Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures

Development (Cambridge)

Volumn 146, Issue 20, 2019, Pages

  Garcıá, Sandra Ruiz ^a   Deprez, Marie ^a   Lebrigand, Kevin ^a   Cavard, Amélie ^a   Paquet, Agnes ^a   Arguel, Marie Jeanne ^a   Magnone, Virginie ^a   Truchi, Marin ^a   Caballero, Ignacio ^b   Leroy, Sylvie ^a   Marquette, Charles Hugo ^a   Marcet, Brice ^a   Barbry, Pascal ^a   Zaragosi, Laure Emmanuelle ^a  

^a UNIVERSITÉ CÔTE D'AZUR   (France)

^b UNIVERSITÉ DE TOURS   (France)

Author keywords

Airway epithelium; Basal cells; Club cells; Deuterosome; Differentiation; Goblet cells; Keratins; Multiciliated cells; Pathways; Single cell RNA seq

Indexed keywords

BONE MORPHOGENETIC PROTEIN; KERATIN; NOTCH RECEPTOR; PEPTIDES AND PROTEINS; PROTEIN CDC20B; PROTEIN DEUP1; PROTEIN FOXN4; PROTEIN HES6; PROTEIN YPEL1; RNA; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; WNT PROTEIN;

ARTICLE; CELL LINEAGE; CILIATED EPITHELIUM CELL; GOBLET CELL; HUMAN; HUMAN CELL; NOSE EPITHELIUM; PRIORITY JOURNAL; RNA SEQUENCE; SINGLE CELL ANALYSIS;

EID: 85074944730     PISSN: 09501991     EISSN: 14779129     Source Type: Journal    
DOI: 10.1242/dev.177428     Document Type: Article

References (87)

