Rapid measure of MicroRNA levels in cancer

Tiny particles developed to measure microRNA levels could help diagnose and monitor many diseases

A team of researchers at the Massachusetts Institute of Technology (MIT), in the US has engineered a way to detect abnormal microRNA levels in the blood of cancer patients, raising the possibility of developing a simple blood test to diagnose or monitor the disease.

The technology, described in two recent papers in the journals Analytical Chemistry and Angewandte Chemie, consists of an array of tiny particles, each designed to latch onto a specific type of microRNA. By exposing blood samples or purified RNA to these particles, the researchers can generate a microRNA profile that reveals whether cancer is present.

MicroRNA appear to contribute to tumours’ uncontrollable growth and each type of cancer — lung, pancreas, and so forth — has its own microRNA signature.

While measuring microRNA levels has clear potential benefits, there are many challenges to detecting microRNA, says Patrick Doyle, a professor of chemical engineering at MIT and leader of the research team. ‘There’s not an accepted gold standard,’ Doyle says. ‘Everybody has their own favourite one.’

Most current microRNA-detection techniques require RNA to be isolated from a blood or tissue sample and purified — a time-consuming process. Detecting microRNA directly from a blood sample would be much more efficient, Doyle says.

In their Angewandte Chemie paper, published in January, Doyle, graduate student Stephen Chapin and their colleagues showed that they could use tiny hydrogel particles, about 200 micrometers in length, to rapidly detect microRNA dysregulation patterns in RNA taken from four individuals with four different types of cancer.

In their Analytical Chemistry paper, which went online in August, their particles successfully detected microRNA in the blood serum of a prostate cancer patient.

The hydrogels used are conducive to the attachment of nucleic acids. Each of the researchers’ particles is decorated with millions of identical strands of DNA that are complementary to a specific microRNA target sequence. When the particles are mixed with a blood sample, any microRNA present binds to its complementary DNA. Each DNA strand also contains a short sequence that binds to a fluorescent probe, added later. Using a custom-built microfluidic scanner, the researchers then rapidly measure each particle’s fluorescence, revealing how much microRNA is present. The scanner also reads a chemical ‘barcode’ imprinted on each particle, which reveals the type of microRNA being detected. The entire process takes less than three hours.

In their second paper, the researchers bumped up their particles’ sensitivity by amplifying the fluorescence generated by each particle. Their new approach is 100 times more sensitive than other particle technologies for detecting microRNA, according to Doyle. The technology can detect as few as 10,000 copies of a particular microRNA, and each serum assay requires only 25 microliters of sample.

The new MIT approach also gives more accurate results than existing techniques that directly label microRNA strands with a fluorescent probe.

Doyle is now starting to work with medical researchers to investigate using microRNA detection to study other diseases such as cardiovascular disease and HIV. He and one of his former graduate students, Daniel Pregibon, have formed a company, Firefly Bioworks, to license the technology and they plan to develop the system for commercial use.