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Superior technique identified that can block CRISPR gene editing

A team led by Stanford ChEM-H Institute Scholar Stanley Qi have identified a potent tool for protecting cells from CRISPR-mediated gene editing.

BY HANAE ARMITAGE

The gene-editing technique CRISPR-Cas9, though less than a decade old, is nearly a household term. Today, it can swap, silence and activate the DNA of plants, animals and even humans.

But for every offense there is a defense, and in recent years a handful of scientists have started researching "anti-CRISPR" approaches, which protect DNA from CRISPR-induced edits.

The CRISPR system is derived from bacteria's natural defense system; the tiny microbes wield a DNA-cutting molecule (Cas9) against viral invaders, or bacteriophages, slicing them into dysfunctional bits. "But bacteriophages have evolved their own defenses," said Stanley Qi, PhD, assistant professor of bioengineering.

Some of those defenses take the form of an anti-CRISPR, of which there are several different types. While there’s been some work to elucidate how anti-CRISPRs inhibit CRISPR’s trademark gene-editing, there’s still more to understand. It's thought that most of them work by binding to the part of Cas9 (the scissors) that typically attaches to DNA, thereby blocking its ability to latch.

And, anti-CRISPRs are not all equal, Qi told me. Recently, his team set out to see which were most potent in blocking CRISPR in yeast and human cells.

In a new paper published in Nature Communications, Qi and colleagues have explored the function of several varieties of "Acrs" (or anti-CRISPRs) that can imbue a cell with resistance. Muneaki Nakamura, PhD, postdoctoral researcher in Qi's lab, is the first author of the paper.

"We tested the efficiency of a panel of Acrs and found that there's one in particular that conveys the most protection — AcrIIA4," said Qi. By administering AcrIIA4 before any CRISPR editing, the scientists saw that AcrIIA4 could not only protect against gene editing, it could protect genes from CRISPR activation or silencing, in which genes are turned off or on entirely.

Qi and Nakamura also demonstrated that this Acr can create "gene circuits" to program, or set, the silencing and re-activation of specific genes to occur at a certain time, which could be used to alter the timing of certain activities in a cell.

So far, Qi’s team has shown that AcrIIA4 can protect both yeast and human cells from edits, a trait that he thinks could one day be developed to help guide and in some cases, rein in, CRISPR-based therapies. While anti-CRISPR research has yet to break the confines of a dish, Nakamura and Qi are excited about its applications in the future.

Some researchers see anti-CRISPR as a way to keep CRISPR-Cas9 editing more targeted, as CRISPR-Cas9 can produce unforeseen "side edits." Others think of anti-CRISPR as a protection mechanism, which, when used to its full potential can render an entire cell or potentially even an organism impervious to CRISPR-Cas9.

Nakamura said that he could see anti-CRISPRs refining gene drives, which consist of genetic edits made in sexually reproducing species that alter the genome for multiple generations. It’s possible, he speculates, that some populations could be rendered un-editable as a safeguard against changing an entire species. Such populations, he said, would theoretically only be introduced if the gene drive needed to be stopped or reversed.

But while applying brakes to CRISPR is thought-provoking, Qi and Nakamura caution that the science of anti-CRISPRs still requires major development and is at an early stage — especially in a living organism, although that is something they plan to pursue.

"I'm hoping that anti-CRISPR technology can be part of a solution that balances and refines the power of gene editing," Qi said.