Pancreatic cancer marked by beacons

Researchers from the Georgia Institute of Technology hope to diagnose pancreatic cancer by using molecular-scale beacons to find genetic signs of cancer.

Pancreatic cancer is a silent killer, often reaching an advanced stage before being diagnosed. Gang Bao and his colleagues at the Georgia Institute of Technology hope to provide early detection of this killer using molecular-scale beacons that would find genetic signs of cancer and signal clinicians with a burst of fluorescence.

The molecular beacons consist of three parts: a fluorescent dye molecule and a ‘quencher’ molecule on opposite ends of an oligonucleotide engineered to match specific genetic mutations associated with cancer. Initially, the two molecules are held close together in a hairpin shape, the quencher preventing fluorescence emission from the dye.

Delivered into cells, the beacons seek out and bind to the mutated genetic material, known as mRNA. This breaks the bonds holding dye and quencher together, producing a fluorescent signal visible microscopically.

The current design of beacons, however, is prone to digestion by cellular enzymes, which activates the beacons to create false signals. To overcome this difficulty, the Bao lab has developed a new dual-beacon system that detects the fluorescence resonance energy transfer (FRET) between two beacons bound to the same mRNA target, significantly increasing the detection sensitivity.

‘This could become a very powerful clinical tool for cancer diagnosis,’ said Bao, associate professor in the Wallace H. Coulter Department of Biomedical Engineering. ‘If there are mutations in the cell, the beacons should find them. Cancer diagnosis based on molecular beacons should be much faster than any technique now available.’

Bao, his Ph.D. student Andrew Tsourkas and collaborators at Emory University have so far shown that the technique can efficiently detect several common genes. They have also shown how the detection time and specificity depend on the structure of the beacons.

But their work faces many challenges. They must demonstrate that their FRET-enhanced molecular beacons will find the mutated mRNA quickly – within 30 minutes. They must also find better dye molecules to provide a detectable signal even if the mutation exists in just one of 10,000 cells under study.

The technique would be useful in diagnostic testing. But to be really useful against pancreatic and other cancers for which no good screening tests exist, it would have to detect cancer markers in blood or other easily collected body fluid. Ultimately, Bao hopes the beacons — just a few nanometers in size — will be able to detect cancerous cells in the human body.

‘Studies show that even if the difference between the mRNA for the cancer and the normal mRNA is only one base pair, the molecular beacons can still differentiate between the two,’ he said. ‘If we can detect the cancer early enough, very likely the outcome of cancer patients can be dramatically improved.’

In more basic research, Bao and his students use optical tweezers – piconewton forces generated by beams of photons from a high-powered laser – to quantify interaction of biomolecules such as proteins and DNA. For example, by anchoring one protein on a surface, they use the tweezers to measure the unbinding force required to separate it from another protein.

‘This is an engineering study similar to the way we study the strength of steel,’ he explained. ‘We just have a nano-scale system and a much more delicate tool.’