August 31, 2016

Will the 2016 Presidential Candidates Debate Science and Technology Policy?

In an effort to import more scientifically-based policy issues into the 2016 election,, a coalition of science-based and academic organizations, has issued a challenge to the Presidential candidates regarding their views on policies impacting the science sector (broadly construed). is calling for a Presidential debate focused on science and technology issues, with an online petition in support of such an event posted on their site. This effort was also conducted in earlier Presidential elections (see 2012 initiative); to date, there have been no such debates. The official Presidential debates are managed by a somewhat ad hoc organization, the Commission on Presidential Debates. The official debates this election cycle do not have subject matter limits. has also posted a list of 20 questions, culled from submissions by the participating organizations, for the candidates (Clinton, Trump, Johnson, Stein), who are invited to submit answers. There are foundational questions that impact the science sector generally, related to innovation, research funding, education, immigration and regulations. The most prominent life science-related questions are the following: 
Biodiversity: Biological diversity provides food, fiber, medicines, clean water and many other products and services on which we depend every day. Scientists are finding that the variety and variability of life is diminishing at an alarming rate as a result of human activity. What steps will you take to protect biological diversity?
Food: Agriculture involves a complex balance of land and energy use, worker health and safety, water use and quality, and access to healthy and affordable food, all of which have inputs of objective knowledge from science. How would you manage the U.S. agricultural enterprise to our highest benefit in the most sustainable way?
Public Health: Public health efforts like smoking cessation, drunk driving laws, vaccination, and water fluoridation have improved health and productivity and save millions of lives. How would you improve federal research and our public health system to better protect Americans from emerging diseases and other public health threats, such as antibiotic resistant superbugs?
Vaccinations: Public health officials warn that we need to take more steps to prevent international epidemics from viruses such as Ebola and Zika. Meanwhile, measles is resurgent due to decreasing vaccination rates. How will your administration support vaccine science?
There are several questions related to mental health issues, and the epidemic of opioid abuse. The rest of the list poses specific questions related to energy, environment, space, and the Internet. 

It is likely that the campaigns will respond to the written questions. Probably the most conspicuous omission (relative to the volume of recent debate and controversy in the life science community) is the emerging issue of the management and uses of gene-editing technologies (see earlier posts here and here). Additionally, there is no explicit acknowledgment of dual-use research in the life sciences (see earlier posts here and here). Nonetheless, the organization does elevate the visibility of science-related policies as central aspects of 21st century governance, and implicitly suggests that any credible candidate in 2016 needs to exhibit some degree of scientific literacy.

July 23, 2016

Congressional Impasse on Zika Virus Funding Impacts Public Health Efforts in Peak Summer Months

