CRISPR and Gene Editing Blueprint Analogy

There was a nice guest post on AgWeb recently titled:

Gene Editing: Building Better Blueprints, One Gene at a Time. 

I really like the blueprint analogy as a means to help people understand how gene editing is similar and different from other technologies. Many consumers that are skeptical of advances in food technology are comfortable with older technologies or don't realize the differences.

As Bob Reiter stated in the article:

"Now consider this: what if there was a defect in the blueprint for the house? If we followed those instructions anyway, the defect would be built into the house – which could later lead to structural problems, ranging from minor to catastrophic, depending on which part the defect involved."

Messing up the blueprint is what a lot of consumers are hesitant about when it comes to traditional recombinant DNA technologies (a.k.a. 'GMOs'). They are worried about unknown downstream structural problems and the impact that could have on human health. To put this in other terms, genomic disruptions. In response they advocate for more regulations, testing, and labeling of 'GMO' foods and many are calling for a similar framework for gene edited foods. And food manufacturers take advantage of the marketing opportunities created by these concerns. Ever heard of the non-GMO Project?

But the blueprint analogy is actually helpful here. As Bob explains, in college he was careful about designing the blueprint. If we think of gene editing like making careful targeted changes to the blueprint, USDA organic approved technologies (methods using radiation or chemical mutagens) are more like his intoxicated fraternity brothers sneaking in making random changes to his plans without him knowing. Perhaps they introduce really cool innovations! On the other hand, the roof might leak, the plumbing could drain backwards, or worse. To put it differently, the number of genomic disruptions are far greater and unknown.

You would think, if customers and regulators were concerned about Bob's targeted changes (maybe they would insist that someone from the county does an inspection before proceeding with the construction) they would really be worried about the changes brought about by his inebriated counterparts. However, if we analogize back to mutagenic conventional and organic food, they don't seem concerned at all. They have accepted a build it and see what happens later attitude. No testing. No labeling. (other than maybe that Butterfly food marketers like to stamp on everything from rock salt to water). Of course, from a scientific risk based perspective, there probably is not a reason for testing or labeling these foods....if consumers already understand and accept this that should be a step further down a path toward newer 'safer' technologies that promise so much more.

You can only take an analogy so far but I like Bob's.

See also: Organic Activists Realize Hypocrisy On Gene Editing and Biotech

References:

Batista R and others (2008). Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proceedings of the National Academy of Sciences of the United States of America 105(9): 3640–3645

Baudo MM, Lyons R, Powers S, Pastori GM, Edwards KJ, Holdsworth MJ, Shewry PR. (2006). Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J. 2006 Jul;4(4):369-80

CRISPR Mediated Off Target Mutations in Mice

In a very recent paper in Nature Methods , researchers used CRISPR technology to repair a gene mutation related to blindness in mice. But what they found was a large number of off target mutations compared to what is typically expected.

An article in The Conversation discusses some of the possible explanations for these findings. Some critics have suggested that the large number of off target mutations could be related to the specific methods used to control the activity of the Cas9 enzyme, which would impact the number of cuts/edits made in the host DNA that occur.

Others have pointed out that there are various flavors of CRISPR, and even temperature can impact enzyme activity and off target impacts, as well as better and worse methods of detection of off target mutations.    

See:
Xiang et al. (2017). Temperature effect on CRISPR-Cas9 mediated genome editing. J. Genetics & Genomics. (Apr 20) 44(4):199-205.

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (28 January 2016)

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases Genome Res. 2014. 24: 132-141

When it comes to food crop applications, critics of CRISPR technology, as well as older recombinant DNA technologies have been largely concerned with genetic disruptions. These criticisms imply that genetic disruptions indicate increased risk to consumers. I think a very relevant question in this regard (give or take the Nature Methods paper) is related to the comparative differences in genetic disruptions between CRISPR mediated genetic improvements vs traditional plant breeding methods including mutation breeding (chemical and radiological mutagenesis used in conventional and organic foods).

