Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition

Nat Med. 2021 May;27(5):806-814. doi: 10.1038/s41591-021-01332-7. Epub 2021 May 6.


Cystic fibrosis (CF) is a lethal autosomal recessive disorder that afflicts more than 70,000 people. People with CF experience multi-organ dysfunction resulting from aberrant electrolyte transport across polarized epithelia due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CF-related lung disease is by far the most important determinant of morbidity and mortality. Here we report results from a multi-institute consortium in which single-cell transcriptomics were applied to define disease-related changes by comparing the proximal airway of CF donors (n = 19) undergoing transplantation for end-stage lung disease with that of previously healthy lung donors (n = 19). Disease-dependent differences observed include an overabundance of epithelial cells transitioning to specialized ciliated and secretory cell subsets coupled with an unexpected decrease in cycling basal cells. Our study yields a molecular atlas of the proximal airway epithelium that will provide insights for the development of new targeted therapies for CF airway disease.

Publication types

  • Multicenter Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation / genetics
  • Cilia / metabolism
  • Cystic Fibrosis / genetics*
  • Cystic Fibrosis / pathology*
  • Cystic Fibrosis Transmembrane Conductance Regulator / biosynthesis
  • Cystic Fibrosis Transmembrane Conductance Regulator / genetics
  • Epithelial Cells / cytology*
  • Epithelial Cells / pathology
  • Gene Expression Profiling
  • Humans
  • Lung / pathology*
  • Respiratory Mucosa / pathology*
  • Single-Cell Analysis / methods
  • Transcriptome / genetics


  • CFTR protein, human
  • Cystic Fibrosis Transmembrane Conductance Regulator