Single-cell atlas of BAL from preschool cystic fibrosis reveals key inflammatory pathways modified by the CFTR modulator ivacaftor in the early life lung

Aberrant inflammation and structural lung damage occurs early in life for people with cystic fibrosis (CF). Even in the era of CFTR modulators, anti-inflammatory therapy may still be needed to prevent establishment and lifelong consequences of bronchiectasis. In this study, we integrated transcriptome-wide single-cell RNA sequencing data, highly multiplexed surface protein expression, and functional pathway analysis to create a comprehensive paediatric lower airway atlas of 44 immune and epithelial cell populations in bronchoalveolar lavage (BAL). We then analysed this atlas to investigate inflammatory cell responses in children with CF to show widespread dysregulation of macrophage function in the preschool CF lung. This included alterations in pathways associated with SARS-COV and influenza responses, TNF/IFN signalling, cholesterol homeostasis, and pulmonary fibrosis that were further altered by the early development of bronchiectasis. We showed that the CFTR modulator ivacaftor restores some of these macrophage-related functional deficits and reduces expression of pathways associated with neutrophil infiltration, however the modulator lumacaftor/ivacaftor was not associated with any detectable change in transcriptional response. This work represents a comprehensive, multi-omic single-cell analysis of bronchoalveolar lavage from preschool children and the results inform the future development of anti-inflammatory therapy for children with CF.