Laser-precise gene-edited accident

August 2021

 Hypothesis -

1. Supposition made as the basis for reasoning, without assumption of its truth, or as a starting-point for investigation 
2. Groundless assumption

(Oxford English Dictionary)

A brief perusal of the website of biotech company, Cibus, will give a you a good idea of what it sells.

Cibus uses its own "unique and proprietary precision gene-editing technologies" to "enable the direct creation of desired traits without integration of foreign material for nature identical non-GMO crops".

Note that "GMO" is not a good selling point. Cibus is plugging the make-believe that gene-edited GMOs are somehow not GMOs and therefore somehow more acceptable to consumers.

The bases of Cibus gene-editing technologies are its 'Rapid Trait Development Systems' (RTDSTM) which involve culturing 'naked' parent plant cells stripped of their protective walls. In this highly unnatural form the cells are unstable and prone to mutation. They're also vulnerable to chemical attack, and this can be used to enable the uptake of a simple synthesized nucleotide* gene editor.

*DNA is a nucleic acid formed from a chain of nucleotide molecules.

Cibus' first commercial RTDS product is 'SU canola', a gene-edited canola tolerant to sulfonylurea herbicide. The novel canola has a single nucleotide change in a gene for an essential enzyme which in its native form is inactivated by the herbicide.

Actually, this first gene-edited crop, Cibus SU canola, is just another version of what all the biotech companies have been churning out for decades: a lucrative package of a GM herbicide-tolerant commodity crop with it's own herbicide.

In 2016, the Canadian regulators who approved Cibus' SU canola for food use noted that it was created using RTDS and a nucleotide-directed mutagenic technique, and that the precision of the edit in the crop had been confirmed by DNA analysis. They also noted that, notwithstanding the use of a precision gene-editing tool and the confirmation of that precision, Cibus "hypothesized that the single nucleotide mutation was the result of a spontaneous somaclonal (culture induced) variation that occurred during the tissue culture process, and not due to the specific oligonucleotide* used in the RTDS protocol".

*An olignucleotide is a short chain of nucleotides

No basis for the latter supposition was given, and the regulators seem unconcerned that Cibus appears not to have mastered its own "laser precise" gene-editing tool which it claimed to be the very foundation of its business model.

Comment. Indeed, it seems somewhat lax of regulators to approve any novel crop on the basis of a 'supposition' or 'groundless assumption' about how it was created in the first place.

Four years later, the hypothesis became an established fact slipped, without fanfare, into select media outlets. Euroseeds, 'the voice of the European seed sector', reported that the SU canola was "in fact developed from spontaneous somaclonal variation".

French campaign group Inf'OGM dug a bit deeper and found Cibus explanation: "the herbicide selection step identified multiple herbicide tolerant plants. These plants came from cells in Petri dishes where an oligonucleotide was added and also from control cell samples in Petri dishes where no oligonucleotide was added ... We were pleased to find that some of the plants had the specific mutation the oligonucleotide was designed to induce, but the majority of the tolerant plants had a variety of different mutations that had arisen spontaneously during the cell culture process." Cibus concludes by saying that it "selected one of the spontaneous mutations ... this became our first SU Canola line".

Cibus seems to be saying its laser-precise gene editor worked in a few plants but that plenty of suitably mutated, non-edited plants arose spontaneously. However, the commercialised SU canola was confirmed by DNA analysis to have the laser-precise edit intended. Since single genes consist of millions of nucleotides within a genome of billions, the chance of one single exact planned laser-precise change in a single nucleotide arising spontaneously in a few cells in a dish is, as Dr John Fagan pointed out, "vanishingly small". He added "it is highly preposterous that a company that has invested tens of millions in developing a particular method of gene editing would turn around and claim that its first commercial product made using this gene editing method was not actually the result of that method but happened accidentally via random mutagenesis."

COMMENT

There would seem to be a vanishingly small chance that Cibus is oblivious to the points made by Dr. Fagan. So, what's going on?

Was Cibus smart enough to give itself a get-out clause for RTDS in case gene-edited GMOs became the liability transgenic GMOs have become? After all, if the first gene-edited crop 'success' story could so easily become a cell culture miracle, so could all the rest.

And, GM proponents keep insisting that gene edited plants are 'nature identical', merely an escalation of what happens in nature, and indistinguishable from what happens in nature, so no one's ever going to be able to prove industry is indulging in wishful thinking. Or are they?

GM-concern groups have pointed out that just before Cibus concluded its four-year deliberation on whether SU canola might have arisen by spontaneous mutation, a study was published inconveniently disproving the claim that gene-edited plants couldn't be identified and therefore couldn't be regulated. The study described analytical methods which "may be applicable to virtually any genome-edited organism", providing that basic information about the DNA edit as supplied to regulators is available. Their methods used widely-available scientific expertise and common equipment already in routine use in laboratories.

To trial their method, the scientists used Cibus SU canola because it has some particularly challenging features.

Challenging features for the analysis of Cibus SU canola include, for example:

1. The edit involved a single-nucleotide edit, the smallest change possible.
2. The gene altered isn't unique in the organism, it's just one member of a set of similar genes.
3. The SU crop Cibus finally commercialised is a hybrid between the RDTS-generated plants and a chemically-mutated version with the same single nucleotide change in a different gene in this set.

With these kinds of challenges, if the techniques work for SU canola, they'll work for any other gene-edited crop.

What better moment to find out that all those annoying tests and inconvenient regulations looming for gene edited crops such as SU canola can be dispensed with because the edit has been declared a natural mutation? Indeed, Euroseeds took pains to announce that the published detection method had merely detected a natural mutation and so was making "much ado about nothing".

OUR COMMENT

There's another explanation which is much, much more likely than that vanishingly unlikely spontaneously laser-precise accident.

During the long procedure of cell culture, molecular treatments and plant regeneration, there's significant scope for operator errors: did the culture plates or the plants get mixed up? was the wrong reagent added to a cell culture? did the labels get mixed up?

Cibus haven't come clean on how it managed to eliminate all these possibilities.

On the other hand, if Cibus is right and its SU canola is a result of spontaneous mutation, there's an interesting implication. Despite all the purposefully gene-edited plants it created, it was one which hadn't been subject to a humanly-contrived nucleotide change which formed the best stock for commercialisation. This would suggest Cibus' miracle plant which had changed by itself was much more robust than the GM ones ... not a great sales pitch for their designed, laser-precise, gene-edited crops.

Bear all this in mind next time you hear how wonderful gene-edited crops promise to be (especially from our own Department of Environment Food and Rural Affairs [1])

Background

[1] THE PRECISION PROBLEM IN GENOME EDITING - June 2021


SOURCES:

• www.cibus.com

• Novel Food Information - Cubus Canola Event 5715 (Imidazolinone and Sulfonylurea Herbicide Tolerant), Novel Food Information, Government of Canada, 27.05.16

• Claire Robinson, Company claims first commercial gene-edited crop wasn't gene-edited after all, GM Watch 21.09.21

• Cibus's canola. The mysterious origin of the mutation, GM Watch 29.09.20

• Greg Gocal, Non-Transgenic Trait Development in Crop Plants Using Oligo-Directed Mutagenesis Cibus' Rapid Trait Development System, Cibus 2014

• Much ado about nothing, really! www.euroseeds.eu, 8.09.20

• First open source detection test for a gene-edited GM crop, GM Watch, 7.09.21

• Pradheep Chhalliyil, et al., 2020, Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plant, Foods 9

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