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 在心脏发育期间，坐标基因表达变化有助于进行性谱系限制 多态祖细胞中的终端身份，该身份在其寿命中保持。妥协 分化和/或细胞状态已与多种疾病有关，包括先天性心脏的方面 疾病和心力衰竭。因此，细胞身份的基础机制具有强烈的关注。型号 基本的命运确定和身份通常集中在转录因子和/或利基信号上。当前的 范式无法调和有限数量的形态和谱系特定数量之间的相互作用 转录因子导致200多个具有不同身份的细胞类型。我假设核 建筑代表了实现数百个基因协调调节的关键机制 通过管理其可访问性或可用性来基本的蜂窝身份。支持我们的假设，我们有 建立了强大的工作，表明核建筑调节心脏细胞身份 发展与疾病。首先，我们发现了关键转录因子不仅 控制转录，但也要编舞基因组折叠以调节心脏神经冠的命运确定。 其次，我们的工作表明，染色质保障心脏细胞身份的空间定位，可能 有助于人类心脏病（即椎板病）。数十年的工作表明基因表达 程序受到激活剂和相对阻遏蛋白的募集和活动的调节。此外 为了彻底改变我们对转录的理解，这项工作导致疗法直接针对转录 因素。同样平衡核构建形成，维护和解散的机制 知之甚少。在EIA应用程序中，我概述了跨学科的愿景，以发现这些愿景 机制控制心脏细胞身份。在主题1中，我提出了识别和破译的策略 分子参与者指导基因组折叠撞击心脏细胞的建立，维护和拆卸 状态。在主题2中，我提出了策略，以发现表观遗传，转录和机械输入如何 调节基因组在生理和病理学中与核椎板相关的空间定位 状况。我们已经建立了一个多收益的程序，该程序将使用高吞吐量3D成像，遗传 具有精确时空分辨率，可调心脏微动物，表观基因组工程的操作， 超分辨率成像和最先进的基因组学以应对提出的研究，重点扎根于 生理相关性。正交方法可促进严格，但需要灵活性。我的出色记录 建立有影响力的工作支持我们追求这一范式转移工作。提出的研究 有可能重塑我们对表观遗传学，转录和机械相关的理解 机制直接3D基因组组织并编排心脏细胞身份。通过观看心脏 通过基因组组织的棱镜疾病，我们预测了许多未实现的治疗机会。