A research technician works to clone DNA in a lab.
Photo: AP Images

When the gene-editing technology CRISPR first made a splash back in 2012, it foretold a future in which curing diseases might simply involve snipping out problematic bits of genetic code. Of course, innovation is rarely so straightforward. As incredible as CRISPR is, it also has some pretty sizable flaws to overcome before it can live up to its hype as a veritable cure-all for human disease.

A new study published this week in the journal Nature Genetics tackles one CRISPR complication. CRISPR gene-editing systems can easily cut many pieces of DNA at once, but actually editing all those genes is a lot more time-consuming. Now, scientists at UCLA have come up with a way to edit multiple genes at once.

When scientists use CRISPR for genetic engineering, they are really using a system made up of several parts. CRISPR is a tool taken from bacterial immune systems. When a virus invades, the bacterial immune system sends an enzyme like Cas9 to the virus and chops it up. The bacteria then adds short bits of virus DNA to its own code, so it can recognize that virus quickly in the future. If the virus shows up again, a guide RNA will lead the Cas9 enzyme to the matching place in the virus code, where it again chops it up. In CRISPR, when that cutting is done, scientists can also insert a new bit of code or delete code, to, for example, fix disease-causing genetic mutations in the code before patching it up. But delivering that new code and making the patch is where it can get especially tricky.

If you try to do that for a whole bunch of cells at once, Leonid Kruglyak, a senior author on the paper, explained to Gizmodo, “the vast majority of cells will end up with a mismatched guide-patch combo.”

In other words, you’ll wind up with a whole lot of broken genes instead of an edited one.

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To solve the problem and speed up the editing process, scientists at UCLA physically connected thousands of RNA guides to DNA-editing code, ensuring that the right place on the genome gets cut and patched each time.

“We figured out how to physically connect the matched guide/patch pairs, and still keep the sequences short enough so we can make many thousands of them cheaply and efficiently,” he said.

To test the new technique, they grew millions of yeast cells inside a flask of fluid, then used CRISPR to deliver a customized set of paired guides and patches to each cell. They altered the yeast cells to give them genetic mutations suspected to be harmful.

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“What we’re doing is making a large library of cells, in which each cell contains exactly one of a large number of desired edits,” Kruglyak said. “We can then screen this library of cells to see which edits have effects we are interested in.”

The real boon here is for research. In just four days, the scientists were able to observe the impact of 10,000 distinct mutations simultaneously. By identifying which cells died and which survived, they gained insight into which genes were truly essential for cellular function and which weren’t.

“The primary use is basic research, although it’s easy to envision applications in genetic diagnostics,” said Kruglyak.

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Down the road, he said, their method could be used to determine whether an unknown genetic mutation in a patient was actually having negative effects.

The bigger news, though, isn’t just this one study on its own, but the flush of recent research seeking to tweak CRISPR to make it live up to its hype. Recent studies have explored combining CRISPR with different enzymes for different purposes, editing individual DNA base pairs, and editing RNA. In the end, CRISPR may be used for far more than DNA editing—it could be a multifunctional tool that also works as a biosensor, a medical detective, and an invaluable instrument for basic research.