In the previous post on the blog, I discussed a question I often receive from clients and other companies, which is whether, under regulations like the U.S. EPA TSCA biotechnology rule, improvements to a previously-approved microbial strain would require a new submission to the agency (such as a new Microbial Commercial Activity Notice). Today, I’d like to discuss another frequently-asked question, which has to do with the status of organisms created solely by gene-editing technologies such as CRISPR (also called genome editing technologies), and whether microorganisms modified solely by gene editing for industrial biotechnology applications would be subject to regulation in the U.S. or other countries.
This is a question that has been frequently raised throughout the world, although most of the public and governmental discussions have focused on the regulation of gene-edited plants. At the risk of over-generalizing, the focus on plants is largely because biotechnology regulatory regimes around the world have striven to avoid regulating plant varieties arising from traditional crop breeding activities, and regulated parties have made the case that the use of gene editing is a faster and more precise way to accomplish changes that could have been derived by plant breeding, and that plants created in this way would not appreciably differ in their risk profile from traditionally-bred varieties. Also, the field testing and growth of GMO plants is a far more prevalent and visible commercial activity than environmental or industrial uses of GMO microorganisms.
There have been at least three recent review articles summarizing the trends in regulation of gene-editing technologies around the world (Sprink et al. (2002); Tachikawa and Matsuo (2023); Buchholzer and Frommer (2023) — see full citations below). These papers are very useful summaries of international developments in recent years regarding movement towards possible down-regulation of organisms derived from genome editing, but the discussions in all three papers are exclusively limited to the impact of these changes on regulation of GMO plants and foods derived from those plants. There is clearly a growing trend towards exempting from GMO regulation those plants modified using genome editing in ways that don’t result in introduction of heterologous DNA, and which can be likened to plants created by traditional breeding. In today’s post, I’d like to focus on the these trends as they relate to the regulation of gene-edited microorganisms for use in industrial applications such as production of chemicals, fuels, enzymes as well as certain environmental or agricultural uses.
There are generally considered to be three types of genome editing by site-directed nucleases (SDNs). As explained in Buchholzer and Frommer (2023), SDN-1 techniques introduce small changes at the target site; SDN-2 methods use template-guided repair by homologous recombination to introduce a specific DNA sequence replacement in the genome; and SDN-3 methods insert larger genetic elements (e.g. full genes) in a similar manner as SDN-2. These distinctions have been important in regulatory decisions regarding gene-edited plants, and may also come into play for oversight of gene-edited microorganisms.
United States
Few countries in the world appear to have addressed this question with regard to regulation of microorganisms. The U.S. is one exception, to some extent attributable to the U.S. philosophy of regulating biotechnology based on the commercial application, which means that multiple agencies, laws and regulations, often with different definitions, are involved in biotechnology oversight. The agency that has historically had the greatest involvement with industrial uses of modified microorganisms is the Environmental Protection Agency, through the New Chemicals Division of its Office of Pollution Prevention and Toxics, which administers biotechnology regulations under the Toxic Substances Control Act (TSCA). As I’ve described previously in the blog, the TSCA regulations govern the uses of certain modified microorganisms intended for use in the production of chemicals, fuels, industrial enzymes and other specialty products as well as some environmental applications, and oversight is limited to those organisms meeting the definition of “new microorganism” under the rule. To fall under this definition, an organism must contain deliberate combinations of coding nucleic acids arising from different genera – so-called “intergeneric” microorganisms. EPA has often been asked whether a microorganism modified solely through gene-editing would be considered “new” and thus subject to the TSCA regulation. EPA’s policy was expressed by EPA staffer Dr. Gwendolyn McClung in a February 2022 presentation. Citing methods such as CRISPR-Cas, TALENS and zinc finger nucleases, Dr. McClung said:
A microbial biotechnology product created using these genome editing techniques would not be regulated under Section 5 of TSCA unless intergeneric genetic material was introduced (“knock-in”) [see slide 26]
Dr. McClung has confirmed this position in e-mail exchanges with me on two occasions. This position is fully consistent with the limitation that the only microorganisms subject to the TSCA regulation are intergeneric organisms, so that if the use of gene-editing accomplishes modifications without introducing any foreign DNA (i.e., through SDN-1 genome editing), such organisms would a priori be outside the scope of this particular rule.
Modified microorganisms used for certain agricultural applications might fall under the biotechnology regulations of the U.S. Department of Agriculture. This regulation, now called the SECURE Rule and found at 7 CFR Part 340, is the rule that is used to regulate field testing and commercialization of transgenic (“GMO”) plants, and the current version of the rule includes exemptions in Section 340.1(b) that cover organisms created through certain gene-editing technologies, but these exemptions are explicitly limited to plants. However, the SECURE rule also covers environmental uses and interstate movement of microorganisms that might present a plant pest risk: under Section 340.2(c), a permit may be required for an organism that “is not a plant but has received deoxyribonucleic acid (DNA) from a plant pest … and the DNA from the donor organism either is capable of producing an infectious agent that causes plant disease or encodes a compound that is capable of causing plant disease”. Thus many microorganisms created using SDN-1 techniques would fall outside this definition because they would not contain any DNA from any donor organism (provided the species itself is not implicated as a plant pest or pathogen). Consultation with USDA may be needed to confirm the exempt status of any specific strain.
