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RNAi Screen Exposes West Nile Virus Players

NEW YORK (GenomeWeb News) – RNA interference is helping scientists ferret out the host genes that help and hinder the West Nile virus as it infiltrates and replicates within human cells.
A team of researchers from Yale University and elsewhere used a genome-wide screen to systematically identify the human genes affecting West Nile virus infections. The findings, appearing online today in Nature, indicate that the West Nile virus relies on hundreds of host proteins to enter and divide in human cells — many of which are also used by the related dengue virus. The findings not only provide a better understanding of these host-virus relationships, but also open the door to potential new antivirals.
West Nile virus belongs to a family of flaviviruses, which also includes tick-borne encephalitis, Japanese encephalitis, yellow fever, and dengue fever. It is usually transmitted to humans by mosquitoes and can have a spectrum of effects — from mild flu-like symptoms to severe conditions, such as brain inflammation or inflammation of tissues surrounding the brain and central nervous system.
The virus was first detected in North America in 1999 when it appeared in New York City. It has since spread across the continental US and into Canada and Mexico. In 2007 alone, the US Centers for Disease Control and Prevention documented more than 3,600 West Nile infections and 124 deaths in the US.
In an attempt to get to the bottom of the specific interactions between West Nile virus and human cells, co-senior author Erol Fikrig, an infectious disease researcher affiliated with Yale University and the Howard Hughes Medical Research Institute, and his colleagues used an RNAi screen to look for mammalian genes and proteins that affect West Nile virus infection.
By silencing 21,121 human genes in HeLa cells the researchers pinpointed 283 host susceptibility factors (which aid infection) and 22 host resistance factors (which discourage infection) for West Nile virus. The majority were previously unknown.
Genes involved in processes such as protein and nucleic acid metabolism, signal transduction, and development frequently showed up in the screen, as did genes with roles in RNA-binding, transcription, transport, and immunity.
The researchers also honed in on pathways that the virus uses to gain entry into cells. For instance, they found that silencing the ubiquitin ligase CBLL1, which participates in cell-surface receptor endocytosis, dramatically decreased the number of infected cells and the number of viruses within those cells that were infected. Similarly, they saw dramatic decreases in infection when they silenced certain genes involved in proteasome function or endoplasmic reticulum-to-proteasome transport.
The researchers also looked at whether the host susceptibility and resistance genes that turned up in the screen influenced West Nile infection in vivo, by looking at their expression in 79 different West Nile-infected tissues. Nearly half of the host susceptibility genes showed increased expression in immune tissue. The expression of almost a third was ramped up in central nervous system tissue.
Intriguingly, many of the same host genes associated with West Nile virus also affected the action of another flavivirus: dengue virus 2. The researchers found overlap between 36 percent of the West Nile and dengue host susceptibility genes. All 22 of the West Nile virus host resistance genes influenced dengue virus infection. In contrast, just five of the 300 or so genes from the West Nile screen affected HIV-2 infection.
That suggests that there may be a common flavivirus pathway, Fikrig told GenomeWeb Daily News, adding that his team is currently using a similar approach to look at how other flaviviruses interact with host cells.
In the future, Fikrig said, he hopes such approaches will provide new insights into the biological mechanism of West Nile and other flaviviruses — and lead to new treatments.
To that end, Fikrig noted that he and his colleagues are trying to pinpoint host pathways that lend themselves to therapeutic interventions. For instance, they plan to look at West Nile virus in mice lacking some of the genes identified in the RNAi screen to determine whether any of the mice exhibit increased resistance to West Nile infection.
“We don’t have a silver bullet yet,” Fikrig said. But, he added, they are hopeful that they will eventually find targets that block flavivirus infection without interfering with essential cellular processes.

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