Transcriptomic analysis of airway macrophages from preschool wheeze

Preschool wheeze is an early life bronchoconstriction disorder with an increased risk of progression to chilhood asthma. Preschool wheeze is typically triggered by respiratory infection, but airway inflammatory phenotypes, including the phenotype of airway macrophages (AMs), in preschool wheeze is not fully understood. In this study, AMs were sorted from preschool wheeze patients and non-wheezing paediatric controls under clinical investigation for chronic cough and gene expression assessed by Illumina mRNA sequencing (110 base pair, paired end reads). A number of differentially expressed genes were observed in AMs from preschool wheeze compared to those from controls, including genes encoding pro-inflammatory chemokines and genes associated with a more immature and inflammatory AM phenotype. These findings suggest that AMs contribute to an altered airway immune landscape in preschool wheeze. CD206+ AMs were bead sorted from bronchoalveolar lavage of children under clinical investigation for preschool wheeze (N=3) or chronic cough without wheeze (N=5). RNA was extracted and converted to mRNA libraries before performing Illumina paired end sequencing. Reads were aligned to the Hg38 genome using COBWeb. Transcripts were quantified from aligned reads using DESeq. Low abundance transcripts were filtered (< 5 reads in < 3 of the samples) and differential expression analysis performed with DESeq2, using the Wald method with Benjamini-Hochberg false discovery rate correction.