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Firefly Bioworks and SomaGenics present new microRNA research technology
Biotech Company “Firefly BioWorks”, develops a new technology, FirePlex, a method of miRNA detection that can been used for both academic and clinical research.

miRNAs have recently emerged as key fine-tune regulators of a large number of genes that control many cellular processes and signaling pathways. These molecules also have specific roles in a variety of diseases, such as cancer and inflammation, and have thus sparked interest for research into their potential as therapeutic and diagnostic biomarker tools.
“microRNA: Targets and Tools for Therapeutic Development” is an upcoming conference by CHI, upon which the latest discoveries regarding miRNA-mediated disease regulation will be address and new methodologies for conducting these studies in a laboratory or clinical setting will be introduced.

To be properly utilized, they must first be detected. Much of the latest research regarding miRNA has focused on improving detection methods. Daniel Pregibon, Ph.D., CTO of Firefly BioWorks, will talk about his firm’s latest technology, FirePlex, a new method of miRNA detection that has been used by both academic and clinical researchers.

Dr. Pregibon explains that , using microarrays or deep sequencing to profile all miRNAs in a single sample, or using single assays to examine individual miRNA expression across many samples are the only two types of technology available for miRNA profiling studies. Unfortunately, these approaches are not suitable for performing biomarker validation studies necessary for developing diagnostic tests.
“What we’re seeing is that there was really nothing in that middle range, if you wanted to look at 25–50 miRNAs over hundreds or thousands of different samples,” he says. FirePlex was designed specifically to to help researchers with these problems and allow high-throughput validation of a certain subset of miRNAs they are interested in studying.
Because each scientist working on miRNA research may be interested in looking at a unique and different set of miRNAs, Dr. Pregibon reported that 99% of the panels they make are custom panels, which can be quickly prepared, one week at the most. FirePlex panels have been developed to run on benchtop flow cytometers, so additional or specialized equipment does not need to be purchased to run an assay.
The FirePlex technology is encoded on hydrogel particles, instead of a glass surface, as with most microarrays. Dr. Pregibon explains that using a hydrogel instead of a glass surface allows each molecule to have many more degrees of freedom, which is useful from a thermodynamics standpoint. This hydrogel base for capturing miRNAs allows for greater sensitivity and specificity. Polyethylene glycol (PEG) is used as a substrate to eliminate nonspecific binding of proteins, lipids, or other complexes.

The FirePlex assay is also based on post-hybridization labeling (the miRNAs are labeled after being hybridized throughout the hydrogel volume), so it can be used with crude samples as well. Any debris will be washed away after immobilizing the miRNAs. Dr. Pregibon states that minimal manipulation of the sample also reduces any bias or mistakes that are consequences of the RNA isolation method used, which can lead to variable RNA yield or selective enrichment. FirePlex has also been expanded to profile miRNAs in cell lysates, fresh tissue, FFPE, and serum/plasma.

Another company, SomaGenics, has developed a method, miR-IDirect, for the direct detection of miRNAs from a plasma sample without total RNA isolation required. Sumedha Jayasena, Ph.D., vp of technology and therapeutic development, says the miR-IDirect platform incorporates SomaGenics’ qPCR-based miR-ID technology. It functions by detecting circulating miRNA in plasma.
This method provides quantification of small RNAs by circularizing them as a first step, then, as the second step creating cDNA by rolling circle amplification of the miRNA circles, and finally amplifying the cDNA further by qPCR using 5´-overlapping PCR primers. miR-ID has been already applied for miRNA detection in total cellular RNA as well as detecting purified RNA from various biological fluids.
miR-ID assays have been developed for about 100 different miRNAs up until now, with even more in development. The miR-ID technology can distinguish miRNAs with terminal modifications, such as 2´-OMe groups at 3´-ends, according to Dr. Jayasena.
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