Genomic structural dynamics in fibroblasts during heart failure

摘要 心力衰竭是一种衰弱综合征，导致关键器官中的氧气和营养物质枯竭 存活并与左心功能不全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、疾病基因表达的病因学 对于没有心力衰竭家族史的患者，常规观察程序和器官水平的病理。在… 在全球水平上，染色质被组织成：更高阶的区域，它们与自己的相互作用比与 其他，所谓的拓扑关联域(TADS)；活动和不活动的隔室，倾向于 分别包含高转录区或低转录区；以及染色体区域。心脏染色质 通过高通量染色质构象捕获(Hi-C)测量，结构与心力衰竭一起错乱。 此外，染色质结构在赋予细胞类型的特定转录本和3D建模方面起着作用 Hi-C接触进入结构群体揭示了细胞类型特异性基因定位和 基因组区划。我们在理解上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与疾病特异性全球核结构的关系。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，以揭示疾病基因的表达 范式是由病理性刺激驱动的。在目标1中，我们将使用高通量测序和 计算建模以生成健康和激活的成纤维细胞基因组的集成3D模型 了解疾病中基因组调节区之间的空间关系。因为建模会生成 对于一组结构，我们可以模拟一组核的结构变化如何对器官做出贡献 水平反应，以及不同类别的基因如何在3D中进行协调行动。在目标2中，我们将推进这些 用正交法验证研究结果，建立基因组模型。我们将对候选基因进行3D FISH 从我们的模型来证实这些在体内的空间变化与压力超负荷介导的心力衰竭。在……里面 分离的成纤维细胞，我们将对这些基因进行功能获得和丧失的研究，以机械地将它们联系在一起 染色质结构、转录和表型。该项目将具有长期的基础性和转化性 影响，最终目标是在3年内将申请者塑造成一名独立的科学家。

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.