The gene-editing tool CRISPR is based on a natural defense system embedded in bacterial cells that recognizes and destroys invading viral DNA.
What if we could add that same attack mechanism to our own cells? A biotech startup, Locana, is trying to do just that by inserting the CRISPR machinery into human cells to equip the body to fight Huntington’s disease and amyotrophic lateral sclerosis, also known as Lou Gehrig’s disease.
To do it, Gene Yeo, the company’s cofounder and a professor of cellular and molecular medicine at the University of California, San Diego, School of Medicine, is repurposing CRISPR to go after a different target: RNA, the messenger molecule involved in transferring and decoding the genetic information stored in DNA.
In diseases like ALS, Huntington’s and some types of muscular dystrophy, RNA builds up and makes aberrant proteins that cause disease. Yeo says he’s particularly interested in these diseases because they have no effective therapies and can be fatal. He wants to use CRISPR to destroy toxic RNAs and reverse the devastating effects of disease.
Normally, CRISPR uses a slicing protein called Cas9 that recognizes and chops up the desired DNA, eliminating a mutated gene. Yeo and his team modified Cas9 to leave DNA alone and instead bind to and cut problematic RNA.
In a study published in August, Yeo and his colleagues used CRISPR-Cas9 to destroy errant repeats in RNA sequences. When tested in the lab, Yeo’s CRISPR tool obliterated 95 percent or more of these RNA knots in cells harboring Huntington’s disease and a type of ALS.
The researchers also tested the approach on a form of inherited muscular dystrophy, called myotonic dystrophy. They were able to eliminate 95 percent of faulty RNAs in muscle cells taken from patients. After they applied CRISPR, the once-diseased cells resembled healthy ones. Yeo thinks more than 20 genetic diseases that are caused by toxic RNA repeats could potentially be treated this way.
Knocking down these RNAs is only temporary, though. RNA constantly regenerates, so its level in cells eventually rebounds back to normal after a few days to a week. Yeo says that’s actually a benefit of using CRISPR to target RNA instead of DNA—the effects aren’t lasting.
“With RNA targeting, there’s no permanent, irreversible damage to the genome,” Yeo says.
This will allow scientists to make temporary changes to RNA and test the effects in animals before injecting people with an experimental CRISPR therapy. Yeo and other labs are designing molecules that could shut off this process if something goes wrong.
A therapy with a temporary effect would work better in some cases, such as for conditions that are not life-threatening or infectious diseases that would only require short-term treatment. But to treat ALS or Huntington’s disease over a person’s lifetime, you need something that will last longer than just a few days or a week.
So Yeo is designing a virus capsule to carry the CRISPR machinery to the right cells. These viral delivery shuttles would allow the Cas protein to stick around in a person’s cells longer—ideally for years, turning Cas into a mini-arsenal to keep unruly RNA at bay.
Mitchell O’Connell, an assistant professor of biochemistry and biophysics at the University of Rochester Medical Center, says the approach would probably require repeat treatments over the years. That’s different from using CRISPR for editing DNA, which would be a one-time injection or procedure.
O’Connell and others studying CRISPR to target RNA think this feature might make the approach safer than DNA editing. Using CRISPR to edit genes comes with the risk of off-target mutations—unwanted genetic cuts that could cause serious side effects in patients, like cancer. So far, Yeo says he has seen few off-target effects by pursuing RNA. He thinks that's because RNA is a more specific target.
“This could be ramped up more quickly because it’s not as dangerous,” O’Connell says.
Other researchers are also interested in using CRISPR to go after RNA. Feng Zhang, a researcher at the Broad Institute of MIT and Harvard, this week published a paper in Nature, where he showed that another cutting protein known as Cas13 could be used to detect, slice, and track RNA in human cells. Previously, Zhang’s lab used CRISPR-Cas13 to target RNA in bacterial cells.
In the new study, Zhang and his colleagues used the same CRISPR editing system to reduce RNA levels expressed by three genes associated with cancer.