Genomic structural dynamics in fibroblasts during heart failure

心力衰竭期间成纤维细胞的基因组结构动态

• 批准号: 10733415
• 负责人: Douglas Joseph Chapski
• 金额: $ 7.63万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10733415
• 关键词: 3-Dimensional; Adopted; Architecture; Binding; Biological Assay; Candidate Disease Gene; Cardiac; Cell Nucleus; Cell Proliferation; Cell Separation; Cells; Chromatin; Chromatin Modeling; Chromatin Structure; Chromosome Territory; Cicatrix; Collaborations; Collagen; Communities; Computer Models; DNA Methylation; DNA Sequence Alteration; Data Set; Death Certificates; Deposition; Dimethyl Sulfoxide; Disease; Disease Progression; Enhancers; Environment; Etiology; Exhibits; Family history of; Fibroblasts; Fibrosis; Functional disorder; Gel; Gene Expression; Gene Expression Regulation; Gene Order; Genes; Genetic Transcription; Genome; Genomic Segment; Genomics; Goals; Heart; Heart failure; High-Throughput Nucleotide Sequencing; Histones; Hypertrophy; Inflammatory; Knowledge; Left Ventricular Dysfunction; Link; Measures; Mediating; Modeling; Mus; Myocardium; Myofibroblast; Neighborhoods; Nuclear; Nuclear Structure; Nucleic Acid Regulatory Sequences; Nucleosomes; Nutrient; Operative Surgical Procedures; Organ; Organ Survival; Oxygen; Pathologic; Pathology; Patients; Phenotype; Physiological; Population; Reader; Resolution; Role; Scientist; Shapes; Signaling Molecule; Small Interfering RNA; Stains; Stimulus; Structural Models; Structure; Synapses; Syndrome; Techniques; Testing; Tissues; Transcriptional Activation; Up-Regulation; Validation; Work; adenoviral mediated; cell type; chromosome conformation capture; clinically relevant; cost; cytokine; experimental study; gain of function; gene repression; genome-wide; genomic locus; in vivo; insight; knock-down; loss of function; mathematical model; member; membrane-associated guanylate kinase; novel; overexpression; periostin; permissiveness; predictive modeling; pressure; programs; promoter; response; spatial relationship; therapeutic target; three dimensional structure; three-dimensional modeling; transcriptome; transcriptome sequencing; translational impact; user-friendly

ABSTRACT Heart failure is a debilitating syndrome that results in depletion of oxygen and nutrients in critical organs for survival and is associated with left ventricular dysfunction and deposition of scar tissue by fibroblasts. Although genetic mutations partially explain the etiology of phenotypic dysfunction in the heart, disease gene expression programs and organ-level pathology are routinely observed in patients with no family history of heart failure. At a global level, chromatin is organized into: higher order regions that interact with themselves more than with others, so-called topologically associating domains (TADs); active and inactive compartments that tend to contain regions of higher or lower transcription, respectively; and chromosome territories. Cardiac chromatin structure is deranged with heart failure, as measured by high-throughput chromatin conformation capture (Hi-C). In addition, chromatin architecture plays a role in conferring cell-type specific transcriptomes and 3D modeling of Hi-C contacts into populations of structures reveals differential rules for cell-type specific gene positioning and genome compartmentalization. A major gap in our understanding is the relationship between local and long range chromatin interactions in conferring disease specific global nuclear structure. To this end, we propose defining 3D chromatin architectural dynamics with fibroblast disease, to reveal how disease gene expression paradigms are driven with pathological stimulus. In Aim 1 we will use high-throughput sequencing and computational modeling to generate integrated 3D models of healthy and activated fibroblast genomes to understand spatial relationships between genomic regulatory regions in disease. Because modeling generates a population of structures, we can model how structural changes in a population of nuclei contribute to organ level response, and how classes of genes undergo coordinated actions in 3D. In Aim 2 we will advance these genomic models by validating findings with orthogonal techniques. We will perform 3D FISH on candidate genes from our models to confirm these spatial changes in vivo with pressure overload mediated heart failure. In isolated fibroblasts, we will perform gain and loss of function studies on these genes to mechanistically link their chromatin structure, transcription, and phenotype. This project will have long-term basic and translational impacts, with the end goal of shaping the Applicant into an independent scientist within 3 years.

摘要 心力衰竭是一种使人衰弱的综合征，其导致关键器官中的氧气和营养物质耗尽， 存活，并与左心室功能障碍和成纤维细胞的瘢痕组织沉积有关。虽然 基因突变部分解释了心脏表型功能障碍的病因，疾病基因表达 在没有心力衰竭家族史的患者中常规观察程序和器官水平的病理学。在 在全局水平上，染色质被组织成：更高阶的区域，它们与自身的相互作用比与 其他的，所谓的拓扑关联域（TADs）;倾向于 分别含有较高或较低转录的区域;和染色体区域。心脏染色质 通过高通量染色质构象捕获（Hi-C）测量，心力衰竭时结构紊乱。 此外，染色质结构在赋予细胞类型特异性转录组和3D建模中起作用 Hi-C接触进入结构群体揭示了细胞类型特异性基因定位的差异规则， 基因组区室化我们理解的一个主要差距是本地和长期之间的关系 范围染色质相互作用赋予疾病特异性的整体核结构。为此，我们建议 定义成纤维细胞疾病的3D染色质结构动力学，以揭示疾病基因表达 范式是由病理刺激驱动的。在目标1中，我们将使用高通量测序， 计算建模，以生成健康和活化的成纤维细胞基因组的集成3D模型， 了解疾病中基因组调控区域之间的空间关系。因为建模会产生 我们可以模拟细胞核群体中的结构变化如何有助于器官 水平反应，以及基因类如何在3D中进行协调行动。在目标2中，我们将推进这些 通过正交技术验证发现的基因组模型。我们将对候选基因进行3D FISH 从我们的模型，以确认这些空间的变化，在体内与压力超负荷介导的心力衰竭。在 分离的成纤维细胞，我们将对这些基因进行功能的获得和丧失研究，以机械地将它们与细胞的功能联系起来。 染色质结构、转录和表型。该项目将有长期的基础和翻译 影响，最终目标是在3年内将申请人塑造成独立的科学家。