Building better base editors

CRISPR-based gene editing has potential therapeutic benefits but also some technical shortcomings. One set of these gene editing tools, base editors, can rewrite the four individual DNA letters, or bases —  A, C, T or G — which represent key chemical building blocks of DNA, adenine, cytosine, thymine, and guanine.

Now, in two papers published in Nature Biotechnology, researchers the Broad Institute of MIT and Harvard, Harvard University, and the Howard Hughes Medical Institute have invented new CRISPR tools that address some of the challenges of base editors by improving their precision and genome-targeting ability.

Base editors work by homing in on specific areas of DNA and swapping out certain bases for others. After that swap, base editors — like the cytosine base editor that converts C•G to T•A — sometimes perform unwanted, off-target edits. And until now, even the best CRISPR tool — SpCas9 — can only bind to about one in 16 locations along DNA, leaving many genetic mutations out of reach.

In the first paper, the research team designed new cytosine base editors that reduced an elusive type of off-target editing by 10- to 100-fold, making these new variants especially promising for treating human disease. In the second study, the team evolved a new generation of CRISPR-Cas9 proteins capable of targeting a much larger fraction of pathogenic mutations, including one responsible for sickle cell anemia. This mutation was, until now, 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 gene editors into people,” said David Liu, senior author of the two papers. “Minimizing this kind of elusive off-target editing, called Cas9-independent editing, is an important step toward achieving that goal. This type of off-target editing can occur at random locations in the genome. When you run the experiment 10 times, you get 10 different answers. That makes it so challenging to study.”

Liu is the Richard Merkin Professor and director of the Merkin Institute of Transformative Technologies in Healthcare at the Broad Institute, a professor of chemistry and chemical biology at Harvard University, and a Howard Hughes Medical Institute investigator.

Read more at Broad Institute (Caitlin McDermott-Murphy)

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