CRISPR gene-editing is a technique that allows the genomes of living organisms to be modified. Naturally, this has been looked at with promise of use in humans to help eradicate disease. However, several recent experiments that use the tool to modify human embryos have revealed large, unintended genomes at or near the target site.
Three different studies showing these results were published without peer review on bioRxiv, where their intention was to edit a single gene. Results from each of the papers showed large-scale, unwanted DNA deletions and rearrangements in the areas surrounding the targeted sequence. Previous research has shown that CRISPR editing can lead to “off-target” gene mutations far away from the target sequence, but the nearby changes identified in the latest studies can be missed by assessment methods.
Gaétan Burgio, a geneticist at the Australian National University in Canberra said: “The on-target effects are more important and would be much more difficult to eliminate”.
As CRISPR gene editing creates permanent changes to the genome that can be passed on to generations, it could lead to unintended and potentially damaging genetic changes in future generations”. In fact, Fyodor Urnov, a researcher studying genome editing at the University of California, Berkeley went as far as to say that “if human embryo editing were space flight, the new data are the equivalent of having the rocket explode at the launch pad before take-off”.
Unwanted side effects
The first experiments using CRISPR to edit human embryos started in 2015 and since, a handful of teams have started to explore the process to make precise edits to genes, but the studies remain strictly regulated and rare.
The latest research highlights how little we know about how human embryos repair the DNA that is cut by genome-editing tools. The first of the pre-prints was posted on the 5th of June by Kathy Niakan from the Francis Crick institute and her colleagues. In the study, the researchers used CRISPR-Cas9 to create mutations in a the POU5F1 gene, a gene that is important for embryonic development. They edited 18 embryos, of which around 22% had an unwanted change that affected large swathes of DNA surrounding the target gene.
Another group led by Dieter Egli of Columbia University in New York studied embryos created with sperm carrying a blindness-causing mutation in the EYS2 gene. The team tried to correct the mutation using CRISPR-Cas9 but found about half of the embryos lost large parts of the chromosome on which EYS is mutated, and in some cases, they lost the entire chromosome.
The third paper was led by Shoukhrat Mitalipov of Oregon Health & Science University in Portland, where the team studied embryos made using sperm that carried a mutation that causes a heart condition, but also found signs that editing led to large regions of the chromosome being altered
CRISPR-Cas9 uses a small strand of RNA to direct the Cas9 enzyme to the target site, which then cuts both strands of DNA and the cells repair systems heal the gap. The edits occur during the imperfect repair process, where a small number of DNA letters are either inserted or removed, but broken DNA can also cause reshuffling or loss of large sections of the genome.
While previous work on mouse embryos has also shown that unwanted effects occur, it was important to demonstrate that it happens in human embryos too, as different cell types might respond to gene editing differently.
The three studies offered different explanations for how the DNA changes arose: with Egli and Niakan’s teams attributing most of the changes to large deletions and rearrangements, while Mitalipov’s group said that up to 40% of the changes were caused by gene conversion.
Gene conversion is a process in which DNA repair processes copy a sequence from one chromosome in a pair to heal the other. Mitalipov and his colleagues reported similar results in 2017, but researchers were sceptical that frequent gene conversions could occur in embryos.
Overall, these studies are likely to be inform the ongoing, controversial debate over whether gene editing in human embryos is safe.
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