Global gene expression and comparison between multiple populations in the mouse epidermis

• The markers CD34, Sca-1, Integrin-α6 and Plet-1 is sufficient for separating previously described populations and identifies new subsets.
• Global transcriptome profiling identifies Hspa2 as a marker of the inner root sheath of the bulge.
• The specific transcriptome profiles that identifies the directly isolated cells are lost during culturing

Several populations with stem cell characteristics have been identified in the mouse hair follicle, and some are characterized by specific subsets of surface markers.Here we investigate to what extend a multicolor panel of the four surface markers CD34, Sca-1, Integrin-α6 and Plet-1 is sufficient for separating previously described populations. We used global transcriptome profiling to characterize these, and we also performed transcriptome analysis of selected populations after two weeks of culturing. This has not been done before in a context of multiple populations.We identified eight populations of which two have not been described previously: A subset expressing integrin-α6 only and a subset expressing all markers but CD34. Both subsets are highly clonogenic. Transcriptome profiling also showed expression of Hspa2 in a population negative to all markers and immunostaining identified this population as inner root sheath keratinocytes.All cultured populations lost characteristics from the parent population and could not be separated based on the gene expression profile.Our data shows that flow cytometry using multicolor panels can identify further subsets of cells within the epidermis and also highlights a marked discrepancy in gene expression between directly isolated cells and tissue cultured cells.