Biomarker profiling or multiplex quantification for everyone

Many researchers would be keen to identify new targets for their research project: add a new cytokine to the classical inflammatory panels, find the missing link between 2 phosphorylation pathways, dig into the miRNA to find a new therapeutic target…
They expect they’ll need dedicated (and expensive) new equipment. Not necessarily! Let’s take a look at assays that use existing and quite common readers, or that can easily be outsourced to reliable labs…

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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.

miRNA mediates gene expression through HDL particles

A recent study published in Nature Communications is the first to report how a mature microRNA (miR-223) actively controls the gene expression of a cell in which it was not originally transcribed. High Density Lypoprotein (HDL), commonly known as “good cholesterol”, is associated with reduced risk of cardiovascular disease.  HDL particles are complex structures composed of many components, including proteins, bioactive lipids and… microRNAs. One of the known benefits of HDL is its ability to reduce inflammation that might integrate miRNA-driven pathways.

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microRNAs: Finding the effector – miRNA detection

Following on from my previous post  in which I started to introduce a series of techniques to investigate the impact of miRNA expression on cell fate, let’s take a look at the first one: miRNA detection

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microRNAs: Keys to open cell biology’s secret chamber

As cell biologist, when working in labs I have in the past witnessed several “X-files” in a flask of cells along my way: all cells of an established cell line are supposed to have the same genetic background and to respond similarly to the same stimuli… but sometimes this is simply not what happens!
I would not risk saying that it all comes down to epigenetics, but much of this “unexpected” behaviour is governed at  mRNA level independently of the genetic background. “Cell personality” is then defined at several levels: genetic background, epigenetics, mRNA modulation and protein/lipid content.

It’s a sophisticated web of positive/negative signals that governs cell fate and behavior. But how do cells cope with this complicated issue? [Read more…]

A new dimension in biomarker profiling: miRNA 3D-arrays by TORAY

Blood sample

Circulating miRNA from blood

miRNA are implicated in a number of diseases and cancers. Despite the fact that their different roles in physiological and pathological cell processes are still under investigation, there is already more and more interest in considering them as future key diagnostic and prognostic biomarkers. Indeed, they are conveniently present in blood, and furthermore, their small size makes them relatively robust compared to messenger RNAs. They are well conserved into poor quality samples such as FFPE samples allowing the best hopes when exploring biobanks of tissues.

Accurate and convenient technologies aimed at profiling miRNA expression from such biobanks and blood opens up a promising era in biomarker discovery for personalized healthcare.
But still, we need to find an efficient profiling approach to cover the full miRnome that contains about 2000 Human miRNA… [Read more…]

Secretome biomarker identification: tech tips for selecting the most suitable tools

In a previous post, I mentioned that the secretome is becoming a very hot topic in the world of proteome analysis, and even a crucial study subject. Today, I’d like go a step further and shed some light on how to analyse it.

Let’s see what the options are…

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Proteome, secretome, kinome… What’s it all about?

Proteome is referenced as the result of expression of the whole genome. With the recent developments of genomics, one could consider that this analysis is enough to decipher any biological mechanism…
But depending on your sample, some regulations occur, that are not directly linked to the genes: isoform splicing, post-translational modifications (such as phosphorylation, acetylation & glycosylation), secretion…

Genomics, although powerful, does not allow the analysis of such protein-specific modifications. To overcome these limits, proteomics emerges, with specific subsets having specific requirements. Here, I’d like to put the Secretome and Kinome in the highlight!

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