发展，影响了750名新生儿中的1个。 DS是由染色体21（T21），导致基因剂量改变，并导致脑细胞类型的比例变化，并且在神经元的形态和成熟中，暗示了神经发育的病因。但是，基础导致观察到的神经病理学和功能缺陷的分子机制仍然很大未知。大脑体系结构的整体复杂性阻碍了进步，这是细胞的不完整知识开发过程中DS的类型和分子途径在DS中失调，与人类相关的实验有限型号。此外，批量转录组和表观基因组分析表明，T21不仅改变了基因剂量在该基因座中，但也会导致基因表达的广泛变化，并可能导致基因调节改变动力学。基于这些数据，我们假设增加ChR21基因剂量会改变全局基因表达在神经祖细胞中，改变神经细胞命运的规范和分化。在这里，我们利用新颖的基因组包括联合单核转录组（SNRNASEQ），单核染色质可及性在内的技术（SNATACSEQ）分析和单细胞关节染色质相互作用和甲基化分析（SC-M3C-SEQ）作为原发性人神经祖细胞（PHNPC），是一种经过验证的人皮质生成模型，以测试这一点假设。我们将首先通过执行DS定义细胞特异性分子和基因调节失调连接SNRNASEQ，SNATACSEQ和SC-M3C-SEQ在一个控制和DS的集合中，一次开发新皮层峰值神经发生的时期。这种全面的多摩尼克分析将发现细胞组成的变化 DS新皮层中的细胞特异性基因表达特征以及细胞谱系的扰动地图和规范。通过整合单细胞表达和表观遗传特征，我们将定义近端和远端基因调节元件以及驱动DS疾病机制的转录因子。最后，我们将利用独特的DS患者衍生和控制PHNPC系列的集合来在体外对疾病进行建模为了表征DS中的神经祖细胞增殖和规范，以及神经元的变化形态发生和突触发生。我们在分化时间表上执行snrnaseq和snatacseq 为了审问细胞，分子和基因 DS中的调节失调，并将该模型与体内DS机制直接进行比较。总共，我们提出一个全面的项目，可提供深入的细胞生物学和DS的分子表征使用体内组织和与人相关的模型进行进展审讯。这项研究的长期目标是提供基础分子知识最终有助于开发DS的治疗方法。