Khaw, C. R. | Search bioRxiv

bioRxiv2026

Persistence of tobacco-mutated alveolar progenitor cells after smoking cessation mirrors long term risk of lung adenocarcinoma

Tobacco smoke shapes mutations, selection and clonal expansion in lung epithelial cells. Smoking cessation leads to divergent epidemiology in the two most common lung cancers: squamous cell carcinoma risk declines sharply, while adenocarcinoma risk is preserved. To investigate this discrepancy, we analysed 806 genomes of alveolar type II (AT2) cells and found persistently elevated mutation burdens after cessation. In contrast, in the proximal airway, rare basal stem cells with near-normal mutation burden expand after cessation, protecting against squamous cell carcinoma. Targeted single-molecule DNA sequencing of AT2 cells revealed positive selection for TP53 and cell cycle and MAPK genes, supporting continued cancer risk. A multistage carcinogenesis model emphasised the importance of a small population of hypermutated cells in the alveoli and reproduced the divergent epidemiological trajectories following cessation due to distinct regenerative dynamics. Our findings suggest that differences in mutational burden and clonal regeneration explain post-cessation trends in lung cancer subtypes. One sentence summaryCancer risk reflects not only cumulative exposure to toxins, but the capacity of tissues to erase genomic damage through regeneration from protected cells with clonal advantage.

genomics↗

bioRxiv2025

Podoplanin expression identifies human airway basal cells with higher progenitor cell potential

Basal cells are key to maintaining and repairing a functioning airway epithelium. Understanding how basal cells maintain normal airways provides a foundation for interpreting their dysfunction in disease states and for the development of novel therapies. The airway epithelium exists in a dynamic state in which basal stem cells replace lost luminal mucosecretory and multiciliated cell types via an intermediate suprabasal cell state. The ability to isolate basal cells with high progenitor cell potential would be beneficial in regenerative medicine applications, but the molecular identity of this population is unclear. Here, we evaluate candidate surface markers to isolate human basal cells. As an individual marker, we found that podoplanin (PDPN) had a favorable sensitivity and specificity compared with integrin alpha 6 (ITGA6) or nerve growth factor receptor (NGFR). We found that KRT5-expressing basal cells could be subdivided into those with high or low PDPN expression; KRT5-negative cells did not express PDPN. In vitro, PDPN-high basal cells had higher colony-forming capacity, increased population doubling potential and formed larger colonies than PDPN-low basal cells. PDPN-high basal cells expressed higher levels of TP63, as well as other genes expressed by quiescent or resting basal cells identified in single cell RNA sequencing studies. PDPN-low basal cells expressed genes associated with a differentiating basal cell state, including KRT4, NOTCH3 and serpin B family genes. Our results demonstrate that PDPN expression can identify basal cells with high progenitor cell potential, enabling high efficiency sorting of airway stem cells.

cell biology↗