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Gene-editing tool CRISPR can now manipulate more types of genetic material

Gene-editing tool CRISPR can now manipulate more types of genetic material


‘It’s another tool in the toolbox’

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CRISPR has generally been engineered to edit DNA (shown here), but a new version targets RNA.
CRISPR has generally been engineered to edit DNA (shown here), but a new version targets RNA.
Illustration: James Bareham / The Verge

The powerful gene-editing tool CRISPR has been making headlines for its ability to edit DNA, which could one day transform how we fight cancer and other life-threatening diseases. Now, scientists have created a new version of CRISPR that can target and edit a different genetic building block: RNA.

The new tool, described in a study published today in Science, offers several advantages: its edits, for instance, aren’t permanent, which makes gene editing much safer. Researchers showed that the new system, called REPAIR, can work relatively efficiently in human cells. In the future, it could be used to treat diseases, as well as better understand the role that RNA plays in causing those diseases.

“It’s another tool in the toolbox.”

“It’s another tool in the toolbox that we didn’t have access to before,” says Mitchell O'Connell, assistant professor in the Department of Biochemistry and Biophysics at the University of Rochester, who was not involved in the research. “It’s like developing new technology that makes you see things that you couldn't see before, or tweak things that you couldn't tweak.”

The gene-editing tool CRISPR is based on a defense mechanism bacteria use to ward off viruses by cutting off bits of their DNA and pasting them elsewhere. Scientists have engineered that mechanism to tweak DNA, creating unusually muscular beagles, for instance, and mosquitoes that don’t transmit malaria. But there are different types of CRISPR, with different types of molecular scissors. The gene-editing tool that’s been making lots of headlines is called CRISPR-Cas9. The CRISPR used in today’s study is called CRISPR-Cas13.

Instead of snipping DNA, this type of CRISPR targets another of the major biological molecules found in all forms of life, RNA. Most of the time, RNA is used inside the body to help DNA build proteins. And proteins play an important role in causing diseases. There are some advantages to editing RNA instead of DNA, says study co-author David Cox, a PhD student in the Zhang Lab at the Broad Institute of MIT and Harvard, which has been doing pioneering work on CRISPR. RNA is constantly being made and recycled inside cells, so an RNA edit is not permanent. (The edits could still be effective, though: the CRISPR system could be kept in cells for, say, months, allowing the scissors to keep editing RNA as it forms.) That makes the whole process safer. If you edit RNA and make a mistake, for instance, the faulty RNA will be degraded likely within 24 hours. Instead, if you edit DNA and make a mistake, that mistake is irreversible and could possible lead to cancer. Certain changes to DNA could also be passed on to future generations, while changes to RNA generally aren’t passed on.

“there are still big risks involved.”

Gene editing “is very exciting, but there are still big risks involved,” O'Connell tells The Verge. Targeting RNA rather than DNA is “a safer strategy, particularly for things where you might not want to make permanent change.”

To create the new editing tool, called REPAIR, the researchers combined CRISPR-Cas13 with a protein called ADAR. It works this way: the Cas13 enzyme is programmed to target a specific RNA sequence that might correspond to a disease mutation; the ADAR protein then makes the edit. In the study, the researchers showed that the system can edit specific RNA bases with 20 to 40 percent efficiency — and up to 90 percent in some instances, says Cox. And the system made few mistakes: even though gene-editing tools are very precise, sometimes they snip pieces of genetic code they weren’t programmed to cut. These off-target cuts can be dangerous, and scientists want to make sure there are as few of them as possible.

A first version of REPAIR caused nearly 20,000 off-target cuts, says study co-author Omar Abudayyeh, also a PhD student in the Zhang Lab. “That was a pretty disappointing moment,” he tells The Verge. But then, the team tweaked the system in a way that reduced the number of off-target cuts to 10 to 20 per target site, making it much more precise — and safe.

O'Connell says he was surprised by how well the system works. RNA has been targeted before in an effort to make drugs to treat disease, O'Connell says. But this CRISPR system makes the whole editing process much easier. In the future, this editing tool could be used to treat life-threatening diseases like hemophilia, as well as a heart condition called hypertrophic cardiomyopathy, which can lead to sudden death, Cox tells The Verge. Before that happens, the system needs to be optimized, and made much more precise. Researchers also need to show that it works in mice, other animals, and eventually in people. “It’s a long road to translate this into any sort of therapy,” says study co-author Jonathan Gootenberg, another PhD student in the Zhang Lab.

“You feel so empowered where you’re in the lab.”

Together with CRISPR-Cas9, this system really has the potential to revolutionize how we treat diseases. And that’s the motivation that keeps Gootenberg, Cox, and Abudayyeh working hard in their lab. Abudayyeh says that when he was in med school, he met a woman with terminal lung cancer, who had maybe a few more months to live. “You feel pretty hopeless in that situation because there’s nothing you can do even as a doctor,” he says. But that’s also what inspired him to get into biotechnology.

“You feel so empowered where you’re in the lab, just thinking about new ways to make new technologies with the potential to hopefully actually help patients like that,” Abudayyeh says. “It’s really exciting.”