Not too long ago, CRISPR was a cryptic acronym — or, to some ears, a drawer to keep lettuce fresh. Today, CRISPR Cas9, the most popular form of the powerful gene-editing technology, is widely used to accelerate experiments, grow pesticide-resistant crops, and design drugs to treat life-threatening genetic diseases like sickle cell anemia.
But CRISPR is not perfect. Base editors (think of them as gene-editing pencils) can rewrite individual DNA letters. They home in on specific areas of DNA and swap out certain bases — A, C, T, or G — for others. But after the swap, base editors—like the cytosine base editor that converts C•G to T•A — perform unwanted off-target edits. Until now, even the best CRISPR tool, SpCas9, could only bind to about one in 16 locations along DNA, leaving many genetic mutations out of reach.
Now, in two papers published in Nature Biotechnology, researchers at Harvard University, the Broad Institute, and the Howard Hughes Medical Institute have invented new CRISPR tools that address both issues. The first paper describes newly designed cytosine base editors that reduce an elusive type of off-target editing by 10- to 100-fold, making new variants that are especially promising for treating human disease. The second describes a new generation of all-star CRISPR-Cas9 proteins the team evolved that are capable of targeting a much larger fraction of pathogenic mutations, including the one responsible for sickle cell anemia, which was prohibitively difficult to access with previous CRISPR methods.
“Since the era of human genome editing is in its fragile beginnings, it’s important that we do everything we can to minimize the risk of any adverse effects when we start to introduce these into people,” said David Liu, the lead author on the papers. “Minimizing this kind of elusive off-target editing is an important step toward achieving that goal.”
Reduced off-target editing
Liu, Richard Merkin Professor, vice chair of the faculty, and director of the Merkin Institute of Transformative Technologies in Healthcare at the Broad Institute of MIT and Harvard, set out with his team to pinpoint those troubling and erratic CRISPR-independent off-target edits.
“That type of off-target editing can occur at random locations in the genome,” said Liu. “When you run the experiment 10 times, you get 10 different answers. That makes it so challenging to study.”