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Genome Editing

Genome editing, also called gene editing, techniques are a type of genetic engineering, resulting in the creation of genetically modified organisms (GMOs). Genome editing is a collection of techniques that alter the genetic material of genetic material of plants, animals and microbes. The aim is to insert, delete or otherwise change a DNA sequence at a specific, targeted site or sites in the genome. These new genetic engineering (genetic modification or GM) techniques raise many of the same risk questions as earlier techniques of genetic engineering, and raise the same environmental, social, economic and ethical concerns.report cover

The new techniques can make it easier and faster to genetically engineer a wider range of organisms, for more purposes. They are powerful research tools that are being used to better understand gene function and, in particular, to genetically modify mice and other research animals to study human diseases. They are also being used to experiment with creating new GM crop plants and farm animals. The biotechnology industry argues that genome editing should not be classified as genetic modification, and should not be regulated or labelled.

CBAN Factsheet: Introduction to Genome Editing, July 2020
CBAN Report:
Genome Editing in Food and Farming: Risks and Unexpected Consequences, July 2020

Updates

September, 2021: Health Canada and the Canadian Food Inspection Agency are proposing new regulatory guidance on genetically engineered plants and foods. The proposals would remove government oversight for some genetically engineered foods and plants, particularly those produced through the new genetic engineering techniques of genome editing (also called gene editing). These proposals would allow some GMOs (genetically modified organisms) into our food system without any government safety assessments – these would be unregulated GMOs that the government may not even know exist. Information and updates are posted at www.cban.ca/NoExemptions

September 2020: The first-ever public detection method for a gene-edited crop has been developed by a group of non-governmental organisations, non-GMO food associations and a food retailer. The new research refutes claims by the biotech industry and some regulators that new genetically modified (GM) crops engineered through gene editing are indistinguishable from similar, non-GM crops and therefore cannot be regulated. Click here to read about what this means, or watch the video.

August 2020: A new scientific paper published in the journal Environmental Sciences Europe finds that the risks associated with genome editing include a wide range of unintended effects that can be triggered by the genome editing process, as well as its intended biological characteristics, irrespective of whether additional genes are introduced into the genome or not.  The paper concludes that “genetic errors, caused by the genome editing process, have potential implications for food, animal feed and environmental safety.”

July 2020: Use of CRISPR by a team at the University of California Davis has resulted in genetic “chaos” in a gene-edited calf, part of an effort to create single-sex species for agriculture (all male calves for the beef industry). Cuts were made to DNA in unintended places and extra unintended DNA was inserted (from the plasmid). A Crispr calf is born. It’s definitely a boy, WIRED, July 24.

June 2020: A suite of new studies has found large, unwanted changes to the genome at or near the target site (on-target effects). See CRISPR gene editing in human embryos wreaks chromosomal mayhem: Three studies showing large DNA deletions and reshuffling heighten safety concerns about heritable genome editing, Heidi Ledford, June 25, 2020, Nature (news) 583: 17-18.

June 2020: CBAN’s Letter to the Editor, “Non-GMO claims cause confusion” in The Western Producer, in response to the article “Transgenic crops: end of an era,” (June 4).

Introduction

Genome editing, also called gene editing, is a term used to describe a collection of new techniques that alter the genetic material (usually DNA) of plants, animals and microbes. In general, these techniques consist of different types of DNA “editing” systems that aim to insert, delete or otherwise change a DNA sequence at specific, targeted sites in the genome. The organism’s genetic material is changed, not through the breeding process, but directly and artificially by humans, making these techniques a type of genetic engineering, resulting in the creation of genetically modified organisms (GMOs).

Genome editing systems are comprised of molecular components that are programmed to make changes (perform “edits”) at a target location in the genome. The most frequently used genome editing technique is CRISPR-Cas9 or CRISPR, but other techniques follow similar principles

Claims that these technologies are safer than other GM techniques are unproven. Each gene editing technique each bring their own set of risks and uncertainties. Whilst many of these are the same as with older genetic engineering techniques, there are also serious additional concerns. There is a strong scientific case for classifying all these techniques as genetic engineering (genetic modification or GM) and regulating their use with as much rigour as previous and current GM techniques.