The Zika virus outbreak is spreading in the U.S., according to local public health authorities and the federal Centers for Disease Control (CDC); international Zika virus cases are also increasing. Infection occurs because of a mosquito bite that transmits the virus, and most public health interventions to date concentrate on limiting exposure to the mosquito (Aedes aegypti). As of yet, there is no vaccine or specific treatment for the Zika virus. The discovery that Zika virus infection in pregnant women can lead to birth defects, including microcephaly, raised the alarm about the spread of the virus in this population (see earlier post here). To date, there are about 1400 reported cases in the U.S; there are about 400 cases of Zika infection in pregnant women. Most cases in the U.S. are traced to individuals traveling outside the country, returning with the infection; Puerto Rico, Brazil and other Caribbean and Latin American countries are some of the hotspots of transmission. Now, however, there  appear to be are several cases of local transmission of the Zika virus in Florida, which means that the virus is gaining a foothold in the U.S. itself. As in most public health crises, the government is tasked with providing increased support to local authorities, funding for treatment developments, and other activities. Congress has been in a stalemate over emergency Zika virus funding over the last month. President Obama sought $1.9 billion in new dedicated funding; the House of Representatives approved $1.1 billion. On to the Senate, where several provisions inserted into the funding bill encountered opposition; most notably, an explicit ban on Planned Parenthood as the recipient of any new funds. As discussed in an earlier post, because of the risk that Zika virus infection poses to pregnant women, who are at risk to give birth to babies with developmental disorders (and not all are known at this point), access to contraception and other reproductive services would appear to be a key ingredient in minimizing the birth of Zika-affected babies. That’s where the usual political conflict over reproductive and family planning funding entered the Zika funding legislation, and created an impasse. So to date, the Senate has not approved the funding that the House approved, and Congress has taken its usual lengthy summer break without acting on emergency funding for Zika virus research and support. The 7-week hiatus in the Zika funding battle has dismayed federal public health officials. The American Medical Association  (AMA) faulted Congress
At a time when concerns continue to mount about the nation's readiness to protect the public from the Zika virus, the AMA is disappointed by Congress' failure to pass legislation before adjourning for summer recess that would provide the resources necessary for our country to respond to this looming public health crisis. Without ensuring there are sufficient resources available for research, prevention, control and treatment of illnesses associated with the Zika virus, the United States will be ill-equipped to deploy the kind of public health response needed to keep our citizens safe and healthy—especially since the spread of mosquito-borne illness is accelerated during the summer months.
Editorials in some of the hardest hit areas of the country noted how the impasse would adversely affect their regions; here is the Palm Beach Post from Florida on the local impact: 
Congress has left the building. And in its dysfunctional wake, it leaves yet another failed effort at passing crucial emergency funding to fight the spread of the dreaded Zika virus. For at least the next seven weeks, Florida — which has distinguished itself as ground zero for cases of the mosquito-borne virus — will just have to hope that the worst part of the rainy storm season doesn’t translate into more infections. (Palm Beach County has seen about 12 cases of travel-related Zika.) It may be a long, hot summer. Mosquitoes that carry the Zika virus breed year-round here, and the number of infections in the continental United States is mounting. On Monday, the state Health Department reported 13 new cases of the Zika virus in Florida - the most reported cases of the virus in a single day. Moreover, federal officials say they will have to postpone a slew of anti-Zika actions. For example, the U.S. Centers for Disease Control and Prevention will have “limited capacity” to help with efforts to counter mosquito populations in the continental U.S. and territories. 
Yes, it should be noted that the CDC is now dispersing about 60 million dollars currently to localities to augment public health efforts, but these are “stopgap” awards that will not approach the scale of the demand. Congress returns on September 6th.

July 17, 2016

Congress Passes Federal Labeling Requirement for Genetically Engineered Foods; State Labeling Laws Would Be Preempted

