Defining the cellular dynamics that orchestrate alveolar epithelial cell repair behaviors in live mammal

项目概述：哺乳动物的肺在各种损伤后具有自我修复的能力。肺泡 修复是一个动态和协调的过程 分化成专门的细胞来修复受损的上皮。最近的研究发现了一种独特的中间体 在干/祖细胞和这些特化细胞之间的转变期间存在的祖细胞状态; 然而，驱动中间祖细胞的动态细胞行为和分子调控景观， 对细胞向修复的转变知之甚少。在这里，我们提出了两个目标，解剖细胞和 在再生的哺乳动物肺中控制肺泡修复的体内分子机制。首先（目标1）， 将利用永久性肺部成像窗口系统来跟踪出现，生活行为和终端 在肺泡修复过程中，个体中间祖细胞随时间的分化。第二个目标（Aim 2） 结合scRNA-seq和scATAC-seq以及先进的动态分析和机器学习 定义细胞状态空间的技术（基因表达和染色质可及性），细胞轨迹 和过渡中间祖细胞的调节景观。我们将通过以下方式实现这两个目标： 补充体内肺损伤模型和荧光报告小鼠，以追踪 对于中间祖细胞是独特的，并且可能依赖于它们的细胞来源和/或损伤背景。 该项目将产生广泛的，高质量的数据集，以实现定量和预测模型的关键 哺乳动物体内驱动肺泡修复的调节机制。考虑到许多细胞和 肺生物学的分子机制在小鼠和人类之间是保守的，我们的发现具有潜在的 揭示在人类疾病背景下调节肺泡修复的假定靶点。

PROJECT SUMMARY: The mammalian lung has the capacity to repair itself following various injuries. Alveolar repair is a dynamic and coordinated process whereby stem/progenitor cells in the lung undergo differentiation into specialized cells to repair the damaged epithelium. Recent studies have uncovered a distinct intermediate progenitor cell state that exists during the transition between stem/progenitor cells and these specialized cells; however, the dynamic cellular behaviors and molecular regulatory landscape that drives intermediate progenitor cell transitions toward repair is poorly understood. Here, we propose two aims to dissect the cellular and molecular mechanisms that control alveolar repair in vivo in the regenerating mammalian lung. First (Aim 1) we will utilize a permanent lung imaging window system to track the emergence, live behaviors and terminal differentiation of individual intermediate progenitor cells over time during alveolar repair. Second (Aim 2) we will utilize combined scRNA-seq and scATAC-seq together with advanced dynamical analysis and machine learning techniques to define the cellular state space (gene expression and chromatin accessibility), cellular trajectories and regulatory landscape of transitioning intermediate progenitor cells. We will perform both aims using complimentary in vivo lung injury models and fluorescent report mice in order to track the mechanisms that are unique to intermediate progenitor cells and potentially dependent on their cellular origin and/or injury context. This project will generate extensive, high quality datasets to enable quantitative and predictive models of the key regulatory mechanisms that mammalian drive alveolar repair in vivo. Given that many of the cellular and molecular mechanisms of lung biology are conserved between mouse and human, our findings have the potential to uncover putative targets for modulating alveolar repair in the context of human disease.