June 22, 2016

RAC Approves First Use of CRISPR Gene-Editing Protocol in Humans

Yesterday, the Recombinant DNA Advisory Committee (RAC), a federal advisory committee to the NIH, held a public meeting to consider the first submission for approval to use a CRISPR/Cas9-based (CRISPR) study protocol with human patients. CRISPR is a technique that allows genes to be edited; it has swept through biomedical science in the last few years as a breakthrough technology. The RAC committee has provided oversight for the field of gene transfer therapies for decades (and supplements FDA and local institutional oversight by IRBs and IBCs). As an advisory committee to NIH, first constituted in 1974, RAC's regulatory portfolio for human experiments began with reviewing gene transfer studies pursuant to the NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules. The field of "gene therapy" has largely been comprised of studies involving gene transfer into patients to correct, replace, or diminish gene activity relevant to various clinical conditions; to date, several thousand gene therapy clinical trials worldwide have been conducted. RAC's jurisdiction extends to the use of gene-editing protocols, as well as other gene-altering technologies such as RNA interference. Now, a collaborative effort from the University of Pennsylvania (Penn), M.D. Anderson Cancer Center, and the University of California, San Francisco produced a proposed study protocol involving CRISPR gene-editing that was discussed and evaluated by the RAC this week at its meeting. The protocol involves an ex vivo technology where T cells of cancer patients will be removed and subject to gene-editing to alter several cell receptors before the cells are infused back into the patient. The goal is to engineer the T cells of the immune system so that they target and destroy cancer cells; this initial study is to identify any safety issues that might emerge. The recruited patients have either myeloma, melanoma, or sarcomas and would be those for which conventional therapies are not available or effective. During the meeting, questions were raised about potential conflicts of interest due to financial interests of some investigators, as well as the involvement of Penn, as it was the site of the now well-known 1999 gene therapy trial that resulted in the death of Jesse Gelsinger; that trial had notable flaws involving the transparency of preclinical testing and of competing financial interests. After public review and discussion of the protocol, the committee voted to approve the protocol. Yesterday's approval marks the first RAC-sanctioned use of CRISPR technology in human patients.

This is the first study protocol submitted to RAC that uses CRISPR in humans, but it is not the first gene-editing human protocol that RAC has considered. Sangamo BioSciences received approval to use its zinc-finger gene-editing technology (ZFN) in two different human trials: an ex vivo protocol approved in 2007, and an in vivo protocol approved in 2015. In what appeared to be a coincidence, yesterday's meeting also considered the first proposed gene therapy trial to treat Ornithine Transcarbamylase (OTC) Deficiency since the 1999 Gelsinger trial. Several discussants referenced the Gelsinger incident in their comments. The committee held a discussion of whether preclinical trials for the gene transfer method in non-human primates were necessary before approval (only mice studies were provided); RAC then voted an approval with stipulated conditions

As gene transfer studies have become more routine over the last several decades, the scope and need for continued RAC oversight has been questioned. A recent study of RAC that was conducted by the Institute of Medicine examined whether gene transfer oversight by RAC continued to be necessary; the report concluded that only new protocols presenting novel vectors or technical approaches needed to be evaluated by RAC. However, the IOM committee explored whether the RAC model of a public advisory committee could be utilized more generically for other emerging biotechnologies. including, for example, protocols from the field of nanobiotechnology or synthetic biology, for example. The IOM report endorsed consideration of an expanded scope for RAC or an advisory committee with similar attributes to provide the kind of oversight for new technologies as RAC has provided for decades in the field of gene therapy.

June 15, 2016

National Academy of Sciences Report on Controversial Gene Drive Technology Endorses Further Research, Controlled Field Trials

