Agarwal, A., Coleno, M.L., Wallace, V.P., Wu, W.Y., Sun, C.H., Tromberg, B.J., and George, S.C. (2001). Two-photon laser scanning microscopy of epithelial cell-modulated collagen density in engineered human lung tissue. Tissue Eng. 7, 191–202. https:// doi.org/10.1089/107632701300062813.
Angelidis, I., Simon, L.M., Fernandez, I.E., Strunz, M., Mayr, C.H., Greiffo, F.R., Tsitsiridis, G., Ansari, M., Graf, E., Strom, T.M., et al. (2019). An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat. Commun. 10, 963. https://doi.org/10.1038/s41467-019-08831-9.
Barkauskas, C.E., Cronce, M.J., Rackley, C.R., Bowie, E.J., Keene, D.R., Stripp, B.R., Randell, S.H., Noble, P.W., and Hogan, B.L. (2013). Type 2 alveolar cells are stem cells in adult lung. J. Clin. Invest. 123, 3025–3036. https://doi.org/10.1172/jci68782.
Basil, M.C., Katzen, J., Engler, A.E., Guo, M., Herriges, M.J., Kathiriya, J.J., Windmueller, R., Ysasi, A.B., Zacharias, W.J., Chapman, H.A., et al. (2020). The cellular and physiological basis for lung repair and regeneration: past, present, and future. Cell Stem Cell 26, 482–502. https://doi.org/10.1016/j.stem.2020.03.009.
Cazzalini, O., Scovassi, A.I., Savio, M., Stivala, L.A., and Prosperi, E. (2010). Multiple roles of the cell cycle inhibitor p21(CDKN1A) in the DNA damage response. Mutat. Res. 704, 12–20. https://doi. org/10.1016/j.mrrev.2010.01.009.
Chen, J.K., Taipale, J., Cooper, M.K., and Beachy, P.A. (2002). Inhibition of Hedgehog signaling by direct binding of cyclopamine to Smoothened. Genes Dev. 16, 2743–2748. https://doi.org/10.1101/ gad.1025302.
Choi, J., Park, J.E., Tsagkogeorga, G., Yanagita, M., Koo, B.K., Han, N., and Lee, J.H. (2020). Inflammatory signals induce AT2 cellderived damage-associated transient progenitors that mediate alveolar regeneration. Cell Stem Cell 27, 366–382.e7. https://doi. org/10.1016/j.stem.2020.06.020.
Coppe´, J.P., Desprez, P.Y., Krtolica, A., and Campisi, J. (2010). The senescence-associated secretory phenotype: the dark side of tumor suppression. Annu. Rev. Pathol. 5, 99–118. https://doi.org/10. 1146/annurev-pathol-121808-102144.
Das, M., Jiang, F., Sluss, H.K., Zhang, C., Shokat, K.M., Flavell, R.A., and Davis, R.J. (2007). Suppression of p53-dependent senescence by the JNK signal transduction pathway. Proc. Natl. Acad. Sci. U S A 104, 15759–15764. https://doi.org/10.1073/pnas. 0707782104.
Desai, T.J., Brownfield, D.G., and Krasnow, M.A. (2014). Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature 507, 190–194. https://doi.org/10.1038/nature12930.
Gotoh, S., Ito, I., Nagasaki, T., Yamamoto, Y., Konishi, S., Korogi, Y., Matsumoto, H., Muro, S., Hirai, T., Funato, M., et al. (2014). Gen eration of alveolar epithelial spheroids via isolated progenitor cells from human pluripotent stem cells. Stem Cell Reports 3, 394–403. https://doi.org/10.1016/j.stemcr.2014.07.005.
Horan, G.S., Wood, S., Ona, V., Li, D.J., Lukashev, M.E., Weinreb, P.H., Simon, K.J., Hahm, K., Allaire, N.E., Rinaldi, N.J., et al. (2008). Partial inhibition of integrin alpha(v)beta6 prevents pulmonary fibrosis without exacerbating inflammation. Am. J. Respir. Crit. Care Med. 177, 56–65. https://doi.org/10.1164/rccm.200706- 805OC
Hubackova, S., Krejcikova, K., Bartek, J., and Hodny, Z. (2012). IL1- and TGFb-Nox4 signaling, oxidative stress and DNA damage response are shared features of replicative, oncogene-induced, and drug-induced paracrine ‘bystander senescence’. Aging 4, 932–951. https://doi.org/10.18632/aging.100520.
