In 2006, Takashi and Yamanaka described that mouse mature cells can be reprogrammed to a pluripotent state by expression of four transcription factors (Oct4, Klf4, Sox2 and cMyc [OKSM]) with obvious implications for the regenerative medicine field.

Recent landmark studies provided detailed molecular roadmaps for these so called induced pluripotent stem cells (iPSCs) generated from fibroblasts, however the molecular events that underpin the reprogramming process of other cell types are still largely unknown. In addition, universal and cell type-specific aspects of reprogramming and whether reprogramming is a universal reversion of the developmental pathway has not been properly addressed yet.

To fill this knowledge gap, we molecularly characterised and profiled the reprogramming pathways of mouse fibroblasts, neutrophils and keratinocytes via fluorescence-activated cell sorting and high-throughput whole transcriptome sequencing in the context of an OKSM reprogrammable mouse model.

Gene expression profiles of intermediates became progressively similar to those of iPSCs confirming that reprogramming occurs molecularly via an ordered sequence of events and that reprogramming pathways of all cell types fully converge at the end of reprogramming. This suggests that transcriptional signatures of early reprogramming stages have a strong cell type-specific component.

Even though we observed a transition through a primitive streak-like state for fibroblasts, neither neutrophils nor keratinocytes appeared to transition through this state during reprogramming, suggesting that this is not a universal feature of mammalian cell reprogramming. Early neutrophil and keratinocyte reprogramming intermediates were more similar to their somatic stem cells than their cell type of origin indicating that early reprogramming processes are characterised by a certain level of cell dedifferentiation along the cellular hierarchy.

Universal aspects of reprogramming of the characterised cell types included the observation of two major transcriptional waves, as previously identified for fibroblasts, at the start and end of the reprogramming process. The first wave was largely associated with cell identity loss and the second with the reactivation of the pluripotency network.

In summary, in depth analysis of transcriptomes of multiple cell types during reprogramming identified cell type-specific components to the reprogramming process which provide a more comprehensive picture compared to previous studies that provided high resolution maps of the reprogramming process of fibroblasts.