The National Academies of Sciences, Engineering, and Medicine (NAS) has issued a report on gene drive technology, Gene Drive Research in Non-Human Organisms: Recommendations for Responsible Conduct. A gene drive is a method by which specific genetic mutations (or alleles) are preferentially inherited, and over time, the effect is to eliminate other competing alleles. This has population-wide consequences for an organism, and can permanently alter (or reduce) the genetic diversity of a species. The phenomenon of a gene drive occurs in nature, and has been observed in many organisms
In nature, certain genes ‘drive’ themselves through populations by increasing the odds that they will be inherited.
Now, however, advances in gene-editing technology have facilitated the development of deliberately engineered gene drives. From the report summary:
A wide variety of gene drives occur in nature. Researchers have been studying these natural mechanisms throughout the 20th century but, until the advent of CRISPR/Casfor gene editing, have not been able to develop a gene drive. Since early 2015, laboratory scientists have published four proofs-of-concept showing that a CRISPR/Cas9-based gene drive could spread a targeted gene through nearly 100% of a population of yeast, fruit flies, or mosquitos.
In other words, use of gene drive technology can impose a specific genetic allele (variant) on a population and eliminate all other forms of the gene. Effectively, the population is now homozygous for the preferred variant. That is both the attraction and the concern regarding the use of this technique. Genetic traits could be eliminated, and at its most extreme, whole populations could be "driven" out of existence. It is simple to imagine particular uses of the technology that would eliminate undesirable traits in a target population, such as the ability of mosquitos to spread malaria, or very currently, the ability of the Aedes aegypti mosquito to transmit the Zika virus. The report summarizes possible applications and the requirement for a deliberative approach to use of the technique:
Gene-drive modified organisms hold promise for addressing difficult-to-solve challenges, such as the eradication of insect-borne infectious diseases and the conservation of threatened and endangered species. However, proof-of-concept in a few laboratory studies to date is not sufficient to support a decision to release gene-drive modified organisms into the environment. The potential for gene drives to cause irreversible effects on organisms and ecosystems calls for a robust method to assess risks. A phased approach to testing, engagement of stakeholders and publics, and clarified regulatory over-sight can facilitate a precautionary, step-by-step approach to research on gene drives without hindering the development of new knowledge.
The report did not recommend a moratorium on research, despite noting the potential for adverse consequences. Instead, it endorsed continued research on the technology with some limited field evaluations:
Although there is insufficient evidence available at this time to support the release of gene-drive modified organisms into the environment, the likely benefits of gene drives for basic and applied research are significant and justify proceeding with laboratory research and highly-controlled field trials.
The current regulatory landscape for gene drive applications is summarized:
In the United States, regulation of gene-drive modified organisms will most likely fall under the Coordinated Framework for the Regulation of Biotechnology, which includes the U.S. Food and Drug Administration, the U.S. Department of Agriculture, and the U.S. Environmental Protection Agency. However, the diversity of potential gene-drive modified organisms and contexts in which they might be used reveals a number of regulatory overlaps and gaps. The U.S. government will need to clarify the assignment of regulatory responsibilities for field releases of gene-drive modified organisms, including the roles of relevant agencies.
At the present time, the patchwork structure for biotechnology regulation is currently under formal review by the Obama administration (see earlier post for more background). In general, as the new products of genetic engineering have been developed over the years, they encounter oversight from any one (or more) of three agencies: the FDA, EPA, or USDA. As the regulatory framework is redesigned, we could expect that various applications of gene drive technology will face an approval process customized to the particular goal and purpose of the technology. The report states:
It is important to note that a one-size-fits-all approach to governance is not likely to be appropriate. Each phase of research activity—from developing a research plan to post-release surveillance—raises different levels of concern depending on the organism being modified and the type of gene drive being developed.
The NAS report has received criticism from opponents of field testing, who noted that precise control of such experiments is not possible, and wider, possiblly uncontrolled spread of altered organisms could occur. Other criticisms suggest that the scope of the report is too limited, and does not adequately address possible dual-use concerns (malevolent uses of the technology). The report has some conceptual overlap with efforts of the World Health Organization (WHO) has previously released a guidance framework for how to introduce genetically engineered mosquitoes that are reproductively disabled, thus reducing the population of a malaria vector. In summary, the NAS panel has cautiously endorsed further gene drive research in the U.S., and contemplates eventual field trials of engineered organisms.

May 27, 2016

NSABB Finalizes Recommendations for Increased Oversight of Gain-of-Function Pathogen Research

