Deciphering how 3D genome organization orchestrates cardiac cellular identity

解读 3D 基因组组织如何协调心脏细胞身份

• 批准号: 10574267
• 负责人: Rajan Jain
• 金额: $ 88.44万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2030-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10574267
• 关键词: 3-Dimensional; Architecture; Cardiac; Cells; Chromatin; Development; Disease; Engineering; Epigenetic Process; Equilibrium; Failure; Gene Expression; Genes; Genetic Materials; Genetic Transcription; Genome; Genomics; Heart Diseases; Heart failure; Human; Human Biology; Link; Longevity; Maintenance; Mechanics; Modeling; Molecular; Multipotent Stem Cells; Neural Crest; Nuclear; Nuclear Lamina; Pathologic; Patients; Physiological; Positioning Attribute; Regulation; Repressor Proteins; Resolution; Shapes; Signal Transduction; Therapeutic; Three-Dimensional Imaging; Tissues; Vision; Work; cardiogenesis; cell type; congenital heart disorder; epigenome; flexibility; genetic manipulation; interest; morphogens; novel therapeutic intervention; programs; recruit; shift work; spatiotemporal; superresolution imaging; transcription factor

Project Summary During cardiac development, coordinate gene expression changes facilitate the progressive lineage restriction of multipotent progenitors into a terminal identity that is maintained over their lifespan. Compromised differentiation and/or cell state have been linked to multiple diseases, including aspects of congenital heart disease and heart failure. Thus, the mechanisms underlying cellular identity are of intense interest. Models underlying fate determination and the identity often focus on transcription factors and/or niche signals. Current paradigms fail to reconcile how the interplay between a finite number of morphogens and lineage specific transcription factors result in 200+ cell types with distinct and stable identities. I hypothesize that nuclear architecture represents a critical mechanism for achieving coordinated regulation of hundreds of genes underlying cellular identity by governing their accessibility or availability. Supporting our hypothesis, we have built a strong body of work demonstrating that nuclear architecture regulates cardiac cellular identity in development and disease. First, we discovered mechanisms by which critical transcription factors not only govern transcription, but also choreograph genome folding to regulate cardiac neural crest fate determination. Second, our work shows that spatial positioning of chromatin safeguards cardiac cellular identity and likely contributes to human cardiac disease (i.e. laminopathies). Decades of work have shown that gene expression programs are regulated by the recruitment and activity of activator and opposing repressor proteins. In addition to revolutionizing our understanding of transcription, this work has led to therapies directly targeting transcription factors. The mechanisms that similarly balance formation, maintenance and dissolution of nuclear architecture are poorly understood. In the EIA application I outline an interdisciplinary vision to uncover how these mechanisms control cardiac cellular identity. In Theme 1, I propose strategies to identify and decipher how molecular players guiding establishment, maintenance and disassembly of genome folding impact cardiac cell state. In Theme 2, I propose strategies to uncover how epigenetic, transcriptional, and mechanical inputs regulate spatial positioning of the genome in relation to the nuclear lamina in physiologic and pathologic conditions. We have established a multipronged program that will use high throughput 3D imaging, genetic manipulations with precise spatiotemporal resolution, tunable cardiac microtissues, epigenome engineering, super-resolution imaging and state-of-the-art genomics to tackle the propose studies, with a focus grounded in physiological relevance. The orthogonal approaches promote rigor, but require flexibility. My strong track record of building an impactful body of work support our pursuit of this paradigm shifting work. The proposed studies have the potential to reshape our understanding of how epigenetics, transcriptional, and mechano-related mechanisms direct 3D genome organization and orchestrate cardiac cellular identity. By viewing cardiac diseases through the prism of genome organization, we predict a wealth of unrealized therapeutic opportunities.

项目摘要 在心脏发育过程中，协调基因表达的变化促进了进行性谱系限制 将多能祖细胞转化为终末身份，并在其整个生命周期中保持不变。损害 分化和/或细胞状态与多种疾病有关，包括先天性心脏病 疾病和心力衰竭。因此，潜在的细胞身份的机制是强烈的兴趣。模型 潜在的命运决定和同一性通常集中在转录因子和/或小生境信号上。电流 范式未能调和有限数量的形态发生素和谱系特异性之间的相互作用， 转录因子导致200+细胞类型具有不同的和稳定的身份。我假设核武器 结构代表了实现数百个基因的协调调节的关键机制 通过管理它们的可访问性或可用性来支持蜂窝身份。支持我们的假设，我们有 建立了一个强大的工作机构，证明核结构调节心脏细胞的身份， 发展和疾病。首先，我们发现了关键转录因子不仅 控制转录，但也编排基因组折叠，以调节心脏神经嵴命运的决定。 其次，我们的工作表明，染色质的空间定位保障了心脏细胞的身份， 导致人类心脏病（即核纤层蛋白病）。几十年的研究表明，基因表达 程序受激活蛋白和相反阻遏蛋白的募集和活性调节。此外 为了彻底改变我们对转录的理解，这项工作已经导致了直接针对转录的疗法， 因素类似地平衡核结构的形成、维持和分解的机制 我们对此知之甚少。在EIA应用程序中，我概述了一个跨学科的愿景，以揭示这些 机制控制心脏细胞的身份。在主题1中，我提出了识别和破译如何 指导基因组折叠建立、维持和拆卸的分子参与者影响心肌细胞 状态在主题2中，我提出了一些策略，以揭示表观遗传、转录和机械输入是如何 调节基因组在生理和病理中相对于核纤层的空间定位 条件我们已经建立了一个多管齐下的计划，该计划将使用高通量3D成像，遗传 具有精确时空分辨率的操作，可调心脏微组织，表观基因组工程， 超分辨率成像和最先进的基因组学来解决拟议的研究，重点是 生理相关性正交方法促进了严谨性，但需要灵活性。我的良好记录 建立一个有影响力的工作机构支持我们追求这种范式转变的工作。拟议的研究 有可能重塑我们对表观遗传学，转录和机械相关的理解 机制指导3D基因组组织并协调心脏细胞身份。通过查看心脏 通过基因组组织的棱镜来研究疾病，我们预测了大量未实现的治疗机会。