Vermont enacted the first state law that requires the manufacturers of food products with genetically engineered (GE) ingredients to label their food products accordingly. Its Act 120 became law on July 1, 2016. However, for decades, there has been an ongoing battle at the federal level over whether a national labeling scheme should be enacted (the term GMO/genetically modified organism is also used). (See earlier posts for more background). So, after the Vermont bill became effective, there was a flurry of activity in Congress again to address the issue of a federal labeling scheme for GE food products. (The FDA has not required labels on food products with GE ingredients, in a policy that dates back to 1992). The Senate recently passed a bill, S. 764, that would mandate a particular federal labeling scheme for GE ingredients, and would also preempt any state labeling laws. The federal bill uses the term "bioengineering" to describe the products covered by the law: 
[F]ood - (A) that contains genetic material that has been modified through in vitro recombinant [DNA] techniques; and (B) for which the modification could not otherwise be obtained through conventional breeding or found in nature. 
There is an explicit statement of the preemption achieved by this legislation: 
No State or a political subdivision of a State may directly or indirectly establish under any authority or continue in effect as to any food or seed in interstate commerce any requirement relating to the labeling of whether a food (including food served in a restaurant or similar establishment) or seed is genetically engineered (which  shall  include such other similar terms as determined by the Secretary of Agriculture) or was developed or produced using genetic engineering, including any requirement for claims that a food or seed is or contains an ingredient that was developed or produced using genetic engineering.
This last provision is aimed at the recent Vermont law, as well as other initiatives in Connecticut, Maine and Alaska. Since its enactment in 2014, the Vermont law had already impacted the food and restaurant industries, with some major players declaring that they would provide labels in anticipation of the law (see here). It was apparent that the Vermont law had immediate national impact, as food manufacturers faced compliance with the statute or avoidance of Vermont’s market (practically unworkable). Now, the House of Representatives has passed a version of the recent Senate bill, and it goes to President Obama for signing; it appears that he will sign it. The clear effect of the federal bill is to preempt the long-sought state labeling laws. However, does this bill actually require a label? The bill departs from other labeling proposals over the years (state and federal) in that it contains no explicit requirement to provide a “GMO” or other GE-related name on the main label of the product. The actual labeling scheme in the new federal law is quite elastic, describing the format of the labeling as follows: 
[T]he form of a food disclosure under this section be a text, symbol, or electronic or digital link. 
Thus, a consumer could use a smartphone to read a QR code, or utilize a provided link to access information, or read whatever disclosure material the manufacturer has chosen to provide. The forms of the notification could be arguably obscure, and indirect. In other words, at least so far, there will be no uniformity of disclosure. Already, there are allegations that the bill is discriminatory in that it will make it harder for some consumers to pursue the informational references; access to digitally formatted information is not universal. The USDA has two years to make the law operational, and may refine the labeling formats in that period, subject to public input.

June 30, 2016

Supreme Court Denies Certiorari in Sequenom v. Ariosa

The Supreme Court has denied certiorari for the appeal in Sequenom v. Ariosa (Fed. Cir. 2015). There has been widespread interest in this case, which invalidated patent claims to a method of performing prenatal diagnosis using cell-free fetal DNA (cffDNA) collected from a maternal blood sample (see earlier post here). The method has been critical to the development of non-invasive prenatal testing (NIPT). NIPT testing can be used to identify chromosomal abnormalities or other genetic aberrations, and it offers an alternative to the invasive techniques of amniocentesis or chorionic villi sampling, both of which carry some risk to the fetus. Sequenom would have followed a sequence of recent Supreme Court decisions, AMP v. Myriad (2013) and Mayo v. Prometheus (2012) (Mayo) that each invalidated patent claims in the life sciences for a lack of patentable subject matter. The most controversy has followed the Mayo decision, which was then followed by a software-related patent case, Alice v. CLS (2014). The Mayo/Alice pair has distilled an analytic framework for determining when method patent claims impermissibly read on a law of nature or a natural phenomenon. The framework has been criticized for being overly broad, and for having a deleterious impact on the viability of method patent claims in the life sciences, particularly in the diagnostic testing sector. In the Federal Circuit decision in Sequenom last year, the concurrence by Judge Linn also took direct issue with the Court’s recent dictates in these method patent cases. But the Court did not take the invitation to focus on its own recently developed test. So in deciding not to take the case, the Court will not - for now - review its Mayo/Alice roadmap. One example of continuing influence of the Court's current paradigm is Cleveland Clinic v. True Health Diagnostics (N.D. Ohio 2016), invalidating the method patent claims on a method of detecting cardiovascular disease by detecting the elevation of specific enzyme levels (see earlier post here).

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.