This week, the National Science Advisory Board for Biosecurity (NSABB) returned to its ongoing deliberation over the scope and form of oversight of gain of function (GOF) research on viruses and other pathogens. Since a moratorium on federal funding was declared in 2014, the NSABB has been working on establishing guidelines both for funding and oversight of this specific research area. The concerns over GOF research are that experiments could produce particularly dangerous pathogens which pose public health risks (see earlier post for background). In this review, the NSABB actually focused its attention on a subset of GOF research, defined as Gain of Function Research of Concern (GOFROC):
[T]he working group identified the attributes of GOFROC, which is research that could generate a pathogen that is: 1) highly transmissible and likely capable of wide and uncontrollable spread in human populations; and 2) highly virulent and likely to cause significant morbidity and/or mortality in humans. 
In its public meeting this week, the NSABB adopted recommendations from a report by its own internal working group; they are as follows (underlined for emphasis): 
1: Research proposals involving GOF research of concern entail significant potential risks and should receive an additional, multidisciplinary review, prior to determining whether they are acceptable for funding. If funded, such projects should be subject to ongoing oversight at the Federal and institutional level. 
2: An external advisory body that is designed for transparency and public engagement should be utilized as part of the U.S. government’s ongoing evaluation of oversight policies for GOF research of concern. 
3: The U.S. government should pursue an adaptive policy approach to help ensure that oversight remains commensurate with the risks associated with the GOF research of concern. 
4: In general, oversight mechanisms for GOF research of concern should be incorporated into existing policy frameworks when possible. 
5: The U.S. government should consider ways to ensure that all GOF research of concern conducted within the U.S. or by U.S. companies be subject to oversight, regardless of funding source
6: The U.S. government should undertake broad efforts to strengthen laboratory biosafety and biosecurity and, as part of these efforts, seek to raise awareness about the specific issues associated with GOF research of concern. 
7: The U.S. government should engage the international community in a dialogue about the oversight and responsible conduct of GOF research of concern. 
This completes the current NSABB review of federal policies pertaining to GOF/GOFROC research. However, the report does recommend an ongoing institutional apparatus to review policies, not individual experiments. It also recommends that privately-funded experiments involving GOFROC receive additional oversight, although that could require Congressional action. Finally, against a backdrop of reported safety lapses at federal laboratories (see here and here), the NSABB locates improved biosafety and biosecurity measures as an equally important concern in establishing how GOFROC can be managed.

May 19, 2016

National Academies of Sciences Report on Genetically Engineered Crops: Safe to Date, No Increased Yields, Insect and Weed Resistance

The National Academies of Sciences, Engineering and Medicine (NAS) have released a report on the safety and impact of genetically engineered (GE) crops: Genetically Engineered Crops: Experiences and Prospects. This was an extensive evaluation by a committee comprised of academic experts to consider health and/or environmental effects of GE crops (note that the term "genetically modified organism/GMO" is used widely as well). As the authors described the scope of the report: 
The committee examined almost 900 research and other publications on the development, use, and effects of genetically engineered characteristics in maize (corn), soybean, and cotton, which account for almost all commercial GE crops to date. 
Here is a summary conclusion from the report:
[T]he study committee found no substantiated evidence of a difference in risks to human health between current commercially available genetically engineered (GE) crops and conventionally bred crops, nor did it find conclusive cause-and-effect evidence of environmental problems from the GE crops. 
The committee noted that the majority of GE crops in commercial use are engineered to carry just a few additional genetic traits: 
The committee used evidence accumulated over the past two decades to assess purported negative effects and purported benefits of current commercial GE crops. Since the 1980s, biologists have used genetic engineering to produce particular characteristics in plants such as longer shelf life for fruit, higher vitamin content, and resistance to diseases. However, the only genetically engineered characteristics that have been put into widespread commercial use are those that allow a crop to withstand the application of a herbicide or to be toxic to insect pests. 
The fact that only two characteristics have been widely used is one of the reasons the committee avoided sweeping, generalized statements about the benefits and risks of GE crops. Claims about the effects of existing GE crops often assume that those effects would apply to the genetic engineering process generally, but different characteristics are likely to have different effects. A genetically engineered characteristic that alters the nutritional content of a crop, for example, is unlikely to have the same environmental or economic effects as a characteristic for herbicide resistance. 
There is a reiteration of the basic U.S. regulatory paradigm, which focuses on the nature of a GE product, rather than a process-based approach:
All technologies for improving plant genetics – whether GE or conventional -- can change foods in ways that could raise safety issues, the committee’s report notes. It is the product and not the process that should be regulated, the new report says, a point that has also been made in previous Academies reports.
In determining whether a new plant variety should be subject to safety testing, regulators should focus on the extent to which the novel characteristics of the plant variety (both intended and unintended) are likely to pose a risk to human health or the environment, the extent of uncertainty about the severity of potential harm, and the potential for human exposure – regardless of whether the plant was developed using genetic-engineering or conventional-breeding processes. ” –omics” technologies will be critical in enabling these regulatory approaches.
The United States’ current policy on new plant varieties is in theory a “product” based policy, but USDA and EPA determine which plants to regulate at least partially based on the process by which they are developed. But a process-based approach is becoming less and less technically defensible as the old approaches to genetic engineering become less novel and as emerging processes — such as genome editing and synthetic biology — fail to fit current regulatory categories of genetic engineering. 
On the contentious issue of labeling food derived from GE crops (see here), the committee did not find a compelling scientific basis to require labeling, but noted that there are other considerations: 
[T]he issue involves social and economic choices that go beyond technical assessments of health or environmental safety; ultimately, it involves value choices that technical assessments alone cannot answer. 
The report therefore endorses the existing product-based framework, but coupled with a nuanced determination of what products should receive enhanced oversight. Critically, the report notes a fact which is not widely appreciated, which is that GE crops largely contain only two added traits: insect or herbicide resistance. Both of these characteristics serve agronomic ends, in contrast to alteration of product attributes, such as nutritional enhancement. As a result, the NAS committee notes that other GE traits could be introduced and require specific regulatory focus. This could be especially true when the goal of a GE alteration is a deliberate change in food composition. Finally, and not insignificantly, the committee finds that GE crops, on balance, have not led to increased yields, and notes the development of resistance in both insects and weeds. These latter conclusions will feature prominently as the cost/benefit calculus for the use of GE crops continues to be debated.

