Short RNAs to the Rescue

Ever since scientists realized, just over a decade ago, that exposing cells to short snippets of RNA could affect the activity of matching genes, they have dreamed if harnessing this RNA interference, or RNAi, to fight diseases. In the past week, two groups have announced progress toward that goal, treating chimpanzees with hepatitis C and mice with lung cancer.

RNAi, which rapidly earned a 2006 Nobel Prize, is just one facet of the many ways in which short RNAs regulate gene activity. Researchers have since found numerous types of naturally occurring short RNA that play important roles in development, stem cells, cancer, and other biological processes. These RNA-based mechanisms could seriously revise the emerging understanding of how cellular processes are controlled.

Over the same period, manipulating genetic activity with short RNAs has become an essential tool in biology labs. Cells process various forms of short RNA, such as short-hairpin RNA (shRNA) and small interfering RNA (siRNA) into RNA-protein complexes that reduce (usually) how much protein is made from a messenger RNA that include a complementary (or nearly complementary) sequence.

This technique gives researchers a quick way to learn about what a particular gene does, at least in culture dishes, sidestepping the laborious creation and breeding of genetically-modified critters. (Or if they do put in the time, they can insert genes that allow them to controllably trigger RNAi to knock down a gene only in particular cells or after it has completed an indispensible task in helping an organism to grow.)

But affecting genetic regulation in patients faces the challenges of "delivery" that are well-known in the pharmaceutical industry: To have a beneficial effect, the short RNA must survive in the body, get inside the right cells in large quantities, and not cause too many other effects in other cells. The New York Academy of Sciences has a regular series on the challenges of using RNA for treatment, and I covered one very interesting meeting in 2008.

Molecular survival is the first challenge. Researchers have developed various chemical modifications that help RNA (or a lookalikes) withstand assaults by enzymes that degrade rogue nucleic acids. Santaris, for example, which helped in the hepatitis project, has developed proprietary modifications it calls "locked nucleic acids," or LNA. Other researchers and companies are exploring similar techniques.

Getting the protected RNA to the right tissue is another challenge. Foreign chemicals are naturally cycled to the liver for processing, so it's fairly easy to target this organ. For this reason, the hepatitis results don't really prove that the technique is useful for other tissues. The Santaris release also neglects to mention any publication associated with the research.

The mouse lung cancer result appears in Oncogene. The lead Yale researcher, Frank Slack, regularly studies short RNAs in the worm C. elegans, as I described in a recent report from the New York Academy of Sciences. In this work, he teamed with Mirna Therapeutics, which aims to use the short-RNA-delivery vehicle to replace naturally occurring microRNA that are depleted in cancer, like the let-7 they used for this study. The mouse cancers did not disappear, but they regressed to about a third of their previous size, according to the release. Mirna says that since they are replacing natural microRNAs, their technique shouldn't induce many side effects in other tissues.

A further risk for small-RNA delivery is immune responses. The field of gene therapy is only now recovering from the 1998 death of Jesse Gelsinger in what looks like a massive immune response to the virus used to insert new genes in his cells. Although the short-RNA response will be different, some cellular systems are primed to respond to the foreign nucleic acids brought in by viruses.

It's likely that there will be many twists and turns along the way, and I haven't solicited expert opinions on these studies, but they seem to be intriguing steps toward the goal of using RNA not just to study biology, but to change people's lives.