MicroRNA was discovered as a new genetic material some ten years ago now. Scientists observed that it seems to turn a cell’s genes on and off. Recent research has shown that these small bundles of genetic code appear to become out of control in cancer cells.

A team at MIT has begun using minute particles that measure microRNA levels in tissue samples to provide a method to scan and diagnose cancer. In theory the process should work with many other diseases.

Two current papers in the journals Analytical Chemistry and Angewandte Chemie, outline the technology which uses an array of particles that attach themselves to a specific type of microRNA. The method exposes tissue, blood samples or purified RNA to these particles, enabling a microRNA profile to be created. Different types of cancer have their own microRNA signature, thus the presence of individual cancers in lung, stomach, pancreas, etc. can be identified and processed by what promises to be a new and effective cancer testing procedure.

Patrick Doyle, a professor of chemical engineering at MIT and leader of the research team, said:

“While measuring microRNA levels has clear potential benefits, there are many challenges to detecting microRNA. There’s not an accepted gold standard,” Doyle says. “Everybody has their own favorite one.”

The problem with most microRNA detection methods is that the RNA must be isolated from the blood or tissue in a purification process that is time consuming and expensive. Doyle and his colleagues, including graduate student Stephen Chapin, outlined in their Angewandte Chemie paper, published in January 2011, that they have successfully used hydrogel particles, with a length of around 200 microns, to more easily and efficiently detect microRNA dysregulation patterns in samples taken from four individuals with cancer.

Hydrogels are a type of polymer chain network that attract water causing the attachment of nucleic acids. The hydrogel particles are ornamented with millions of identical strands of DNA. The strands are complimentary to a specific microRNA target sequence. Thus microRNA in a blood sample will be attracted to and attach to the DNA on the hydrogel particle.

Following on from their first paper, their more recent report in this month’s Analytical Chemistry shows the hydrogel particle test, successfully identifying a patient with prostate cancer.

By mixing the hydrogel particles with a blood sample, any microRNA present binds to its respective DNA. The DNA strands on the hydrogel contain a short sequence that then binds to a fluorescent probe at the completion of the test. They then use a custom designed microfluidic scanner to rapidly measure each particle’s fluorescence, thus revealing how much microRNA is present. The scanner also reads a chemical barcode imprinted on each hydrogel particle, which identifies the type of microRNA being detected. The entire process is complete in under three hours.

The second paper goes on to outline how the researchers, in adding multiple DNA label sequences to each microRNA target, have increased the sensitivity of the hydrogel microRNA detection particles by as much as 100 times. (The DNA attaches to the fluorescent probes). This has enabled them to detect as few as 10,000 copies of a particular microRNA sequence in samples as small as 25 microliters.

In addition, this new approach from Doyle at MIT is more accurate because different microRNA strands have different shapes which affect how easily they bind to the DNA markers. Using mixed DNA markers helps avoid this anomaly.

Doyle and colleagues are now beginning work with medical researchers to study the use of microRNA detection for use in other diseases such as heart disease and HIV. He has also formed a company, Firefly Bioworks, with a former graduate student, Daniel Pregibon. Firefly Bioworks will license the technology for the custom made scanner that is needed to detect the fluorescence of the hydrogels, with an aim of providing a unit for commercial use.

Written by Rupert Shepherd B.Sc.