Epithelial cells possess a remarkable capacity to rapidly adapt their cell fate programme in response to changing tissue demands. Upon tissue injury or environmental perturbations, adult committed cells can reacquire stem cell properties, thereby expanding the pool of cells that contribute to tissue regeneration. Notably, this ability to rewire the cell fate programme – known as cell fate plasticity – extends beyond physiological constraints. When exposed to ectopic cues, epithelial cells can alter their identity as directed by the surrounding microenvironment. A deeper understanding of the mechanisms that govern these changes in cell identity holds great promise for regenerative medicine. However, our current knowledge of these processes is very limited.

Here, I adapted an ex vivo regenerative model to investigate adult oesophageal cell fate in response to the ectopic microenvironment of the skin. For this, I exposed the appendage-free mouse oesophageal epithelium to the mouse skin dermis, bearing empty niches for hair follicles. Whole-mount techniques together with immunofluorescence analysis revealed that oesophageal cells re-epithelialized the skin dermis and underlying niches, forming a new epithelium with associated appendages structurally similar to hair follicles.

By looking into surrogate markers of oesophageal and skin lineages, I found that oesophageal cells were instructed to change towards the skin lineage. Further investigation confirmed that the cues dictating lineage conversion emerged from the skin dermis. Yet, histological characterization and transcriptomic analysis unveiled high heterogeneity in response to dermal signals, denoting the inefficiency of the lineage conversion process.

To investigate the mechanisms promoting/preventing oesophageal-to-skin lineage conversion, I made use of an in-depth single cell RNA sequencing dataset. Interestingly, cells transitioning towards skin identity showed a regenerative profile defined by a marked hypoxic signature. To further study the relevance of this signature for lineage conversion, I used gain and loss of function experiments targeting the hypoxia-inducible factor-1α (HIF1a) and its downstream target SRY-box transcription factor 9 (SOX9). These results unveiled that the HIF1a-SOX9 axis poses a barrier to oesophageal-to-skin lineage conversion. In turn, when this barrier is lifted cells respond better to the dermal signals instructing alternative fate choices.

Finally, I explored the contribution of oesophageal cells to hair follicle formation following transplantation into the skin. These in vivo experiments confirmed that oesophageal cells have the ability to reconstitute functional hair follicles giving rise to hair.

Taken together, the results of my PhD project reveal the existence of barrier mechanisms to cell fate plasticity, whereby the same cues that promote tissue regeneration prevent free-access to alternate fates. Future studies will be needed to investigate the physiological relevance of these mechanisms in the context of wound-healing and cancer, where plasticity is known to operate.