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17 Nov 2019 20:33
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  •   Home > News > International

    More accurate than CRISPR? Prime editing is the latest tool in the gene editing toolbox

    A newly announced gene editing tool called prime editing, could be more accurate and make fewer byproducts than CRISPR-Cas9, scientists say.

    Scientists have developed a new gene editing tool called prime editing, which has the potential to correct 89 per cent of the known human genetic variants that can cause disease, including those that cause sickle cell anaemia and cystic fibrosis.

    The announcement, made in Nature on Tuesday, said the new technology could be more accurate and versatile than well-known gene editing technique CRISPR-Cas9, while sidestepping some of its shortcomings.

    "There are more than 75,000 currently known human DNA changes associated with genetic diseases," said chemist and co-author of the paper David Liu of the Broad Institute during a press briefing.

    These include 12 types of mutations in which a single DNA base (adenine, cytosine, guanine or thymine, represented as A, C, G or T respectively) is changed to a different letter, deletions of letters, insertions of letters or combinations of multiple changes.

    For example, sickle cell anaemia is most often caused by a specific A that has been mutated to a T in a gene that encodes one of your haemoglobins, Professor Liu said.

    And most cystic fibrosis cases are caused by the deletion of three consecutive letters in the CFTR gene.

    What gene editing tools do we currently use?

    Currently, there are two frequently used methods of gene editing that work well in human and other mammal cells.

    The first involves programmable DNA-cutting enzymes or nucleases which make double stranded breaks of the DNA double helix.

    CRISPR-Cas9 is an example of this method, with Cas9 being the enzyme that does the cutting.

    It was heralded as a revolutionary technology when it first used for gene editing in 2013.

    "It was kind of like discovering the Moon at that time," said geneticist Gaetan Burgio of the Australian National University who was not involved in this study.

    "It was a very exciting period."

    But CRISPR-Cas9 also has downsides. Making double strand breaks in the DNA can lead to uncontrollable insertions and deletions at the cut site, these are also known as indels.

    There can be off-target events, where edits are also made at locations in the genome that look similar to the target site but were not intended to be edited.

    And the efficiency of CRISPR-Cas9, or how often the edits or corrections are successful, can also be low, particularly when it is being used in therapy.

    The second method is called base editing and was developed by Professor Liu's lab in 2016.

    Instead of cutting the DNA double helix it directly converts one DNA letter into another letter, but it can only correct four of the 12 possible point mutations in DNA.

    It also cannot make precise insertions or deletions, such as the insertions needed to fix the CFTR gene in cystic fibrosis.

    Enter prime editing

    That's part of the appeal of this new method of prime editing, Dr Burgio said.

    "What the prime editing does is some sort of base editing with the advantages, but without the inconvenience," he said.

    "It's really versatile, you can edit pretty much whatever you want in high efficiency."

    It can edit all possible point mutations, as well as being able to make precise insertions and deletions, all without making a double strand break of the DNA.

    Professor Liu compares it to swapping from CRISPR-Cas9's molecular scissors to prime editing's molecular word processor.

    "If CRISPR-Cas9 and other programmable nucleases are like scissors, and if base editors are like pencils, then you can think of prime editors to be like word processors, capable of searching for target DNA sequences and precisely replacing them with edited DNA sequences," he said.

    Another advantage of prime editing is that is has the potential to cause fewer off-target events, said bioinformatician Denis Bauer of the CSIRO, who was not involved in the research.

    "This is because prime editing needs three components to 'line up' for an edit to happen," Dr Bauer said.

    Although she notes, the authors haven't ruled out the technique may create novel or unknown off-target events.

    Dr Burgio said he can think of a couple of instances where this new tool could be really transformative.

    The much higher efficiency of prime editing compared to CRISPR-Cas9, could make a massive difference to a patient with sickle cell anaemia for example.

    Like base editing, prime editing also allows you to edit non-dividing cells like neurons and some muscle cells, Dr Bauer said.

    This would be useful for being able to eventually treat adults with precise 'gene surgery' approaches she said.

    Otherwise, genetic diseases not treatable by base editing could only be treated at the single cell stage.

    The consequences of this is that the edits would be in all cells and the person would pass the change onto their offspring, which scientists have called for a moratorium against.

    What are the downsides?

    There is still a lot of work to be done fully assessing the capabilities of prime editing and understanding its effects, Professor Liu said.

    And seeing this technique being used in clinical practice could be many years away, said Dr Bauer, after the safety, effectiveness and viability of the approach is more carefully looked at.

    It's also not going to work for every genetic correction, Dr Burgio said.

    "If the gene is difficult to edit, it will remain difficult to edit, regardless of the technique."

    What does the future of gene editing look like?

    Like any exciting new tool in the gene editing toolbox, prime editing has both unique strengths and weaknesses, Dr Bauer said.

    And both Professor Liu and Dr Burgio think it's unlikely that one technique will win out over all the others.

    "Nucleases, base editors and prime editors each have complementary strengths and weaknesses, just as scissors, pencils and word processors each have unique and useful roles," Professor Liu said.

    "We anticipate that all three classes of editing agents in mammalian cells have or will have roles in basic research, and in applications such as human therapeutics and agriculture."

    © 2019 ABC Australian Broadcasting Corporation. All rights reserved

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