A new study has contradicted a finding of CRISPR-Cas9 off-target activity, instead finding that "unexpected mutations" were due to two closely related mice:
In May, a study claimed that the revolutionary CRISPR gene editing technique can cause thousands of unwanted and potentially dangerous mutations. The authors called for regulators to reassess the safety of the technique. But doubts were raised about these claims from the very beginning, not least because it was a tiny study involving just three mice. Some critics have called for the paper to be withdrawn. Now a paper posted online on 5 July has proposed a simple and more plausible explanation for the controversial results. If it's right, the authors of the original study were wrong.
[...] When Stephen Tsang of Columbia University Medical Center and colleagues compared the entire genomes of two CRISPR-edited mice with a third one, they found thousands of shared mutations in the two edited mice. Tsang and co attributed to these mutations to CRISPR, and issued a widely-covered press release that suggested CRISPR is far riskier than dozens of other studies had suggested.
[...] But there is a much simpler explanation, says the latest study: the two CRISPR-edited mice just happened to be more closely related and thus shared more mutations. [...] "I agree the two mice are indeed more likely to be closely related," says geneticist Gaetan Burgio of the Australian National University, one of the many critics of the original paper. He says its publication in a prominent journal was a failure of peer review.
"Unexpected mutations after CRISPR-Cas9 editing in vivo" are most likely pre-existing sequence variants and not nuclease-induced mutations (open, DOI: 10.1101/159707) (DX)
The disputed press release from May, and the study it was based on:
Unexpected mutations after CRISPR–Cas9 editing in vivo (DOI: 10.1038/nmeth.4293) (DX)
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A disputed paper that raised questions about the safety of CRISPR has been retracted:
A scientific paper that purported to lay bare serious flaws in the gene-editing tool known as CRISPR and briefly tanked shares of genome-editing companies has been retracted by its publisher.
The paper [DOI: 10.1038/nmeth.4293] [DX], published last year in Nature Methods, claimed that CRISPR wreaked havoc on the genome, causing hundreds of unintended mutations in mice — and that the algorithms typically used to detect these changes were routinely missing them.
[...] Two months after publication of the paper, Nature Methods published an "an expression of concern" about the paper in July. The retraction notice, appended Friday, goes further, saying the authors did not use mice that had been bred in their own laboratory — so they could not know if any genetic mutations were the result of their intervention with CRISPR editing, or if it stemmed from variations in the mice's own genomes.
Nature Methods editorial discussing the retraction: CRISPR off-targets: a reassessment (open, DOI: 10.1038/nmeth.4664) (DX)
Previously: CRISPR Safer than Thought; Misleading Study Found Shared Mutations in Closely Related Mice
One of the barriers to using CRISPR-Cas9 gene editing in the clinic is the possibility that the enzyme will clip DNA in the wrong spot. In a study published in Nature [DOI: 10.1038/s41586-018-0500-9] [DX] today (September 12), researchers describe a strategy to predict these off-target mutations throughout the genome and show in mice that a carefully designed guide RNA strand does not produce any detectable slip-ups.
The study confirms that "you'd better make sure that you've got a really accurate guide RNA," says Janet Rossant, a developmental biologist at the University of Toronto and the Hospital for Sick Children who did not participate in the work. "This [method] is a better way of testing for how specific that guide RNA will be before you go into animal models and, of course, into humans," she adds.
According to coauthor Marcello Maresca, a biologist at AstraZeneca in Sweden, one long-term goal of his company is to be able to use therapeutic gene editing to address a number of human diseases. "However, realizing the potential of CRISPR medicines requires the development of methods to enable the efficient modification of the target gene with no effects elsewhere in the genome," he writes in an email to The Scientist.
VIVO = "verification of in vivo off-targets".
Related: CRISPR Safer than Thought; Misleading Study Found Shared Mutations in Closely Related Mice
CRISPR Becomes More Precise
Paper That Found CRISPR "Off-Target Effects" Retracted
Repair of Double-Strand Breaks Induced by CRISPR Leads to Large Deletions and Complex Rearrangements
Did CRISPR Really Fix a Genetic Mutation in These Human Embryos?