April 29, 2016

Zika Virus Outbreak: Research Funding, Commercial Test, U.S. Risk Map

In the ongoing outbreak of Zika virus infection across parts of North and South America, there are several developments which signal increasing concern over the exact impact and geographic reach of the virus (the first death in the U.S. linked to the virus has been reported). At least 55 countries report Zika outbreaks, according to the World Health Organization. The virus is spread by mosquitos, specifically the Aedes aegypti. In the U.S., 426 cases of Zika-infected individuals have been reported. Although a course of infection may be mild and easily resolved in most individuals, Zika has become a high-profile infectious disease because viral infection in pregnant women has been linked to an increased risk of microcephaly in offspring. There are suspicions that more developmental risks to the child of an infected mother may exist, possibly unknown and only seen as development unfolds. In general, the mosquito thrives in warm and tropical climates, but seasonal weather patterns can shift the field of exposure. NASA scientists and other colleagues have published an Aedes aegypti risk map of the U.S., showing that a wide swath of the eastern U.S. is potentially susceptible to mosquito (and thus virus) spread, especially in the upcoming summer of 2016; the potential spread goes north as far as New York City. A commercially available test for detection of the Zika virus received an Emergency Use Authorization (EUA) from the FDA (the Quest Diagnostics Zika RT-PCR test). A current legislative battle over possible increased funding for public health responses to Zika reached a stalemate before Congress adjourned. One bill calls for $1.6 billion in supplemental funding for dedicated Zika virus research and public health capabilities, but is encountering Republican opposition. Some of the political infighting over a federal response to the Zika outbreak recalls earlier conflicts during the Ebola virus crisis. However, the Zika virus is already in the U.S., cases are officially documented, and the upcoming summer portends more infections, not less. The 2016 Summer Olympics in Brazil this summer have already caused concern among attending athletes; the current understanding of transmission suggests that Zika virus cases in the U.S. are largely explained by travel to countries with high risk of infection; that fact will also impact the Olympics participation. No effective treatment or vaccine for the Zika virus is yet developed; increased NIH funding would certainly allow research to expand. Another target for intervention is to reduce the Aedes aegypti mosquito population; already, a British biotechnology has produced a genetically engineered (GE) mosquito that is reproductively crippled and is hoping to conduct trials in the U.S. An upcoming post will examine that option in more detail.

April 7, 2016

Major Overhaul of Federal Biotechnology Regulation is Underway; National Academy of Sciences Invites Public Participation

The federal regulation of biotechnology products is grounded in a design that was first announced in 1986 as the Coordinated Framework (CF) for the Regulation of Biotechnology, later updated in 1992. Those documents have largely shaped the the federal regulatory regime for biotechnology. A key concept in this original framework was that products produced through genetic engineering (or recombinant DNA) techniques would not receive special oversight because of the processes used to produce them. Instead, a risk-based approach was instituted that focused on the characteristics of actual products, not underlying production techniques. In 2015, the White House, through its Office of Science and Technology (OSTP), announced that it would launch an overhaul of the 1992 policy. In the memorandum, the OSTP provided a definition of “biotechnology products” to be included in the review: 
For the purpose of this memo, “biotechnology products” refers to products developed through genetic engineering or the targeted or in vitro manipulation of genetic information of organisms, including plants, animals, and microbes. It also covers some of the products produced by such plants, animals, and microbes or their derived products as determined by existing statutes and regulations. Products such as human drugs and medical devices are not the focus of the activities described in this memorandum. 
Since the 1980’s, the existing coordinated framework has divided the primary regulation of biotechnology products among three agencies: the U.S. Environmental Protection Agency (EPA), the U.S. Department of Agriculture (USDA), and the U.S. Food and Drug Administration (FDA). The OSTP is involved in a more general role as overseer of the regulatory design, rather than as a formal regulatory body. In the memorandum sent to the heads of the EPA, FDA and USDA, the OSTP alludes to the regulatory overlap, redundancy and confusion that has arisen with the multi-agency design: 
Each of the Federal regulatory agencies with jurisdiction over the products of biotechnology has developed regulations and guidance documents to implement its authority under existing laws, resulting in a complex system for assessing and managing health and environmental risks of the products of biotechnology. While the current regulatory system for the products of  biotechnology effectively protects health and the environment, in some cases unnecessary costs and burdens associated with uncertainty about agency jurisdiction, lack of predictability of time frames for review, and other processes have arisen.
As part of the modernization initiative, the Administration held 3 meetings organized by the relevant agencies to receive feedback on the proposed overhaul. Two documents were issued that are helpful to understanding the current climate that is precipitating calls for redesign: a table of current agency responsibilities, and a series of case studies illustrating how a singular GE product can be subject to multi-agency review. Pursuant to the OSTP charge, a committee formed by the National Academy of Sciences, Medicine and Engineering was commissioned to conduct a formal study, “Future Biotechnology Products and Opportunities to Enhance Capabilities of the Biotechnology Regulatory System.” This committee has set the following objectives:
Describe the major advances and the potential new types of biotechnology products likely to emerge over the next 5-10 years. 
Describe the existing risk analysis system for biotechnology products including, but perhaps not limited to, risk analyses developed and used by EPA, USDA, and FDA, and describe each agency’s authorities as they pertain to the products of biotechnology. 
Determine whether potential future products could pose different types of risks relative to existing products and organisms. Where appropriate, identify areas in which the risks or lack of risks relating to the products of biotechnology are well understood. 
Indicate what scientific capabilities, tools, and expertise may be useful to the regulatory agencies to support oversight of potential future products of biotechnology. 
The first public meeting of the NAS committee will be held on April 18, 2016. The agenda for the meeting is posted here.