The term “editing” implies a level of precision that is not currently, and may never be possible. It suggests the ability to rewrite the genetic code and to simply cut and paste DNA but, in reality, the results are still determined by processes in the organism that we neither fully understand nor control.

Gene editing can more efficiently target sites in the genome but the enzymes used in gene editing have been shown to cut DNA in the wrong spots and create off-target mutations. After a cut is made, the cell’s DNA repair mechanisms are in control of what happens next for the organism. The results can be alterations – such as deletions, insertions, and rearrangements – at the intended site, but also at unintended, off-target sites.

Precise edits, even if possible, do not necessarily yield precise outcomes. Even a simple genetic “tweak” can have wide-ranging effects on an organism’s genome.

“In general, greater precision at the molecular level does not directly result in greater safety or higher success rates in plant development.” – Testbiotech (2020), Overview of genome editing applications using SDN-1 and SDN-2 in regard to EU regulatory issues

CBAN Factsheet: Introduction to Genome Editing, July 2020
CBAN Report:
Genome Editing in Food and Farming: Risks and Unexpected Consequences, July 2020

Unexpected effects

Any attempt to engineer genomes with such invasive methods can cause unexpected and unpredictable effects. Genome editing can cause genetic errors, including “off-target” effects in the genome, unintended “on-target” effects, interference with gene regulation, and intended and unintended insertion of DNA. These genetic errors are important because they can lead to unexpected and unpredictable effects in the resultant genome-edited organisms, that could be important for food and environmental safety.

Unexpected large deletions or rearrangements of DNA can take place at the intended editing site or elsewhere, and can disrupt the function of non-target genes. Unwanted changes may slip by undetected. Even the intended alteration can inadvertently alter other important genes, causing changes in chemistry or protein production that can be important for food and environmental safety. Genome editing may also have unintended impacts on an organism’s ability to express or suppress other genes. The orchestration of gene function in an organism is part of a complex regulatory network that is poorly understood.

For an overview of the genetic errors that can be caused by genome editing processes, see CBAN’s report Genome Editing in Food and Farming: Risks and Unexpected Consequences, July 2020.

March 2021: A new study shows genome editing (also called gene editing) causes drastic unwanted effects in plants including severe deformities, even when the changes are intended to be small “tweaks”, such as gene knockouts in existing genes. Kawall, K. Genome-edited Camelina sativa with a unique fatty acid content and its potential impact on ecosystems. Environ Sci Eur 33, 38 (2021).

Case Study: Genome-Edited Hornless Cows

In 2020, scientists at the US Food and Drug Administration (FDA) reported errors in the genome of cows that were genetically engineered to not grow horns. The genome edited hornless cows had been held up as a positive example of the power and ease of genome editing, and discussed as a demonstration of why genome-edited animals do not need to be regulated. However, the case of the hornless cows shows the potential for errors in the genome editing process, and the need for independent safety assessment.

The dairy cows were genome-edited to be hornless (polled), to eliminate the practice of manually dehorning cows. Two cows were developed by university researchers in collaboration with the U.S. company Recombinetics. The developers reported that they were created without foreign genes and “our animals are free of off-target effects”. However, in 2019, researchers at the U.S. Food and Drug Administration (FDA) found unexpected foreign DNA in the cows (on-target effects).

Read the full story (page 12-13) in CBAN’s new report: Genome Editing in Food and Farming: Risks and Unexpected Consequences.

