Oxygen and miRNAs in Cosmetology and Dermatology

A recent review by Nadim et al. casts some light on a Cosmetology and Dermatology, where circulating biomarkers, though studied to a certain extent so far, are yet unknown for many skin models. (1) A first element to have in mind when considering the skin-related experimental model is the “Oxygen level”. Oxygen levels may contribute to different findings, and the in vitro models used so far may not be so physiologically relevant as initially thought.

Hypoxia and miRNAs

Tissue oxygenation (which is a major part of the cell microenvironment) regulates the expression of the microRNAs called oxymiRs. OxymiRs may be categorized into three groups:

  1. microRNAs whose expression is directly modied by the Oxygen partial pressure,
  2. microRNAs whose expression is indirectly (pH, metabolites, etc.) modified by the Oxygen partial pressure, andpO2 percentage levels in various tissues
  3. microRNAs that target mediators of Oxygen sensing pathways to regulate biological networks for cell survival.

Examples of miRNAs important in skin physiology include miR-17, miR-21, miR-24, miR-27, miR-29b, miR-99 family, miR-125, miR-146a, miR-155, miR-203 and miR-205, among many other.

For example, in injured tissue, disruption of the vascular supply is associated with a low oxygen partial pressure, or hypoxia, which induces the expression of specic microRNAs referred to as HypoxamiRs (included in group (1) of the oxymiRs classification).

miR-210, known as the master HypoxamiR, is robustly induced under hypoxic conditions in nearly all kinds of cells. Under hypoxia, miR-21 also induces angiogenesis by targeting PTEN, leading to activation of AKT and ERK1/2 signaling pathways.

Transfection Factors and microRNAs

Other transcription factors such as p53 and NF-kB have been shown to affect the expression of microRNAs under hypoxia/anoxia conditions.

Numerous studies have demonstrated the modulation of microRNA expression and particularly that of the miR-200 family with oxidative stress due to excessive ROS levels.

Up to now, very few studies have shown the role of the intermediate Oxygen level (physioxia) in regulating microRNA expression in skin cells. Taken together, these results strongly support the idea that physioxia should be an important criterion in determining the microRNA expression level and consequently protein expression and skin functions.

Therefore, when trying to understand the role of microRNAs in skin models, it is important to choose a cell culture system that is as physiological as possible, and have the tools to analyse the different biomarkers (no only microRNA, but also signaling pathways, secretome, etc).

Should you like to have more information on this review, or know what we can do for you to support you with cell culture technologies with controlled oxygen levels or to support you for your biomarker discovery studies, do not hesitate to contact me by leaving a message below.

Source:

(1) Nadim M. et al. “Physioxia and MicroRNAs As Key Factors in the Skin Microenvironment” (2015) FSCC Magazine, Vol. 18 – #1, pp: 35-43

miRNAs: potent biomarkers in cancer research?

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Expression signals of validated miRNAs that differentiated pancreato-biliary cancer from non-malignant abnormalities (A), or from cancers of other types (B).

A recent paper by Kojima, M. et al. has found a signature of miRNAs to identify patients with pancreato-biliary cancers who could benefit from surgical intervention.

Namely, a combination of eight miRNAs (miR-6075, miR-4294, miR-6880-5p, miR-6799-5p, miR-125a-3p, miR-4530, miR-6836-3p, and miR-4476) achieved a sensitivity, specificity, accuracy and AUC of 80.3%, 97.6%, 91.6% and 0.953, respectively.

In contrast, CA19-9 and CEA gave sensitivities of 65.6% and 40.0%, specificities of 92.9% and 88.6%, and accuracies of 82.1% and 71.8%, respectively, in the same test cohort. This diagnostic index identified 18/21 operable pancreatic cancers and 38/48 operable biliary-tract cancers in the entire cohort.

Finding of this eight miRNAs was possible by using Toray’s 3D profiling technology. This finding is especially important, as it is difficult to detect pancreatic cancer or biliary-tract cancer at an early stage using current diagnostic technology.

microRNAs are stably present in peripheral blood, and are therefore a good candidate for finding prognostic or diagnostic biomarkers.

Studying only the miRNAs available in the literature may limit the novelty of the biomarkers found, so for a wide variety of diseases, a profiling is mandatory in order to find really specific circulating biomarkers.

Toray’s technology is available in Europe as fee-for-services via tebu-bio Laboratories (see Press Release). By exploring the full miRnome (composed by 2,000 miRNAs) with Toray’s 3D-Gene® technology, one might identify slight miRNA expression level changes (including low abundance miRNAs) in blood samples, biopsies FFPE specimens…

Interested in miRNA profiling in cancer research? Leave a message below or browse tebu-bio’s 3D-Gene® miRNA profiling platform web page!

