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Gene gold turning to dust?

Governments are sinking further billions into genomics and related research but a new study finds no sign of revolution in healthcare.

Controversy over Gene Therapy 'Breakthrough'

A 'precision' gene therapy turns out to have significant off-target effects Dr. Mae-Wan Ho

Collateral damage from 'precision' gene therapy

A gene therapy technique, hailed as 2002's 'breakthrough of the year' in its ability to shut down specifically and precisely any chosen gene, has been found not to be so specific or precise after all. The technique involves RNA interference ("Subverting the genetic text", SiS 24), the ability of a short specific duplex sequence of RNA to target the transcript of gene, thereby shutting it down. Unfortunately, there are "off-target" effects on other genes and proteins.

The technique depends on a perfect match between the siRNA (small interfering RNA) introduced and its complementary sequence in the gene transcript. Only sequences of 19-21 base pairs are generally used, as longer sequences induce nonspecific immune reactions.

However, various mismatches between the siRNA and its target appear to be tolerated, so that other transcripts with similar sequences are also affected.

Peter Linsley, executive director of cancer biology for Rosetta Inpharmatics, a company based in Seattle, Washington, USA, and a subsidiary of drug giant Merck, was using siRNAs to design more targeted drugs. The plan was to use siRNA to shut down a particular gene, and then add a compound that also targets the gene to see if additional genes are affected.

But his team found that the siRNAs were shutting down more genes than just the one intended. "The siRNAs were dirtier than our compounds," Linsley said. They kept finding the same results, and finally concluded that the siRNA could "cross-react" with other genetic targets. They had trouble convincing reviewers to get their results eventually published in Nature Biotechnology in June 2003.

At first skeptical of the findings, the RNA interference community was gradually prodded by Linsley's work to look more carefully at their own findings. "We saw more and more unexplained phenomena," admitted Rene Benards, a cancer geneticist at the Netherlands Cancer Institute in Amsterdam. Similarly, Phillip Zamore, a biochemist at the University of Massachusetts Medical School in Worcester, now believes that the limitation of the technique should have been obvious, and it was "incredibly unreasonable" to have presumed absolute specificity.

Using microarrays to screen for off-target effects, researchers are finding in general that a dozen genes may be affected by a single siRNA; although Linsley has recorded on average at least 40genes affected. But microarrays only show the effect on RNA transcripts, and not on proteins (and microarrays themselves are proving unreliable, see "Biotech wonder tool in disarray", this series). So the off-target effects could be even more extensive.

This is especially understandable in hindsight, as geneticists have discovered numerous species of microRNAs interfering naturally and copiously in gene and protein functions. Putting in siRNAs is rather like throwing a monkey wrench randomly into the incredibly complicated and sophisticated machinery that RNA interference has turned out to be.

Predictably, proponents remain hopeful that such off-target effects may not matter, and could be addressed by further research.

The first clinical trial of siRNA therapy was launched in October 2004 by the Philadelphia company Acuity Pharmaceuticals on macular degeneration, a breakdown of the small area at the back of the eye that's responsible for acuity in vision, which causes blindness. Because the treatment is restricted to the eye, it is hoped that the risk of off-target effects is of less concern. Another candidate for treatment is hepatitis B, where the hope is that the siRNA could disable the virus without causing too much off-target damage.

But it would be irresponsible to proceed in the absence of further research, given the sorry record of gene therapy thus far ("Gene therapy woes", this series).

Article first published 05/04/05


  1. "RNAi shows cracks in its armor", Jennifer Couzin, News Focus, Science 2004, 306, 1124-5.

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