Transcriptome analysis of human airway stem cells at their early and late passages expanded in dual SMAD signaling inhibitors

SUMMARY of the associated publication: Many adult epithelial stem cells cannot undergo prolonged expansion. This may be due to a cell autonomous limitation or a lack of necessary culture conditions. Thus far, the long-term culture of adult stem cells has required the use of Matrigel organoid culture or feeder co-culture systems. We demonstrate that the TGFbetaBMP/SMAD signaling pathway is highly active in the luminal cells of diverse p63+ basal cell-containing epithelia. Indeed, the activation of SMAD signaling in airway stem cells causes their differentiation, while conversely, inhibition of SMAD signaling leads to stem cell hyperplasia and compromised differentiation. Consistently, TGFbetaBMP/SMAD signaling activation prevents mature cell dedifferentiation. Using pharmacologic dual SMAD inhibition, we developed a feeder-free culture system that allows the cloning of single airway basal stem cells and the expansion of airway stem cells from clinical non-invasively obtained samples with high efficiency. Furthermore, the expansion protocols are applicable not only to human cells but also to those of mouse, ferret, and pig. When differentiated epithelia are produced from expanded cells, they exhibit proper epithelial physiology, and respond to clinically relevant pharmacologic agents. Most remarkably, a very wide variety of functional adult epithelial basal stem cells can be expanded despite their differing origins. The goal of this microarray analysis: It has been shown that inhibition of TGFbeta signaling leads to tumorigenesis (e.g. Guasch et al., 2007, and others). It will be important to show whether the dual inhibited population assumes a tumorigenic status in the same or different manner compared to directly isolated progenitor cells. To address this concern, we have done comprehensive transcriptome analysis comparing gene expression signature of airway stem cells at their early and late passages. We do not find tumor-associated gene signatures during stem cell expansion.