Single-cell RNA sequencing reveals novel cell differentiation dynamics during human airway epithelium regeneration

Sandra Ruiz García, Marie Deprez, Kevin Lebrigand, Agnès Paquet, Amélie Cavard, Marie-Jeanne Arguel, Virginie Magnone, Ignacio Caballero, Sylvie Leroy, Charles-Hugo Marquette, Brice Marcet, Pascal Barbry, Laure-Emmanuelle Zaragosi

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Nov 26, 2018

Received Date: 12th November 18

The upper airway epithelium is mainly composed of multiciliated, goblet, secretory and basal cells, which collectively constitute a first line of defense against inhalation of noxious substances. Upon injury, regeneration can restore a proper mucociliary function through proliferation and differentiation. In chronic airway diseases, the injured epithelium frequently displays defective repair and tissue remodeling, characterized by loss of multiciliated cells and mucus hyper-secretion. Delineating the drivers of the dynamics of differentiation and cell fate in human airway epithelium can help define the minimal set of rules that control epithelial homeostasis.

We have used single-cell transcriptomics to characterize sequences of cellular and molecular processes that take place during human airway epithelium regeneration. We have characterized airway cell subpopulations with high resolution. Using lineage inference algorithms, we have unraveled cell trajectories from basal to luminal cells, providing novel markers for specific cell populations. This is illustrated with precursors of multiciliated cells that we have termed deuterosomal cells, for which we identify highly specific markers, such as YPEL1HES6CDC20B, and a splice variant of this latter that encodes microRNA-449abc. We report that secretory cells are not the only precursors of multiciliated cells, but that goblet cells can also play this role. This likely explains the presence of dual cells, expressing markers of both cells, so far interpreted as transdifferentiating multiciliated cells. Finally, our study provides a repertoire of molecules involved in key successive steps of the regeneration process, corresponding either to structural molecules such as keratins or components of the Notch, Wnt or BMP/TGFb signaling pathways. Our findings were independently confirmed in experiments performed on fresh human and pig airway samples, and on mouse tracheal epithelial cells.

Through the characterization of goblet cell and multiciliated cell lineages, and the identification of specific association between cell populations and key components of signaling pathways, our single-cell RNA-seq study describes novel elements to the molecular and cellular choreography at work during mucociliary epithelium differentiation.

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This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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