March 31, 2016

Lawsuit Challenges FDA Approval of Genetically Engineered Salmon

This week, a coalition of environmental, food safety and consumer groups has filed suit against the FDA for its 2015 approval of a genetically engineered (GE) salmon product in 2015 (following several decades of review). The product is AquaAdvantage, made by Aqua Bounty, Inc.  This is the first transgenic animal to be approved by the FDA for food consumption. To produce the GE salmon, Atlantic salmon is engineered to contain the growth hormone gene from Pacific Chinook salmon, which causes the fish to grow in less time; the gene is placed under the control of a promoter from ocean pout, which causes elevated expression of the hormone. The fish are to be only sterile females. The production plans submitted to the FDA describe the preparation of the GE fish eggs in Canada, and the actual production of the fish in Panama (with eventual location in the U.S. as well). Following the approval, Alaska Sen. Lisa Murkowski, an opponent of the FDA's actions (see here), inserted a legislative provision into the 2015 omnibus spending bill, requiring the FDA to develop a labeling scheme for the GE salmon before they enter the market. As a result of that maneuver, the FDA is in the process of complying with that mandate, and the GE salmon is not yet commercially available.

In their press release, the plaintiffs assert several grounds on which the agency’s action does not comply with existing federal law: 
The lawsuit challenges FDA’s claim that it has authority to approve and regulate GE animals as “animal drugs” under the 1938 Federal Food, Drug, and Cosmetic Act. Those provisions were meant to ensure the safety of veterinary drugs administered to treat disease in livestock and were not intended to address entirely new GE animals that can pass along their altered genes to the next generation. The approval of the GE salmon opens the door to other genetically engineered fish and shellfish, as well as chickens, cows, sheep, goats, rabbits and pigs that are reportedly in development. 
The lawsuit also highlights FDA’s failure to protect the environment and consult wildlife agencies in its review process, as required by federal law. U.S. Atlantic salmon, and many populations of Pacific salmon, are protected by the Endangered Species Act and in danger of extinction. Salmon is a keystone species and unique runs have been treasured by residents for thousands of years. Diverse salmon runs today sustain thousands of American fishing families, and are highly valued in domestic markets as a healthy, domestic, “green” food.
The lawsuit was filed in the Northern District of California. The suit could directly test the applicability of the FDA's determination that the insertion of new genetic material amounts to a kind of "veterinary  drug" and thus applications for approval of food from GE animals require a new drug application under the Federal Food, Drug, and Cosmetic Act. According to the FDA: 
FDA regulates GE animals under the new animal drug provisions of the law, and the agency must approve them before they are allowed on the market. Food and animal feed from GE animals will undergo FDA review before the food or feed can be marketed. The Federal Food, Drug, and Cosmetic Act defines a drug as "an article (other than food) intended to affect the structure or any function of the body of man or other animals." Therefore, the rDNA construct intended to change the structure or function of the body of the GE animal is a drug.
The suit also challenges the legitimacy of the FDA's determination that the GE salmon posed no environmental risk, based on an Environmental Assessment; the plaintiffs argue that the FDA is required to perform the more rigorous Environemntal Impact Statement (EIS). The food and restaurant industries had earlier indicated some resistance to selling the GE salmon; Red Lobster and Costco have already announced that the product will not be carried.

