A multimodal cell atlas of the pediatric lower airway

Abstract

Many childhood respiratory diseases are characterised by chronic inflammation, however, the immune landscape of the pediatric airway remains largely uncharacterised. This is due, in part, to difficulties obtaining tissue-specific samples in early life as well as limited application of technologies that permit deep profiling from small sample volumes.

Here, we employed multiomic single-cell sequencing to generate the first immune cell atlas of the pediatric lower airway with more than 44,800 cells across 12 preschool aged children. By integrating transcriptome-wide gene expression, assessment of 154 surface proteins, and functional pathway analysis, we extensively characterised immune and epithelial cell populations present in the bronchoalveolar lavage of 11 children with cystic fibrosis and an age-matched healthy control. Paired spectral flow cytometry analysis of over 256,000 cells revealed high correlation in cell subset proportions and protein expression across the two techniques. We further revealed that pediatric alveolar macrophages consist of 12 functionally distinct sub populations, and that the childhood lung is enriched for IFN-α/β signalling. Whilst we showed no significant difference in overall cell proportions between CF and healthy lung, we observed significant differential gene expression in the alveolar macrophage population, including genes associated with lung inflammation and fibrosis.

Our work provides a comprehensive cellular analysis of the pediatric lower airway, reveals key immune signatures of early life lung disease, and provides a reference for investigations of respiratory immunity in children.