Identification of senescent-like cells in airway organoids using single cell sequencing

Chronic lung diseases (e.g. chronic obstructive pulmonary disease, cystic fibrosis) are incurable. Epithelial senescence, a state of dysfunctional cell cycle arrest, contributes to the progression of such diseases. We differntiated basal cells to airway (bronchial) organoids. The organoids were treated with doxorubicin (Dox), quercetin (Quer) and the combination of Dox and Quer. Single cell sequencing showed that the organoids were composed of (transitional) basal, secretory, goblet, deuterosomal and ciliated cells. In addition, we identified a cluster, here defined as senescent cells, with high expression for the common senescence markers CDKN1A (p21), CDKN2A (p16), TIMP2, and GDF15. Senescent cells were marked by an increased activity of the BATF and PRDM1 regulons. Pathway enrichment analysis showed enrichment of the cellular senescence pathway in the senescent cell cluster. Transitional basal cells and secretory cells showed velocity towards senescent cells. Quer treatment resulted in a reduced proportion of senescent cells, whereas Dox treatment resulted in an increased proportion of goblet cells with increased expression of genes associated with detoxification (e.g. CYP1A1, ALDH13A). Quercetin antagonized doxorubicin-induced activity of senescence associated galactosidase without compromising organoid integrity. Further studies need to clarify to what extent such senescent cells are present in the airways of patients with chronic lung diseases and whether they affect the differentiation of the airway epithelium.