Given that previous risk management/regulatory reviews and agencies have found little evidence to restrict or highly regulate traditional and mutagenic crop improvement methods, if genetic disruptions for CRISPR mediated crop improvements are comparable the argument for increased scrutiny of CRISPR based crops is weakened. Previous research indicates that genetic disruptions for traditional plant breeding methods are actually greater than what we observe in recombinant DNA methods.

See:
Batista R, Saibo N, Lourenço T, Oliveira MM. Microarray analyses reveal that
plant mutagenesis may induce more transcriptomic changes than transgene
insertion. Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3640-5. doi:
10.1073/pnas.0707881105. PubMed PMID: 18303117; PubMed Central PMCID: PMC2265136

Baudo MM, Lyons R, Powers S, Pastori GM, Edwards KJ, Holdsworth MJ, Shewry PR. (2006). Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J. 2006 Jul;4(4):369-80

 To reiterate two important questions in relation to the Nature Methods paper as it may apply to food seem to be:

1) are the drastically higher than expected off target mutations based on sound methods/application of CRISPR

2) What is the weight of evidence comparing genetic disruptions in CRISPR vs conventional crop improvement methods.

Organic Activists Realize Hypocrisy On Gene Editing and Biotech

There is a segment of the organic movement that wants to get their ducks in a row so that they can oppose gene editing technologies without hypocrisy. Quote:

“Without regulatory review” is bad enough. But to allow the use of mutagenesis, a process that involves “dousing seeds with chemicals,” in organic is a serious breach of consumer trust in the USDA organic certification program.”

Well no kidding. Not that I agree that this is a concern for safety, but its always been odd to me that recombinant DNA technologies would be ineligible for certified organic labeling (especially when Bt traits would make it much easier to exclude pesticides) while the gross number of other foods produced via mutagenesis were perfectly fine. Perhaps this cognitive dissonance was just fine until recent advances in gene editing technologies like CRISPR-Cas9. With the FDA taking comments regarding regulation of gene editing in new plant varieties, this is likely not a coincidence. 

As I stated in my comments:

"Similar to organically certified crop varieties that use chemical and radiological methods to create in-genome changes, gene edited technologies operate within genome, vs. across species.  (one popular example of gene editing includes the CRISPR-Cas9 system).  Unlike mutagenic approaches used in organically approved plant breeding systems,  these in-genome tweaks are planned, controlled, and designed to bring about very specific outcomes."

This presents a problem. Of course the page I have linked to does not explicitly state this as their rationale, you can't oppose new technologies that are actually more precise and safer than the old technologies you stand by unappologetically. (I realize in terms of safety we are splitting hairs but those hairs represent lots of money and marketing opportunities). So I don't blame this group for trying to get everyone on the same page.  Another quote:

"How do you know if your organic food comes from mutant seeds? You don’t. If you buy local, you can ask your local farmer. Alternatively, you can avoid rice, wheat, barley, pears, cotton, peppermint, sunflowers and grapefruit. These are the only mutant crops that you could potentially find in the organic section."

Slim pickings if you want to oppose gene editing with integrity.

See also: Fat Tails, the Precautionary Principle, and GMOs.

Comments on Rules for Gene-Editing Technology

From the literature:

“We found that the improvement of a plant variety through the acquisition of a new desired trait, using either mutagenesis or transgenesis, may cause stress and thus lead to an altered expression of untargeted genes. In all of the cases studied, the observed alteration was more extensive in mutagenized than in transgenic plants” - (Batista, et al; 2008)

So what are the implications of this? Currently the FDA is accepting public comments related to genome editing in new plant varieties used for foods. https://www.regulations.gov/document?D=FDA-2016-N-4389-0001

