From the earliest days of the CRISPR-Cas9 era, scientists have known that the first step in how it edits genomes — snipping DNA — creates an unholy mess: Cellular repairmen frantically try to fix the cuts by throwing random chunks of DNA into the breach and deleting other random bits. Research published on Monday suggests that’s only the tip of a Titanic-sized iceberg: CRISPR-Cas9 can cause significantly greater genetic havoc than experts thought, the study concludes, perhaps enough to threaten the health of patients who would one day receive CRISPR-based therapy.

The results come hard on the heels of two studies that identified a related issue: Some CRISPR’d cells might be missing a key anti-cancer mechanism and therefore be able to initiate tumors.

The DNA damage found in the new study included deletions of thousands of DNA bases, including at spots far from the edit. Some of the deletions can silence genes that should be active and activate genes that should be silent, including cancer-causing genes.

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The DNA chaos that CRISPR unleashes has been “seriously underestimated,” said geneticist Allan Bradley of England’s Wellcome Sanger Institute, who led the study. “This should be a wake-up call.”

Leading CRISPR companies scrambled to play down the latest threat to what they hope will be a multibillion-dollar business and to their stock prices, but investors reacted with alarm. Within the first 20 minutes of when the study was released, the three publicly traded CRISPR companies lost more than $300 million in value, and it was downhill from there: CRISPR Therapeutics ended down 8.6 percent, Editas Medicine fell 7 percent, and Intellia Therapeutics lost nearly 10 percent.

The companies questioned whether the CRISPR-caused DNA damage reported in the new study applied to the kind of cells they’re planning to CRISPR. They emphasized that if genomic scrambling is at all common then it should also be seen in earlier forms of genome-editing such as zinc fingers and TALENs (but apparently isn’t). And they insisted they’re on the case.

“We’re not Pollyannaish about this,” said geneticist Tom Barnes, chief innovation officer at Intellia. For its mouse experiments, Intellia analyzes edited genomes for collateral damage both near the editing target and tens of thousands of DNA letters away, he said, but “we have not seen any [cancer-causing] transformation of these cells, even with all the edits we’ve introduced.”

In a statement, Editas spokeswoman Cristi Barnett said the possibility of genetic chaos from CRISPR is “an interesting topic” that the company “actively examine[s].” The reported DNA havoc, she said, is not “specifically problematic in our work to make CRISPR-based medicines.” CRISPR Therapeutics did not respond to requests for comment.

Academic scientists were less dismissive of the new study, in Nature Biotechnology. One leading CRISPR developer called it “well-done and credible,” “a cautionary note to the [genome-editing] community,” and consistent with other research showing that the DNA cuts that CRISPR makes, called double-stranded breaks, “can induce the types of genomic DNA rearrangements and deletions they report.” He asked not to be identified so as not to jeopardize business relationships with genome-editing companies.

But just as critics of last month’s studies asked why, if CRISPR’d cells can initiate cancer, no CRISPR’d mice had turned up with tumors, so scientists raised similar questions about the new genomic havoc finding: Why don’t scientists see it when they analyze the DNA of CRISPR’d cells?

“You find what you look for,” said Bradley. “No one is looking at the impact [of these DNA changes] on downstream genes.”

And few studies conduct full-out genome sequencing of CRISPR’d cells. Moreover, scientists typically search for one form of the collateral damage the Sanger study found — deletions of thousands of DNA bases (the double helix’s famous A’s, T’s, C’s, and G’s) — using a standard technique called PCR, which makes millions of DNA copies. But to work, PCR must attach to a “binding site” on DNA; CRISPR sometimes deletes that binding site, said Bradley, whose team used a different technique to analyze the double helix for collateral damage from CRISPR.

The Sanger scientists didn’t set out to find collateral DNA damage from CRISPR. As they investigated how CRISPR might change gene expression, a “weird thing” showed up, Bradley said: The target DNA was accurately changed, but that set off a chain reaction that engulfed genes far from the target. The scientists therefore changed course.

When they aimed CRISPR at different targets in mouse embryonic stem cells, mouse blood-making cells, and human retinal cells, “extensive on-target genomic damage [was] a common outcome,” they wrote in their paper. In one case, genomes in about two-thirds of the CRISPR’d cells showed the expected small-scale inadvertent havoc, but 21 percent had DNA deletions of more than 250 bases and up to 6,000 bases long.

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Since therapeutic uses of CRISPR would edit the genomes of billions of cells in, say, a patient’s liver, even rare DNA damage “makes it likely that one or more edited cells … would be endowed with an important [disease-causing] lesion,” the scientists wrote.

Nature Biotechnology took a year to publish the paper, after asking Bradley numerous variations of “are you sure?” and “did you consider this?” and asking him to run additional experiments, Bradley said. The results all held up.

The one U.S. clinical trial using CRISPR’d cells began recruiting patients this year. It will use CRISPR to make immune cells, removed from patients with any of four types of cancer, attack telltale molecules on the tumor cells’ surface. Asked what genome analysis he plans to do, lead investigator Dr. Edward Stadtmauer of the University of Pennsylvania said, “We are doing extensive testing of the final cellular product as well as the cells within the patient.”