May 12, 2016

Gene-Edited Mushroom Is First CRISPR-Generated Product to Avoid Federal USDA Regulation

Genetic alteration since the beginning of the biotechnology age has largely relied on the introduction of new genetic material into an organism to create a genetically engineered (GE) bacterium, plant or animal (also known as a genetically modified organism, GMO). Regulatory schemes reflected that dominant paradigm. Now, however, the use of gene-editing technology for genetic manipulation in plants can result in genetically altered plants that bypass the regulatory requirements for the introduction of standard GE plants into the marketplace. The traditional genetic engineering of crops employed the introduction of foreign genetic material into the crop; such gene transfer generally triggered formal review of the altered product because of the phenotype conveyed by the introduced gene(s), or because of the use of a vector that had plant pest characteristics. A GE plant product would trigger review if the newly introduced trait posed environmental or other safety-related risks. The review was conducted by the Animal and Plant Health Inspection Service (APHIS) of the USDA, pursuant to its statutory authority under the Plant Protection Act of 2000. (Depending on the product, additional oversight by the FDA or EPA could be required). Today, genetic alteration has moved beyond simple gene transfer into more precise techniques for changing the genome of an organism. Now, in a regulatory first, APHIS has made a determination that a white button mushroom altered by CRISPR/Cas9 gene editing technology to exhibit reduced browning is an “unregulated article” that will not require the kind of formal review usually applied to traditionally genetically engineered products containing foreign DNA: 
APHIS does not consider CRISPR/Cas9-edited white button mushrooms as described in your October 30, 2015 letter to be regulated. 
Here, CRISPR/Cas9 gene editing technology was used to introduce a small deletion in a polyphenol oxidase gene in the mushroom, with the result that the altered enzyme cannot produce the browning that shortens shelf life. The final product has no foreign DNA and no plant pest characteristics. This decision by APHIS follows earlier determinations that have resulted in at least 10 genetically altered products being approved without requiring a formal review. These products have been produced with, e.g., techniques that did not rely on the introduction of new genetic material using any plant pest vector, or non-CRISPR gene editing technologies. This shift in regulation highlights how modern genetic alteration writ large encompasses multiple technologies, some of which fall into an existing regulatory mandate, and some of which do not. The central theme of biotechnology regulation to date has been to focus on the product, not the process. As far back as the introduction of the federal Coordinated Framework for Regulation of Biotechnology in 1986, the prevailing scheme ensured that genetically engineered products would not be singled out for heightened review simply because of the way they were produced. The product was the focus; more precisely, the actual phenotypes of the GE plants or insects were evaluated to identify traits that required additional oversight. The traditional dichotomy between product-based or process-based paradigms for regulation biotechnology products has been criticized as a poor fit for the realities of the biotech marketplace. Evidence for an evolution of the regulatory scheme has been provided by the Obama administration’s announcement of a deliberative process to overhaul and modernize the regulation of biotech products, with the recruitment of the FDA, EPA, and USDA in the process (see earlier post). This regulatory renewal will no doubt eliminate a strict focus on gene transfer as the only genetic technology producing altered organisms, and strive to broaden the definition of the field of genetic alteration to reflect new realities, such as CRISPR and other gene-editing technologies. Then the calculus of risk/benefit analysis will need to be applied, in the context of emerging genetic technologies where risk profiles are not yet established.