Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020).
Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen Emphysema Conf. https://europepmc.org/article/med/5610792 10, 433–441 (1967).
Tanabe, N. et al. Micro-computed tomography comparison of preterminal bronchioles in centrilobular and panlobular emphysema. Am. J. Respir. Crit. Care Med. 195, 630–638 (2017).
Weibel, E. R. & Gomez, D. M. Architecture of the human lung. Use of quantitative methods establishes fundamental relations between size and number of lung structures. Science 137, 577–585 (1962).
Kobayashi, Y. et al. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat. Cell Biol. 22, 934–946 (2020).
Strunz, M. et al. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis. Nat. Commun. 11, 3559 (2020).
Choi, J. et al. Inflammatory signals induce AT2 cell-derived damage-associated transient progenitors that mediate alveolar regeneration. Cell Stem Cell 27, 366–382 (2020).
Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).
Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015).
Travaglini, K. J. et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature 587, 619–625 (2020).
Habermann, A. C. et al. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci. Adv. 6, eaba1972 (2020).
Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci. Adv. 6, eaba1983 (2020).
Carraro, G. et al. Single-cell reconstruction of human basal cell diversity in normal and idiopathic pulmonary fibrosis lungs. Am. J. Respir. Crit. Care Med. 202, 1540–1550 (2020).
Okuda, K. et al. Secretory cells dominate airway CFTR expression and function in human airway superficial epithelia. Am. J. Respir. Crit. Care Med. 203, 1275–1289 (2021).
Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377–381 (2018).
Montoro, D. T. et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 560, 319–324 (2018).
Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153–1163 (2019).
Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. Site and nature of airway obstruction in chronic obstructive lung disease. N. Engl. J. Med. 278, 1355–1360 (1968).
Hogg, J. C. et al. The nature of small-airway obstruction in chronic obstructive pulmonary disease. N. Engl. J. Med. 350, 2645–2653 (2004).
Cosio, M. et al. The relations between structural changes in small airways and pulmonary-function tests. N. Engl. J. Med. 298, 1277–1281 (1978).
Weibel, E. R. A retrospective of lung morphometry: from 1963 to present. Am. J. Physiol. Lung Cell. Mol. Physiol. 305, L405–L408 (2013).
Deprez, M. et al. A single-cell atlas of the human healthy airways. Am. J. Respir. Crit. Care Med. 202, 1636–1645 (2020).
Buechler, M. B. et al. Cross-tissue organization of the fibroblast lineage. Nature 593, 575–579 (2021).
Schittny, J. C. Development of the lung. Cell Tissue Res. 367, 427–444 (2017).
Pan, H., Deutsch, G. H. & Wert, S. E. Comprehensive anatomic ontologies for lung development: a comparison of alveolar formation and maturation within mouse and human lung. J. Biomed. Semant. 10, 18 (2019).
Jeffrey, P. K. The development of large and small airways. Am. J. Respir. Crit. Care Med. 157, S174–S180 (1998).
Miller, A. J. et al. In vitro and in vivo development of the human airway at single-cell resolution. Dev. Cell 53, 117–128 (2020).
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
Wolf, F. A. et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 59 (2019).
Jin, S., MacLean, A. L., Peng, T. & Nie, Q. scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. Bioinformatics 34, 2077–2086 (2018).
Zhou, P., Wang, S., Li, T. & Nie, Q. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics. Nat. Commun. 12, 5609 (2021).
Katsura, H. et al. Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2-mediated interferon responses and pneumocyte dysfunction. Cell Stem Cell 27, 890–904 (2020).
Plantier, L. et al. Ectopic respiratory epithelial cell differentiation in bronchiolised distal airspaces in idiopathic pulmonary fibrosis. Thorax 66, 651–657 (2011).
Weibel, E. R. Morphometry of the Human Lung (Springer-Verlag, 1963).
Castleman, W. L., Dungworth, D. L. & Tyler, W. S. Intrapulmonary airway morphology in three species of monkeys: a correlated scanning and transmission electron microscopic study. Am. J. Anat. 142, 107–121 (1975).
Pinkerton, K. E. & Joad, J. P. The mammalian respiratory system and critical windows of exposure for children’s health. Environ. Health Perspect. 108, 457–462 (2000). Suppl 3.
Hyde, D. M., Samuelson, D. A., Blakeney, W. H. & Kosch, P. C. A correlative light microscopy, transmission and scanning electron microscopy study of the ferret lung. Scan. Electron Microsc. 3, 891–898 (1979).
Miller, L. A., Royer, C. M., Pinkerton, K. E. & Schelegle, E. S. Nonhuman primate models of respiratory disease: past, present, and future. ILAR J. 58, 269–280 (2017).
Rogers, C. S. et al. The porcine lung as a potential model for cystic fibrosis. Am. J. Physiol. Lung Cell Mol. Physiol. 295, L240–L263 (2008).
Plopper, C. G., Heidsiek, J. G., Weir, A. J., George, J. A. & Hyde, D. M. Tracheobronchial epithelium in the adult rhesus monkey: a quantitative histochemical and ultrastructural study. Am. J. Anat. 184, 31–40 (1989).
Ma, S. et al. Single-cell transcriptomic atlas of primate cardiopulmonary aging. Cell Res. 31, 415–432 (2021).
Boucher, R. C. Muco-obstructive lung diseases. N. Engl. J. Med. 380, 1941–1953 (2019).
Bhandari, A. & McGrath-Morrow, S. Long-term pulmonary outcomes of patients with bronchopulmonary dysplasia. Semin. Perinatol. 37, 132–137 (2013).
Jiang, Y. et al. Alteration of cystic airway mesenchyme in congenital pulmonary airway malformation. Sci. Rep. 9, 5296 (2019).
Kim, C. F. B. et al. Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell 121, 823–835 (2005).
Giangreco, A., Reynolds, S. D. & Stripp, B. R. Terminal bronchioles harbor a unique airway stem cell population that localizes to the bronchoalveolar duct junction. Am. J. Pathol. 161, 173–182 (2002).
Williams, S. E., Beronja, S., Pasolli, H. A. & Fuchs, E. Asymmetric cell divisions promote Notch-dependent epidermal differentiation. Nature 470, 353–358 (2011).
Kumar, P. A. et al. Distal airway stem cells yield alveoli in vitro and during lung regeneration following H1N1 influenza infection. Cell 147, 525–538 (2011).
Nagendran, M., Riordan, D. P., Harbury, P. B. & Desai, T. J. Automated cell-type classification in intact tissues by single-cell molecular profiling. eLife 7, e30510 (2018).
Kwapiszewska, G. et al. Transcriptome profiling reveals the complexity of pirfenidone effects in idiopathic pulmonary fibrosis. Eur. Respir. J. 52, 800564 (2018).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience 9, giaa151 (2020).
Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
Lambert, S. A. et al. The human transcription factors. Cell 172, 650–665 (2018).
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
Jin, S. et al. Inference and analysis of cell–cell communication using CellChat. Nat. Commun. 12, 1088 (2021).