Taking Down “Bad” Genes with RNAi

There are three basic approaches to gene therapy. The most studied strategy thus far is to add a fully functioning gene to replace a broken one. This is the rationale behind the AAV vectors carrying RPE65 in the eye trials, for example. Alternatively, a faulty gene can be edited while it sits in the genome, the process of using zinc finger nucleases.

The third and perhaps most experimental tactic is RNA interference (RNAi), which is typically used to reduce the expression of a gene that’s making a harmful product.

RNAi made waves in 1998, when researchers inserted small, double-stranded pieces of RNA into worm cells. The fragments initiated a process that destroyed matching sequences in the worm’s messenger RNA, preventing them from being translated into protein. A few years later, the process was repeated in human cells. Voilà: a way to silence specific genes.

“That field has totally exploded,” notes Mark Kay of Stanford. Still, the approach is very new and has already hit significant roadblocks. Here’s a sampling of attempts—and failures—of using RNAi in the clinic.


Three years ago, German doctors used a bone marrow transplant to cure HIV in a middle-aged man. The bone marrow produces immune cells that are attacked by HIV. The man also had leukemia, and his doctors had the wherewithal to find a donor who carried a variation of a gene called CCR5. Its protein product prevents the virus from working. After the procedure, the man stopped taking antiretroviral drugs and still has no detectable HIV in his blood.

Now, John Rossi, of the Beckman Research Institute of City of Hope in Duarte, California, and colleagues are trying to replicate this success in other HIV patients by using RNAi to knock down CCR5, a molecular gate that HIV must traverse to get into a cell. Last summer the team reported results of using a lentivirus ex vivo to insert three different RNAi tools into the cells of four HIV patients. These cells were safely and permanently transformed and injected back into patients, but there were not enough of them to reduce the participants’ viral load.

Transthyretin amyloidosis

Massachusetts biotech company Alnylam Pharmaceuticals is working on a slew of RNAi drugs. One of them, for example, treats transthyretin amyloidosis, a rare, progressive disease caused by the build-up of a protein in nerves and organs. In animal models, the drug, dubbed ALN-TTR, blocks production of this protein in the liver. The company plans to release data from a phase 1 human safety trial of the drug this fall.

Despite promising early results on this and other compounds, last year, Pharma giant Novartis pulled out of a five-year partnership with Alnylam. Part of the problem is that RNAi molecules are fragile and are not easily directed to places in the body where they’re most needed. Novartis is not the only drug developer with a change of heart about RNAi. After investing three years and $500 million in RNAi drug development, the pharmaceutical company Roche dropped its RNAi program in 2010.

Age-related macular degeneration

Another cautionary tale comes from Bevasiranib, an RNAi drug for age-related macular degeneration. This condition, a common cause of blindness in older people, stems from an overgrowth of blood vessels in the retina. The drug was thought to work by using RNAi to silence VEGF, a gene that encodes a growth factor. Early trials were encouraging, with many patients showing slightly better vision.

In 2007, biotech company Opko Health launched a phase 3 trial of Bevasiranib—a first for RNAi drugs. But two years later, the company decided to terminate the trial because participants’ vision did not improve significantly.

A mouse study published in Nature in 2008 suggested that rather than selectively suppressing VEGF, Bevasiranib works because it triggers an immune response in the eye, which happens to curb growth of the blood vessels.

-- Virginia Hughes
HHMI Bulletin, August 2011

Return to main article >