Alber, A.B., Marquez, H.A., Ma, L., Kwong, G., Thapa, B.R., Villacorta-Martin, C., Lindstrom-Vautrin, J., Bawa, P., Luo, Y., Ikonomou, L., et al. (2022). Directed differentiation of mouse pluripotent stem cells into functional lung- specific mesenchyme. Preprint at bioRxiv. https://doi.org/10.1101/2022.08. 12.502651.
Aros, C.J., Pantoja, C.J., and Gomperts, B.N. (2021). Wnt signaling in lung development, regeneration, and disease progression. Commun. Biol. 4, 601. https://doi.org/10.1038/s42003-021-02118-w.
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.M. (2013). Type 2 alveolar cells are stem cells in adult lung. J. Clin. Invest. 123, 3025–3036. https://doi.org/10.1172/JCI68782.
Chen, S., Zhou, Y., Chen, Y., and Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. https://doi.org/10.1093/ bioinformatics/bty560.
Chen, Y.W., Huang, S.X., de Carvalho, A.L.R.T., Ho, S.H., Islam, M.N., Volpi, S., Notarangelo, L.D., Ciancanelli, M., Casanova, J.L., Bhattacharya, J., et al. (2017). A three-dimensional model of human lung development and dis- ease from pluripotent stem cells. Nat. Cell Biol. 19, 542–549. https://doi.org/ 10.1038/ncb3510.
Cohen, E.D., Miller, M.F., Wang, Z., Moon, R.T., and Morrisey, E.E. (2012). Wnt5a and Wnt11 are essential for second heart field progenitor development. Development 139, 1931–1940. https://doi.org/10.1242/dev.069377.
Dobbs, L.G., Gonzalez, R.F., Allen, L., and Froh, D.K. (1999). HTI56, an integral membrane protein specific to human alveolar type I cells. J. Histochem. Cyto- chem. 47, 129–137. https://doi.org/10.1177/002215549904700202.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21. https://doi.org/10.1093/bioinformatics/ bts635.
Dye, B.R., Hill, D.R., Ferguson, M.A., Tsai, Y.H., Nagy, M.S., Dyal, R., Wells, J.M., Mayhew, C.N., Nattiv, R., Klein, O.D., et al. (2015). In vitro generation of human pluripotent stem cell derived lung organoids. Elife 4. https://doi. org/10.7554/eLife.05098.
Evseenko, D., Zhu, Y., Schenke-Layland, K., Kuo, J., Latour, B., Ge, S., Scholes, J., Dravid, G., Li, X., MacLellan, W.R., and Crooks, G.M. (2010). Map- ping the first stages of mesoderm commitment during differentiation of human embryonic stem cells. Proc. Natl. Acad. Sci. USA 107, 13742–13747. https:// doi.org/10.1073/pnas.1002077107.
Frank, D.B., Peng, T., Zepp, J.A., Snitow, M., Vincent, T.L., Penkala, I.J., Cui, Z., Herriges, M.J., Morley, M.P., Zhou, S., et al. (2016). Emergence of a wave of Wnt signaling that regulates lung alveologenesis by controlling epithelial self- renewal and differentiation. Cell Rep. 17, 2312–2325. https://doi.org/10.1016/ j.celrep.2016.11.001.
Goss, A.M., Tian, Y., Tsukiyama, T., Cohen, E.D., Zhou, D., Lu, M.M., Yamagu- chi, T.P., and Morrisey, E.E. (2009). Wnt2/2b and beta-catenin signaling are necessary and sufficient to specify lung progenitors in the foregut. Dev. Cell 17, 290–298. https://doi.org/10.1016/j.devcel.2009.06.005.
Gotoh, S., Ito, I., Nagasaki, T., Yamamoto, Y., Konishi, S., Korogi, Y., Matsu- moto, H., Muro, S., Hirai, T., Funato, M., et al. (2014). Generation of alveolar epithelial spheroids via isolated progenitor cells from human pluripotent stem cells. Stem Cell Rep. 3, 394–403. https://doi.org/10.1016/j.stemcr. 2014.07.005.
