CRISPR screen identifies Zika-fighting gene

UT Southwestern researchers used CRISPR screening to identify a gene that helps cells resist viruses like Zika, which is spread by mosquitoes. (auimeesri/iStock/Getty Images Plus/Getty Images)

The gene editing system CRISPR is being widely adopted as a tool for genome-scale screening. Now researchers at the University of Texas Southwestern Medical Center are reporting that they successfully used CRISPR to pinpoint a gene that helps human cells resist infection from flaviviruses like Zika.

They did it by knocking out every gene in the genome one at a time and then examining how cells respond to flavivirus infection. The gene IFI6 gene emerged as a potent inhibitor, the team reported in the journal Nature Microbiology.

The scientists' approach centered around a cytokine called interferon, which plays an important role in cells’ response against pathogens. These proteins are released once a virus has been detected, setting off an alarm to other cells so that they can prepare a defense by inducing the transcription of interferon-stimulated genes.

“In the CRISPR screen, we used human liver cells and knocked out every gene in the genome—about 19,000 genes—one at a time. We then stimulated the cells with interferon, knowing that this stimulation would normally allow the cells to resist viral infection," explained John Schoggins, assistant professor of microbiology and leader of the team, in a release. "For the cells that did not resist infection—because they were missing a gene due to the CRISPR knockout—we used next-generation sequencing to figure out the identity of the relevant genes.”

Cells with the IFI6 gene showed robust inhibition of yellow fever, dengue, Zika and West Nile viruses, said Schoggins, while the IFI6-knockout lines were notably susceptible to infections.

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Because flaviviruses can cause serious symptoms—Zika, for example, has been linked to neurological defects in infants—scientists have been looking for different ways to tackle them. Researchers at Albert Einstein College of Medicine and Pennsylvania State University recently found the RSAD2 gene could naturally create a compound that’s effective against Zika. According to researchers at the Washington University School of Medicine in St. Louis, the widely known malaria drug hydroxychloroquine can block the transmission of Zika to the fetus because it suppresses a waste-management process in cells called autophagy.

Previous studies used CRISPR screening to identify genes that give rise to flavivirus infection, and a Broad Institute-led team has also created a sensitive Zika diagnostic based on the gene-editing technology.

The UT Southwestern researchers hope their study can also serve as a foundation for developing therapies against flavivirus. That said, additional studies would need to be done to show whether CRISPR screens in other cell types would yield the same result. For instance, studying neurons would be helpful for unlocking clues to Zika, but the team will have to figure out how to get around logistical challenges that CRISPR screening in brain cells presents, he said.