Worms feed gene function analysis using RNAi

BOSTON (04/07/02)—High-throughput studies of gene inhibition in a popular worm model are being served up on a commercial platform by Devgen, a Belgian biotech company.

Gene expression inhibition has become a popular tool for drug developers eager to evaluate the overabundance of new genomics-generated targets. A variety of conventional tools, including antisense inhibitors, ribozymes, and DNA-binding proteins, can be used to inhibit gene activity, shedding light on gene function that can then be used to home in on the best targets for new drugs.

RNA inhibition, or RNAi, uses fragments of double-stranded RNA (dsRNA) to degrade messenger RNA (mRNA), the chemical replica of the genetic code that is read by the cellular machinery to make proteins. The 2-millimeter long, soil-dwelling nematode worm Caenorhabditis elegans, a popular animal model in genetics and developmental biology, easily absorbs RNAi molecules either by soaking in a dsRNA-containing solution, or by eating dsRNA-loaded bacteria.

Devgen has created a library of Escherichia coli bacteria, in which each microbe contains a specific dsRNA fragment targeting one of the worm's 19,000 or so genes. By exploiting the worm's appetite, researchers can generate a virtual sea of C. elegans, each animal having a specific gene down-regulated. The company plans to use the technology internally and in collaborations.

"We are still learning the rules for generating the right dsRNAs to get optimal results from RNAi," says Elisabetta Ullu, a professor at Yale Medical School, who studies RNAi in an even more primitive organism — the trypanosome. "It will never be the equivalent of a knockout mouse in terms of level of inhibition. But the effect is exquisitely specific, and you can get as much as 90 to 95 percent degradation of the targeted mRNA."

RNAi has been well-studied in several systems. In C. elegans (and reportedly the fruit fly), the effect is heritable. The use of RNAi in mammalian systems was only worked out within the past year, and it is still unclear if it will work in a whole mammal. But the technique appears to have important advantages. "I have not heard anyone report failure to down-regulate when using RNAi," says Ullu, who credits the success of RNAi partly to the fact that it exploits native cellular machinery. The technique also is relatively simple and inexpensive.

Whether RNAi proves a more commercially popular tool than more established methods for modulating gene function, such as antisense, remains to be seen. "I don't think one approach will rule," says Nicholas Dean, vice president of functional genomics at ISIS Pharmaceuticals' Gene Trove division. "In some instances one technique is better than another, but in other cases they are complementary."

Antisense can be used in live mammals, and a goal of Gene Trove is to produce a library of antisense inhibitors for about 2,000 genes by the end of this year, and for 10,000 genes within three years. The resulting assays will be useful for studying cancer, diabetes, inflammation, and angiogenesis. "It's a high throughput way of doing gene function studies," Dean says.

With huge stashes of putative drug targets still on hand, the use of such libraries is bound to increase. "The screening approaches that are going to be implemented," says Ullu, "are as important as the high throughput methods themselves."