Han, L., Chaturvedi, P., Kishimoto, K., Koike, H., Nasr, T., Iwasawa, K., Gies- brecht, K., Witcher, P.C., Eicher, A., Haines, L., et al. (2020). Single cell tran- scriptomics identifies a signaling network coordinating endoderm and meso- derm diversification during foregut organogenesis. Nat. Commun. 11, 4158. https://doi.org/10.1038/s41467-020-17968-x.
Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W.M., 3rd, Zheng, S., Butler, A., Lee, M.J., Wilk, A.J., Darby, C., Zager, M., et al. (2021). Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29. https://doi.org/10.1016/ j.cell.2021.04.048.
Hardy, K.M., Garriock, R.J., Yatskievych, T.A., D’Agostino, S.L., Antin, P.B., and Krieg, P.A. (2008). Non-canonical Wnt signaling through Wnt5a/b and a novel Wnt11 gene, Wnt11b, regulates cell migration during avian gastrulation. Dev. Biol. 320, 391–401. https://doi.org/10.1016/j.ydbio.2008.05.546.
Hein, R.F.C., Wu, J.H., Holloway, E.M., Frum, T., Conchola, A.S., Tsai, Y.H., Wu, A., Fine, A.S., Miller, A.J., Szenker-Ravi, E., et al. (2022). R-SPONDIN2+ mesenchymal cells form the bud tip progenitor niche during human lung devel- opment. Dev. Cell 57, 1598–1614.e8. https://doi.org/10.1016/j.devcel.2022. 05.010.
Horie, M., Miyashita, N., Mikami, Y., Noguchi, S., Yamauchi, Y., Suzukawa, M., Fukami, T., Ohta, K., Asano, Y., Sato, S., et al. (2018). TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts. Am. J. Physiol. Lung Cell Mol. Physiol. 314, L177–L191. https://doi.org/10.1152/ajplung.00193.2017.
Jacob, A., Morley, M., Hawkins, F., McCauley, K.B., Jean, J.C., Heins, H., Na, C.L., Weaver, T.E., Vedaie, M., Hurley, K., et al. (2017). Differentiation of human pluripotent stem cells into functional lung alveolar epithelial cells. Cell Stem Cell 21, 472–488.e10. https://doi.org/10.1016/j.stem.2017.08.014.
Kishimoto, K., Furukawa, K.T., Luz-Madrigal, A., Yamaoka, A., Matsuoka, C., Habu, M., Alev, C., Zorn, A.M., and Morimoto, M. (2020). Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. Nat. Commun. 11, 4159. https://doi.org/10.1038/ s41467-020-17969-w.
Konishi, S., Gotoh, S., Tateishi, K., Yamamoto, Y., Korogi, Y., Nagasaki, T., Matsumoto, H., Muro, S., Hirai, T., Ito, I., et al. (2016). Directed induction of functional multi-ciliated cells in proximal airway epithelial spheroids from hu- man pluripotent stem cells. Stem Cell Rep. 6, 18–25. https://doi.org/10. 1016/j.stemcr.2015.11.010.
Kopylova, E., Noe´ , L., and Touzet, H. (2012). SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217. https://doi.org/10.1093/bioinformatics/bts611.
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 Rep. 12, 431–440. https://doi.org/ 10.1016/j.stemcr.2019.01.014.
Li, B., and Dewey, C.N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 12, 323. https://doi.org/10.1186/1471-2105-12-323.
Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550. https://doi.org/10.1186/s13059-014-0550-8.
Mikels, A.J., and Nusse, R. (2006). Purified Wnt5a protein activates or inhibits beta-catenin-TCF signaling depending on receptor context. PLoS Biol. 4, e115. https://doi.org/10.1371/journal.pbio.0040115.
