DNA base editors not as safe as previously thought

The past few years have seen a large number of research articles showing that the CRISPR gene-editing tool, designed to make a double-strand break in the DNA in a targeted location, may also cause many unintended mutations (damage to DNA).

Genetic engineers have tried to get around this problem by adapting the CRISPR gene-editing tool so that it no longer makes a double-strand break in the DNA. One adaptation consists of piggybacking onto the CRISPR tool an enzyme that changes individual DNA bases (so called “base editing”).

Base editing has been touted as a way of introducing changes in genes while avoiding the unintended effects, such as large deletions or rearrangements, which can arise from DNA repair processes following the usual CRISPR-induced double-strand DNA break.

Researchers have applied to Defra for consent to conduct field trials of genetically modified (GM) wheat and gene-edited Brassica.

The two small-scale field trials are planned to take place at the John Innes Centre on the Norwich Research Park between April and September in each year from 2019 to 2022.

The wheat trial follows research at the John Innes Centre that identified a gene, TaVIT2 which encodes for an iron transporter in wheat.

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In the same application to Defra, researchers have requested consent to trial Brassica oleracea plants, modified using CRISPR-Cas9 gene-editing technology.

A tightening of restrictions on the insecticides known as neonicotinoids has brought hope that the decline in honey bees and wild pollinators can be reversed. Yet concerns are growing as to how new technology could radically change the landscape. Are we heading towards a world of ‘frankenbees’, in which gene-edited bees are resistant to pesticides and where only the rich can afford to pay for pollinated crops?

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ROBOT SWARMS

Technological advances are likely to shift the parameters of the debate. Depending on your perspective, the potential opportunities offered by robotics and genetic engineering will either be reassuring or deeply disturbing.

At least five companies are working to develop robot bees that could be controlled in swarms to pollinate crops and be impervious to insecticides. Last year scientists at Delft University of Technology developed a prototype bee-like drone, whose wings beat 17 times per second to generate the lift needed to stay airborne. The robotic insect has a 33cm wingspan and weighs 29 grams, making it 55 times the size of a fruit fly. Harvard is also looking at such developments. ‘If we’re not careful we could end up with a situation where we have an environmental market for something we get for free,’ says Matt Shardlow of Buglife. ‘It could be in some companies’ financial interests to keep that going.’

Other researchers are studying whether it is possible to genetically engineer bees to be resistant to pesticides. By using CRISPR technology – a molecular tool that can amend an organism’s genetic code – it is possible to insert a desired trait into the specimen in question, such as a honey bee. Inevitably, bee keepers have labelled these ‘frankenbees’. The first genetically modified honey bee queens were born in a laboratory at Heinrich Heine University in Dusseldorf in 2014.

We are not nearly as determined by our genes as once thought.

We’ve all seen the stark headlines: “Being Rich and Successful Is in Your DNA” (Guardian, July 12); “A New Genetic Test Could Help Determine Children’s Success” (Newsweek, July 10); “Our Fortunetelling Genes” make us (Wall Street Journal, Nov. 16); and so on.

The problem is, many of these headlines are not discussing real genes at all, but a crude statistical model of them, involving dozens of unlikely assumptions. Now, slowly but surely, that whole conceptual model of the gene is being challenged.

We have reached peak gene, and passed it.

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In a paper in Physics of Life Reviews in 2013, James Shapiro describes how cells and organisms are capable of “natural genetic engineering.” That is, they frequently alter their own DNA sequences, rewriting their own genomes throughout life. The startling implication is that the gene as popularly conceived—a blueprint on a strand of DNA, determining development and its variations—does not really exist.

So it is, in a review in the journal Genetics in 2017, that the geneticists Petter Portin and Adam Wilkins question “the utility of the concept of a basic ‘unit of inheritance’ and the long implicit belief that genes are autonomous agents.” They show that “the classic molecular definition [is] obsolete.”

These radical revisions of the gene concept need to reach the general public soon—before past social policy mistakes are repeated.

Caution required for using CRISPR in potential gene therapies – and food plants

Scientists at the Wellcome Sanger Institute have discovered that CRISPR/Cas9 gene editing can cause greater genetic damage in cells than was previously thought. These results create safety implications for gene therapies using CRISPR/Cas9 in the future as the unexpected damage could lead to dangerous changes in some cells. Potential consequences could include triggering cancer.

Reported on 16 July 2018 in the journal Nature Biotechnology, the study also revealed that standard tests for detecting DNA changes miss finding this genetic damage, and that caution and specific testing will be required for any potential gene therapies.

As usual we see far more honesty about the off-target effects of CRISPR from genetic engineers in the field of medical research than we see from the plant genetic engineers. However, the technique as used in plants is the same, as are the mechanisms of DNA repair. These off-target effects in food plants could have possible knock-on effects on food safety, including unexpected toxicity and allergenicity.

Soil Association rejects suggestion by farm minister George Eustice that the recent ECJ ruling on genome editing should be ignored

EXCERPT: “The Soil Association will continue to encourage the cultivation of open pollination seeds, which can help farmers adapt to a changing climate by breeding drought and pest tolerant plants. Breeding crops in this way has proven to be lower-cost, faster and more effective than GM, particularly when informed by new technologies like Marker Assisted Selection, based on our new knowledge of the genome.”

We take a science-based approach to GM regulation: UK to consider relaxing gene editing ban post Brexit

The UK has confirmed it will ‘consider’ relaxing the European Union’s controversial decision to include gene editing techniques within its regulatory framework that restricts the use of genetically modified organisms (GMOs) in the food chain after Brexit.

CRISPR/Cas9 is one of the newest genome editing tools. It can alter sections of DNA in cells by cutting at specific points and introducing changes at that location. Scientists at the Wellcome Sanger Institute carried out a full systematic study in both mouse and human cells and discovered that CRISPR/Cas9 frequently caused extensive mutations, but at a greater distance from the target site.

Published in the journal Nature Biotechnology, the study found that CRISPR/Cas9 gene editing can cause greater genetic damage in cells than was previously thought. The researchers found that many of the cells had large genetic rearrangements such as DNA deletions and insertions.

These results create safety implications for gene therapies using CRISPR/Cas9 in the future as the unexpected damage could lead to dangerous changes in some cells. In addition, some of these changes were too far away from the target site to be seen with standard genotyping methods. The researchers stressed that standard tests for detecting DNA changes miss finding this genetic damage, and that caution and specific testing will be required for any potential gene therapies.

Abstract

CRISPR–Cas9 is poised to become the gene editing tool of choice in clinical contexts. Thus far, exploration of Cas9-induced genetic alterations has been limited to the immediate vicinity of the target site and distal off-target sequences, leading to the conclusion that CRISPR–Cas9 was reasonably specific. Here we report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors and a human differentiated cell line. Using long-read sequencing and long-range PCR genotyping, we show that DNA breaks introduced by single-guide RNA/Cas9 frequently resolved into deletions extending over many kilobases. Furthermore, lesions distal to the cut site and crossover events were identified. The observed genomic damage in mitotically active cells caused by CRISPR–Cas9 editing may have pathogenic consequences.

UK umbrella campaign GM Freeze today welcomed a European Court of Justice (ECJ) decision to ensure proper regulation of controversial new genetic engineering techniques.

Supporting the position taken by environmental campaigners, the judgement states that organisms obtained by mutagenesis are Genetically Modified Organisms (GMOs). In addition, it states clearly that the only techniques that can escape full GMO regulation are those that already had a history of safe use in 2001.