A gene therapy ‘breakthrough’ in precision turns out to have many off-target effects and killed more than 150 mice. Time for gene therapist to take a system’s view of genetics and biology before proceeding. Dr. Mae-Wan Ho
A gene therapy ‘breakthrough’ in precision touted by medical researchers for treating HIV, cancer, neuro-degenerative diseases, hepatitis, and more, was found to have many off-target effects in 2005  (Controversy over gene therapy ‘breakthrough’, SiS 26), raising considerable concerns over safety.
The technique is based on RNA interference (RNAi), using short stretches of RNA to target genes, in theory, in a sequence-specific manner and silence them. Unfortunately, many other genes and proteins were affected, the precision was illusory. Undaunted, proponents carried on, hoping that the off-target effects would be addressed by further research.
Then in May 2006, the nightmare unfolded. RNAi gene therapy ended up killing mice by the dozens [2, 3]. The finding came from the laboratory of gene therapist Mark Kay of Stanford University California, USA, whose research team reported 3 years ago that RNAi inhibited the hepatitis B virus in mouse livers.
The team has administered a refined version of the RNAi treatment to infected mice, using short hairpin RNA (shRNA), a precursor to the microRNA (miRNA) species  (Subverting the genetic text, SiS 24) previously used. For the first couple of days, everything was as expected. But within a week or two, the mice began to fall ill, their skin turning yellow from liver damage. More than 150 animals died, and many others suffered liver toxicity. Kay and postdoctoral fellow Dirk Grimm, while taken aback by the toxicity of the treatment, said they and others still had confidence in RNAi. “I really think it can still work,” said Kay.
It has better work, because companies have been testing RNAi on people for treating a respiratory virus and macular degeneration since October 2004.
“There’s something that we don’t understand going on here”, said Timothy Nilsen, head of the Center for RNA Molecular Biology at Case Western Reserve University Cleveland, Ohio, USA
Kay’s team packaged genes encoding the shRNA molecules into viruses stripped of other genetic material, and injected the viruses into the mice. The viruses then infected the cells and kept producing the shRNAs, thus making a single dose go much further. The virus used was an adeno-associated virus (AAV) that homes in on the liver, and sure enough 90 percent of the virus-delivered genes ended up there.
Is the virus to blame? Apparently not, there were no problems injecting ‘empty’ virus without the RNA genes.
Was it the shRNA? Kay’s team created dozens of viruses making other RNA sequences and injected those into mice without hepatitis B. Out of all 49 sequences, 36 were severely toxic; 23 were lethal in every case, killing the animals within two months. So the effect had nothing to do with any specific gene targeted by the shRNA.
Was it an overdose of small RNA? Kay’s team found that death was associated with low levels of the mice liver’s own miRNA, which are necessary to the liver’s function, indicating that perhaps the shRNA injected was competing for processing or transport of the small RNAs. The mice were dying from liver failure possibly from an overload of shRNA in their livers. The team had apparently safely inhibited the hepatitis B in mice by injecting an AAV that made less RNA.
John Rossi of City of Hope in Duarte California, who is working on RNAi therapy for HIV, said the results were “not surprising in retrospect”. Too many extra RNA molecules may disrupt the cells’ own RNAi machinery. Kay’s group suggested that the extra small RNA compete for a protein, exportin-5, that transports the cell’s own small RNAs out of the nucleus.
Despite these setbacks and warnings, a company called Sirna Therapeutics in San Franscisco California is still planning to test a nonviral RNAi strategy on people with hepatitis C next year. Sirna’s chief scientific officer Barry Polisky said that the company “has spent a hell of a lot of time and effort” putting small RNAs into animals and nonhuman primates looking for toxicity and haven’t seen anything like what Kay’s team has found.
But Nilsen for one is not convinced. “I think it is premature to say anything is safer at this point”, he said.
People in the field understood that this wasn’t any kind of show-stopper – if anything it offered further information to move things forward,” Kay said .
The only reason to cling to the belief that current RNAi therapy in humans is safe is that Kay’s group has used shRNA rather than miRNA, which is downstream of shRNA. But if shRNA competes for limiting amounts of a protein exporting the small RNA out of the nucleus, then it would happen whether miRNA or shRNA is used.
In my opinion, RNAi gene therapy is unsafe on the whole because the effects are not, and cannot be specific, even more so than conventional DNA gene therapy  (Gene therapy woes, SiS 26). Numerous RNA species interfere at every level of gene function  (Subverting the genetic text, SiS 24), and it is impossible to target the effects precisely because the RNA interference underworld is huge, comprising some 97 to 98 percent of the transcription activity in the cell, and the specificity depends on low levels of the correct sequences being produced at the right time in the appropriate places in a dynamic molecular consensus, ‘a dance of life’ that’s the essence of the fluid genome  (Living with the Fluid Genome).
Gene therapist should really take an appropriately holistic and systems view of genetics and biology before they create more diseases than they cure.
Article first published 12/07/06
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