Scientists: New technique identifies molecular ‘biomarkers’ for disease

March 31, 2008

GAINESVILLE, Fla. — University of Florida chemists are the first to use a new tool to identify the molecular signatures of serious diseases — without any previous knowledge of what these microscopic signatures or “biomarkers” should look like.

Reported this month in the online edition of the Journal of Proteome Research, the advance could one day lead to earlier detection and improved treatment of some types of cancer as well as other diseases.

“With many diseases, the problem has been that we really don’t know what to look for,” said Weihong Tan, a professor of chemistry and the lead author of the paper. “What we’ve done is create a technique to identify the biomarkers despite that limitation.”

Doctors often diagnose cancer and other diseases based on the appearance of a tumor or a patient’s symptoms. While such traditional methods can be effective, they sometimes identify a disease only after it is established. For example, clinicians may get tipped off to the presence of lung cancer — which kills more people than any other type of cancer — based on visible images of a tumor that appear on radiological exams of a patient’s lungs.

Because earlier detection typically improves outcomes, doctors would like to spot disease at the molecular level, before it grows or spreads and manifests itself in more obvious and harmful ways. Given that diseased cells’ molecular structures differ from those of healthy ones, that approach should be possible, and researchers have had some success finding such “biomarkers” using antibodies, Tan said. But despite years of research, biomarkers for most diseases remain elusive or unreliable, he said.

His group turned to “aptamers,” single-strand chains of DNA or RNA that recognize and bind to target protein molecules, as a new tool. His paper reports the first-ever successful use of the aptamers to discover a molecular biomarker — in this case, one for leukemia.

Tan said his group used cell-SELEX, a process his group developed and patented.

Researchers create trillions of different varieties of aptamers in a solution. They then immerse cells known to carry the sought-after disease in the solution. After an incubation period, they rinse the cells.

The vast majority of the aptamers wash away, but those with stronger molecular affinity for the diseased cells remain. The researchers repeat the process several times, eventually shrinking the pool of aptamers to as few as 10 to 25 very strongly attached aptamers — those most closely associated with the diseased cells. Analysis then reveals these aptamers’ molecular structure, as well as the molecular structure of the cells’ biomarkers they bind to.

“As long as the molecules in question are expressed in a substantially different way on diseased and normal cells, they can be identified,” Tan said.

Rebecca Sutphen, associate professor and director of the Genetic Counseling & Testing Service at the H. Lee Moffitt Cancer Center & Research Institute in Tampa, said improved diagnosis may not be the only application of the research.

“The opportunity to identify cancer cell-specific biomarkers and potentially detect small numbers of cancer cells has many potential clinical applications, including disease detection, better imaging of tumors and even potential application for stem cells,” she said.

Other biomarkers have been found for leukemia, but none is particularly reliable, Tan said. Tan and his colleagues reported using aptamers to recognize cancer cells in a 2006 paper in the Proceedings of the National Academy of Sciences. Tan said the latest paper advances that work by revealing the target biomarkers the selected aptamers recognize, Tan said. These targets will form a molecular foundation in understanding diseases, he said.

“In 2006, we did not know what the aptamer recognized on the cancer cell surface,” he said. “In this current work, we report discovering these biomarkers, which then form the molecular foundation for us to understand the cancer and to prepare different molecular tools for molecular medicine.”

Tan said the research is particularly promising because aptamers are relatively easy and inexpensive to manufacture compared with antibodies. “This offers the potential for wider application,” he said, adding that aptamers could one day be used not only to detect disease, but also to ferry therapeutic agents to diseased cells.

The research was funded in part with two grants from the National Institutes of Health. It was also funded with two grants from Florida’s Bankhead-Coley Cancer Research Program and one grant from the State of Florida Center of Excellence in Bio/nano sensors.

The paper’s co-authors are Dihua Shangguan, Zehui Cao, Ling Meng, Prabodhika Mallikaratchy, Kwame Sefah, Hui Wang and Ying Li.