Mayo Clinic researchers teach RNA to act as decoy inside living cell to prevent disease activation

Discovery points to one possible path to novel drug development for cancer, AIDS, some inflammation

Using a new approach, Mayo Clinic researchers have successfully “taught” an RNA molecule inside a living cell to work as a decoy to divert the actions of the protein NF-kappaB, which scientists believe promotes disease development. The findings are published in the current issue of Proceedings of the National Academy of Sciences.

Although it also plays helpful roles in the body, NF-kappaB (pronounced “en-ef-kappa-bee):

• activates genes that promote cancer-cell survival
• enables the HIV virus to reproduce, contributing to the onset of AIDS
• promotes the inflammation process involved in many chronic diseases, such as rheumatoid arthritis

The good news is that once it is diverted by the RNA decoys, NF-kappaB should no longer be available to play its negative role in the chain of molecular events that leads to disease. Mayo’s experimental findings suggest that this could be a new and effective strategy for developing drugs capable of halting the disease process.

In the paper, L. James Maher, III, Ph.D., and Laura Cassiday, Ph.D., Mayo Clinic Department of Biochemistry and Molecular Biology, describe their success with yeast cells and decoy RNA. Under natural conditions in the body, RNA delivers DNA’s plans to cells, which make all the worker proteins to carry out DNA’s executive orders. Drs. Maher and Cassiday have used the RNA/NF-kappaB pairs to divert the NF-kappaB protein. This diversion ensures that the disease-directing capability of NF-kappaB never reaches the DNA.

“We’re trying to develop a somewhat nontraditional drug that is made out of RNA — which is similar to DNA — because it has some advantages over other drugs,” says Dr. Maher, a molecular biologist. The experiment was performed in his laboratory. “One advantage is that it can be produced by the body’s own cells using a gene-therapy approach in which cells are given the gene for this decoy RNA. But this is a long way off. What’s exciting for us at this point are two discoveries: One is that the small RNAs that we are studying can be taught to do new and exciting things inside living cells. The other is that we have found a new way to use yeast cells as a powerful test system for helping us find the RNAs that are most likely to work in mammalian cells.”

“Theoretically, if we want to stop any of these diseases in which NF-kappaB is known to be involved — cancers, AIDS, some inflammatory diseases — we’d like to stop the action of this protein; that would be a long-term goal,” adds Dr. Cassiday, who is a post-doctoral fellow at Mayo Graduate School. “Our short-term goal is to learn the capabilities of these small, folded RNAs.”

The Experiment: How It Works, Where It Leads

Step 1: Test tube experiments

In Dr. Maher’s lab, researchers used a novel approach to finding the right decoy RNAs. Lori Lebruska, Ph.D., a graduate of Mayo Graduate School, took a random collection of one hundred thousand billion (that’s one followed by 14 zeroes) small RNAs. She then mixed the RNAs with NF-kappaB protein and captured the “smartest” RNAs on a filter. After many repeated capture cycles, the RNAs that stuck best to NF-kappaB were the most likely to be competent decoys.

Step 2: Testing the RNA decoy in a living cell.

Drs. Maher and Cassiday had to see if the decoy RNA could bind NF-kappaB not just in a test tube but in the chaos of a cell.

“It’s a whole different ball game in the cell, because there are thousands of other proteins that the RNA might bind to,” says Dr. Cassiday. “These proteins could distract it from what we want it to do: find and bind to NF-kappaB. We weren’t sure the RNA was specific enough to target NF-kappaB under these conditions. Also, there are all sorts of enzymes that degrade RNA within a cell. We weren’t sure the RNA would be stable enough to survive and do its job. These were all considerations that needed to be resolved in our cellular experiments.”

To test the RNA decoy’s ability to adapt to life inside cells, the researchers chose yeast, which is very similar to human cells, as a model organism.

“The rules change inside the cell,” says Dr. Maher. “The real question becomes how can we send the RNA molecules back to school to adapt to these new cellular rules when all they previously knew how to do was succeed with test-tube rules?”

After simultaneously screening thousands of RNA variations in yeast, Drs. Cassiday and Maher found one RNA that had learned to do it all. Dr. Maher notes that by increasing the amount of this molecule, bigger and bigger decoy effects emerge, allowing for significant inhibition of NF-kappaB’s disease capabilities.

The next step for the Mayo research team is to adapt this RNA decoy to life in mammalian cells to see if it can “learn” the additional rules necessary to survive and foil NF-kappaB in its natural setting. If it does, it might one day be a candidate for a new kind of drug therapy.

Shelly Plutowski
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email: newsbureau@mayo.edu