Epigenenomic and transcriptomic networks in normal and defective lung development

 描述（由申请人提供）：先天性或新生儿肺部疾病导致婴儿的发病率和死亡率相当高，并导致幸存者终身肺功能障碍和呼吸困难。新兴的系统生物学领域有很大的潜力来阐明复杂的基因调控网络和相互作用的机制，控制正常的肺发育，并在异常发育过程中出错，导致疾病。这种方法首先需要访问定义肺发育遗传程序的数据库，但迄今为止，系统科学家所需的数据库还没有从正常或患病肺发育期间的纯人类肺谱系中制备出来。这项建议准备了数据库，并启动了分析和计算的方法，需要建立一个肺儿童出生缺陷的发育系统生物学研究。我们试图通过使用诱导多能干细胞（iPSC）在培养中的分化来制备基因表达和全局组蛋白修饰的第一个动态人类肺发育数据库，来了解正常和患病的人类肺发育。在这个提议中，我们汇集了肺发育生物学家，干细胞生物学家，临床医生，物理学家，和计算研究人员应用这种新的体外模型系统来绘制正常人肺发育的表观基因组和转录组，并使用NKX2.1中天然存在或工程改造的扰动来构建发育的基因调控网络，会导致肺部先天缺陷在目标1中，我们使用能够概括肺上皮谱系特化和分化的发育序列的新型人胚胎干细胞（ESC）/iPSC体外模型系统来定义在正常人肺发育期间出现的全局表观基因组和转录组学程序。在目的2中，我们确定动态候选基因调控网络，组蛋白-DNA相互作用，增强子/启动子元件使用的时间序列数据在建立正常肺上皮细胞的命运。在目标3中，我们开发了系统发育生物学方法，用于使用从患有肺出生缺陷的儿童产生的疾病特异性iPSC来理解肺儿童出生缺陷的发病机制。

 DESCRIPTION (provided by applicant): Congenital or neonatal lung diseases cause considerable morbidity and mortality in infants and lead to life-long lung dysfunction and dyspnea in survivors. The emerging field of systems biology has great potential to illuminate the complex gene regulatory networks and interacting mechanisms that control normal lung development and go awry during abnormal development leading to disease. This approach first requires access to databases that define the genetic programs of lung development, yet to date no databases required by systems scientists have been prepared from pure human lung lineages during normal or diseased lung development. This proposal prepares the databases and initiates the analytical and computational approaches required to found a developmental systems biology study of lung child birth defects. We seek to understand normal and diseased human lung development by preparing the first dynamic human lung developmental databases of gene expression and global histone modifications using differentiation of induced pluripotent stem cells (iPSCs) in culture In this proposal, we bring together lung developmental biologists, stem cell biologists, clinicians, physicists, and computational researchers to apply this new in vitro model system to map the epigenome and transcriptome of normal human lung development and to construct gene regulatory networks of development using naturally occurring or engineered perturbations in NKX2.1 that are known to lead to lung birth defects. In aim 1, we define the global epigenomic and transcriptomic programs emerging during normal human lung development using a novel human embryonic stem cell (ESC)/iPSC in vitro model system able to recapitulate the developmental sequence of lung epithelial lineage specification and differentiation. In Aim 2 we identify dynamic candidate gene regulatory networks, histone-DNA interactions, and enhancer/promoter elements using time-series data obtained during the establishment of normal lung epithelial cell fate. In aim 3 we develop systems developmental biology approaches for understanding the pathogenesis of lung child birth defects using disease-specific iPSCs generated from children with lung birth defects.