Jassal, B., Matthews, L., Viteri, G., Gong, C., Lorente, P., Fabregat, A., Sidiropoulos, K., Cook, J., Gillespie, M., Haw, R., et al. (2020). The reactome pathway knowledgebase. Nucleic Acids Res. 48, D498–D503. https://doi.org/10.1093/nar/gkz1031.
Kanagaki, S., Ikeo, S., Suezawa, T., Yamamoto, Y., Seki, M., Hirai, T., Hagiwara, M., Suzuki, Y., and Gotoh, S. (2021a). Directed induction of alveolar type I cells derived from pluripotent stem cells via Wnt signaling inhibition. Stem Cells 39, 156–169. https:// doi.org/10.1002/stem.3302.
Kanagaki, S., Suezawa, T., Moriguchi, K., Nakao, K., Toyomoto, M., Yamamoto, Y., Murakami, K., Hagiwara, M., and Gotoh, S. (2021b). Hydroxypropyl cyclodextrin improves amiodarone-induced aberrant lipid homeostasis of alveolar cells. Am. J. Respir. Cell Mol. Biol. 64, 504–514. https://doi.org/10.1165/rcmb.2020-0119OC.
Katsura, H., Sontake, V., Tata, A., Kobayashi, Y., Edwards, C.E., Heaton, B.E., Konkimalla, A., Asakura, T., Mikami, Y., Fritch, E.J., et al. (2020). Human lung stem cell-based alveolospheres provide insights into SARS-CoV-2-mediated interferon responses and pneumocyte dysfunction. Cell Stem Cell 27, 890–904.e8. https://doi. org/10.1016/j.stem.2020.10.005.
Katzen, J., and Beers, M.F. (2020). Contributions of alveolar epithelial cell quality control to pulmonary fibrosis. J. Clin. Invest. 130, 5088–5099. https://doi.org/10.1172/jci139519.
Knight, Z.A., and Shokat, K.M. (2005). Features of selective kinase inhibitors. Chem. Biol. 12, 621–637. https://doi.org/10.1016/j. chembiol.2005.04.011.
Kobayashi, Y., Tata, A., Konkimalla, A., Katsura, H., Lee, R.F., Ou, J., Banovich, N.E., Kropski, J.A., and Tata, P.R. (2020). Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat. Cell Biol. 22, 934–946. https://doi.org/10. 1038/s41556-020-0542-8.
Korogi, Y., Gotoh, S., Ikeo, S., Yamamoto, Y., Sone, N., Tamai, K., Konishi, S., Nagasaki, T., Matsumoto, H., Ito, I., et al. (2019). In vitro disease modeling of Hermansky-Pudlak syndrome type 2 using human induced pluripotent stem cell-derived alveolar organoids. Stem Cell Reports 12, 431–440. https://doi.org/10.1016/j. stemcr.2019.01.014.
Lederer, D.J., and Martinez, F.J. (2018). Idiopathic pulmonary fibrosis. N. Engl. J. Med. 378, 1811–1823. https://doi.org/10. 1056/NEJMra1705751.
Moeller, A., Ask, K., Warburton, D., Gauldie, J., and Kolb, M. (2008). The bleomycin animal model: a useful tool to investigate treatment options for idiopathic pulmonary fibrosis? Int. J. Biochem. Cell Biol. 40, 362–382. https://doi.org/10.1016/j.biocel. 2007.08.011.
Montesano, R., and Orci, L. (1988). Transforming growth factor beta stimulates collagen-matrix contraction by fibroblasts: implications for wound healing. Proc. Natl. Acad. Sci. U S A 85, 4894– 4897. https://doi.org/10.1073/pnas.85.13.4894.
