Childhood-onset asthma is characterized by airway epithelial hillock-to-squamous differentiation in early life

Childhood-onset asthma is characterized by Type 2-inflammation and airway wall remodeling, but mechanisms of asthma development in the first years of life remain unclear. Here, we investigate transcriptional changes in airway wall biopsies of 22 symptomatic one year old children and relate these to asthma at school age. We demonstrate that pre-asthmatic children (n = 10) overexpressed a gene signature characteristic for an airway epithelial differentiation trajectory via hillock cells towards squamous cells (adjusted p-value 8.06e-16), whilst there was no association with gene signatures of Type 2-inflammation or eosinophil activation. Genes expressed along this trajectory are linked to an altered epithelial barrier function, innate immune activation and extracellular matrix remodeling. Functional GWAS analysis supports a causal link between childhood-onset, but not adult-onset asthma, and the hillock-squamous cell differentiation trajectory. Next, we confirmed the presence of hillock-like cells at the RNA and protein level in pediatric upper and lower airway samples. These findings identify a novel mechanism by which an aberrant airway epithelial differentiation trajectory may contribute to a pre-asthmatic state, highlighting the difference between the early origins of childhood-onset asthma and adult asthma, and point to possible new targets for the early diagnosis and treatment of asthma in the first two years of life. One Sentence Summary RNA sequencing in bronchial biopsies from wheezing infants and children < 2 years shows evidence for an airway epithelial hillock-to-squamous differentiation pathway that marks the development of asthma.