Progenitor identification and SARS-CoV-2 infection in human distal lung organoids

Nature. 2020 Dec;588(7839):670-675. doi: 10.1038/s41586-020-3014-1. Epub 2020 Nov 25.


The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate the investigation of pathologies such as interstitial lung disease, cancer and coronavirus disease 2019 (COVID-19) pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we describe the development of a long-term feeder-free, chemically defined culture system for distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids were able to differentiate into AT1 cells, and basal cell organoids developed lumens lined with differentiated club and ciliated cells. Single-cell analysis of KRT5+ cells in basal organoids revealed a distinct population of ITGA6+ITGB4+ mitotic cells, whose offspring further segregated into a TNFRSF12Ahi subfraction that comprised about ten per cent of KRT5+ basal cells. This subpopulation formed clusters within terminal bronchioles and exhibited enriched clonogenic organoid growth activity. We created distal lung organoids with apical-out polarity to present ACE2 on the exposed external surface, facilitating infection of AT2 and basal cultures with SARS-CoV-2 and identifying club cells as a target population. This long-term, feeder-free culture of human distal lung organoids, coupled with single-cell analysis, identifies functional heterogeneity among basal cells and establishes a facile in vitro organoid model of human distal lung infections, including COVID-19-associated pneumonia.

Publication types

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

MeSH terms

  • Alveolar Epithelial Cells / cytology
  • Alveolar Epithelial Cells / metabolism
  • Alveolar Epithelial Cells / virology
  • COVID-19 / metabolism
  • COVID-19 / pathology
  • COVID-19 / virology*
  • Cell Differentiation
  • Cell Division
  • Clone Cells / cytology
  • Clone Cells / metabolism
  • Clone Cells / virology
  • Humans
  • In Vitro Techniques
  • Influenza A Virus, H1N1 Subtype / growth & development
  • Influenza A Virus, H1N1 Subtype / physiology
  • Integrin alpha6 / analysis
  • Integrin beta4 / analysis
  • Keratin-5 / analysis
  • Lung / cytology*
  • Models, Biological*
  • Organoids / cytology*
  • Organoids / metabolism
  • Organoids / virology*
  • Pneumonia, Viral / metabolism
  • Pneumonia, Viral / pathology
  • Pneumonia, Viral / virology
  • SARS-CoV-2 / growth & development
  • SARS-CoV-2 / physiology*
  • Single-Cell Analysis
  • TWEAK Receptor / analysis
  • Tissue Culture Techniques*


  • ITGA6 protein, human
  • ITGB4 protein, human
  • Integrin alpha6
  • Integrin beta4
  • KRT5 protein, human
  • Keratin-5
  • TNFRSF12A protein, human
  • TWEAK Receptor