Cellular organization and biology of the respiratory system Brigid L. M. Hogan and Purushothama Rao Tata

The lungs, which evolved in early terrestrial vertebrates, mediate the vital processes of supplying various mesenchymal cell types, including smooth muscle and fibroblasts that support epithelial

O2 to the blood and removing CO2. Air enters through the mouth and trachea and is distributed homeostasis and lung functions as well as ectoderm-derived neurons. Although respiratory tract through the lung lobes by a highly branched, tree-like system of tubes lined by pseudostratified tissue shows limited turnover in homeostasis, damage to the respiratory epithelium can be epithelium. The intralobar airways supported by cartilage are known as bronchi; the smaller repaired by resident tissue stem cells. Furthermore, immune cells within the lung help protect branches lacking cartilage are known as bronchioles. The bronchioles terminate in millions of the lungs from infection and promote repair. Defects in the homeostatic and reparative tiny, thin-walled, highly vascularized sacs (alveoli) composed of specialized epithelial cells mechanisms may lead to diseases such as chronic obstructive pulmonary disease, asthma, where gas exchange takes place. In addition to epithelial cells, the respiratory tract contains fibrosis and cancer, which together make a major contribution to mortality worldwide.

Tissue organization and cell function Cell lineages Human respiratory system Respiratory diseases

Airways Airways Asthma Cystic fibrosis Pseudostratified Basal cells: TP63, KRT5, NGFR • Obstruction of small airways by goblet cell • Reduced airway surface fluid and thickened Self-renewal epithelium Function as multipotent stem cells Only hyperplasia and excessive mucus inhibit mucociliary clearance and Basal cell after mucus production promote airway colonization by microbes Club cells: SCGB1A1, injury • Constriction of small airways and reduced • Risk factors: mutations (loss of function SCGB3A2 (data from mice) air flow caused by hypersensitive smooth of CFTR) Immunomodulatory functions muscles and tissue fibrosis • Inflammation due to accumulation of Goblet cells: MUC5AC, FOXA3, SPDEF eosinophils and other immune cells Idiopathic pulmonary fibrosis Secrete mucins Bronchial circulation Basal lamina in airways • Progressive, irreversible replacement of NE Ionocyte Tuft Ciliated Club Goblet Nerve • Risk factors: allergens, environmental alveoli with scar-like deposits of ECM, cell cell cell cell cell Ciliated cells: FOXJ1, β-tubulin IV pollutants, obesity, maternal–fetal containing hyperplastic AEC2s, cysts of Remove mucus out of the lung exposure, family history bronchiolar epithelium and inflammatory cells • Risk factors: advanced age, male sex, SMGs Upper smoking, mutations (loss of function of NE cells: ASCL1, CALCA Mucous respiratory Bronchopulmonary dysplasia Act as sensory cells; cell Acinus tract telomerase genes (TERT, TR), surfactant communicate with neurons Only Myoepithelial • Delayed development of alveolar region proteins, and polymorphisms in MUC5B after cell Cartilage • NE cell hyperplasia, inflammation gene regulatory elements) injury Only • Risk factors: premature birth, Rare cells maternal exposures Ionocytes: FOXI1, CFTR high after Serous Tuft (brush) cells: TRPM5, GNG13 Basal Self-renewal injury cell Vocal folds Pulmonary arterial hypertension cell Bronchiolitis • Expansion of the tunica media in arterioles, endothelial plexiform lesions SMGs • Inflammation in small conducting airways SMG Trachea • Risk factors: mutations (BMPR2, ALK1), Cartilage • Risk factors: viral infection, connective Myoepithelial cells: TP63, ACTA2 Pulmonary drug toxicity (fen-phen), HIV, connective blood circulation tissue disease, lung transplant rejection, Multipotent stem cells; expel mucins tissue disease out by contraction Alveoli burn-pit exposure, diacetyl exposure (rare)