March 30, 2016

Vermont Law Requiring Labeling of Genetically Engineered Foods Set to Take Effect as Congressional Opposition Fails

Vermont is on track to implement the nation’s first law requiring the labeling of foods with genetically engineered (GE) ingredients, whether raw or processed. (The term "genetically modified organism" (GMO) is often seen in discussions as well). The state’s Act 120, passed in 2014, was enacted to advance several objectives related to “public health and food safety, environmental impacts” and avoidance of “consumer confusion and deception.” The law states: 
[F]ood offered for sale by a retailer after July 1, 2016 shall be labeled as produced entirely or in part from genetic engineering if it is a product:
(1) offered for retail sale in Vermont; and 
(2) entirely or partially produced with genetic engineering. 
The law further describes the labeling: 
[I]n the case of any processed food that contains a product or products of genetic engineering, the manufacturer shall label the package in which the processed food is offered for sale with the words: “partially produced with genetic engineering;" “may be produced with genetic engineering;" or “produced with genetic engineering.” 
In the two years since its passage, there have been several efforts in Congress to enact a federal law that would reassert federal jurisdiction over the labeling issue and preempt any state labeling laws. The House considered bills in 2015, and the Senate just this month considered its own version. Although a House bill passed, the attempts to establish a federal counterweight to state labeling efforts failed as a similar bill was defeated in the Senate. Efforts to mandate the labeling of GE food products at the national level have consistently failed in Congress, and the FDA has resisted all calls for a national mandate on labeling. Now, as Vermont’s law will take effect on July 1, 2016, preparations for compliance are evident on a number of fronts. The Attorney General has issued a memorandum detailing its enforcement strategy which states: 
Our Office expects that most GE foods on Vermont grocery store shelves will be properly labeled by July 1, 2016. Out of recognition that some food products have longer shelf lives, CP (Consumer Protection Rule) 121 creates a six-month “safe harbor” for foods distributed before July 1, 2016, and offered for retail sale through December 31, 2016. During this six-month period, unless there is evidence that a manufacturer distributed a mislabeled product after July 1, 2016, we will not bring an enforcement action or seek fines for those products. 
Beyond these developments in Vermont, Connecticut and Maine have also passed mandatory GE labeling laws; however, their implementation will only be triggered when a number of states join the effort (see here). On the commercial front, with the Vermont mandate looming, major food manufacturers are releasing plans to add labeling labeling regarding the “genetically engineered” attributes of their food products. General Mills issued a statement
As the discussions continue in Washington, one thing is very clear: Vermont state law requires us to start labeling certain grocery store food packages that contain GMO ingredients or face significant fines. We can’t label our products for only one state without significantly driving up costs for our consumers and we simply will not do that. The result: consumers all over the U.S. will soon begin seeing words legislated by the state of Vermont on the labels of many of their favorite General Mills products. 
Other major companies following suit include Kellogg’s, ConAgra Foods, and Campbell’s Foods. In a departure from other manufacturers, Campbell’s has called for a federally mandated labeling system to systematize labeling, and the company formally withdrew from food industry efforts to oppose GE food labeling laws and initiatives. The effect of the Vermont law is now being realized across the food industry; however, a lawsuit filed against Vermont's law by the Grocery Manufacturers Association (GMA) is still working through the federal courts: the trial judge denied summary judgment and a preliminary injunction for GMA; an appeal of the district court's injunction ruling is on appeal at the Second Circuit.