Gene editing represents an opportunity to move forward with advanced technologies to sustainably feed the planet without the same regulatory hurdles that make development costs for transgenic plant varieties (aka GMO) up to 20x greater than conventionally bred plants(Conko and Miller, 2003). Similar to organically certified crop varieties that use chemical and radiological methods to create in-genome changes, gene edited technologies operate within genome, vs. across species.  (one popular example of gene editing includes the CRISPR-Cas9 system).  Unlike mutagenic approaches used in organically approved plant breeding systems,  these in-genome tweaks are planned, controlled, and designed to bring about very specific outcomes. Gene edited plants are not ‘gmo’ in the manner that the term has traditionally been used (or misused) by regulatory proponents, and in fact are just as natural as their organically approved counterparts in terms of their development. However they stand out in very important and positive ways.

The article above (see also Baudo  et al; 2006) does not specifically address gene edited plants, while it does indicate that genomic disruptions are greater in mutagenic plants vs standard transgenic plants. (one common argument for increased regulation related to transgenic crops has been based on the concern that the introduction of new genes can have unknown consequences and genomic disruptions are one way of characterizing this*) With greater disruptions, one might favor increased regulatory scrutiny similar to the existing framework in place for transgenics. However, we do not have a framework in place for mutagenically improved crop varieties that have been safely used for decades and approved by the organic food industry as well as consumers.  Because both mutagenic and gene edited technologies represent similar in-genome approaches to crop improvement, this in fact argues against additional regulation for both mutagenic and gene edited plants, or it begs for the possibility of a revision of the existing regulatory framework for transgenics.

The benefits of gene editing technology offer far greater option value* than either conventional and organic mutagenically improved or even traditional ‘GMO’ or transgenic crops while the risks to human health and the environment are equally minimal. To impose new costly regulations on gene-edited plants would be to create huge hurdles for the development of next generation green technologies in food and fiber production in the United States and have significant environmental, public, and personal health implications for the rest of the world.

References:

Batista R, Saibo N, Lourenço T, Oliveira MM. Microarray analyses reveal that
plant mutagenesis may induce more transcriptomic changes than transgene
insertion. Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3640-5. doi:
10.1073/pnas.0707881105. PubMed PMID: 18303117; PubMed Central PMCID: PMC2265136

Baudo MM, Lyons R, Powers S, Pastori GM, Edwards KJ, Holdsworth MJ, Shewry PR. (2006). Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J. 2006 Jul;4(4):369-80

Henry Miller and Gregory Conko. Bootleggers and Biotechs. Regulation. Summer 2003

 *this post has been modified to better clarify some posited arguments some have made for regulation of genetically modifed crop plants as well as to express the potential option value that gene editing might provide in addition to previously existing technologies. Special thanks to input via twitter from @CosmicHominid for constructive input

CRISPR Technology

A nice article related to CRISPR technology and an application with waxy corn in a recent DTN article:

https://www.dtnpf.com/agriculture/web/ag/news/article/2016/06/17/gene-editing-comes-agriculture 

A very nice description of CRISPR technology:

"The letters CRISPR stand for "clustered regularly interspaced short palindromic repeats," that is, snippets of DNA….They work as part of the bacteria's defense system, in partnership with a group of special, DNA-cutting Cas ("Crispr-associated") proteins and RNA molecules….When viruses invade, the bacterial CRISPR-Cas copies DNA sequences from the virus and saves this information as a short CRISPR repeat -- a sort of molecular mug shot. When that virus invades again, these repeats are remobilized as RNA molecules, which recognize the virus DNA sequence and guide the CRISPR complex to it. There, the Cas protein snips the offending DNA sequence out, disabling the virus."

"Using a specific protein, Cas9, researchers are now using this CRISPR complex to target specific genes in the genome of plants, animals and even humans. The RNA guides the CRISPR complex to the gene sequence in question, and Cas9 cuts it out. Researchers can leave the DNA to heal on its own or they can insert a desired gene in its place."

The article goes on to discuss the regulatory environment and applications related to a new variety of waxy corn in the development pipeline for Pioneer.