Multi-modal characterization of three human lung niches at the single cell level

摘要 呼吸系统在结构上是复杂的，由许多隔间或壁龛组成 用于呼吸过程中的独特功能。虽然人类呼吸系统表现出很大程度的相似性 对于老鼠等啮齿动物，它含有独特的隔间和结构，人们对此知之甚少，但很可能 对了解疾病的病因和进展具有重要意义。作为一个例子，沿 人类呼吸道的近-远端轴与小鼠的有显著不同，这可能是缺乏的原因。 许多人类肺部疾病的合适的啮齿动物模型。这种缺乏理解的情况对人类来说是相似的 肺血管系统，几乎不存在肺动脉高压等疾病的动物模型。一个详细的 对发育中的人类肺中这些间隔和其他间隔的分析将导致识别新的 单个细胞的细胞谱系和分子特征横跨呼吸道近-远轴线和沿 肺血管系统。这些数据需要与高分辨率成像技术相结合才能建立 发育中的人类肺的细胞图谱。LUNGMAP联盟第二阶段的主要目标之一是， 它最初是在2014年发起的，旨在定义独特的架构、细胞和基因表达复杂性 使用包括单细胞分析在内的尖端和新兴技术对发育中的人类肺进行研究。 鉴于人类肺在空间上的特定结构复杂性，我们建议重点关注三个重要的 隔室或壁龛：1)近端气道，2)远端气道和肺泡，包括终末和 呼吸性细支气管(TBS和RBS)；3)肺血管。我们将利用多模式基因组， 表观基因组学和蛋白质组学技术来确定这三个生态位中的细胞和分子异质性 在单细胞水平上，并传播这些信息以允许研究人员提取细胞间的串扰 在发育中的人类肺中定义并维持这三个生态位。我们的团队已经开发并应用了 新的基因组和成像工具以及设计的交互式Web应用程序，以显示和询问多个 维度数据，允许对中生成的数据进行特定、交互和持续的持续分析 LUNGMAP联盟。重要的是，我们的团队已经证明了定义细胞间相互作用的能力 通过将基因组数据与高分辨率成像相结合，在特定的肺部利基中进行研究。我们的最终目标是 建议是1)识别和绘制发育中的人类三个关键生态位内的细胞谱系 呼吸系统，2)定义它们相对于彼此的空间组织，3)提供新的数据集以允许 研究人员确定对其出生后发育至关重要的细胞-细胞相互作用，并4)组织 并使用多维基因组和 蛋白质组分析工具。

ABSTRACT The respiratory system is architecturally complex and comprised of many compartments or niches responsible for unique functions during respiration. While the human respiratory system exhibits a significant level of similarity with rodents such as mice, it contains unique compartments and structures that are poorly understood but likely to be important in understanding disease etiology and progression. As an example, the heterogeneity along the proximal-distal axis of the human airway is significantly different than in the mouse, which may underlie the lack of appropriate rodent models for many human lung diseases. This lack of understanding is similar for the human pulmonary vasculature, where few animal models of diseases such as pulmonary hypertension exist. A detailed analysis of these compartments and others in the developing human lung will result in the identification of new cell lineages and molecular signatures of individual cells across the proximal-distal axis of the airways and along the pulmonary vasculature. These data will need to be coupled with high resolution imaging techniques to build a cellular atlas of the developing human lung. One of the major goals of Phase 2 of the LungMAP Consortium, which was originally initiated in 2014, is to define the unique architectural, cell, and gene expression complexities of the developing human lung using sophisticated and emerging technologies including single cell analytics. Given the spatially specific architectural complexities of the human lung, we propose to focus on three important compartments or niches: 1) the proximal airways, 2) the distal airways and alveolus including the terminal and respiratory bronchioles (TBs and RBs), and 3) the pulmonary vasculature. We will utilize multi-modal genomic, epigenomic, and proteomic techniques to define the cellular and molecular heterogeneity in these three niches at the single cell level, and disseminate this information to allow investigators to extract cell-cell crosstalk that defines and maintains these three niches in the developing human lung. Our group has developed and applied novel genomic and imaging tools and designed interactive web applications to display and interrogate multi- dimensional data that allows for specific, interactive, and continuous ongoing analysis of the data generated in the LungMAP Consortium. Importantly, our group has demonstrated the ability to define cell-cell interactions within specific lung niches by integrating genomic data with high resolution imaging. The ultimate goals of our proposal are to 1) identify and map the cell lineages within three critical niches of the developing human respiratory system, 2) define their spatial organization in relation to each other, 3) provide novel datasets to allow researchers to identify the cell-cell interactions that are critical for their postnatal development, and 4) organize and display the data for broad access throughout the scientific community using multi-dimensional genomic and proteomic analysis tools.