1. Adam, M., Potter, A. S. and Potter, S. S. (2017). Psychrophilic proteases dramatically reduce single-cell RNA-seq artifacts: a molecular atlas of kidney development. Development 144, 3625-3632. doi:10.1242/dev.151142
2. Al Jord, A., Shihavuddin, A., Servignat d’Aout, R., Faucourt, M., Genovesio, A., Karaiskou, A., Sobczak-Thépot, J., Spassky, N. and Meunier, A. (2017). Calibrated mitotic oscillator drives motile ciliogenesis. Science 358, 803-806. doi:10.1126/science.aan8311
3. Bae, S., Bessho, Y., Hojo, M. and Kageyama, R. (2000). The bHLH gene Hes6, an inhibitor of Hes1, promotes neuronal differentiation. Development 127, 2933-2943.
4. Bauer, A., Chauvet, S., Huber, O., Usseglio, F., Rothbächer, U., Aragnol, D., Kemler, R. and Pradel, J. (2000). Pontin52 and Reptin52 function as antagonistic regulators of beta-catenin signalling activity. EMBO J. 19, 6121-6130. doi:10. 1093/emboj/19.22.6121
5. Boers, J. E., Ambergen, A. W. and Thunnissen, F. B. (1998). Number and proliferation of basal and parabasal cells in normal human airway epithelium. Am. J. Respir. Crit. Care. Med. 157, 2000-2006. doi:10.1164/ajrccm.157.6. 9707011
6. Boers, J. E., Ambergen, A. W. and Thunissen, F. B. J. M. (1999). Number and proliferation of Clara cells in normal human airway epithelium. Am. J. Respir. Crit. Care Med. 159, 1585-1591. doi:10.1164/ajrccm.159.5.9806044
7. Brechbuhl, H. M., Ghosh, M., Smith, M. K., Smith, R. W., Li, B., Hicks, D. A., Cole, B. B., Reynolds, P. R. and Reynolds, S. D. (2011). Β-catenin dosage is a critical determinant of tracheal basal cell fate determination. Am. J. Pathol. 179, 367-379. doi:10.1016/j.ajpath.2011.03.016
8. Chen, G., Korfhagen, T. R., Xu, Y., Kitzmiller, J., Wert, S. E., Maeda, Y., Gregorieff, A., Clevers, H. and Whitsett, J. A. (2009). SPDEF is required for mouse pulmonary goblet cell differentiation and regulates a network of genes associated with mucus production. J. Clin. Invest. 119, 2914-2924. doi:10.1172/ JCI39731
9. Cheng, P., Kumar, V., Liu, H., Youn, J.-I., Fishman, M., Sherman, S. and Gabrilovich, D. (2014). Effects of Notch signaling on regulation of myeloid cell differentiation in cancer. Cancer Res. 74, 141-152. doi:10.1158/0008-5472.CAN-13-1686
10. Chevalier, B., Adamiok, A., Mercey, O., Revinski, D. R., Zaragosi, L.-E., Pasini, A., Kodjabachian, L., Barbry, P. and Marcet, B. (2015). miR-34/449 control apical actin network formation during multiciliogenesis through small GTPase pathways. Nat. Commun. 6, 8386-8400. doi:10.1038/ncomms9386
11. Cohn, L. (2006). Mucus in chronic airway diseases: Sorting out the sticky details. J. Clin. Invest. 116, 306-308. doi:10.1172/JCI27690
12. Cole, B. B., Smith, R. W., Jenkins, K. M., Graham, B. B., Reynolds, P. R. and Reynolds, S. D. (2010). Tracheal basal cells: a facultative progenitor cell pool. Am. J. Pathol. 177, 362-376. doi:10.2353/ajpath.2010.090870
13. Colopy, S. A., Bjorling, D. E., Mulligan, W. A. and Bushman, W. (2014). A population of progenitor cells in the basal and intermediate layers of the murine bladder urothelium contributes to urothelial development and regeneration. Dev. Dyn. 243, 988-998. doi:10.1002/dvdy.24143
14. Coraux, C., Roux, J., Jolly, T. and Birembaut, P. (2008). Epithelial cell-extracellular matrix interactions and stem cells in airway epithelial regeneration. Proc. Am. Thorac. Soc. 5, 689-694. doi:10.1513/pats.200801-010AW
15. Cruciat, C.-M. (2014). Casein kinase 1 and Wnt/β-catenin signaling. Curr. Opin. Cell Biol. 31, 46-55. doi:10.1016/j.ceb.2014.08.003
