Infectious diseases: “Deleting” diseases from human bodies

One effort being funded under Safe Genes is a $2.5 million, two-year project led by Jennifer Doudna’s laboratory at the University of California, Berkeley, in partnership with Sandia, and the University of California, San Francisco. Doudna is a pioneer in the development of CRISPR. If the early research is fruitful, DARPA could extend this effort for another two years, bringing the total to four years and $5 million.

Viruses are skilled at changing their DNA and generating new anti-CRISPR proteins to block the bacterial immune systems. This is the other side of the bacteria-virus “arms race.” These proteins can function as antidotes, allowing gene editors to be turned off if needed.

The Safe Genes team is taking advantage of these proteins to develop inhibitors that can control off-target effects of CRISPR. Schoeniger said that should a dose of a gene editor need to be administered, it could be followed by a dose of the inhibitor to shut it off, minimizing the amount of time in which off-target effects could take place.

Remaking the cargo
This Safe Genes project builds on work ongoing at Sandia which also is focused on fighting infectious disease using gene editing.

Normally, the CRISPR system targets DNA, but Sandia has been collaborating with Doudna’s team to create a CRISPR system that targets RNA instead. Attacking virus RNA directly is likely to be effective against most pathogens of biosafety concern, said Negrete.

CRISPR systems already exist that target RNA, but these systems result in general RNA degradation. This new RNA-targeting system can affect specific human or animal RNA, including those known to encode proteins that aid viral infection.

“Some proteins are known gateways for invaders,” Negrete explained. “If you knock out these proteins via their coding RNAs, the pathogens can’t get into your cells and you haven’t made any permanent changes to your genome.”

Developing safe CRISPR applications
Sandia notes that for the Safe Genes project, Sandia will test the RNA-targeting CRISPR technology against a variety of viruses. The Sandia team will deliver the CRISPRs to mammalian cells infected with a variety of RNA viruses, including Ebola and Rift Valley Fever Virus, that cause symptoms such as hemorrhagic fever. Then they’ll measure the level of virus remaining in the cells after treatment.

“Ideally, we’d like to see the level of virus reduced to zero. If it isn’t, the CRISPR technology would have to be modified,” Negrete said.

In addition, the UCSF team is developing CRISPR-derived technologies to turn genes on and off without editing DNA. For this application, the team is harnessing CRISPR for targeted DNA methylation. DNA methylation is a non-destructive mechanism of gene expression regulation that occurs naturally throughout the mammalian life cycle.

Negrete believes this work, if successful, would represent a quantum leap forward for virology because the new CRISPR technologies would attack illnesses in multiple ways. Currently, vaccines target single strains of a virus. Sandia’s Safe Genes project is working toward solutions that target all the strains of a virus, as well as finding ways to repair infected host and human cells.

“It’s cumbersome to create new treatments for each and every bug, and not feasible for quickly responding to emerging threats. One treatment for each and every strain that appears, as well as all the related viruses – it’s a much better strategy,” Negrete said. “It’s like the leap from eliminating one letter with a pencil eraser to hitting control-A and deleting an entire paragraph.”