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miRNAs are short (~22 bp) non-coding RNA sequences shown to regulate almost every known cellular activity. Collectively, it’s estimated that miRNAs regulate up to 60% of all genes.
It’s not surprising, then, that miRNAs play an important role in gene regulation that controls embryonic stem cell (ESC) pluripotency and differentiation, as well as induced pluripotent stem cell (iPSC) reprogramming.
The process of stem cell differentiation has been a focus of biomedical research for tissue engineering and stem cell therapy. One current issue in the field is not only defining these mechanisms, but identifying different developmental stages and cell types.
miRNAs in ESC pluripotency and differentiation
Cells express different levels of various miRNAs that can target genes involved in promoting differentiation or maintaining pluripotency at each stage of development. This provides a miRNA signature useful for identifying the developmental stage of that cell type. Therefore, studying ESC-specific miRNAs can yield useful biomarkers for stem cell differentiation.
Screening the expression of 40 ESC-associated miRNAs led to the identification of 14 novel differentiation‐associated miRNAs that provide a unique signature for ESCs that are poised to undergo differentiation (Ma et al,. 2015). Among those were miR‐27a and miR‐24 that block self‐renewal by targeting several pluripotency‐associated factors.
When the researchers deleted these two miRNAs in mouse embryonic fibroblasts, cells started undergoing somatic cell reprogramming, confirming the roles of miR-27a and miR-24 as suppressors of ESC pluripotency and drivers of stem cell differentiation.
While the above miRNAs are linked to ESC differentiation, others have been shown to suppress it. For example, a recent study by Guo et al. (2015) demonstrated that the ESC-enriched miR-294/302 family stabilizes pluripotency by suppressing apoptotic pathways.
miRNAs in somatic cell reprogramming
There are several types of pluripotent stem cells: ESCs, somatically reprogrammed iPSC and now the new F-class of iPSCs, so called because of their fuzzy appearance under a microscope (Tonge et al., 2014).
Studies discussed in the previous section used miRNA signatures to identify the developmental stage of the cell. Now the question has been raised of whether we can use miRNA expression profiling to distinguish between these various types of stem cells. The answer, it seems, is yes. In a recent publication, Clancy et al. (2014) demonstrated that different stem cell types display distinct miRNA expression profiles during reprogramming.
Using next-generation sequencing, the researchers showed that while the overall miRNA abundance was comparable between the cell types, there were changes in the levels of specific miRNAs during reprogramming. These changes were characteristic of the traditional ESC class, reprogrammed iPSC class or the F-class.
Interestingly, these specific miRNAs were regulated by different mechanisms. Twelve of the ESC-specific miRNA loci, including miR-302/367 and miR-290/295, were regulated transcriptionally by DNA methylation, which allowed miRNA expression to be turned on in the later phases of reprogramming.
On the other hand, the F-class miRNAs encompassed 22 genomic loci, including certain members of the let-7 family, miR196a-5p, and miR-181a-5p. Unlike the ESC class, the expression of these miRNAs was regulated at the post-transcriptional level.
These recent results demonstrate that unique miRNA signatures of ESC, iPSC and F-class stem cells provide useful biomarkers for identifying the specific class and developmental stage of that particular stem cell.
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