Multiscale functional characterization of genomic variation in human developmental disorders

人类发育障碍基因组变异的多尺度功能表征

• 批准号: 10473897
• 负责人: Gary Chung Hon
• 金额: $ 195.93万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10473897
• 关键词: 3-Dimensional; Address; Adult; Affect; Alleles; Binding Proteins; Cardiac; Cardiac Myocytes; Catalogs; Cell Line; Cells; Chromatin Loop; Clone Cells; Communities; Complex; Coupling; Data; Data Set; Defect; Detection; Development; Disease; Disease susceptibility; Elderly; Elements; Enhancers; Evaluation; Foundations; Future; Gene Expression; Gene Expression Regulation; Gene Targeting; Genetic Transcription; Genetic Variation; Genome; Genome engineering; Genomics; Goals; Human; Human Development; Human Genetics; Image; Knowledge; Link; Mass Spectrum Analysis; Measures; Molecular; Morphology; Mosaicism; Neurons; Outcome; Pathway interactions; Patients; Phenotype; Placenta; Predisposition; RNA; Regulatory Element; Repression; Research Personnel; Resources; Risk; Series; Techniques; Tissues; Variant; autism spectrum disorder; cell type; combinatorial; congenital heart disorder; data interoperability; developmental disease; disease phenotype; experimental study; functional genomics; gene network; genetic variant; genome wide association study; genomic variation; high throughput analysis; human disease; human embryonic stem cell; human model; improved; insight; molecular phenotype; multimodality; novel; pleiotropism; predictive modeling; recruit; risk variant; screening; single cell technology; single-cell RNA sequencing; technological innovation; tool; trophoblast

Project Summary/Abstract Large-scale studies have identified thousands of genetic variants linked to developmental defects, together with the regulatory elements harboring these variants and the cell types in which these variants likely function. This diversity of variants, regulatory elements, and cell types indicates that multiple mechanisms contribute to developmental defects. One key challenge to our understanding of these mechanisms is that the molecular, cellular, and functional phenotypes of each variant remain largely uncharacterized. Until these critical gaps in knowledge are addressed, the underlying molecular and cellular determinants of developmental disease susceptibility will remain incomplete. To bridge these gaps, we propose to establish the “UT Southwestern Center for Regulatory Element Variation and Function”. The primary goal of this Center is to systematically catalog molecular and cellular phenotypes for disease-associated enhancers in human development, with a focus on gaining insights into mechanisms of non-canonical human genetics and gene regulation. To build a generalizable framework to understanding the impact of human genetic variation on function, we propose a high throughput perturbation platform with three primary goals: (1) Contribute to a variant/element/phenotype catalog with relevance to diseases of human development, focusing on elements genetically associated with congenital heart disease (cardiomyocytes), autism (neurons), and placental defects (trophoblasts); (2) Contribute to a variant/element/phenotype catalog for non-canonical human genetics, focusing on two understudied topics in human genetics: pleiotropic effects and non-cell autonomous effects; and (3) Contribute to a variant/element/phenotype catalog with relevance to mechanisms of gene regulation, focusing on enhancer RNAs. The Center will take advantage of recent technological innovations in genome engineering, single-cell genomics, and high content screening to enable the multiscale functional characterization of genomic variation in human developmental disorders. Several of these techniques have been pioneered by investigators contributing to this project, including: the development of novel tools for enhancer perturbation and the coupling of endogenous enhancer perturbations with a single-cell RNA-Seq readout (Mosaic-Seq). Impact and Significance: The efforts on this project will lead to a number of key outcomes and deliverables, including (1) greater understanding of the relationships between sequence variation and genome function, (2) an extensive variant/element/phenotype catalog for the community, (3) tools for generating predictive models for the community, and (4) resources to enable future functional genomics studies. Together, our multifaceted and combinatorial approaches will open new horizons to understanding the impact of regulatory variants on developmental disease phenotypes.

项目概要/摘要 大规模研究已经确定了数千种与发育缺陷相关的遗传变异， 以及含有这些变体的调控元件以及这些变体可能存在的细胞类型 功能。变异、调控元件和细胞类型的多样性表明多种机制 导致发育缺陷。我们理解这些机制的一个关键挑战是 每个变体的分子、细胞和功能表型在很大程度上仍然未知。直到这些关键的 解决了知识差距，发育疾病的潜在分子和细胞决定因素 敏感性将保持不完全。为了弥合这些差距，我们建议建立“UT Southwestern 监管元件变异和功能中心”。该中心的主要目标是系统地 编目人类发育中与疾病相关的增强子的分子和细胞表型， 专注于深入了解非规范人类遗传学和基因调控的机制。 建立一个通用框架来理解人类遗传变异对功能的影响， 我们提出了一个高通量扰动平台，具有三个主要目标：（1） 与人类发展疾病相关的变异/元件/表型目录，重点关注元件 与先天性心脏病（心肌细胞）、自闭症（神经元）和胎盘缺陷遗传相关 （滋养层）； (2) 为非规范人类遗传学的变异/元素/表型目录做出贡献， 重点关注人类遗传学中两个尚未研究的主题：多效性效应和非细胞自主效应；和 (3) 为与基因调控机制相关的变异/元件/表型目录做出贡献，重点关注 关于增强子 RNA。该中心将利用基因组工程方面的最新技术创新， 单细胞基因组学和高内涵筛选，以实现基因组的多尺度功能表征 人类发育障碍的变异。其中一些技术是由研究人员首创的 为该项目做出贡献，包括：开发用于增强子扰动和耦合的新颖工具 使用单细胞 RNA 测序读数 (Mosaic-Seq) 检测内源性增强子扰动。 影响和意义：该项目的努力将带来许多关键成果和成果 可交付成果，包括（1）更好地理解序列变异与基因组之间的关系 函数，(2) 社区的广泛变异/元素/表型目录，(3) 生成工具 社区的预测模型，以及（4）支持未来功能基因组学研究的资源。一起， 我们的多方面和组合方法将为理解监管的影响开辟新的视野 发育疾病表型的变异。