March 26, 2016

Sequenom Petitions Supreme Court to Review Denial of Prenatal DNA Testing Patent

In the closely-watched patent law case with significant implications for the patenting of diagnostic and other methods in biomedicine, Ariosa v. Sequenom (Fed. Cir. 2015), new developments could result in the case finally reaching the Supreme Court. Sequenom (the assignee of the patent) has now filed a petition for certiorari at the Supreme Court, seeking to overturn the ruling of the Federal Circuit that invalidated its patent to a method of performing prenatal diagnosis using cell-free fetal DNA (cffDNA) collected from a maternal blood sample (see here). Here is Claim 1 of U.S. Patent No. 6,258,540: 
A method for detecting a paternally inherited nucleic acid of fetal origin performed on a maternal serum or plasma sample from a pregnant female, which method comprises amplifying a paternally inherited nucleic acid from the serum or plasma sample and detecting the presence of a paternally inherited nucleic acid of fetal origin in the sample. 
The Federal Circuit applied a two-part test from  Mayo v. Prometheus (2011) and found a lack of patentable subject matter: 
Thus, in this case, appending routine, conventional steps to a natural phenomenon, specified at a high level of generality, is not enough to supply an inventive concept. Where claims of a method patent are directed to an application that starts and ends with a naturally occurring phenomenon, the patent fails to disclose patent eligible subject matter if the methods themselves are conventional, routine and well understood applications in the art. The claims of the ’540 patent at issue in this appeal are not directed to patent eligible subject matter and are therefore, invalid. 
The petitioners argue that earlier Supreme Court case law does not mandate the result that the Federal Circuit arrived at. Citing the landmark case of Diamond v. Diehr (1981), concerning whether a patent claim to a rubber-curing method preempted the use of a mathematical formula, the petition notes that Diehr stated that “[i]n determining the eligibility of respondents’ claim[s]...under §101, their claims must be considered as a whole.” The petition further notes that the recent Mayo test is not rooted in the central imperative for excluding certain subject matter from patenting, which is a preemption of fundamental knowledge that becomes an obstacle to scientific progress. They characterize the Mayo test as a rote application of a two-step formula that avoids an actual analysis of whether a patent claim “preempts” further use of fundamental subject matter in the field. The petitioners argue that no preemption occurs here: 
Demonstrated methods show that cffDNA may be used without practicing each of the patent’s core steps: One need not fractionate the sample; one may forego  amplification; and one can use cffDNA without distinguishing paternally inherited sequences at all. These non-preempted innovations are conclusive evidence that petitioner’s patent does not claim the natural phenomenon itself —instead claiming merely one set of applications then  known only to the inventors. 
The petition further develops the impact of the Ariosa (and Mayo) decisions on a wide swath of method patents in the life sciences: 
[T]he decision below threatens to destroy the predictability and certainty the patent system needs to do its job. At a minimum, the biomedical community is now adrift in determining whether or not patents will ever be available in these or related fields. And that’s essentially the ballgame, because once you must seriously question the availability of patent protection, you cannot: (1) confidently invest in research; (2) confidently invest in clinical validation and commercialization of existing patents; or (3) confidently predict that it is better to disclose your discoveries through the patent system than it is to keep them a trade secret. 
In the denial for rehearing en banc, several judges of the Federal Circuit noted their disagreement with an outcome mandated by the Mayo test, but not commanded by the overall objectives of the patentable subject matter doctrine. This case is well-positioned to provide the Court with an opportunity to investigate the method (diagnostic, therapeutic, etc.) claims in biotechnology and consider whether the Mayo test has imposed a rigid formula that short-circuits case-by-case consideration of preemption. For that reason, the Court may respond to the appeal for clarification and review and accept the case; if so, this case would add to an unprecedented involvement by the Court in this patent law doctrine (5 cases in 6 years).

