Researchers use novel technology to extract RNA from archive formalin-fixed paraffin-embedded tissue

High quality outcomes allow researchers to identify cancer-related genetic changes that span years

For the first time, Fox Chase Cancer Center researchers have demonstrated the ability to extract RNA from formalin-fixed, paraffin-embedded tissue samples archived for up to five years. What’s more, the technology used retrieves high-quality samples, allowing researchers to identify cancer-related genetic changes. Accepted as a “late-breaking” abstract, the research was presented today at the 95th Annual Meeting of the American Association for Cancer Research by Renata Coudry, M.D., a research pathologist at Fox Chase Cancer Center.

“Recent advances in both laser-capture microdissection (LCM) technology and microarray technology have revolutionized our investigation of the genetic basis of human cancer,” said Coudry. “Pure cell populations can now be isolated by LCM and evaluated for changes in gene expression that accompany the development of cancer. However, applying these techniques to archived clinical specimens has been limited by our inability to extract high-quality genetic material from routinely processed clinical samples.”

Hospitals are required to store tumor samples from surgical procedures in case further testing is needed. Biopsy tissue and other tissue specimens are universally preserved by being fixed in formalin and embedded in paraffin, a process that was thought to compromise DNA and RNA integrity. Messenger RNA (mRNA) indicates the activity of genes, or gene expression.

The Paradise Reagent System developed by Arcturus Bioscience Inc. provides an integrated system to isolate and amplify mRNA for analyzing global gene expression in archival specimens.

By retrospectively correlating treatment outcomes and genetic profiles, scientists could learn what genes are involved in certain forms of a specific cancer and tailor individual therapy for each patient. “At Fox Chase, we used the technology with great success to compare the gene expression profiles of normal and colorectal tumor tissue that had been archived for up to five years,” Coudry said. “We are already applying this methodology to the identification of new molecular targets that may serve as biomarkers of cancer risk and chemopreventive response.”

The Fox Chase group used laser capture to microdissect colonic crypt tissues from the archived samples. They then developed genetic profiles using microarray, or “gene chip,” technology to evaluate the genetic changes in the tissue. The procedure uses glass “chips” to hold thousands of gene fragments that can be visualized by a computer. Because genes RNA extracted from in a blood or tissue sample will bind to the corresponding gene fragment on the chip, researchers can analyze the expression of thousands of the sample’s genes at once.

As research pathologist, Coudry works in the Fox Chase laboratory of cell biologist Margie L. Clapper, Ph.D., director of chemoprevention research at Fox Chase. In addition to Coudry and Clapper, Fox Chase co-authors of the study include postdoctoral associate Sibele I. Meireles, Ph.D.; bioinformatician Radka Stoyanova, Ph.D.; Harry S. Cooper, M.D., vice chairman of clinical laboratories and chief of surgical pathology and immunohistochemistry; and Paul F. Engstrom, M.D., senior vice president for population science

Fox Chase Cancer Center, one of the nation’s first comprehensive cancer centers designated by the National Cancer Institute in 1974, conducts basic and clinical research; programs of prevention, detection and treatment of cancer; and community outreach. For more information about Fox Chase activities, visit the Center’s web site at www.fccc.edu.