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：
10588168
负责人：
Luis de la Torre-Ubieta
金额：
$ 23.46万
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 2025-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10588168
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 Future Gene Dosage Gene Expression Gene Expression Profile Gene Expression Regulation Gene Mutation Genes Genome Genomics Goals Human Impairment In Vitro Individual Joints Knowledge LGALS3BP gene Language Development Learning Maps Memory Methylation Methyltransferase Modeling Molecular Molecular Profiling Morphogenesis Morphology Neocortex Neurodevelopmental Disorder Neuroglia Neuronal Differentiation Neurons Newborn Infant Pathogenesis Pathology Pathway interactions Patients Pregnancy Process Proliferating Proteins Publishing Regulator Genes Regulatory Element Reporting Research Resolution Role Sampling Specific qualifier value Technology Testing Therapeutic Time Tissue-Specific Gene Expression Tissues arm brain cell brain tissue cell cortex cell fate specification cell type comparison control epigenomic profiling epigenomics experimental study gene regulatory network human model in vitro Model in vivo mRNA Differential Displays multiple omics neocortical nerve stem cell neurodevelopment neurogenesis neuropathology novel progenitor sex single nucleus RNA-sequencing stem cell biology stem cell model synaptogenesis therapy development timeline transcription factor transcriptome transcriptome sequencing transcriptomic profiling 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，会导致认知缺陷，包括学习障碍以及记忆和语言发展，影响着每 750 名新生儿中的 1 人。 DS 是由三倍引起的 21号染色体（T21），导致基因剂量改变，并导致脑细胞类型比例变化，以及神经元形态和成熟，提示神经发育病因。然而，底层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程度上未知。大脑结构的整体复杂性以及对细胞的不完整了解阻碍了进展 DS在发育过程中的类型和分子途径失调，以及有限的人类相关实验模型。此外，大量转录组和表观基因组分析表明 T21 不仅改变基因剂量在位点内，但也会导致基因表达的广泛变化，并可能导致基因调控的改变动力学。基于这些数据，我们假设增加 chr21 基因剂量会改变整体基因表达在神经祖细胞中，改变神经细胞的命运规范和分化。在这里，我们利用新颖的基因组技术包括联合单核转录组 (snRNAseq)、单核染色质可及性 (snATACseq) 分析，以及单细胞联合染色质相互作用和甲基化分析 (sc-m3C-seq) 作为人类初级神经祖细胞（phNPC），一种经过验证的人类皮质生成模型，来测试这一点假设。我们将首先通过执行以下操作来定义 DS 中细胞特异性分子和基因调节失调将 snRNAseq、snATACseq 和 sc-m3C-seq 联合到一组对照和 DS 发育新皮质中，一次神经发生高峰期。这种全面的多组学分析将揭示细胞组成的变化 DS 新皮质中的细胞特异性基因表达特征以及揭示细胞谱系的扰动地图和规格。通过整合单细胞表达和表观遗传图谱，我们将定义近端和远端基因调控元件，以及驱动 DS 疾病机制的转录因子。最后，我们将利用一系列独特的 DS 患者来源和对照 phNPC 系来建立体外疾病模型为了表征 DS 中神经祖细胞的增殖和规范，以及神经元的变化形态发生和突触发生。我们在分化时间线上联合执行 snRNAseq 和 snATACseq 重现胚胎至妊娠中期的皮质发生，以探究细胞、分子和基因 DS 的调节失调，并直接将该模型与体内 DS 机制进行比较。总而言之，我们提出一个综合项目，提供 DS 的深入细胞生物学和分子表征使用体内组织和人类相关模型进行进展，并为未来的机制建立该模型审讯。这项研究的长期目标是提供基础分子知识，最终为 DS 治疗方法的开发做出贡献。