March 15, 2016

More Diagnostic Method Patent Claims Found Invalid Under Mayo/Alice Framework

Some instability in the interpretation of allowable subject matter in biotechnology patent law continues, as the life science sector contends with recent Supreme Court decisions affecting both composition of matter and method claims. For composition of matter claims, the AMP v. Myriad (2013) Supreme Court case established that an isolated gene was not patentable because it is a product or law of nature, while synthetic non-natural DNA sequences (cDNA) were patentable. The method claims in that case (largely directed to methods to identify mutations in the BRCA1 and BRCA2 genes) were held to be invalid, on the basis that such claims were directed to abstract ideas. Two other cases from the Court established a test for method claims in order to differentiate between impermissible claims to abstract ideas, laws of nature, natural phenomena, and permissible claims to applications or inventive manipulation of such subject matter. The test from Mayo v. Prometheus (2011) (a case with patent claims to method of drug optimization using metabolite testing) was as follows
First, we determine whether the claims at issue are directed to a patent-ineligible concept. If the answer is yes, then we next consider the elements of each claim both individually and “as an ordered combination” to determine whether additional elements “transform the nature of the claim” into a patent-eligible application. 
Later, in the software-based Alice v. CLS (2014), the Court reaffirmed this test. In the last several years, lower court cases have contended with applying this test to challenged life science method claims. Most notably, in Ariosa v. Sequenom (Fed. Cir. 2015), using the Mayo test, the Federal Circuit decided that methods for the detection of fetal DNA in maternal serum were invalid as directed to natural laws (see here). That case is likely to be appealed to the Supreme Court.  A recent district court case illustrates the ongoing impact of all of these decisions on patent claims to diagnostic methods iin biotechnology. In Cleveland Clinic v. True Health Diagnostics (N.D. Ohio 2016), the court considered a defendant’s invalidity challenge on its motion to dismiss under Rule 12(b)6. A representative claim from one of the patents in suit is as follows: 
14. A method of assessing a test subject's risk of developing a complication of atherosclerotic cardiovascular disease, comprising: 
determining levels of myeloperoxidase (MPO) activity, myeloperoxidase (MPO) mass,or both in a bodily sample of the test subject, said bodily sample being blood,serum, plasma, blood leukocytes selected from the group consisting of neutrophils and monocytes, or any combination thereof; 
wherein elevated levels of MPO activity or MPO mass or both in the subject's bodily sample as compared to levels of MPO activity, MPO mass or both, respectively,in comparable bodily samples obtained from control subjects diagnosed as not having the disease indicates that the test subject is at risk of developing a complication of atherosclerotic cardiovascular disease. 
Effectively, the method utilizes the observation that levels of the enzyme MPO correlate with blood vessel inflammation, and can thus be indicative of an elevated risk of a cardiovascular event. The patent claim is somewhat similar to the method claim in Mayo, where the observation of a metabolite level was indicative of pharmaceutical effectiveness (or toxicity). On a motion to dismiss by the defendant, the district court applied the Alice/Mayo test and decided that the correlation between MPO and cardiovascular risk was a law of nature, and that the addition of claim steps to “determining” and “comparing” only supplied routine and conventional processes that did not constitute an “inventive concept.” The court noted its standard that it would only “grant the motion only if defendant is able to show invalidity by clear and convincing evidence,” which it found here. The Cleveland Clinic decision (and other similar opinions) reflect the continuing influence of the Mayo/Alice test on life science method claims despite judicial criticism; the field awaits a possible return by the Supreme Court to these issues if Sequenom files a petition for certiorari this year and the Court accepts review.