microRNA signatures of iPSCs and endoderm-derived tissues. Mus musculus

MicroRNAs (miRNAs), small non-coding RNAs that fine-tune gene expression, play multiple roles in the cell, including cell fate specification. We have analyzed the differential expression of miRNAs during fibroblast reprogramming into induced pluripotent stem cells (iPSCs) and endoderm induction in iPSCs upon treatment with high concentrations of Activin-A in reduced serum. During reprogramming, adult mouse fibroblasts are converted into cells that resemble embryonic stem cells (ESCs) according to standard molecular and functional assays for pluripotency. The reprogrammed iPSCs assume an ESC-like miRNA signature, marked by the strong induction of pluripotency clusters miR-290-295 and miR-302/367 and conversely the downregulation of the let-7 family. On the other hand, endoderm induction in iPSCs results in the upregulation of 13 miRNAs. Given that the liver and the pancreas are common derivatives of the endoderm, the comparison of the expression levels of these 13 upregulated miRNAs with those in hepatocytes and pancreatic islets suggests a trend of miRNA upregulation in the endoderm tending towards an islet phenotype rather than that of a hepatocyte. These observations provide insights into how differentiation may be guided more efficiently towards the endoderm and further into the liver or pancreas. Moreover, we also report novel miRNAs enriched for each of the cell types analyzed. Overall design: Stemloop RT-qPCR gene expression profiling. REPROGRAMMING: Differentially expressed miRNAs were determined between iPSCs (n=5 clones) and parent tail-tip fibroblasts (n=5) using mESCs R1 (n=3) and D3 (n=3). DIFFERENTIATION: Differentially expressed miRNAs were also analyzed in two iPSC clones upon treatment with Activin-A (n=2 each), and between primary mouse hepatocytes (n=3) and pancreatic islets (n=3).