16. Curran, D. R. and Cohn, L. (2010). Advances in mucous cell metaplasia: a plug for mucus as a therapeutic focus in chronic airway disease. Am. J. Respir. Cell Mol. Biol. 42, 268-275. doi:10.1165/rcmb.2009-0151TR
17. DiMeo, T. A., Anderson, K., Phadke, P., Feng, C., Perou, C. M., Naber, S., Kuperwasser, C. and Kuperwasser, C. (2009). A Novel lung metastasis signature links Wnt signaling with cancer cell self-renewal and epithelial-mesenchymal transition in basal-like breast cancer. Cancer Res. 69, 5364-5373. doi:10.1158/0008-5472.CAN-08-4135
18. Durham, A. L., McLaren, A., Hayes, B. P., Caramori, G., Clayton, C. L., Barnes, P. J., Chung, K. F. and Adcock, I. M. (2013). Regulation of Wnt4 in chronic obstructive pulmonary disease. FASEB J. 27, 2367-2381. doi:10.1096/fj.12-217083
19. Estrach, S., Ambler, C. A., Lo Celso, C. L., Hozumi, K. and Watt, F. M. (2006). Jagged 1 is a β-catenin target gene required for ectopic hair follicle formation in adult epidermis. Development 133, 4427-4438. doi:10.1242/dev.02644
20. ã, O. H., Nieto, M. A. and Galceran, J. (2009). Attenuation of Notch signalling by the Down-syndrome-associated kinase DYRK1A. J. Cell Sci. 122, 1574-1583. doi:10.1242/ jcs.044354
21. Fletcher, R. B., Das, D., Gadye, L., Street, K. N., Baudhuin, A., Wagner, A., Cole, M. B., Flores, Q., Choi, Y. G., Yosef, N. et al. (2017). Deconstructing olfactory stem cell trajectories at single-cell resolution. Cell Stem Cell 20, 817-830.e8. doi:10.1016/j.stem.2017.04.003
22. Giovannini-Chami, L., Paquet, A., Sanfiorenzo, C., Pons, N., Cazareth, J., Magnone, V., Lebrigand, K., Chevalier, B., Vallauri, A., Julia, V. et al. (2018). The “one airway, one disease” concept in light of Th2 inflammation. Eur. Respir. J. 52, 1800437-1800454. doi:10.1183/13993003.00437-2018
23. Gomperts, B. N., Kim, L. J., Flaherty, S. A. and Hackett, B. P. (2007). IL-13 regulates cilia loss and foxj1 expression in human airway epithelium. Am. J. Respir. Cell Mol. Biol. 37, 339-346. doi:10.1165/rcmb.2006-0400OC
24. Gras, D., Chanez, P., Vachier, I., Petit, A. and Bourdin, A. (2013). Bronchial epithelium as a target for innovative treatments in asthma. Pharmacol. Ther. 140, 290-305. doi:10.1016/j.pharmthera.2013.07.008
25. Guha, A., Vasconcelos, M., Zhao, R., Gower, A. C., Rajagopal, J. and Cardoso, W. V. (2014). Analysis of notch signaling-dependent gene expression in developing airways reveals diversity of Clara cells. PLoS ONE 9, e88848. doi:10.1371/journal.pone.0088848
26. Haghverdi, L., Lun, A. T. L., Morgan, M. D. and Marioni, J. C. (2018). Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat. Biotechnol. 36, 421-427. doi:10.1038/nbt.4091
27. Hogan, B. L. M., Barkauskas, C. E., Chapman, H. A., Epstein, J. A., Jain, R., Hsia, C. C. W., Niklason, L., Calle, E., Le, A., Randell, S. H. et al. (2014). Repair and regeneration of the respiratory system: Complexity, plasticity, and mechanisms of lung stem cell function. Cell Stem Cell 15, 123-138. doi:10. 1016/j.stem.2014.07.012
28. Hsieh, J. J.-D., Zhou, S., Chen, L., Young, D. B. and Hayward, S. D. (1999). CIR, a corepressor linking the DNA binding factor CBF1 to the histone deacetylase complex. Proc. Natl. Acad. Sci. USA 96, 23-28. doi:10.1073/pnas.96.1.23
29. Hudson, D. L., Guy, A. T., Fry, P., O’Hare, M. J., Watt, F. M. and Masters, J. R. W. (2001). Epithelial cell differentiation pathways in the human prostate: identification of intermediate phenotypes by keratin expression. J. Histochem. Cytochem. 49, 271-278. doi:10.1177/002215540104900214