Miller, A.J., Dye, B.R., Ferrer-Torres, D., Hill, D.R., Overeem, A.W., Shea, L.D., and Spence, J.R. (2019). Generation of lung organoids from human pluripotent stem cells in vitro. Nat. Protoc. 14, 518–540. https://doi.org/10.1038/s41596- 018-0104-8.
Mulay, A., Konda, B., Garcia, G., Jr., Yao, C., Beil, S., Villalba, J.M., Koziol, C., Sen, C., Purkayastha, A., Kolls, J.K., et al. (2021). SARS-CoV-2 infection of pri- mary human lung epithelium for COVID-19 modeling and drug discovery. Cell Rep. 35, 109055. https://doi.org/10.1016/j.celrep.2021.109055.
Nabhan, A.N., Brownfield, D.G., Harbury, P.B., Krasnow, M.A., and Desai, T.J. (2018). Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells. Science 359, 1118–1123. https://doi.org/10.1126/science.aam6603.
Park, J., Ivey, M.J., Deana, Y., Riggsbee, K.L., So¨ rensen, E., Schwabl, V., Sjo¨ - berg, C., Hjertberg, T., Park, G.Y., Swonger, J.M., et al. (2019). The Tcf21 line- age constitutes the lung lipofibroblast population. Am. J. Physiol. Lung Cell Mol. Physiol. 316, L872–L885. https://doi.org/10.1152/ajplung.00254.2018.
Sakurai, H., Era, T., Jakt, L.M., Okada, M., Nakai, S., Nishikawa, S.i., and Nish- ikawa, S. (2006). In vitro modeling of paraxial and lateral mesoderm differenti- ation reveals early reversibility. Stem Cell. 24, 575–586. https://doi.org/10. 1634/stemcells.2005-0256.
Shu, W., Guttentag, S., Wang, Z., Andl, T., Ballard, P., Lu, M.M., Piccolo, S., Birchmeier, W., Whitsett, J.A., Millar, S.E., and Morrisey, E.E. (2005). Wnt/ beta-catenin signaling acts upstream of N-myc, BMP4, and FGF signaling to regulate proximal-distal patterning in the lung. Dev. Biol. 283, 226–239. https://doi.org/10.1016/j.ydbio.2005.04.014.
Sone, N., Konishi, S., Igura, K., Tamai, K., Ikeo, S., Korogi, Y., Kanagaki, S., Namba, T., Yamamoto, Y., Xu, Y., et al. (2021). Multicellular modeling of ciliop- athy by combining iPS cells and microfluidic airway-on-a-chip technology. Sci. Transl. Med. 13, eabb1298. https://doi.org/10.1126/scitranslmed.abb1298.
Soneson, C., Love, M.I., and Robinson, M.D. (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res. 4, 1521. https://doi.org/10.12688/f1000research.7563.2.
Wu, T., Hu, E., Xu, S., Chen, M., Guo, P., Dai, Z., Feng, T., Zhou, L., Tang, W.,
Zhan, L., et al. (2021). clusterProfiler 4.0: a universal enrichment tool for inter- preting omics data. Innovation 2, 100141. https://doi.org/10.1016/j.xinn.2021. 100141.
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.
Yeo, S.Y., Lee, K.W., Shin, D., An, S., Cho, K.H., and Kim, S.H. (2018). A positive feedback loop bi-stably activates fibroblasts. Nat. Commun. 9, 3016. https://doi.org/10.1038/s41467-018-05274-6.
Zacharias, W.J., Frank, D.B., Zepp, J.A., Morley, M.P., Alkhaleel, F.A., Kong, J., Zhou, S., Cantu, E., and Morrisey, E.E. (2018). Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor. Nature 555, 251–255. https://doi.org/10.1038/nature25786.
Zepp, J.A., Zacharias, W.J., Frank, D.B., Cavanaugh, C.A., Zhou, S., Morley, M.P., and Morrisey, E.E. (2017). Distinct mesenchymal lineages and niches promote epithelial self-renewal and myofibrogenesis in the lung. Cell 170, 1134–1148.e10. https://doi.org/10.1016/j.cell.2017.07.034.
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