The possibility of adverse consequences from CRISPR’d cells has caused some company officials to argue that if, say, their therapy cures a child of a devastating disease, but increases her risk of cancer, that might be an acceptable trade-off.

That argument may well prevail. In 2003, however, when a boy in a gene therapy trial in France developed leukemia because the repair gene landed in the wrong place in his genome and activated a cancer-causing gene, it shut down gene therapy development on both sides of the Atlantic for years.

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  • CRISPR still needs to be used to get more data. Like pharmaceuticals lots of trials happen before the final drug is made. Stuff like CRISPR needs to be used to learn from.The cause may be the same bacteria doing the editing not the siding itself.

    • I was thinking exactly that! I shouldn’t have to Google the topic of an article to find out what it is you’re talking about.

    • Why not? That’s what researchers and well-informed people do. If every article had to explain every thing that somebody might not know, then the authors would need to write a book every time. STAT is about becoming well-informed. CRISPR is a common term in the medical and biological fields, and is not a particular mystery. Please do use your intelligence and curiosity to do a little exploration to learn about it without expecting someone else to anticipate what you don’t know.

  • Poor journalism as America contintues to slip into the black hole of ignorance.

    Miss Begley if you are going to publish an article could you at least cite current technology? You make no reference to Cas-13, evolved about a year ago that used the #1 genetic deficiency in the US, hemochromatosis, to be corrected. Important to me because I have hemochromatosis. Yet, no mention regarding the corrective advancements of Cas-13.

    Begley uses keen buzz words such as unholy knowing that Christiandom is edged over the entire issue pandering to the panic that it instills in Christians, or at least the ones that self proclaim themselves as Christ-like. I am a beleiver in Yeshua and as I sat a “Creation Club” meeting last week, I raised the issue of CRISPR. Why? Because it places the faithful, which includes me, in a corner, and forces a major issue:

    If science is God allowed, as most of us at the Creation Club cleave to our heart and other kinds of meds, then partaking in them to stay alive is valid.
    However CRISPR challenges the paradigm by challenging creation with solid evolutionary science. If science is God allowed, and CRISPR is science, then access is not a challenge to ones faith. As applied, CRISPR quickly takes flawed, inherited, DNA and corrects your God given/allowed defects.

    This tips the tables. God gives me flaws, man corrects them. Humanism vs Faith. Incidentally, I still love Jesus/Yeshua, for I walk by faith and not sight, call me ignorant, call me what you will. However, this article is intentionally skewed.

    Even without flaw, if ever achieved, CRISPRwill still need to be accompanied by epigenetics, specifically mRNA. mRNA the uptake into the mothership, DNA, is evirnonmentally influneced. In theory even if CRISPR corrected all mutations or flaws, then there would still be the need for eventual “DNA Tune Ups” because of environmental impacts via RNA. The proving grounds rests with mRNA.

    Further, now that the genome has been mapped over a decade ago and that AI and robotics are finally starting to realize, what awaits is a mass cleansing and culling by the elite, those above being governered. It is the old story of have or have nots. For imagine if the commoner had access to CRISP? Does any rational human believe this will be the case.

    The playing down of CRISPR is by design, for as the elite and rulers will enjoy significantly extended longevities and possibly immortality, the rest of us in the swill will start to eat each other alive. Why taunt the masses with a sceince fix. Trend and play down the silver bullet all you want, the science cat is out of the bag.

    • God does not “give me flaws” but we are born into a “flawed” Universe that is not what God intended for us originally, and so Jesus paid the price that we may be “bought” out of slavery to sin and death into the incorruptible Heaven. And so there is no “immortality” here in this world or in some other part of the Universe. One may avoid death for a time but then there still is “time” and corruption abounds with all it’s imperfections in various forms throughout every structure… death still remains. No matter how long, caught in that realm is hardly immortality, rather delayed death. Being a Christian as you say you are, there is a much greater Hope of eternity free from corruption and death; a Hope and certainty in Jesus Christ who frees us from sin and death to open wide the doors to Heaven for all those who believe and follow Him.

    • For me, a fellow Christian, it has nothing to do with being presumptuous or challenging God. For me, it’s about knowledge, or rather, a lack of knowledge. I’m humble enough to realize that we still don’t know enough about genetics to be messing around with them. We are still unable to accurately predict the consequences of modifying just a single gene.

    • What are you talking about…? You have completely gone off base from the topic of the article. The piece wasn’t about people’s morals or belief systems and their interactions with genetics (and gene-editing). It was about a study that raised serious questions of exactly how much CRISPR affects the cells edited by it – that scientists had not exclusively been looking for (and subsequently overlooked to a degree).

      How did you manage to break into that with your personal worldview and breakdown of how your faith and modern genetic science’s techniques interact? I’m not questioning or in any way denouncing your personal beliefs, but it’s so far off base from what is being reported on and discussed that I wondered what you were thinking…

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