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At the Bench: Tarnished Treasures?
A method currently used by thousands of laboratories across the country to preserve tissue could render samples useless over time for a common test to assess gene activity, according to a new study by Johns Hopkins researchers.
For more than a century, biomedical scientists have been preserving some tissue samples harvested from patients and research animals in the same way: by soaking these tissues in the preservative formalin and then embedding them in blocks of a wax called paraffin. Perhaps more than 1 billion of these blocks containing formalin-fixed paraffin-embedded (FFPE) tissues are thought to be housed in labs around the world.
“We have a warehouse of these blocks at Johns Hopkins that go back to at least the 1918 flu pandemic,” says Angelo De Marzo, professor of pathology. The gold standard has been to leave these FFPE blocks at room temperature. Then, when laboratories are ready to use the samples, they cut thin slices of the embedded tissue and place them on slides to stain for the presence of various molecules.
One test that’s become increasingly useful is RNA in situ hybridization (RISH), which assesses the activity of particular genes. Those findings might be able to tell doctors or researchers whether certain viruses are present in tissue, or how a patient’s cells responded to particular therapies, for example.
Several years ago, De Marzo, who studies prostate cancer, and his colleagues noticed that prostate tissue samples that should have roughly the same amount of activity in specific genes had wide variations in those genes’ RISH signals. “It occurred to us that the blocks stored for longer might be producing less signal because their RNA was degrading,” he says.
To test the theory, he and his colleagues embarked on a series of tests, which ultimately suggested that storing tissues at room temperature could weaken RISH signals over time, potentially leading to misleading results: low or no activity of targeted genes in older tissue samples even though activity of those genes was high at harvest.
“There’s no reason to think that this isn’t happening around the world with the millions of tissue samples that are harvested every year,” says De Marzo. “These blocks are thought to be a treasure trove of data, but with every year that goes by, they might lose their effectiveness for this technique.”
In contrast, the team found that fresh tissues that were flash-frozen and stored in freezers showed significantly higher levels of RISH signals compared with those stored at room temperature.
Although freezing does appear to preserve function for RISH, De Marzo adds, the long-term answer won’t be to freeze every tissue sample—there isn’t room or other resources to house these numerous tissue samples. Thus, he says, researchers may want to start freezing select samples they predict to be especially useful rather than storing them at room temperature.
The team members published their findings in the American Journal of Clinical Pathology.