Single keratinocyte analysis uncovers Foxm1 as a Yap-dependent regulator of human epidermal stem cells (scRNA-Seq)

Autologous epidermal cultures can permanently restore a functional epidermis on severely burned patients. Transgenic epidermal grafts do so also in genetic skin diseases as Junctional Epidermolysis Bullosa. Clinical success strictly requires an adequate number of epidermal stem cells, detected as holoclone-forming cells. To date, such cells can be only partially distinguished from the other transient amplifying clonogenic keratinocytes and cannot be prospectively isolated. Here we show that genome-wide single-cell transcriptome analysis performed on primary human epidermal keratinocyte cultures identified categories of genes clearly distinguishing the different clonal types, unveiled that holoclone-forming cells are enriched in genes regulating cell cycle, DNA repair (including telomerase), chromosome segregation and spindle organization, confirmed that human epidermal keratinocytes are hierarchically organized along a continuous, mainly linear trajectory showing that stem cells sequentially generate progenitors producing terminally differentiated cells and uncovered the role of FOXM1 as a YAP-dependent key regulator of normal and adhesion-defective epidermal stem cells. Overall design: The purpose of this study is to define, at single-cell levels, transcriptional profile of keratinocytes stem cells and transient amplifying progenitors. Single-cell RNA seq data from two human primary keratinocyte cultures (K82 and K86) harvest at early passsages (t1, profiled 3.367 and 3.978 cells respectively) and after serial cultivation (t2, profiled 4292 and 3576 cells respectively) were obtained with 10X Genomics Chromium Technology.