Epigenenomic and transcriptomic networks in normal and defective lung development

 描述(申请人提供)：先天性或新生儿肺部疾病在婴儿中造成相当大的发病率和死亡率，并导致幸存者终生肺功能障碍和呼吸困难。新兴的系统生物学领域具有很大的潜力来阐明复杂的基因调控网络和相互作用机制，这些基因调控网络和相互作用机制控制着正常的肺发育，并在异常发育导致疾病的过程中出错。这种方法首先需要访问定义肺发育基因程序的数据库，但到目前为止，还没有系统科学家从正常或患病肺发育期间的纯人类肺系中准备出所需的数据库。这项建议准备了数据库，并启动了建立肺性出生缺陷发育系统生物学研究所需的分析和计算方法。我们试图通过利用诱导多能干细胞(IPSCs)在培养中的分化来准备第一个动态的人类肺发育基因表达和组蛋白修饰的动态数据库来了解正常和疾病的人类肺发育。在这个建议中，我们聚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，应用这个新的体外模型系统来绘制正常人类肺发育的表观基因组和转录组，并使用Nkx2.1中自然发生的或经工程处理的扰动构建发育的基因调控网络。在目标1中，我们使用一种新的人类胚胎干细胞(ESC)/IPSC体外模型系统来定义在正常人类肺发育过程中出现的全球表观基因组和转录转录程序，该系统能够概括肺上皮细胞谱系指定和分化的发育序列。在目标2中，我们使用在建立正常肺上皮细胞命运过程中获得的时间序列数据来识别动态候选基因调控网络、组蛋白-DNA相互作用和增强子/启动子元件。在目标3中，我们开发了系统发育生物学方法，利用肺部出生缺陷儿童产生的疾病特异性IPSCs来了解肺性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.