In vitro gene signature of volar keratinocytes at early vs late passage

How cell and tissue identity persist despite constant cell turnover is an important biologic question with cell therapy implications. While many mechanisms exist, we investigated the controls for site-specific gene expression in skin given its diverse structures and functions. For example, the transcriptome of in vivo palmoplantar (i.e. volar) epidermis is globally unique including Keratin 9 (KRT9). While volar fibroblasts have the capacity to induce KRT9 in non-volar keratinocytes, we demonstrate here that volar keratinocytes continue to express KRT9 in vitro solo-cultures. Despite this, KRT9 expression is lost with volar keratinocyte passaging, in spite of stable hypo-methylation of its promoter. Coincident with KRT9 loss is a gain of the primitive Keratin 7 and a signature of dsRNA sensing, including the dsRNA receptor DDX58. Exogenous dsRNA inhibits KRT9 expression in early passage volar keratinocytes or in vivo footpads of wild-type mice. Loss of DDX58 in passaged volar keratinocytes rescues KRT9 and inhibits KRT7 expression. Additionally, DDX58 null mice are resistant to the ability of dsRNA to inhibit KRT9 expression. These results demonstrate that the sensing of dsRNA is critical for loss of cell specific gene expression; our results have important implications of how dsRNA sensing is important outside of immune pathways. Keratinocytes were expanded from the sole of the foot and at passage 4 or 8, RNA was harvested to identify unique transcripts The same single volar isolate was tested one time at passage 4 and one time at passage 8. Total RNA was extracted and sent for microarray analysis