Acinar cells Self-renewal Lung cancer Intralobar Serous: LTF, DCPP1 Chronic obstructive pulmonary disease Major types of lung cancers include: Mucous: MUC5B, TFF2 bronchi Elastin Heterogeneous disorder including: ADCs (40% of cases): Endothelial Emphysema: AEC2 AEC1 cell bundles • Originate from AEC2s with five subtypes Alveoli • Abnormal, permanent enlargement of differing in morphology and alveoli; reduced surface area for clinical characteristics AEC2s: SFTPC, DC-LAMP gas exchange • Risk factors: mutations (gain of function: Bronchioles ECM Stem cells; produce surfactant Mouse–human dierences • Loss of alveolar septa and reduced KRAS, EGFR; loss of function: CDK2A, lung elasticity KEAP1, STK11) AEC1s: PDPN, AGER • Risk factors: smoking, mutations (loss of SCCs (30% of cases): Large surface area; facilitate • Lung tidal volume is much smaller in mouse function of SERPINA) • Originate from basal cells and are gas exchange • Goblet cells are less abundant in mouse Chronic bronchitis: characterized by stratified layers of flat, thin • SMGs are present only in upper-most • Inflammation of mucosa in large airways, squamous cells trachea in mouse Bronchi increased mucus production, cough • Risk factors: smoking, mutations (TP53, Mesenchymal cells • NE cells are mostly solitary and scattered in • Risk factors: smoking, inhalational SOX3, TP63, PI3KCA, CDK2A, and FGFR1) human airways Respiratory Distal exposures, infection, gastroesophageal reflux SCLCs (15% of cases): • Cartilage and basal cells are absent from bronchioles bronchioles • Originate from neuroendocrine cells and Smooth muscle cells: ACTA2, MYH11 mouse intralobar airways Pleura are one of the most aggressive cancer • Respiratory bronchioles are absent from with Alveoli lymphatic (~400 million) types in humans mouse airways Peribronchial fibroblasts: GLI1, LGR6 circulation • Risk factors: smoking, mutations Myofibroblasts: ACTA2 (RB1, TP53)

AEC2 associated fibroblasts Lung cell culture models (lipofibroblast-like): PDGFRA 2D cultures 3D cultures (organoids) Pericytes: PDGFRB • Use primary cells isolated from donor lungs after proteolytic digestion Side chambers Lung on a chip • HBECs are seeded into ECM gels and • Undifferentiated basal cells, known as HBEs, and Air–liquid interface generate spheres with basal, ciliated AEC2s can be cultured in 2D and 3D modules • A microfluidic-based assembly Immune cells • HBECs are grown on transwell inserts in and secretory cells • Used to identify growth and differentiation factors in which lung epithelial cells are specialized cell culture medium • AEC2s are seeded into ECM gels with and screen for drugs to treat respiratory diseases Pseudostratified grown on one side of a epithelium • After reaching confluence, the liquid is fibroblasts and/or endothelial cells Dendritic cells • 2D cultures also allow measurement of membrane and stromal cells on removed to expose cells to air and the • In mouse-derived cultures, both AEC2s transepithelial resistance (and hence, evaluate the other surface medium is changed to induce differentiation and AEC1s are present in these epithelial integrity) Lung epithelium Air • Liquid and air are circulated Alveolar resident macrophages, • By 2–4 weeks, pseudostratified epithelium organoids; the efficiency of generating interstitial macrophages • 3D cultures are amenable for high-throughput Membrane through the system to mimic air is formed AEC1s from human AEC2s is screens Endothelial cells Medium/blood and blood flow in the lung currently limited • 2D and 3D cultures allow measurement of ion Growth Polyporous Basophils, eosinophils medium membrane substitute channel activity (e.g., CFTR) Lymphoid cells (T and B cells)

