miRNA Profiling for Stem Cell Identification

MicroRNAs (miRNAs) are small (less than 22 base pair), non-coding RNA sequences that play a significant role in the regulation of pluripotent cell development and reprogramming.

miRNAs are known to regulate a great number of cellular activities, with research showing miRNAs may regulate approximately 60% of genes (Friedman et al., 2009). For this reason, it is to be expected that miRNAs also play a role in the regulation of genes that control embryonic stem cell (ESC) pluripotency, and how they differentiate, as well as the reprogramming of pluripotent stem cells (iPSC).

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Understanding the mechanics of stem cell differentiation has been a key goal for researchers involved in stem cell therapy and other forms of tissue engineering.

miRNAs in ESC Pluripotency and Differentiation

During every step in their development, cells express changing levels of certain miRNAs that regulate genes associated with pluripotency and differentiation. The different levels of miRNA expression mean that different cell types have a different miRNA profile that can be used to identify the cell type, like a signature. Studying embryonic specific miRNAs could therefore help researchers find biomarkers for cell differentiation.

Looking at the expression of 40 miRNAs associated with embryonic cells allowed researchers to identify 14 novel miRNAs associated with differentiation processes (Ma et al,. 2015), which can be used as a signature to show which ESCs are differentiating. The 14 miRNAs identified included miR-27a and miR-24, which prevent self-renewal by regulating factors associated with pluripotency.

Deleting these two miRNAs in the ESCs of mice resulted in somatic cell reprogramming and showed that miR-27a and miR-24 promote the differentiation of stem cells and therefore remove ESC pluripotency.

While miR-27a and miR-24 promote cell differentiation, other miRNAs block it. Other research showed the miR-294/302 family, found in embryonic cells, suppresses apoptotic pathways, which stabilizes the cells pluripotent state (Guo et al., 2015).

The Role of miRNAs in Reprogramming Somatic Cells

There are multiple types of pluripotent stem cells, which include ESCs, somatically reprogrammed iPSCs, and also an F-family of iPSCs, which have been characterized (and named) by their fuzzy appearance underneath a microscope. (Tonge et al., 2014).

The research explored so far introduced the use of miRNAs signatures to identify the development of the cell. However, can this method also be used to identify the type of stem cell? Research by Clancy et al. (2014) says yes, who showed that different cell types have characteristic miRNA expressions when reprogramming.

Using advanced sequencing techniques the researchers demonstrated that the volume of miRNA was similar between cell types, but that particular miRNAs constituted this volume changed during reprogramming. These changes in miRNA profile could be used to identify if the cells were ESC, iPSC, or F-class.

The characteristic miRNAs were regulated by different mechanisms. Of the embryonic miRNAs, 12 (including miR-290/295 and miR-302/367) were regulated via DNA methylation, which allows the miRNA expression to be turned back on for further reprogramming.

For the F-class, there were 22 characteristic miRNAs (including miR196a-5p, miR-181a-5p and some let-7 miRNAs). However, unlike ESCs, their expression was regulated post-transcriptionally.

This recent research shows that the unique miRNA signatures of different stem cell types can be used as biomarkers to identify the stage of development of a stem cell.

Pre-Designed Panels for miRNA Profiling

Abcam have produced a panel focussed on miRNA profiling for stem cell research. The panel contains 68 miRNA probes, chosen from peer-reviewed studies. The chosen miRNAs were selected for their roles in stem cell differentiation and reprogramming, with a focus on iPSCs and ESCs.

Using panels allows researchers to avoid searching through the literature and start research straight away. Researchers can accurately profile miRNA directly either from crude biofluids or purified RNA.


  1. Clancy JL, Patel HR, Hussein SM, Tonge PD, Cloonan N, Corso AJ et al (2014). Small RNA changes en route to distinct cellular states of induced pluripotency. Nat Commun 5, 5522.
  2. Friedman RC, Farh KK, Burge CB, Bartel DP (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan; 19(1):92-105
  3. Guo WT, Wang XW, Yan YL, Li YP, Yin X, Zhang Q et al (2015). Suppression of epithelial-mesenchymal transition and apoptotic pathways by miR-294/302 family synergistically blocks let-7-induced silencing of self-renewal in embryonic stem cells. Cell Death Differ 22(7):1158-1169.
  4. Ma Y, Yao N, Liu G, Dong L, Liu Y, Zhang M et al (2015). Functional screen reveals essential roles of miR-27a/24 in differentiation of embryonic stem cells. EMBO J 34.3, 361-378.
  5. Tonge PD, Corso AJ, Monetti C, Hussein SM, Puri MC, Michael IP et al (2014). Divergent reprogramming routes lead to alternative stem-cell states. Nature516(7530), 192-197.

About Abcam

Abcam is a global life sciences company providing highly validated antibodies and other binders and assays to the research and clinical communities to help advance the understanding of biology and causes of disease.

Abcam’s mission is to serve life scientists to help them achieve their mission faster by listening to their needs, continuously innovating and improving and by giving them the tools, data and experience they want. Abcam’s ambition is to become the most influential life science company for researchers worldwide.

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Last updated: Apr 1, 2019 at 6:42 AM


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