Munger, J.S., Huang, X., Kawakatsu, H., Griffiths, M.J., Dalton, S.L., Wu, J., Pittet, J.F., Kaminski, N., Garat, C., Matthay, M.A., et al. (1999). The integrin alpha v beta 6 binds and activates latent TGF beta 1: a mechanism for regulating pulmonary inflammation and fibrosis. Cell 96, 319–328. https://doi.org/10.1016/s0092- 8674(00)80545-0.
Munger, J.S., and Sheppard, D. (2011). Cross talk among TGF-b signaling pathways, integrins, and the extracellular matrix. Cold Spring Harb. Perspect. Biol. 3, a005017. https://doi.org/10.1101/ cshperspect.a005017.
Neumark, N., Cosme, C., Jr., Rose, K.A., and Kaminski, N. (2020). The idiopathic pulmonary fibrosis cell atlas. Am. J. Physiol. Lung Cell Mol. Physiol. 319, L887–L893. https://doi.org/10.1152/ajplung.00451.2020.
Okita, K., Yamakawa, T., Matsumura, Y., Sato, Y., Amano, N., Watanabe, A., Goshima, N., and Yamanaka, S. (2013). An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells. Stem Cells 31, 458–466. https://doi.org/10.1002/stem.1293.
Paez-Ribes, M., Gonza´lez-Gualda, E., Doherty, G.J., and Mun˜oz-Espı´n, D. (2019). Targeting senescent cells in translational medicine. EMBO Mol. Med. 11, e10234. https://doi.org/10.15252/emmm. 201810234.
Paris, A.J., Hayer, K.E., Oved, J.H., Avgousti, D.C., Toulmin, S.A., Zepp, J.A., Zacharias, W.J., Katzen, J.B., Basil, M.C., Kremp, M.M., et al. (2020). STAT3-BDNF-TrkB signalling promotes alveolar epithelial regeneration after lung injury. Nat. Cell Biol. 22, 1197– 1210. https://doi.org/10.1038/s41556-020-0569-x.
Popova, A.P., Bozyk, P.D., Goldsmith, A.M., Linn, M.J., Lei, J., Bentley, J.K., and Hershenson, M.B. (2010). Autocrine production of TGF-beta1 promotes myofibroblastic differentiation of neonatal lung mesenchymal stem cells. Am. J. Physiol. Lung Cell Mol. Physiol. 298, L735–L743. https://doi.org/10.1152/ajplung.00347.2009.
Reyfman, P.A., Walter, J.M., Joshi, N., Anekalla, K.R., McQuattie-Pimentel, A.C., Chiu, S., Fernandez, R., Akbarpour, M., Chen, C.I., Ren, Z., et al. (2019). Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 199, 1517–1536. https:// doi.org/10.1164/rccm.201712-2410OC.
Riemondy, K.A., Jansing, N.L., Jiang, P., Redente, E.F., Gillen, A.E., Fu, R., Miller, A.J., Spence, J.R., Gerber, A.N., Hesselberth, J.R., and Zemans, R.L. (2019). Single cell RNA sequencing identifies TGFb as a key regenerative cue following LPS-induced lung injury. JCI Insight 5, e123637. https://doi.org/10.1172/jci.insight.123637.
Rouillard, A.D., Gundersen, G.W., Fernandez, N.F., Wang, Z., Monteiro, C.D., McDermott, M.G., and Ma’ayan, A. (2016). The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database 2016, baw100. https://doi.org/10.1093/database/baw100.
Sisson, T.H., Mendez, M., Choi, K., Subbotina, N., Courey, A., Cunningham, A., Dave, A., Engelhardt, J.F., Liu, X., White, E.S., et al. (2010). Targeted injury of type II alveolar epithelial cells induces pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 181, 254–263. https://doi.org/10.1164/rccm.200810-1615OC.
Spagnolo, P., Kropski, J.A., Jones, M.G., Lee, J.S., Rossi, G., Karampitsakos, T., Maher, T.M., Tzouvelekis, A., and Ryerson, C.J. (2020). Idiopathic pulmonary fibrosis: disease mechanisms and drug development. Pharmacol. Ther. 222, 107798. https://doi.org/10. 1016/j.pharmthera.2020.107798.
