New Version of CRISPR Can Treat RNA-based Diseases Like ALS and Huntington’s


New research from the University of California San Diego has expanded the possible uses of the CRISPR/Cas9 gene editing tool.

Previously, CRISPR/Cas9 was only able to make edits in DNA. In a paper published yesterday in the journal Cell, the researchers report on a modified version of CRISPR/Cas9 that is able to track RNA in live cells in a method called RNA-targeting Cas9.

They also report on a new step that allows their RNA-targeting Cas9 to correct molecular mistakes that lead to microsatellite repeat expansion diseases, which include myotonic dystrophy types 1 and 2, the most common form of hereditary ALS, and Huntington’s disease.

 “This is exciting because we’re not only targeting the root cause of diseases for which there are no current therapies to delay progression, but we’ve re-engineered the CRISPR-Cas9 system in a way that’s feasible to deliver it to specific tissues via a viral vector,” said senior author Gene Yeo, PhD, professor of cellular and molecular medicine at UC San Diego School of Medicine.
Muscle cells from a patient with myotonic dystrophy
Muscle cells from a patient with myotonic dystrophy type I, untreated (left) and treated with the RNA-targeting Cas9 system (right). Credit: UC San Diego Health

Microsatellite repeat expansion diseases are caused by errors in RNA sequences that prevent production of crucial proteins making them toxic to the cell. These errors in the RNA accumulate in the nucleus or cytoplasm of cells.

The researchers used RNA-targeting Cas9 to remove RNA errors associated with ALS, and Huntington’s disease in patient-derived cells. The researchers found that their RNA-targeting Cas9 was able to remove 95%+ the accumulated RNA linked to one type of ALS and Huntington’s disease. The approach also eliminated 95% of the RNA errors in myotonic dystrophy patient cells cultured in the laboratory.

Prof. Gene Yeo discussing previous work on reprogramming Cas9 to target RNA:

Another measure of success centered on MBNL1, a protein that normally binds RNA, but is sequestered away from hundreds of its natural RNA targets by the RNA foci in myotonic dystrophy type 1. When the researchers applied RNA-targeting Cas9, they reversed 93 percent of these dysfunctional RNA targets in patient muscle cells, and the cells ultimately resembled healthy control cells.

“The main thing we don’t know yet is whether or not the viral vectors that deliver RCas9 to cells would illicit an immune response,” Prof. Yeo said. “Before this could be tested in humans, we would need to test it in animal models, determine potential toxicities and evaluate long-term exposure.”

Prof. Yeo and his team have formed a startup company called Locana to do the animal testing for their RNA-targeting Cas9 tool and hopefully move into clinical trials to treat  RNA-based diseases.

“We are really excited about this work because we not only defined a new potential therapeutic mechanism for CRISPR-Cas9, we demonstrated how it could be used to treat an entire class of conditions for which there are no successful treatment options,” said David Nelles, PhD, co-first author of the study with Ranjan Batra, PhD, both postdoctoral researchers in Yeo’s lab.

“There are more than 20 genetic diseases caused by microsatellite expansions in different places in the genome,” Batra said. “Our ability to program the RCas9 system to target different repeats, combined with low risk of off-target effects, is its major strength.