Single cell RNA analysis of cellular niche in normal and impaired late lung development

Abstract

The chronic lung disease bronchopulmonary dysplasia (BPD) is the most common complication in preterm infants. It is characterized by alveolar hypoplasia and dysmorphic vasculature. Changes in cellular composition and gene expression underlying the development of BPD are not fully understood. Here we created a detailed temporal map of normal and aberrant late lung development using single-cell RNA sequencing on lung cells from 36 mice at postnatal days (P) 3, 7 and 14. BPD was mimicked by exposure to hyperoxia (85% O2). The MULTI-seq labeling was used in order to minimize experimental bias and increase the reproducibility. A total of 66.200 cells were analyzed throughout three crucial time points of late lung development, across which we identified 1 mesothelial, 5 epithelial, 6 stromal, 5 endothelial, 8 myeloid and 9 lymphoid cell clusters. All cell compartments followed developmental trajectories and hyperoxic exposure impaired the composition and expression patterns in all compartments. Specifically, hyperoxia impaired epithelial surfactant homeostasis and halted fibroblasts maturation. The number of capillary endothelial cells was significantly reduced, suggesting that hyperoxia impairs endothelial maturation at a critical stage of capillary development. Hyperoxia altered lung macrophage populations by reducing the number of homeostatic alveolar macrophages and diminishing the proliferating macrophages. Additionally, we identified the effector cells of the innate immune response, thought to orchestrate pivotal processes resulting in lung impairment. Understanding the temporal changes on transcriptional level provides new means to study the pathogenesis and novel therapies for BPD.