30. Ji, H., Goode, R. J. A., Vaillant, F., Mathivanan, S., Kapp, E. A., Mathias, R. A., Lindeman, G. J., Visvader, J. E. and Simpson, R. J. (2011). Proteomic profiling of secretome and adherent plasma membranes from distinct mammary epithelial cell subpopulations. Proteomics 11, 4029-4039. doi:10.1002/pmic.201100102
31. Jones, K. G., Holland, J. F., Foureman, G. L., Bend, J. R. and Fouts, J. R. (1983). Xenobiotic metabolism in Clara cells and alveolar type II cells isolated from lungs of rats treated with beta-naphthoflavone. J. Pharmacol. Exp. Ther. 225, 316-319.
32. Jumppanen, M., Gruvberger-Saal, S., Kauraniemi, P., Tanner, M., Bendahl, P.-O., Lundin, M., Krogh, M., Kataja, P., Borg, A., Fernö, M. et al. (2007). Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers. Breast Cancer Res. 9, R16. doi:10.1186/bcr1649
33. Karamitros, D., Stoilova, B., Aboukhalil, Z., Hamey, F., Reinisch, A., Samitsch, M., Quek, L., Otto, G., Repapi, E., Doondeea, J. et al. (2018). Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells. Nat. Immunol. 19, 85-97. doi:10.1038/s41590-017-0001-2
34. Kessler, M., Hoffmann, K., Brinkmann, V., Thieck, O., Jackisch, S., Toelle, B., Berger, H., Mollenkopf, H.-J., Mangler, M., Sehouli, J. et al. (2015). The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids. Nat. Commun. 6, 8989. doi:10.1038/ncomms9989
35. Kiselev, V. Y., Yiu, A. and Hemberg, M. (2018). scmap: projection of single-cell RNAseq data across data sets. Nat. Methods 15, 359-362. doi:10.1038/nmeth.4644
36. Koopmans, T., Kumawat, K., Halayko, A. J. and Gosens, R. (2016). Regulation of actin dynamics by WNT-5A: implications for human airway smooth muscle contraction. Sci. Rep. 6, 30676. doi:10.1038/srep30676
37. Kotton, D. N. and Morrisey, E. E. (2014). Lung regeneration: mechanisms, applications and emerging stem cell populations. Nat. Med. 20, 822-832. doi:10. 1038/nm.3642
38. La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A. et al. (2018). RNA velocity of single cells. Nature 560, 494-498. doi:10.1038/s41586-018-0414-6
39. Laoukili, J., Perret, E., Willems, T., Minty, A., Parthoens, E., Houcine, O., Coste, A., Jorissen, M., Marano, F., Caput, D. et al. (2001). IL-13 alters mucociliary differentiation and ciliary beating of human respiratory epithelial cells. J. Clin. Invest. 108, 1817-1824. doi:10.1172/JCI200113557
40. Lun, A. T. L., McCarthy, D. J. and Marioni, J. C. (2016). A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000 Res. 5, 2122. doi:10.12688/f1000research.9501.2
41. Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M. et al. (2015). Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214. doi:10.1016/j.cell.2015.05.002
42. Malleske, D. T., Hayes, D., Lallier, S. W., Hill, C. L. and Reynolds, S. D. (2018). Regulation of human airway epithelial tissue stem cell differentiation by β-catenin, P300, and CBP. Stem Cells 36, 1905-1916. doi:10.1002/stem.2906
43. Marcet, B., Chevalier, B., Luxardi, G., Coraux, C., Zaragosi, L.-E. E., Cibois, M., Robbe-Sermesant, K., Jolly, T., Cardinaud, B., Moreilhon, C. et al. (2011a). Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat. Cell Biol. 13, 693-699. doi:10.1038/ncb2241
44. Marcet, B., Chevalier, B., Coraux, C., Kodjabachian, L. and Barbry, P. (2011b). MicroRNA-based silencing of Delta/Notch signaling promotes multiple cilia formation. Cell Cycle 10, 2858-2864. doi:10.4161/cc.10.17.17011
