Tumour microenvironment and miRNA biomarkers

In previous posts, we have seen the role of inflammation and glycosylation in the tumour microenvironment (TME). All these are mainly factors at the protein level causing the tumour cells to evade the immune system and metastasise. But what about other factors?

One of the areas that has raised quite some interest recently are microRNAs (miRNAs). If you’d like to brush up your knowledge on miRNAs, you might be interested in this post by my colleague Paola Vecino. miRNAs are becoming trendy, as they seem to be involved in several disease mechanisms (not only in cancer, but also in some other pathologies, including some inflammatory diseases), and they can be used as diagnostic and/or prognostic biomarkers.

In cancer, miRNAs seem to be involved both in the cancer stem cell phenotype and in the ability of specific cancer cells to produce metastases, meaning that they represent a link between the starting and ending points of tumorigenesis (1). Hypoxia-mediated miRNAs can have a role in either oncogenesis or tumour-supression (2). Finally, different studies on animal models as well as profiling clinical cancers for miRNA expression identify miRNAs as potent regulators of the crosstalk between cancer and stroma cells in the TME. As TME is key not only to determine the clinical characteristics of the tumour, but also to define the efficacy of some anticancer therapies, miRNAs are emerging as attractive therapeutic targets (3).

Therefore, one of the first questions that we can ask ourselves is: what do I know about the role of miRNAs in my experimental / clinical model?miRNA PCR array experimental workflow

Case # 1 – I know everything

If you know which miRNAs are key in your model to explain tumorigenesis and metastasis, then you can use the solutions included in a previous series of posts to validate their specific role in either cellular or animal models, and consider them (or not) as valuable Biomarkers.

Case # 2 – I don’t know everything but other people do

If this is your case, you can stand in the shoulder of giants, and analyse the miRNAs that have been described to have a role in specific types of cancer. You can either search publications and gather the information, or use ready-to-use qPCR arrays including miRNAs that have been described previously in the literature.

qPCR is a technology with a very low CV (R2>0.99) for inter- and intra-experimental conditions. It also requires minimum amounts of starting sample (around 10 pg of small RNA or 20 pg of total RNA). Also, the primers included in ready-to-use arrays means that they are validated, so you don’t have to go through the fuss of designing your own primers. The primers are designed in such a way that they are able to identify a single nucleotide mismatch.

You may either decide to go for a generic “cancer” qPCR array, or go to more specific profiles, such as bladder cancer, brain cancer, colorectal cancer, head & neck cancer, hepatocellular carcinoma, leukemia, lung cancer, melanoma, lymphoma, ovarian cancer, or pancreatic cancer, either in mouse or human samples.

Case # 3 – I don’t know everything and other people may not know it either

If you want to stand on the shoulder of giants, but go a step further, you may consider to do a search on the whole miRnome (i.e. all the miRNAs known to date), meaning that you would search miRNAs key to your experimental / clinical model vs. the whole miRBase (up to 2,000 miRNAs described up to date). This means that you will probably discover the miRNAs that have been previously described… and a few more that can make the difference in your specific model.

When you are searching for new miRNA biomarkers at this level, it is important to keep in mind several things regarding the technology used:

  • The technology should be able to detect low-abundance miRNAs
  • The technology might have a high correlation with qPCR results, meaning that it has both profiling as well as quantitative power
  • The technology allows to study not only serum and plasma, but also FFPE samples, so that you can get the most out of the histological samples that have been collected in your biobank for years
  • The technology is accurate and sensitive

Recently, a new array technology has been developed (Toray’s 3D-gene) which is currently being used in a study in Japan with 65,000 cancer patients to discover new miRNA biomarkers.

Interestingly, the 3D-gene RNA profiling technology meets all the criteria above described for (miRNA and mRNA) Biomarker discovery, and is also available in Europe as lab services.

So… which case does your research match?

Leave a comment if you want to share your experiences with miRNA biomarkers!

3D-Gene sensitivity







  1. Nicoloso, M. et alNature Reviews Cancer 9, 293-302 (April 2009) | doi:10.1038/nrc2619.
  2. Jin, H. et al. Chin. Sci. Bull, Vol. 59 (19) 2223-2231. doi: 10.1007/s11434-014-0273-y.
  3. Soon, P. and Kiaris, H. Endocr Relat Cancer 20 (5) R257R267, doi:10.1530/ERC-13-0119.


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