Other uses of modified microorganisms might be regulated differently under the U.S. biotechnology framework. Microorganisms might be regulated as pesticides, or may be used for the production of products subject to the jurisdiction of the Food and Drug Administration, but for these applications, the regulations would apply regardless of whether the organism was genetically modified, whether by classical recombinant DNA techniques or by the newer methods of genome editing. There is one minor exception: under EPA’s pesticide regulations, nonmodified microbial pesticides can be used in outdoor field tests below 10 acres in size without a permit or notice to EPA, but proposed field tests of live genetically modified microbial pesticides require notification to the agency under 40 CFR Part 172.45, regardless of the size of the test. However, Section 172.45(d)(i) exempts from this requirement “microbial pesticides resulting from deletions or rearrangements within a single genome that are brought about by the introduction of genetic material that has been deliberately modified”. It would appear that microorganisms created using SDN-1 genome editing would be eligible for this exemption, and could be field tested below 10 acres without EPA notification, but I don’t know if EPA has ever confirmed such an interpretation.
Australia
I’m aware of only one other country that has formally adopted a policy that excludes from regulation both plants and microorganisms created using certain gene editing technologies, and that is Australia. As previously described in the blog, biotechnology in Australia is regulated under the Gene Technology Act of 2000 and regulations implemented under the Act, which were most recently revised in 2019. Many activities using genetically modified organisms would require approval under the Act from the Office of the Gene Technology Regulator (OGTR), which plays the key role in assessing, regulating and licensing GMOs and enforcing license conditions. In the terminology used in these regulations, a proposed activity with a GMO is called a “dealing”, many of which would require a license from the government.
The Gene Technology Regulations include a detailed definition of which organisms are to be considered as GMOs. The definition largely depends on the use of what is called “gene technology” which is defined as:
any technique for the modification of genes or other genetic material, but does not include:
(a) sexual reproduction; or
(b) homologous recombination; or
(c) any other technique specified in the regulations for the purposes of this paragraph.
Clause (c) requires one to look to the regulations for more clarity on what is and what is not included. Specifically, Schedule 1 of the Regulations lists organisms that are not GMOs for the purposes of the Act and Schedule 1A includes a list of techniques that are not considered to be “gene technology” under the Act. Schedule 1 includes the following category of exemption:
An organism modified by repair of single‑strand or double‑strand breaks of genomic DNA induced by a site‑directed nuclease, if a nucleic acid template was not added to guide homology‑directed repair.
This policy is explained in an October 2021 document available on the OGTR website. The document explains that “organisms modified through unguided repair of site-directed nuclease (SDN) activity, also known as SDN-1 organisms, from regulation as GMOs. Unguided repair means that no nucleic acid template was added to cells to guide genome repair following SDN application. SDNs include, but are not limited to, CRISPR/Cas9, zinc finger nucleases, meganucleases and TALENs”.
It is clear from the text of the regulations that this policy applies to both plants and microorganisms, a position that was confirmed in a conversation one of my clients and I had recently with OGTR staffers. However, the policy is explicitly limited to organisms modified using SDN-1 techniques and may not apply to uses of SDN-2 or SDN-3 methods, so that in many cases the use of a gene editing technology that utilizes target DNA or which results in the insertion of heterologous DNA into the organism’s genome would not be covered by the exemption and would be considered a GMO. Here too, prior consultation with the regulatory agency might be desirable.
Other countries
There have been recent significant developments on exemptions for genome edited plants that have taken place in the EU and UK. Although these are expressly limited in applicability to plants, I plan to summarize these activities in a future blog post.
The following are the citations for the review articles mentioned above:
Tachikawa M and Matsuo M (2023) Divergence and convergence in international regulatory policies regarding genome-edited food: How to find a middle ground. Front. Plant Sci. 14:1105426. https://doi.org/10.3389/fpls.2023.1105426.
Thorben Sprink, Ralf Wilhelm, Frank Hartung, Genome editing around the globe: An update on policies and perceptions, Plant Physiology, Volume 190, Issue 3, November 2022, Pages 1579–1587, https://doi.org/10.1093/plphys/kiac359.
Buchholzer, M. and Frommer, W.B. (2023), An increasing number of countries regulate genome editing in crops. New Phytol, 237: 12-15. https://doi.org/10.1111/nph.18333.
D. Glass Associates, Inc. is a consulting company specializing in government and regulatory affairs support for renewable fuels and industrial biotechnology. David Glass, Ph.D. is a veteran of over thirty-five years in the biotechnology industry, with expertise in industrial biotechnology regulatory affairs, U.S. and international renewable fuels regulation, patents, technology licensing, and market and technology assessments. In addition to his work as a consultant assisting industrial biotechnology companies prepare for and comply with government regulations, he has served as Director of Regulatory Affairs for Joule Unlimited Technologies and Vice President of Government and Regulatory Affairs for BioTechnica International. Dr. Glass has extensive experience with the biotechnology regulations of the U.S. EPA and other agencies, and has coordinated or assisted in the preparation and submission of 18 successful Microbial Commercial Activity Notices and several other biotechnology submissions in the U.S. and other countries. Dr. Glass holds a B.S. in Biological Sciences from Cornell University and a Ph.D. in Biochemical Sciences from Princeton University.
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