  • Read the paper Template plasmid integration in germline genome-edited cattle, Alexis L. Norris et al, July 2019: “We analyzed publicly available whole genome sequencing data from cattle which were germline genome-edited to introduce polledness. Our analysis discovered the unintended heterozygous integration of the plasmid and a second copy of the repair template sequence, at the target site. Our finding underscores the importance of employing screening methods suited to reliably detect the unintended integration of plasmids and multiple template copies.”
  • “No matter how “precise” the initial gene-editing event is in terms of location, undesirable outcomes can occur at the intended site stemming from the DNA repair processes that follow the cutting of the DNA by the editing tool. The findings described in the paper by the US FDA scientists are yet another illustration that looking only for off-target effects from a gene-editing procedure is not enough to identify the full spectrum of undesirable outcomes, which can occur even at the intended gene-editing site.” – from Gene-edited hornless cattle: Flaws in the genome overlooked, GMWatch, August 9, 2019.
  • “...the new FDA finding demonstrates is that the Recombinetics gene-edited cattle do contain DNA unnatural to cattle, despite the claims of their developers to the contrary. Thus FDA does have the authority to regulate.” – from FDA Finds Unexpected Antibiotic Resistance Genes in ‘Gene-Edited’ Dehorned Cattle Independent Science News, August 12, 2019.
  • Background on the company Recombinetics from Testbiotech.

Regulation

January 2021: Health Canada has announced its intention to change guidance on the risk assessment of genetically modified (“novel”) foods, for public consultation starting in mid-February. Changes are expected to propose removing regulation from some products of genetic engineering, particularly some products of the new gene editing techniques. Health Canada – Notice of Intent: To develop and publish new guidance for the Novel Food Regulations, focussed on plant breeding.

The biotechnology, seed and pesticide industry argues that gene editing should not be classified as genetic engineering and that the products should be exempt from regulation. The industry commonly argues that regulation is an expensive and time-consuming obstacle to innovation.

Canada assesses the risks of genetically engineered organisms under regulations for “Novel Foods” and “Plants with Novel Traits”. Most, but not necessarily all, gene edited products will be covered by these regulations because the Canadian government regulates products if they have a “novel” trait, regardless of the process used to make them.

The US, Australia, Argentina, Brazil, Chile and Japan are excluding some genome edited products from risk assessment. However, European regulations for genetically modified organisms cover genome editing: In July 2018, the European Court of Justice ruled that genome-edited organisms (obtained by directed mutagenesis techniques) are genetically modified organisms (GMOs) and therefore subject to existing EU GMO regulations.

Products


GM Waxy Corn, Corteva, North America and Latin America

The large seed and pesticide company Corteva Agriscience (formerly DowDupont) has clearance – in Canada and the US, as well as in Argentina, Brazil and Chile – to introduce a genetically engineered (genetically modified or GM) corn (maize) produced through CRISPR-Cas9. The company refers to it as “CRISPR-Cas waxy corn” or “Next Gen waxy”. Waxy corn has a different starch profile from other corn. In Corteva’s initial target markets of North America and Latin America, waxy corn is currently a minor crop used for food starch and some industrial products. However, waxy corn, also known as sticky or glutinous corn, is a major food crop in East and Southeast Asia, where it originates. This is the first GM waxy corn. Corteva is using its GM waxy corn to test out the regulation of, and public response to, the new genetic engineering technique of CRISPR. In February 2020, Health Canada determined that Corteva’s GM waxy corn was “non-novel” and did not therefore need to undergo a government safety assessment,: this product “is equivalent to varieties that have a history of safe use as food”. This decision was made public in September 2020.

Market Status: The market status of this GM waxy corn is unknown.

