Georgetown cancer researchers develop high throughput method

Cutting edge matrix assembly can be used to analyze large numbers of tumors

Scientists at Georgetown University’s Lombardi Comprehensive Cancer Center have devised a new low-cost technology that allows thousands of tumor slices to be screened side-by-side, an improvement over current and more expensive methods that can analyze only several hundred tumors at once. The researchers anticipate that this technology could someday lead to more reliable prediction of patient prognosis and improved selection of optimal treatments for cancer and other diseases.

The new technology, details of which are published in the July 2005 issue of Nature Methods, “may lead to a better understanding of human cancer, as well as other human disorders, because it will let scientists discover and then detect unique biomarkers of disease in patients,” says Hallgeir Rui, M.D., Ph.D., associate professor of oncology at Georgetown and principal investigator of the study.

Rui and the study’s first author, postdoctoral researcher Matthew LeBaron, Ph.D., created the technology, which they call cutting edge matrix assembly (CEMA), to construct what are known in the field as tissue microarrays. This new method can be done by using the tools that are already available in a medical center’s pathology laboratory, they say.

Researchers now analyze tumors or tissues in large numbers by embedding cylindrical core samples of tissue, each taken from an individual patient, into a cube-like paraffin block, which is then sliced thin and stained in order to show proteins or molecules that scientists think may be involved in a disease. The cores, however, must be spaced a certain distance apart within the paraffin structure or else the cube will crack, Rui says. “This is both laborious and tricky.”

The CEMA technology uses a simple strategy of stacking “plates” of individual tissue, and bonding them with glue. The multiple stacks are then transversely cut and bonded edge-to-edge to assemble the high density arrays or matrices. These arrays, which are then also thinly sliced for analysis, can hold more than 10,000 tissue samples, the researchers say.

“Just like cars used to be built on a heavy frame but are now assembled with a self-supporting construction, CEMA arrays do not require a space-wasting scaffold or frame but samples are instead bonded directly to each other,” Rui says.

“The statistical power inherent in the larger sample numbers of CEMA arrays are expected to strengthen the discovery of new diagnostic markers,” LeBaron says. “Such markers will allow more accurate patient diagnosis and predict outcome more effectively, and ultimately tailor treatments to an individual’s disease.”

“In addition to tumor analyses, CEMA arrays will be useful for large scale studies of whether drugs or environmental contaminants have toxic effects on healthy tissues,” says Heidi Crismon, a medical student who assembled the so far largest array of nearly 12,000 individual pieces of liver and kidney tissues for this study.

With CEMA, the investigators have also solved the problem of creating arrays of thin-walled or multilayered tissues such as intestine, skin, and blood vessels which can not be arrayed by existing technologies.