45. McCarthy, D. J., Campbell, K. R., Lun, A. T. L. and Wills, Q. F. (2017). Scater: preprocessing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 33, btw777. doi:10.1093/bioinformatics/btw777
46. Mercey, O., Popa, A., Cavard, A., Paquet, A., Chevalier, B., Pons, N., Magnone, V., Zangari, J., Brest, P., Zaragosi, L.-E. et al. (2017). Characterizing isomiR variants within the microRNA-34/449 family. FEBS Lett. 591, 693-705. doi:10. 1002/1873-3468.12595
47. Merigo, F., Benati, D., Piacentini, G., Boner, A. and Sbarbati, A. (2002). The ultrastructure of nasal mucosa in children with asthma. Ultrastruct. Pathol. 26, 293-298. doi:10.1080/01913120290104566
48. Montoro, D. T., Haber, A. L., Biton, M., Vinarsky, V., Lin, B., Birket, S. E., Yuan, F., Chen, S., Leung, H. M., Villoria, J. et al. (2018). A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 560, 319-324. doi:10. 1038/s41586-018-0393-7
49. Mori, M., Mahoney, J. E., Stupnikov, M. R., Paez-Cortez, J. R., Szymaniak, A. D., Varelas, X., Herrick, D. B., Schwob, J., Zhang, H. and Cardoso, W. V. (2015). Notch3-Jagged signaling controls the pool of undifferentiated airway progenitors. Development 142, 258-267. doi:10.1242/dev.116855
50. Morimoto, M., Liu, Z., Cheng, H.-T., Winters, N., Bader, D. and Kopan, R. (2010). Canonical Notch signaling in the developing lung is required for determination of arterial smooth muscle cells and selection of Clara versus ciliated cell fate. J. Cell Sci. 123, 213-224. doi:10.1242/jcs.058669
51. Mou, H., Vinarsky, V., Tata, P. R., Brazauskas, K., Choi, S. H., Crooke, A. K., Zhang, B., Solomon, G. M., Turner, B., Bihler, H. et al. (2016). Dual SMAD signaling inhibition enables long-term expansion of diverse epithelial basal cells. Cell Stem Cell 19, 217-231. doi:10.1016/j.stem.2016.05.012
52. Nam, S. M., Kim, Y. N., Kim, J. W., Kyeong, D. S., Lee, S. H., Son, Y., Shin, J. H., Kim, J., Yi, S. S., Yoon, Y. S. et al. (2016). Hairy and Enhancer of Split 6 (Hes6) deficiency in mouse impairs neuroblast differentiation in dentate gyrus without affecting cell proliferation and integration into mature neurons. Cell. Mol. Neurobiol. 36, 57-67. doi:10.1007/s10571-015-0220-8
53. Ordovas-Montanes, J., Dwyer, D. F., Nyquist, S. K., Buchheit, K. M., Vukovic, M., Deb, C., Wadsworth, M. H., Hughes, T. K., Kazer, S. W., Yoshimoto, E. et al. (2018). Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature 560, 649-654. doi:10.1038/s41586-018-0449-8
54. Pal, B., Chen, Y., Vaillant, F., Jamieson, P., Gordon, L., Rios, A. C., Wilcox, S., Fu, N., Liu, K. H., Jackling, F. C. et al. (2017). Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling. Nat. Commun. 8, 1627. doi:10.1038/s41467-017-01560-x
55. Pardo-Saganta, A., Law, B. M., Gonzalez-Celeiro, M., Vinarsky, V. and Rajagopal, J. (2013). Ciliated cells of pseudostratified airway epithelium do not become mucous cells after ovalbumin challenge. Am. J. Respir. Cell Mol. Biol. 48, 364-373. doi:10.1165/rcmb.2012-0146OC
56. Pardo-Saganta, A., Law, B. M., Tata, P. R., Villoria, J., Saez, B., Mou, H., Zhao, R. and Rajagopal, J. (2015a). Injury induces direct lineage segregation of functionally distinct airway basal stem/progenitor cell subpopulations. Cell Stem Cell 16, 184-197. doi:10.1016/j.stem.2015.01.002
57. Pardo-Saganta, A., Tata, P. R., Law, B. M., Saez, B., Chow, R. D.-W., Prabhu, M., Gridley, T. and Rajagopal, J. (2015b). Parent stem cells can serve as niches for their daughter cells. Nature 523, 597-601. doi:10.1038/nature14553
58. Plaisier, S. B., Taschereau, R., Wong, J. A. and Graeber, T. G. (2010). Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res. 38, e169-e169. doi:10.1093/nar/ gkq636