GM High GABA Tomato, Sanatach Seeds, Japan

This tomato is being called world’s first direct consumption genome-edited tomato. The GM tomato created via the use of CRISPR-Cas9 contains higher levels of gamma-aminobutyric acid (GABA), an amino acid believed to aid relaxation and help lower blood pressure. It is a Sicilian Rouge variety and will be sold by Pioneer EcoScience in Japan. “Sicilian Rouge is a popular tomato, and consumers are already used to buying other products with a high GABA content so we felt it was important to introduce them to the technology in a way that was already familiar to them,” Shimpei Takeshita, President of Sanatech Seed and Chief Innovation Officer of Pioneer EcoScience

Market Status: Sanatech Seeds says it plans to introduce the GM tomatoes through the home gardening channel. “The seedlings will be distributed free of charge to home gardeners and if people like the product they will hopefully share their experience and help spread the word…We opened up a campaign via our website inviting people to join and so far we’ve had 5,000 applicants, each of whom will be given five seedlings to plant. We’re in no rush to introduce the tomato commercially, the important thing is to win over the consumer.” Shimpei Takeshita, President of Sanatech Seed and Chief Innovation Officer of Pioneer EcoScience

GM Herbicide Tolerant Canola, Cibus, North America

Update – 2020: The company Cibus has changed its description of its canola and no longer says it is the product of gene editing (via the technique of oligonucleotide-directed mutagenesis). In 2020, the Canadian Food Inspection Agency (CFIA) changed its 2013 summary of approval (“Decision Document”) that described how Cibus created its canola because it was notified by the company that the description was incorrect. In a letter to CBAN, the CFIA said: “The CFIA was notified by Cibus that the text could be erroneously misinterpreted to mean that Cibus canola event 5715 was developed as a direct result of an oligonucleotide-directed mutagenesis approach known as the Rapid Trait Development System (RTDS). The description now correctly states that this canola was selected during the tissue culture process.” Click here to read the letter from CBAN to the CFIA, December 16, 2020 See below for details.

Market Status: Cibus’ herbicide-tolerant canola was noted as the first genome-edited crop sold in Canada and the US. There are two Cibus canola varieties on the market in Canada, sold in Manitoba and Saskatchewan, under the seed brand Falco™ and was introduced in the U.S. in 2016, and in Canada in 2018. Cibus is a US-based company that is now owned by Farmer Business Network (FNB).

Cibus’ Canola

 

Update – 2020: The company Cibus has changed its description of its canola and no longer says it is the product of gene editing (via the technique of oligonucleotide-directed mutagenesis). In 2020, the Canadian Food Inspection Agency (CFIA) changed its 2013 summary of approval (“Decision Document”) that described how Cibus created its canola because it was notified by the company that the description was incorrect. In a letter to CBAN, the CFIA said: “The CFIA was notified by Cibus that the text could be erroneously misinterpreted to mean that Cibus canola event 5715 was developed as a direct result of an oligonucleotide-directed mutagenesis approach known as the Rapid Trait Development System (RTDS). The description now correctly states that this canola was selected during the tissue culture process.” Click here to read the letter from CBAN to the CFIA, December 16, 2020

Background:

Cibus’ herbicide-tolerant canola was noted as the first genome-edited organism sold in Canada. There are two Cibus canola varieties on the market in Canada, sold in Manitoba and Saskatchewan, under the seed brand Falco™ and was introduced in the U.S. in 2016, and in Canada in 2018.

Cibus initially advertised the canola as “non-GMO” but then more commonly advertised it as “non-transgenic”. While Cibus described their canola as gene edited, it also referred to it as non-GMO. However, all gene edited crops are regulated as GMOs in Europe. North America’s largest non-GMO product certifier, the Non-GMO Project, also defines genome editing as GM and will not certify the Cibus canola as Non-GMO Project Verified.

In September 2020, a public detection method for the Cibus gene-edited canola was developed by a group of non-governmental organisations, non-GMO food associations and a food retailer. The new research refuted claims by the biotech industry and some regulators that new GM crops engineered through gene editing are indistinguishable from similar, non-GM crops and therefore cannot be regulated. Click here to read about what this means, or watch the video. The timing of Cibus’ change to their description of their technology, as non-gene edited, coincided with the release of this detection method.

In 2010 the Flax Council of Canada and Cibus entered in to an agreement to collaborate in developing a herbicide tolerant variety of flax.

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