(Score: 2) by Gaaark on Saturday July 08 2017, @02:06PM (7 children)
but there WERE mutations.... is this still not a bad thing?
Did not read article and am not a biologist or whatever.
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(Score: 2) by c0lo on Saturday July 08 2017, @02:17PM (4 children)
But of course they were, CRISPR is a technique for genome editing
https://www.youtube.com/watch?v=aoFiw2jMy-0
(Score: 2) by Gaaark on Saturday July 08 2017, @02:22PM (3 children)
I just figured by 'mutations', they meant the 2 headed mouse kind of thing: they meant to give it bigger eyes, but got 2 heads instead.
Errrgh.... still too much to learn, too little time.
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(Score: 4, Informative) by takyon on Saturday July 08 2017, @02:31PM (2 children)
Off-target activity refers to random splices or mutations caused by an imperfect CRISPR method. It's as if you used Find and Replace on a document but it would add your replacement string in places you don't want it to go, change single characters, delete characters, etc.
There are already some ways to make CRISPR more precise. What this new study suggests is that at least one alarmist perspective of the accuracy/precision of CRISPR was very flawed.
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(Score: 1, Interesting) by Anonymous Coward on Saturday July 08 2017, @04:16PM (1 child)
Not really, it is more that their understanding of how CRISPR works is wrong:
It seems to primarily work by selecting for pre-existing mutants... this is something I have been saying since the hype started. The critique paper is just as clueless but at least now people are starting to recognize the existence of these pre-existing variants. Once they get around to looking closer at their data and quantifying this they will "discover" about 1/100 to 1/10k cells are mutants already *anywhere* they look.
(Score: 0) by Anonymous Coward on Sunday July 09 2017, @04:07PM
Bullshit.
Your explanation is inconsistent with just about any genomic sequencing result. If what you are saying were true, then all the studies reporting the fidelity of DNA and RNA polymerases are wrong as well as just about every study involving quantitative sequencing.
(Score: 3, Insightful) by kanweg on Saturday July 08 2017, @03:35PM (1 child)
The way I understand it is more like this. If my brother and I were CRISPR treated and you were not, comparison of our DNA would show that there are many mutation in the DNA of the CRISPR treated people (my brother and me) not present in the control (you). So, it would be concluded that these are caused by CRISPR. But that is not the case, of course. We were already not very much related and thus our DNA more different from yours.
Bert
(Score: 2) by Gaaark on Saturday July 08 2017, @04:41PM
Ah!, now THAT makes sense (hope it's right, because it sure does SEEM correct, lol).
Modding insightful! :)
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(Score: 0) by Anonymous Coward on Saturday July 08 2017, @03:36PM (1 child)
I love how all of a sudden the CRISPR researchers are aware that there are other reasons to see "mutations" than gene "editing". Usually this goes totally ignored as they kill 90% + of the cells they treat and they fail to wonder why some survive and others don't.
(Score: 0) by Anonymous Coward on Sunday July 09 2017, @03:56PM
Citation needed.
(Score: 3, Interesting) by Immerman on Saturday July 08 2017, @06:10PM
Seems to me they've called into question the CRISPR-mutation link, but not actually shown it to be false.
Now, if they found all/most of the same mutations in a third unedited relative, that would be good evidence against off-target mutations, but that doesn't seem to be the case.
As things stand now, I seem to recall that there has only been one or two full-genome analyses of post-CRISPR organism, and they showed problems. If the studies are faulty then that's certainly good to know, and means we shouldn't take their findings too seriously on their own, but it would still be a good motive to do more rigorous full-genome analysis to see if the exploratory study has indeed uncovered a major problem with CRISPR, or just fallen victim to statistical noise.
Because right now, I don't think there has been a single full-genome analysis that *hasn't* shown problems. And if there really are problems, even if they're associated with careless use of CRISPER, then that is very important information to have before the technology becomes far more widely used than it already is.