59. Plass, M., Solana, J., Wolf, F. A., Ayoub, S., Misios, A., Glažar, P., Obermayer, B., Theis, F. J., Kocks, C. and Rajewsky, N. (2018). Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science 360, eaaq1723-eaaq1735. doi:10.1126/science.aaq1723
60. Plasschaert, L. W., Žilionis, R., Choo-wing, R., Savova, V., Knehr, J., Roma, G., Klein, A. M. and Jaffe, A. B. (2018). A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377-381. doi:10.1038/ s41586-018-0394-6
61. Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A. and Trapnell, C. (2017). Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979-982. doi:10.1038/nmeth.4402
62. Rawlins, E. L., Okubo, T., Xue, Y., Brass, D. M., Auten, R. L., Hasegawa, H., Wang, F. and Hogan, B. L. M. (2009). The role of Scgb1a1+ Clara cells in the long-term maintenance and repair of lung airway, but not alveolar, epithelium. Cell Stem Cell 4, 525-534. doi:10.1016/j.stem.2009.04.002
63. Revinski, D. R., Zaragosi, L.-E., Boutin, C., Ruiz-Garcia, S., Deprez, M., Thomé, V., Rosnet, O., Gay, A.-S., Mercey, O., Paquet, A. et al. (2018). CDC20B is required for deuterosome-mediated centriole production in multiciliated cells. Nat. Commun. 9, 4668-4683. doi:10.1038/s41467-018-06768-z
64. Reynolds, S. D., Reynolds, P. R., Pryhuber, G. S., Finder, J. D. and Stripp, B. R. (2002). Secretoglobins SCGB3A1 and SCGB3A2 define secretory cell subsets in mouse and human airways. Am. J. Respir. Crit. Care Med. 166, 1498-1509. doi:10.1164/rccm.200204-285OC
65. Robinson, M. D., McCarthy, D. J. and Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. doi:10.1093/bioinformatics/btp616
66. Rock, J. R., Onaitis, M. W., Rawlins, E. L., Lu, Y., Clark, C. P., Xue, Y., Randell, S. H. and Hogan, B. L. M. (2009). Basal cells as stem cells of the mouse trachea and human airway epithelium. Proc. Natl. Acad. Sci. USA 106, 12771-12775. doi:10.1073/pnas.0906850106
67. Rock, J. R., Gao, X., Xue, Y., Randell, S. H., Kong, Y.-Y. and Hogan, B. L. M. (2011). Notch-dependent differentiation of adult airway basal stem cells. Cell Stem Cell 8, 639-648. doi:10.1016/j.stem.2011.04.003
68. Schmid, A., Sailland, J., Novak, L., Baumlin, N., Fregien, N. and Salathe, M. (2017). Modulation of Wnt signaling is essential for the differentiation of ciliated epithelial cells in human airways. FEBS Lett. 591, 3493-3506. doi:10.1002/1873-3468.12851
69. Setty, M., Kiseliovas, V., Levine, J., Gayoso, A., Mazutis, L. and Pe’er, D. (2019). Characterization of cell fate probabilities in single-cell data with Palantir. Nat. Biotechnol. 37, 451-460. doi:10.1038/s41587-019-0068-4
70. Smith, M. K., Koch, P. J. and Reynolds, S. D. (2012). Direct and indirect roles for β-catenin in facultative basal progenitor cell differentiation. Am. J. Physiol. Lung Cell. Mol. Physiol. 302, 580-594. doi:10.1152/ajplung.00095.2011
71. Teixeira, V. H., Nadarajan, P., Graham, T. A., Pipinikas, C. P., Brown, J. M., Falzon, M., Nye, E., Poulsom, R., Lawrence, D., Wright, N. A. et al. (2013). Stochastic homeostasis in human airway epithelium is achieved by neutral competition of basal cell progenitors. eLife 2, e00966. doi:10.7554/eLife.00966
72. Tözser, J., Earwood, R., Kato, A., Brown, J., Tanaka, K., Didier, R., Megraw, T. L., Blum, M. and Kato, Y. (2015). TGF-β signaling regulates the differentiation of motile cilia. Cell Rep. 11, 1000-1007. doi:10.1016/j.celrep.2015.04.025
73. Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A. and Quake, S. R. (2014). Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371-375. doi:10.1038/nature13173
74. Tsao, P.-N., Vasconcelos, M., Izvolsky, K. I., Qian, J., Lu, J. and Cardoso, W. V. (2009). Notch signaling controls the balance of ciliated and secretory cell fates in developing airways. Development 136, 2297-2307. doi:10.1242/dev.034884
75. Turner, J., Roger, J., Fitau, J., Combe, D., Giddings, J., Van Heeke, G. and Jones, C. E. (2011). Goblet cells are derived from a FOXJ1-expressing progenitor in a human airway epithelium. Am. J. Respir. Cell Mol. Biol. 44, 276-284. doi:10. 1165/rcmb.2009-0304OC
76. Tyner, J. W., Kim, E. Y., Ide, K., Pelletier, M. R., Roswit, W. T., Morton, J. D., Battaile, J. T., Patel, A. C., Patterson, G. A., Castro, M. et al. (2006). Blocking airway mucous cell metaplasia by inhibiting EGFR antiapoptosis and IL-13 transdifferentiation signals. J. Clin. Invest. 116, 309-321. doi:10.1172/JCI25167
77. van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D. et al. (2018). Recovering gene interactions from single-cell data using data diffusion. Cell 174, 716-729.e27. doi:10.1016/j.cell.2018.05.061
78. Vieira Braga, F. A., Kar, G., Berg, M., Carpaij, O. A., Polanski, K., Simon, L. M., Brouwer, S., Gomes, T., Hesse, L., Jiang, J. et al. (2019). A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153-1163. doi:10.1038/s41591-019-0468-5
79. Vladar, E. K., Stratton, M. B., Saal, M. L., Salazar-De Simone, G., Wang, X., Wolgemuth, D., Stearns, T. and Axelrod, J. D. (2018). Cyclin-dependent kinase control of motile ciliogenesis. eLife 7, e36375. doi:10.7554/eLife.36375
80. Wang, S.-Z., Rosenberger, C. L., Bao, Y.-X., Stark, J. M. and Harrod, K. S. (2003). Clara cell secretory protein modulates lung inflammatory and immune responses to respiratory syncytial virus infection. J. Immunol. 171, 1051-1060. doi:10.4049/ jimmunol.171.2.1051
81. Wang, X., Gupta, P., Fairbanks, J. and Hansen, D. (2014). Protein kinase CK2 both promotes robust proliferation and inhibits the proliferative fate in the C. elegans germ line. Dev. Biol. 392, 26-41. doi:10.1016/j.ydbio.2014.05.002
82. Wang, B., Zhu, J., Pierson, E., Ramazzotti, D. and Batzoglou, S. (2017). Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nat. Methods 14, 414-416. doi:10.1038/nmeth.4207
83. Watson, J. K., Rulands, S., Wilkinson, A. C., Wuidart, A., Ousset, M., Van Keymeulen, A., Göttgens, B., Blanpain, C. C., Simons, B. D., Rawlins, E. L. et al. (2015). Clonal dynamics reveal two distinct populations of basal cells in slow-turnover airway epithelium. Cell Rep. 12, 90-101. doi:10.1016/j.celrep.2015. 06.011
84. Weiske, J. and Huber, O. (2005). The histidine triad protein Hint1 interacts with Pontin and Reptin and inhibits TCF-β-catenin-mediated transcription. J. Cell Sci. 118, 3117-3129. doi:10.1242/jcs.02437
85. Wolf, F. A., Angerer, P. and Theis, F. J. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15-20. doi:10.1186/s13059-017-1382-0
86. Yang, L.-T., Nichols, J. T., Yao, C., Maniley, J. O., Robey, E. A. and Weinmaster, G. (2004). Fringe glycosyltransferases differentially modulate Notch1 proteolysis induced by Delta1 and Jagged1. Mol. Biol. Cell 16, 927-942. doi:10.1091/mbc. e04-07-0614
87. Zemke, A. C., Teisanu, R. M., Giangreco, A., Drake, J. A., Brockway, B. L., Reynolds, S. D. and Stripp, B. R. (2009). β-Catenin is not necessary for maintenance or repair of the bronchiolar epithelium. Am. J. Respir. Cell Mol. Biol. 41, 535-543. doi:10.1165/rcmb.2008-0407OC