Identification of a MicroRNA signature for Fibromyalgia diagnosis

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Heatmap of PBMCs miRNome from FM patients and controls. The microarray analysis was performed with Toray’s 3D-Gene Human miRNA Oligo chips (v.16.0; current version is v21.0). Patient samples are labeled (FM 1–11) and controls (C 1–10). Color palette is included to indicate signal intensity.

A recent paper by Cerdá-Olmedo, G. et al. unravels the miRNA signature in fibromyalgia (FM). Diagnosis of FM, a chronic musculoskeletal pain syndrome characterised by generalized body pain, hyperalgesia and other functional and emotional comorbidities, is a challenging process hindered by symptom heterogeneity and clinical overlap with other disorders. No objective diagnostic method exists at present.

This study aimed at identifying changes in miRNA expression profiles (miRNome) of FM patients for the development of a quantitative diagnostic method of FM. In addition, knowledge of FM patient miRNomes would lead to a deeper understanding of the etiology and/or symptom severity of this complex disease.

A broad profiling was first performed using Toray’s technology. miRNAs found were validated by qPCR in a later step. The profiling of FM patients PBMCs showed a marked downregulation of hsa-miR223-3p, hsa-miR451a, hsa-miR338-3p, hsa-miR143-3p, hsa-miR145-5p and hsa-miR-21-5p (4-fold or more).

Globally, 20% of the miRNAs analyzed (233/1212) showed downregulation of at least 2-fold in patients. This might indicate a general de-regulation of the miRNA synthetic pathway in FM. No significant correlations between miRNA inhibition and FM cardinal symptoms could be identified. However, the patient with the lowest score for mental fatigue coincided with the mildest inhibition in four of the five miRNAs associated with the FM-group.

Therefore, the authors propose a signature of five strikingly downregulated miRNAs (hsa-miR223-3p, hsa-miR451a, hsa-miR338-3p, hsa-miR143-3p and hsa-miR145-5p) to be used as biomarkers of FM. Validation in larger study groups would be required before the results can be transferred to the clinic, as the authors indicate.

Looking for miRNA signatures? Don’t hesitate to leave your comments below!

Circulating Biomarkers in Cardiovascular Disease

Cardiovascular diseases (CVD) are one of the the primary causes of morbidity and mortality worlwide. Therefore, more accurate Blood cardiac biomarkers (CB) are needed for a correct handling of patients, at the diagnostic and prognostic level. CVDs are a myriad of diseases with different molecular mechanisms, so it is important to have CBs specific for each pathology.

Toray's 3D-Gene sensitive and accurate miRNA and mRNA microarray service by tebu-bio

Toray’s 3D-Gene technology enables sensitive and accurate miRNA and mRNA analysis through tebu-bio services

Biomarkers are a significant tool to better identify high-risk individuals, to diagnose disease conditions promptly and accurately, and to efficiently prognose and treat patients with disease. Circulating biomarkers, such as miRNAs, have been used in other fields (e.g. Oncology), but their use in clinical practice for CVD patients is still scarce. [Read more…]

miRNAs and Autoimmune Glomerulonephritis

Correlation of findings in animal models (e.g. mouse) and its validation in human samples lies at the basis of Translational medicine. Nowadays, hypothesis established in mouse models must, at some stage, be validated in a cohort of patients. [Read more…]

CleanTag small RNA library kit with no Gel Purification

 

Next generation sequencing has quickly become the preferred method over tiling arrays for most genomics and transcriptomics needs. The major exception has been the study of microRNAs, where highly sensitive probe arrays such as the 3D-Gene® miRNA profiling platform are still widely used. A large part of the reason for the persistence of array dominance in small RNA expression profiling is caused by the variability introduced in sequencing library prep protocols involving complicated hands-on PAGE purification steps.