Abbreviations 3. Barkauskas, C. E. et al. Lung organoids: current uses and 9. Barkauskas, C. E. et al. Type 2 alveolar cells are stem cells in The poster content is peer reviewed, editorially independent and STEMCELL Technologies • Supports more rapid expansion and at least two additional Transwell® Inserts (#38023/#38024) ADC, adenocarcinoma; AEC, airway epithelial cell; CFTR, cystic future promise. Development 144, 986–997 (2017). adult lung. J. Clin. Invest. 123, 3025–3036 (2013). the sole responsibility of Springer Nature Limited. passages with sustained differentiation potential compared • The recommended cultureware to use with PneumaCult™ fibrosis transmembrane conductance regulator; ECM, 4. Montoro, D. T. et al. A revised airway epithelial hierarchy 10. Desai, T. J., Brownfield, D. G. & Krasnow, M. A. Alveolar Edited by Christine Weber and Paulina Strzyz; copyedited by PneumaCult™ is a serum- and bovine-pituitary extract (BPE)- to conventional expansion medium. products for optimal differentiation of airway epithelial cells at extracellular matrix; EGF, epidermal growth factor; HBECs, human includes CFTR-expressing ionocytes. Nature 560, 319–324 progenitor and stem cells in lung development, renewal and Lauren Beer; designed by Lauren Heslop. free culture system that supports the expansion and • See the data at www.stemcell.com/ExPlus-data the ALI. bronchial epithelial cells; NE, neuroendocrine; SCC, squamous (2018). cancer. Nature 507, 190–194 (2014). © 2019 Springer Nature Limited. All rights reserved. differentiation of human airway epithelial cells, with the key cell carcinoma; SCLC, small-cell lung carcinoma; 5. Plasschaert, L. W. et al. A single-cell atlas of the airway 11. Tata, A. et al. Myoepithelial cells of submucosal glands can https://www.nature.com/articles/s41556-019-0357-7 PneumaCult™ -ALI (#05001) Together, these products provide an optimized culture system for SMG, submucosal gland epithelium reveals the CFTR-rich pulmonary ionocyte. function as reserve stem cells to regenerate airways after feature being a pseudostratified epithelium consisting of goblet • Differentiation medium for human airway epithelial cells in vitro human airway modelling, supporting basic respiratory Nature 560, 377–381 (2018). injury. Cell Stem Cell 22, 668–683.e6 (2018). Affiliations cells, basal cells, and motile cilia. cultured at the air–liquid interface (ALI). research, toxicity studies, and drug discovery studies. 6. LungMAP - Available at: https://www.lungmap.net/ B.L.M.H. and P.R.T are at the Department of Cell Biology, References • Promotes extensive mucociliary differentiation with 7. Chakarov, S. et al. Two distinct interstitial macrophage Duke University Medical Center, Durham, NC, USA. At STEMCELL, science is our foundation. We are Scientists 1. Weibel, E. R. Lung morphometry: the link between structure populations coexist across tissues in specific subtissular Contact information: [email protected] or morphological and functional characteristics similar to the PneumaCult™ -Ex Plus (#05040) Helping Scientists dedicated to making sure your research works. and function. Cell Tissue Res. 367, 413–426 (2017). niches. Science 363, eaau0964 (2019). Acknowledgements [email protected] • Long-term expansion medium for primary human airway in vivo human airway. 2. Hogan, B. L. M. et al. Repair and regeneration of the 8. Okuda, K. et al. Localization of secretory mucins MUC5AC We thank S. Randell and C. Barkauskas for valuable advice on the epithelial cells. • See the data at www.stemcell.com/ALI-data For more information, visit www.PneumaCult.com respiratory system: complexity, plasticity, and mechanisms of and MUC5B in normal/healthy human airways. Am. J. Respir. cellular composition of the human lung and human respiratory Competing interests lung stem cell function. Cell Stem Cell 15, 123–138 (2014). Crit. Care Med. 199, 715–727 (2019). diseases, respectively. The authors declare no competing interests.