A cell atlas of mouse lung development reveals a signaling role for lung basophils in alveolar macrophage maturation

Lung development and function arises from the interactions between diverse cell types and lineages. Using single cell RNA-seq we characterize the cellular composition of the lung during development and identify vast dynamics in both the composition of cells and their molecular characteristics. Analyzing 818 ligand-receptor interaction pairs within and between cell lineages, we identify broadly interacting cells, including AT2, ILC and basophils. Using IL33-receptor knockout mice and in vitro experiments, we show that basophils establish a lung-specific function imprinted by IL-33 and GM-CSF, characterized by unique signaling of cytokines and growth factors important for stromal, epithelial and myeloid cell fates. Antibody depletion strategies, diphtheria toxin-mediated selective depletion of basophils, and co-culture studies, show that lung resident basophils are important regulators of alveolar macrophage development and function. Together, our study demonstrates how whole tissue cell interaction analysis on the single cell level can broaden our understanding of cellular networks in health and disease. Transcriptional profiling of single cells from the different timepoints of lung development, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500 metadata.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts肺脏发育与生理功能源于多种细胞类型及细胞谱系间的相互作用。本研究采用单细胞RNA测序（single cell RNA-seq）技术，对发育进程中肺脏的细胞组成进行表征，并揭示了细胞组成及其分子特征层面的广泛动态变化。通过分析细胞谱系内部及谱系间的818个配体-受体相互作用对，本研究鉴定出了具有广泛相互作用的细胞类群，包括AT2、ILC及嗜碱性粒细胞。本研究借助IL-33受体敲除小鼠模型与体外实验，证实嗜碱性粒细胞可形成由IL-33与粒细胞-巨噬细胞集落刺激因子（GM-CSF）所印记的肺脏特异性功能，其特征为对基质细胞、上皮细胞及髓系细胞命运至关重要的细胞因子与生长因子的独特信号调控模式。通过抗体耗竭策略、白喉毒素介导的嗜碱性粒细胞选择性耗竭实验以及共培养研究，本研究证实肺驻留嗜碱性粒细胞是肺泡巨噬细胞发育与功能的重要调控因子。综上，本研究阐明了单细胞水平的全组织细胞相互作用分析如何能够拓展我们对健康与疾病状态下细胞调控网络的认知。本研究针对肺脏发育不同时间点的单细胞开展转录组分析，该分析通过对数万个细胞进行深度测序完成，测序工作在Illumina Nextseq500平台上分多批次进行。metadata.txt：该元数据文件用于将每个单细胞与其扩增批次及指数分选结果进行关联。