The CleanTag™ Ligation Kit for Small RNA Library Preparation now allows users to remove the Gel Purification steps from their protocols and shift to more automated bead purification protocols. This is particularly important for cases when RNA quantity is limiting. Traditional small RNA library prep protocols will result in the formation of adapter dimers (similar to primer dimers) when RNA quantities are limiting, thus greatly reducing the number of usable reads. [Read more…]

Circulating biomarkers – there’s more than human

In a previous post, we discussed about how important it is to have research tools that allow to study secretome biomarkers outside the usual human and rodents. Either because other species are important research models, or more importantly, because they are the final patient that will be treated, such as pets or cattle.

miRNAs are key mediators in cell processes, allowing to activate or inhibit the expression of certain genes important in different physiological processes. How miRNAs work, and which ones are relevant, are a hot topic of research nowadays, and important advances are being made in areas such as Oncology and the Immune response. [Read more…]

New: CleanTag Ligation Kit for Small RNA Library Prep

As detailed in a previous post, chemically-modifying oligonucleotide adapters is an effective means to prevent adapter dimer formation during small RNA library prep. Just as primer dimers form when very little template DNA is used for PCR, adapter dimers can form with low starting concentrations of RNA. The CleanTag™ Ligation Kit for Small RNA Library Prep is a complete kit which is compatible with Illumina® technology that makes use of such modified adapters in optimized buffer conditions. The kit includes CleanTag™ chemically modified adapters that greatly reduce adapter dimer formation and is optimized for total RNA input from 1-1000 ng. [Read more…]

tebu-bio supports post-transcriptional gene regulation course

tebu-bio is pleased to announce their sponsorship of the 1st Course on “Post-transcriptional gene regulation: mechanisms at the heart of networks” (Institut Curie, March 23-27, 2015) that will be training 40 PhD students and postdoctoral fellows from 10 countries. Post-transcriptional gene regulation refers to every level of gene-expression control in a cell that occurs between transcription and the resulting protein levels. Specialists in this field study such things as polyadenylation, miRNAs, RNA binding proteins, signal transduction, and (pre)mRNA splicing. [Read more…]

Direct access to Biomarker Profiling identification tools

Profiling tools have an increasing interest for identifying new biomarkers. Different tools are available, from classical gene profiling on DNA chips, RT-qPCR arrays, Protein arrays for secretome or transcriptome, mRNA arrays and finally miRNA arrays. All these techniques sometimes require specific material for reading arrays, and some bioanalytics to extract valuable markers of interest.

Expand your knowledge – a new visionArrays - Blog Thumbnail

The increasing focus on these tools is obvious as they help to expand scientific knowledge on sometimes well-known pathways. Why restrict your analysis to classical markers instead of checking the impact on more than 100 biomarkers… at a similar cost? Value of results is obvious as well, as it offers a convenient way to identify original pathways.

The “Start smart” attitude

Facing a new project is always a stressful situation. Biomarkers chosen are generally based on literature, which may lead to duplicating, more or less, already existing information. Searching for innovative pathways looks more like a cherry-picking, highly risky strategy. At the end, this may lead to rather conservative conclusions. A striking example concerns Western blots (WB) which everybody knows may be time consuming, rather expensive and for sure limited in number for a given project. Nobody will ever make the decision to perform more than 100 WB to explore all the potential targets available. Lab’s budgets can’t survive such a strategy, and probably the time allocated to a project cannot suffer such delays…

Protein profiling on secretome or transcriptome now allows you to study more than 1000  targets from a single sample at once. Pricing is equivalent to 10 to 20 WB traditional WB. Results obtained are of top value as they immediately orientate research focus to appropriate pathways without having the risk of missing crucial information. This helps to speed up projects, focus research towards original biomarkers and at the end deeply differentiate published results.

But not everybody has the appropriate material to perform these assays, nor is used to handling these arrays. This generally needs adapted scanners to perform readouts and once results are obtained, spots need to be further analyzed to guarantee final quality. It requires some skill. One can understand the reluctance to jump into these technologies when they are only of occasional need.

So where’s the solution?

For these reasons, tebu-bio has developed over these last years a complete Profiling – Biomarker identification platform that offers researchers access to various solutions. With a complete offer including RT-qPCR arrays, protein arrays for soluble or signal transduction markers, mRNA and miRNA arrays, we help researchers to immediately identify biomarkers involved in their domains. This information, which often appears as the initial step in project management, drives studies in the appropriate direction, rapidly and in a cost effective way.

The service process is extremely simple. After defining the most appropriate solution regarding goals of interest, your samples are tested and results sent back. Time frame is generally 2 to 4 weeks depending on starting material. A dedicated project manager is always available for any questions throughout the project. There is no license involved in these studies, which are performed in our own, European-based labs near Paris.

For those who don’t have access to cell culture facilities, our cell culture platform is also ready to collaborate, with access to a large stock of primary cells.

And the next step…

Well, if you’re curious to know how this could help boost your research, get in touch to see exactly how it can work! Just leave your question or comments below.