Strunz, M., Simon, L.M., Ansari, M., Kathiriya, J.J., Angelidis, I., Mayr, C.H., Tsidiridis, G., Lange, M., Mattner, L.F., Yee, M., et al. (2020). Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis. Nat. Commun. 11, 3559. https://doi.org/10.1038/s41467-020-17358-3.
Tan, Q., Ma, X.Y., Liu, W., Meridew, J.A., Jones, D.L., Haak, A.J., Sicard, D., Ligresti, G., and Tschumperlin, D.J. (2019). Nascent lung organoids reveal epithelium- and bone morphogenetic proteinmediated suppression of fibroblast activation. Am. J. Respir. Cell Mol. Biol. 61, 607–619. https://doi.org/10.1165/rcmb.2018- 0390OC.
Tomasek, J.J., Gabbiani, G., Hinz, B., Chaponnier, C., and Brown, R.A. (2002). Myofibroblasts and mechano-regulation of connective tissue remodelling. Nat. Rev. Mol. Cell Biol. 3, 349–363. https:// doi.org/10.1038/nrm809.
Wilkinson, D.C., Alva-Ornelas, J.A., Sucre, J.M., Vijayaraj, P., Durra, A., Richardson, W., Jonas, S.J., Paul, M.K., Karumbayaram, S., Dunn, B., and Gomperts, B.N. (2017). Development of a threedimensional bioengineering technology to generate lung tissue for personalized disease modeling. Stem Cells Transl. Med. 6, 622–633. https://doi.org/10.5966/sctm.2016-0192.
Wu, H., Yu, Y., Huang, H., Hu, Y., Fu, S., Wang, Z., Shi, M., Zhao, X., Yuan, J., Li, J., et al. (2020). Progressive pulmonary fibrosis is caused by elevated mechanical tension on alveolar stem cells. Cell 180, 107–121.e17. https://doi.org/10.1016/j.cell.2019.11.027.
Xie, T., Wang, Y., Deng, N., Huang, G., Taghavifar, F., Geng, Y., Liu, N., Kulur, V., Yao, C., Chen, P., et al. (2018). Single-cell deconvolution of fibroblast heterogeneity in mouse pulmonary fibrosis. Cell Rep. 22, 3625–3640. https://doi.org/10.1016/j.celrep.2018.03. 010.
Yamaguchi, Y., Hearing, V.J., Itami, S., Yoshikawa, K., and Katayama, I. (2005). Mesenchymal-epithelial interactions in the skin: aiming for site-specific tissue regeneration. J. Dermatol. Sci. 40, 1–9. https://doi.org/10.1016/j.jdermsci.2005.04.006.
Yamamoto, Y., Gotoh, S., Korogi, Y., Seki, M., Konishi, S., Ikeo, S., Sone, N., Nagasaki, T., Matsumoto, H., Muro, S., et al. (2017). Long-term expansion of alveolar stem cells derived from human iPS cells in organoids. Nat. Methods 14, 1097–1106. https://doi. org/10.1038/nmeth.4448.
Yao, C., Guan, X., Carraro, G., Parimon, T., Liu, X., Huang, G., Mulay, A., Soukiasian, H.J., David, G., Weigt, S.S., et al. (2021). Senescence of alveolar type 2 cells drives progressive pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 203, 707–717. https://doi.org/10. 1164/rccm.202004-1274OC.
Youk, J., Kim, T., Evans, K.V., Jeong, Y.I., Hur, Y., Hong, S.P., Kim, J.H., Yi, K., Kim, S.Y., Na, K.J., et al. (2020). Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2. Cell Stem Cell 27, 905–919.e10. https://doi.org/10. 1016/j.stem.2020.10.004.
Zepp, J.A., Morley, M.P., Loebel, C., Kremp, M.M., Chaudhry, F.N., Basil, M.C., Leach, J.P., Liberti, D.C., Niethamer, T.K., Ying, Y., et al. (2021). Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus. Science 371, eabc3172. https://doi.org/10.1126/science.abc3172.