Novel Dynamics of Human Mucociliary Differentiation Revealed by Single-cell RNA Sequencing of Nasal Epithelial Cultures

Overview

Journal Development

Specialty Biology

Date 2019 Sep 28

PMID 31558434

Citations 141

Authors

Sandra Ruiz Garcia

Marie Deprez

Kevin Lebrigand

Amelie Cavard

Agnes Paquet

Marie-Jeanne Arguel

Virginie Magnone

Marin Truchi

Ignacio Caballero

Sylvie Leroy

Charles-Hugo Marquette

Brice Marcet

Pascal Barbry

Laure-Emmanuelle Zaragosi

Affiliations

Soon will be listed here.

Abstract

The upper airway epithelium, which is mainly composed of multiciliated, goblet, club and basal cells, ensures proper mucociliary function and can regenerate in response to assaults. In chronic airway diseases, defective repair leads to tissue remodeling. Delineating key drivers of differentiation dynamics can help understand how normal or pathological regeneration occurs. Using single-cell transcriptomics and lineage inference, we have unraveled trajectories from basal to luminal cells, providing novel markers for specific populations. We report that: (1) a precursor subgroup of multiciliated cells, which we have entitled deuterosomal cells, is defined by specific markers, such as DEUP1, FOXN4, YPEL1, HES6 and CDC20B; (2) goblet cells can be precursors of multiciliated cells, thus explaining the presence of hybrid cells that co-express markers of goblet and multiciliated cells; and (3) a repertoire of molecules involved in the regeneration process, such as keratins or components of the Notch, Wnt or BMP/TGFβ pathways, can be identified. Confirmation of our results on fresh human and pig airway samples, and on mouse tracheal cells, extend and confirm our conclusions regarding the molecular and cellular choreography at work during mucociliary epithelial differentiation.

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References

Jumppanen M, Gruvberger-Saal S, Kauraniemi P, Tanner M, Bendahl P, Lundin M . Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers. Breast Cancer Res. 2007; 9(1):R16. PMC: 1851391. DOI: 10.1186/bcr1649. View

Zemke A, Teisanu R, Giangreco A, Drake J, Brockway B, Reynolds S . beta-Catenin is not necessary for maintenance or repair of the bronchiolar epithelium. Am J Respir Cell Mol Biol. 2009; 41(5):535-43. PMC: 2778160. DOI: 10.1165/rcmb.2008-0407OC. View

Wang S, Rosenberger C, Bao Y, Stark J, Harrod K . Clara cell secretory protein modulates lung inflammatory and immune responses to respiratory syncytial virus infection. J Immunol. 2003; 171(2):1051-60. DOI: 10.4049/jimmunol.171.2.1051. View

Schmid A, Sailland J, Novak L, Baumlin N, Fregien N, Salathe M . Modulation of Wnt signaling is essential for the differentiation of ciliated epithelial cells in human airways. FEBS Lett. 2017; 591(21):3493-3506. PMC: 5683904. DOI: 10.1002/1873-3468.12851. View

Rawlins E, Okubo T, Xue Y, Brass D, Auten R, Hasegawa H . The role of Scgb1a1+ Clara cells in the long-term maintenance and repair of lung airway, but not alveolar, epithelium. Cell Stem Cell. 2009; 4(6):525-34. PMC: 2730729. DOI: 10.1016/j.stem.2009.04.002. View

Ordovas-Montanes J, Dwyer D, Nyquist S, Buchheit K, Vukovic M, Deb C . Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature. 2018; 560(7720):649-654. PMC: 6133715. DOI: 10.1038/s41586-018-0449-8. View

Brechbuhl H, Ghosh M, Smith M, Smith R, Li B, Hicks D . β-catenin dosage is a critical determinant of tracheal basal cell fate determination. Am J Pathol. 2011; 179(1):367-79. PMC: 3123883. DOI: 10.1016/j.ajpath.2011.03.016. View

Gras D, Chanez P, Vachier I, Petit A, Bourdin A . Bronchial epithelium as a target for innovative treatments in asthma. Pharmacol Ther. 2013; 140(3):290-305. DOI: 10.1016/j.pharmthera.2013.07.008. View

Mercey O, Popa A, Cavard A, Paquet A, Chevalier B, Pons N . Characterizing isomiR variants within the microRNA-34/449 family. FEBS Lett. 2017; 591(5):693-705. PMC: 5363356. DOI: 10.1002/1873-3468.12595. View

10.

Rock J, Onaitis M, Rawlins E, Lu Y, Clark C, Xue Y . Basal cells as stem cells of the mouse trachea and human airway epithelium. Proc Natl Acad Sci U S A. 2009; 106(31):12771-5. PMC: 2714281. DOI: 10.1073/pnas.0906850106. View

11.

La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V . RNA velocity of single cells. Nature. 2018; 560(7719):494-498. PMC: 6130801. DOI: 10.1038/s41586-018-0414-6. View

12.

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View

13.

Wang X, Gupta P, Fairbanks J, Hansen D . Protein kinase CK2 both promotes robust proliferation and inhibits the proliferative fate in the C. elegans germ line. Dev Biol. 2014; 392(1):26-41. DOI: 10.1016/j.ydbio.2014.05.002. View

14.

Cole B, Smith R, Jenkins K, Graham B, Reynolds P, Reynolds S . Tracheal Basal cells: a facultative progenitor cell pool. Am J Pathol. 2010; 177(1):362-76. PMC: 2893679. DOI: 10.2353/ajpath.2010.090870. View

15.

Kessler M, Hoffmann K, Brinkmann V, Thieck O, Jackisch S, Toelle B . The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids. Nat Commun. 2015; 6:8989. PMC: 4686873. DOI: 10.1038/ncomms9989. View

16.

Marcet B, Chevalier B, Luxardi G, Coraux C, Zaragosi L, Cibois M . Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat Cell Biol. 2011; 13(6):693-9. DOI: 10.1038/ncb2241. View

17.

Hogan B, Barkauskas C, Chapman H, Epstein J, Jain R, Hsia C . Repair and regeneration of the respiratory system: complexity, plasticity, and mechanisms of lung stem cell function. Cell Stem Cell. 2014; 15(2):123-38. PMC: 4212493. DOI: 10.1016/j.stem.2014.07.012. View

18.

Vieira Braga F, Kar G, Berg M, Carpaij O, Polanski K, Simon L . A cellular census of human lungs identifies novel cell states in health and in asthma. Nat Med. 2019; 25(7):1153-1163. DOI: 10.1038/s41591-019-0468-5. View

19.

Vladar E, Stratton M, Saal M, Salazar-De Simone G, Wang X, Wolgemuth D . Cyclin-dependent kinase control of motile ciliogenesis. Elife. 2018; 7. PMC: 6145839. DOI: 10.7554/eLife.36375. View

20.

Setty M, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Peer D . Characterization of cell fate probabilities in single-cell data with Palantir. Nat Biotechnol. 2019; 37(4):451-460. PMC: 7549125. DOI: 10.1038/s41587-019-0068-4. View