New CRISPR alternative can 'install' whole genes, paving the way to treatment for many genetic disorders

Scientists have developed a new gene-editing system that can weave whole genes into human DNA. It could one day lead to a better method of treating genetic diseases triggered by a diverse range of mutations.

So far, the approach has been tested only in human cells in the laboratory. But if it's shown to be safe and effective for patients, it could provide an alternative to gene-editing tools that target only specific typos in DNA. Rather than correcting a single gene mutation, the new technique would instead introduce a working copy of the gene into a person's cells.

"A single genetic disease can be caused by many different mutations in that gene," said Isaac Witte, a doctoral student at Harvard University and co-lead author of the new research. For example, cystic fibrosis can be triggered by more than 2,000 different mutations in a specific gene. "Treating it [these types of conditions] with genome editing often requires many, mutation-specific approaches. That's labor-intensive, and also intensive from a regulatory standpoint" to get all those approaches approved, Witte told Live Science.

An alternative strategy is to introduce a whole new gene to make up for the broken one. The gene editor, described in a report published Thursday (May 15) in the journal Science, enables these types of edits and can insert the new gene directly "upstream" of where the broken one is found in human DNA. More work is needed to get the new gene editor out of the lab and into medical practice, but "we are quite excited by this," Witte said.

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Directing evolution in the lab

Classical CRISPR systems are often nicknamed "molecular scissors" because they use proteins to cut DNA. These systems are found naturally in bacteria, which use CRISPR to defend themselves against invaders, such as viruses.

The core of the new gene editor is also borrowed from bacteria, but it does not cut DNA. Rather, it moves large sections of a host's DNA from one location to another in a highly targeted manner. These systems — called CRISPR-associated transposases (CASTs) — have been known about since 2017 and act as a way for "jumping genes" to leap around, either within the same cell's DNA or possibly into other cells' genomes.

CASTs are attractive for gene editing because, unlike molecular scissors, they don't cut DNA and thus don't rely on cellular machinery to patch up the DNA that's sustained the cut. That repair process makes it tricky to add new DNA to the genome, in part because it can introduce unwanted mutations. CASTs, on the other hand, sidestep that issue.

But CASTs found naturally in bacteria don't play well with human cells. In previous studies led by Samuel Sternberg, an associate professor of biochemistry and molecular biophysics at Columbia University and a co-senior author of the new paper, researchers characterized naturally occurring CASTs and then attempted to use them to edit DNA in human cells. But the systems proved very inefficient, inserting DNA into only 0.1% or less of the cells, Witte said.

So Witte, Sternberg and colleagues set out to make CASTs more useful for human therapies. They started with a CAST from Pseudoalteromonas bacteria, which, in previous studies, had shown a teensy bit of activity in human cells. Then, they used an experimental approach called PACE to speed up the evolution of that CAST, introducing new tweaks to the system in each successive round.

Through this process, the team evolved a new CAST that could integrate DNA into human cells with 200-fold more efficiency than the original, on average.

"It took over 200 hours in PACE, which corresponds to several hundreds of evolutionary generations," Witte said. The same process would have taken years with more conventional methods of directing evolution in lab dishes.

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Next steps

The evolved CAST — dubbed evoCAST — includes 10 key mutations that are needed for it to work well in human cells, Witte said. However, the system works better in some types of human cells than in others, and more research will be needed to understand why that is, he said.

The team assessed how well evoCAST worked at regions of the genome that carry genes that are mutated in certain diseases, such as Fanconi anemia, Rett syndrome and phenylketonuria. The team found evoCAST worked in about 12% to 15% of treated cells. Although 100% efficiency is likely not necessary to treat genetic diseases, Witte noted, the exact efficiency needed to cure a given condition likely varies and will require study.

The team also tested evoCAST as a method for editing immune cells used in CAR T-cell therapy, a cancer treatment, and found it was similarly efficient for that purpose. That raises the idea of using this gene-editing approach not only inside the human body, but also in the lab to manufacture these types of cell-based therapies.

Future research will need to figure out how to best deliver evoCAST to the right cells in the body. "There are a lot of areas for further studies," Witte said.

Of course, those studies will need to be funded, and on that front, "it's a difficult time," he added. The new Science study was supported, in part, by the National Institutes of Health (NIH). Now, the NIH's funding has been slashed by sweeping cuts, some of which specifically singled out Ivy League universities like Harvard. "It is something that we're actively dealing with," Witte said.