Tracking down HIV propagation

Source: Harvard Medical School

Using RNA interference (RNAi) to screen thousands of genes, researchers from Harvard Medical School have identified 273 human proteins required for HIV propagation. The vast majority had not been connected to the virus by previous studies.

The work appeared online in Science Express on January 10.

Current drugs attack HIV itself, leaving patients vulnerable to counterattack by the rapidly mutating virus, which often evolves resistance.

HIV contains just nine genes encoding 15 proteins, which wreak havoc on the human immune system. Lacking robust machinery, HIV hijacks human proteins to propagate, and these might represent powerful therapeutic targets.

"Antiviral drugs are currently doing a good job of keeping people alive, but these therapeutics all suffer from the same problem, which is that you can get resistance, so we decided to take a different approach centred on the human proteins exploited by the virus," senior author Professor Stephen Elledge said. "The virus would not be able to mutate to overcome drugs that interact with these proteins."

Over the last two decades, researchers around the world have identified dozens of human proteins, or host factors, required for HIV propagation. The new study builds on this work, essentially quadrupling the list of host factors to include proteins involved with a surprising array of cellular functions ranging from protein trafficking to a type of programmed cell death called autophagy.

"The expanded list is a hypothesis generation machine," Elledge said. "Scientists can look at the list, predict why HIV needs a particular protein, and then test their hypothesis."

To create the list, postdoctoral researcher and first author Abraham Brass, working with Derek Dyxkhoorn and Nan Yan, began with a library of short interfering RNAs (siRNAs) targeting specific human genes. Each siRNA disrupts the gene's ability to produce a particular protein.

Brass placed the siRNAs on thousands of human cells, with just one gene being targeted in each well of cells. Thus each well contained cells lacking a particular protein.

Next, he unleashed HIV on the cells. If HIV replication was inhibited in a given well, it suggested the missing protein was involved.

Of the 273 proteins he identified, just 36 had been previously implicated in the HIV life cycle. He picked three of the other 237 proteins, and subjected them to a host of careful genetic experiments, proving they too truly play a role in HIV propagation.

Immune cells-the very cells HIV attacks-contain high concentrations of many of the 273 host factors, offering further proof of the list's validity.

"This is the first whole genome screen for human proteins required by HIV, and we're confident that it netted real results," Brass said. "Given the method, we missed some proteins, but the majority of the ones we found are highly likely to play a role in HIV propagation."

"Identification of host proteins required for HIV infection through a functional genomic screen" is scheduled for print publication in the February 8 issue of Science.