The new bacterial enzyme has the ability to cut and modify RNA with the exquisite precision that has only been possible so far for DNA editing.
Just when we thought the world of CRISPR gene editing couldn’t get any hotter, two biologists at MIT’s McGovern Institute have announced the discovery of a new CRISPR protein called Cas7-11, and it could make a world of difference for patients with diseases like Huntington’s and muscular dystrophy that are caused by spelling errors in RNA.
The new bacterial enzyme, which McGovern fellows Omar Abudayyeh and Jonathan Gootenberg describe in a newly published Nature article, has the ability to cut and modify RNA with the exquisite precision that has only been possible so far for DNA editing.
Abudayyeh expressed confidence in the protein akin to the discovery of the printing press.
“This new enzyme is like the Cas9 of RNA,” he stated. “It creates two precise cuts and doesn’t destroy the cell in the process like other enzymes.”
Abudayyeh and Gootenberg, friends and colleagues since their time in Feng Zhang’s lab at MIT and co-founders of Sherlock Biosciences, originally discovered the Cas13 enzyme, which has been developed for RNA targeting applications. But Cas13 had a problem—when it recognizes its target, it goes crazy, shredding any RNA in the cell and the cell along with it.
The discovery of Cas7-11 is the result of an intensive exploration of the CRISPR systems found in the vast microbial ecosphere. All CRISPR proteins, at least the ones discovered so far, including Cas7-11, are used by bacteria as a defense against viruses. The protein stores a memory of the pathogen in its genetic material, and guided by a small piece of RNA, it targets and destroys the infection. As such, they are a natural breeding ground for potential therapeutic tools, and not only for viruses.
“Some target DNA, some target RNA. Some are very efficient in cleaving the target but have some toxicity, and others do not. They introduce different types of cuts, they can differ in specificity—and so on,” said Eugene Koonin, an evolutionary biologist and senior investigator at the National Center for Biotechnology Information (NCBI).
While most CRISPR proteins work within a system to cleave their targets, Abudayyeh, Gootenberg and Koonin identified one that had the capacity to operate on its own, meaning that it had a lot of advantages from an engineering perspective. They named it Cas7-11.
The authors explained that, through the process of evolution, the components of a more complex Cas machine had fused together to make the Cas7-11 protein.
Gootenberg hinted that this discovery could have even broader implications.
“It totally changes the landscape of how these systems are thought about, both functionally and evolutionarily,” he said.
With an inkling of the enzyme’s therapeutic potential, Gootenberg and Abudayyeh began experimenting and discovered that, when introducing it into cells partnered with an RNA guide, Cas7-11 made precise cuts and, importantly, left other RNA alone. They concluded that it had the capacity to edit letters in the RNA code and the flexibility to either stabilize or destroy specific RNA molecules, allowing them to adjust protein levels.
This could potentially allow scientists to turn down the level of a protein that is causing harm due to genetic diseases like Huntington’s, which occurs due to a single sequence of RNA stuck on repeat that causes irreparable damage to neurons.
“It’s yet another great example of how these basic-biology-driven explorations can yield new tools for therapeutics and diagnostics,” Gootenberg said. “We’re certainly still just scratching the surface of what’s out there in natural diversity.”
Introducing CasMINI
Elsewhere in the CRISPR universe, scientists at Stanford University have engineered what they are calling CasMINI. While CRISPR systems Cas9 and Cas12a use 1000 and 1,500 amino acids respectively, CasMINI has only 529 amino acids.
The researchers hope the discovery will make it easier to deliver into cells and drive high levels of gene activation.
“The work presents the smallest CRISPR to date, according to our knowledge, as a genome-editing technology. If people sometimes think of Cas9 as molecular scissors, here we created a Swiss knife containing multiple functions. It is not a big one, but a miniature one that is highly portable for easy use,” said senior study author Stanley Qi, Ph.D., an assistant professor of chemical and systems biology in the Stanford School of Medicine.
In a paper published Friday in Molecular Cell, researchers confirmed that the miniature system demonstrated the ability to delete, activate, and edit target gene sequences just like the originals. They hypothesize that CasMINI could overcome some critical challenges and take CRISPR to the next level.
“The large size of CRISPR-Cas effectors and their fusion proteins has posed a challenge for efficient cell engineering and in vivo delivery,” the investigators stated. “There is a great need to engineer highly efficient, compact Cas systems to facilitate the next generation of genome engineering applications.”
