Oct4-mediated reprogramming induces embryonic-like microRNA expression signatures in human fibroblasts

Lucie Peskova,Jan Oppelt,Katerina Cerna,Tomas Barta,Marek Mraz

doi:10.1038/s41598-019-52294-3

Abstract

Oct4-mediated reprogramming has recently become a novel tool for the generation of various cell types from differentiated somatic cells. Although molecular mechanisms underlying this process are unknown, it is well documented that cells over-expressing Oct4 undergo transition from differentiated state into plastic state. This transition is associated with the acquisition of stem cells properties leading to epigenetically “open” state that is permissive to cell fate switch upon external stimuli. In order to contribute to our understanding of molecular mechanisms driving this process, we characterised human fibroblasts over-expressing Oct4 and performed comprehensive small-RNAseq analysis. Our analyses revealed new interesting aspects of Oct4-mediated cell plasticity induction. Cells over-expressing Oct4 lose their cell identity demonstrated by down-regulation of fibroblast-specific genes and up-regulation of epithelial genes. Interestingly, this process is associated with microRNA expression profile that is similar to microRNA profiles typically found in pluripotent stem cells. We also provide extensive network of microRNA families and clusters allowing us to precisely determine the miRNAome associated with the acquisition of Oct4-induced transient plastic state. Our data expands current knowledge of microRNA and their implications in cell fate alterations and contributing to understanding molecular mechanisms underlying it.

Highlights

The forced expression of defined transcription factors in cells is capable of inducing dramatic cell-fate conversions
It has been demonstrated that Oct[4] expression induces state unlike that of being observed during reprogramming to induced pluripotent stem cells (iPSCs) with a lack of molecular hallmarks of iPSCs formation[4,5]. This plastic state is characterised by loss of cell identity, de-differentiation and onset of a stem cell-like state associated with mixed expression of developmentally related genes that are linked to multiple lineages, but not with pluripotency status[5]
We found that human dermal fibroblasts over-expressing Oct[4] lose their cell identity demonstrated by down-regulation of fibroblast-specific genes and elevated expression of epithelial genes

Summary

Introduction

The forced expression of defined transcription factors in cells is capable of inducing dramatic cell-fate conversions. Increasing number of studies suggests that this approach leads to a transient induction of pluripotency[8,9] Still, this method has the advantage of higher efficiency, elevated proliferation, and erasure of epigenetic memory, when compared to direct cell lineage conversion[7]. It has been demonstrated that Oct[4] expression induces state unlike that of being observed during reprogramming to iPSCs with a lack of molecular hallmarks of iPSCs formation[4,5] This plastic state is characterised by loss of cell identity, de-differentiation and onset of a stem cell-like state associated with mixed expression of developmentally related genes that are linked to multiple lineages, but not with pluripotency status[5]. This study provides a novel insight into understanding of the molecular profile of cell plasticity, which is necessary for reprogramming strategies optimisations and their successful implementations

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