Animal Biotechnology: Opportunities and Obstacles Alison Van Eenennaam, Ph.D.

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University of California, Davis, USA Email: alvaneenennaam@ucdavis.

1 Animal Biotechnology: Opportunities and Obstacles Alison Van Eenennaam, Ph.D. Cooperative Extension Specialist Animal Biotechnology and Genomics Department of Animal Science University of California, Davis, USA Photo credit: Cornell Alliance for Science Animal Genomics and Biotechnology Education

2 Animal breeders have made remarkable genetic progress based solely on phenotype-based selection Animal Genomics and Biotechnology Education

3 The 8-week old body weight of broiler (meat) chickens has increased from 0.81 kg to 3.14 kg over the period 1957 to 2001, and approximately 80% of this four-fold increase has been the result of genetic selection. Havenstein, G., et al. (2003). Growth, livability, and feed conversion of 1957 versus 2001 broilers when fed representative 1957 and 2001 broiler diets. Poultry Science 82, Animal Genomics and Biotechnology Education

4 Genetic engineering (GE) can be defined as the manipulation of an organism s genes by introducing, eliminating, or rearranging specific genes using the methods of modern molecular biology, particularly those techniques referred to as recombinant deoxyribonucleic acid (rdna) techniques

5 Approved commercially-available Genetically Engineered (GE) food animals in the United States Animal Genomics and Biotechnology Education

6 Genetically engineered animals for agricultural applications

7 Genetic improvement (permanent, cumulative) as a solution to animal disease rather than chemicals

8 Mastitis-resistant cows (inflammation of mammary gland) Nature Biotechnology 23:

9 Mad cow -resistant cows (bovine spongiform encephalopathy (BSE)) Nature Biotechnology 2007 PNAS 2006

2011 Science 331:223-226. www.roslin.ed.ac.

10 GE Chickens That Don't Transmit Bird Flu Breakthrough could prevent future bird flu epidemics 2011 Science 331: Animal Genomics and Biotechnology Education

TRYPANOSOMIASIS (African sleeping sickness) in SUB-SAFARAN

sickness and 3 million cattle deaths annually 35 million

to these drugs 90% of the crops grown in sub- Saharan Africa

more than $4 billion in losses every year http://www.ilri.

11 TRYPANOSOMIASIS (African sleeping sickness) in SUB-SAFARAN AFRICA Several thousand people die of African sleeping sickness and 3 million cattle deaths annually 35 million doses/year of Trypanocidal drugs 13 economies have resistance to these drugs 90% of the crops grown in sub- Saharan Africa are produced without animal power, which costs the continent more than $4 billion in losses every year Slides: Jayne Raper; CUNY Animal Genomics and Biotechnology Education

$2 million grant from the Bill & Melinda Gates Foundation and the US National Science Foundation to develop trypanosomiasis-resistant ApoL-1 GE cattle.

12 $2 million grant from the Bill & Melinda Gates Foundation and the US National Science Foundation to develop trypanosomiasis-resistant ApoL-1 GE cattle. Trypanosomiasis is a disease caused by blood parasites of the genus Trypanosoma and transmitted in Africa by tsetse flies (Glossina spp). More than 30 tsetse fly species and subspecies infest an area of 8.7 million Animal Genomics and Biotechnology Education

13 What is the problem we are trying to solve? Foot and Mouth Disease

14 Foot & Mouth Disease in UK 6 to 10 million animals slaughtered from 10,000 farms $ 3.5 to $ 6 billion lost, Numerous producer suicides

15 What is the problem we are trying to solve? Twenty percent of animal protein production is lost to disease Van Eenennaam, A.L. and A.E. Young Animal agriculture and the importance of agnostic governance of biotechnology. Agriculture and Food Security 4:21

16 The Fearmongering

17 Animal Genomics and Biotechnology Education

18 Animal Genomics and Biotechnology Education

19 Fast growing salmon The founder female was generated in years ago Nature Biotechnology 10:

21 Fish reach adult size in 16 to 18 months instead of 30 months

The regulation of genetically engineered (GE) animals in US is under Food & Drug Administration The Food and Drug Administration s Center for Veterinary Medicine evaluates GE animals under the new

22 The regulation of genetically engineered (GE) animals in US is under Food & Drug Administration The Food and Drug Administration s Center for Veterinary Medicine evaluates GE animals under the new animal drug provisions of the Federal Food Drug and Cosmetic Act (FFDCA). The act defines drugs as articles (other than food) intended to affect the structure or any function of the body of man or other animals. The rdna construct in the resulting GE animal is thus a regulated article that meets the drug definition; the GE animal itself is not a drug.. rdna construct

24 Timeline of AquAdvantage regulatory process 27 years from discovery to approval? Year Event 1989 Founder AquAdvantage fish produced in Canada 1995 FDA review of AquAdvantage salmon begins (INAD) 2001 First regulatory study submitted by Aqua Bounty Technologies to U.S. FDA for a New Animal Drug Applications (NADA) 2009 FDA guidance on how GE animals will be regulated Final AquAdvantage regulatory study submitted to FDA 2010 FDA VMAC meeting on AquAdvantage salmon (9/20/10) 2015 November 19 th, 2015 Approval (>$60 million to bring the AquAdvantage salmon through the regulatory approval process) 2016 January: US FDA issues a ban on the import and sale of GE salmon until FDA publishes final labeling guidelines for informing consumers of such content. The ban was the result of language Alaska Sen. Lisa Murkowski introduced into the 2016 fiscal budget, or omnibus, bill. It also authorizes an independent scientific review of the effects of GE salmon on wild salmon stocks and for human consumption. March: a coalition of environmental organizations sues US FDA over approval of GE salmon approval May: Canadian Approval of AquAdvantage for sale in Canada December: FDA bills AquaBounty for $113,000 Animal Drug User Fee for their approved animal drug product despite continued FDA ban on the import and commercial sale of AquAdvantage fillets

25 What is the problem we are trying to solve? To efficiently produce land-based Atlantic salmon in on-land systems More efficient: Less feed to produce a serving of fish Less disease spread to wild populations Decreased use of antibiotics ScienceLaw

26 Gene or Genome Editing What are we talking about? Meganuclease Zinc finger TALENs CRISPR/Cas9 Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotech 2014;32:

27 How might gene editing be used in animal breeding? Species Target TargetedTrait/Goal Cattle Intraspecies POLLED allele substitution No horns Myostatin gene knockout Increased muscle yield Beta-lactoglobulin gene knockout Elimination of milk allergen Insertion of lysostaphin transgene Disease resistance Insertion of lysozyme transgene Disease resistance Insertion of SP110 transgene Resistance to tuberculosis Chicken Ovalbumin gene knockout Elimination of ovalbumin in egg Insertion of Immunoglobulin heavy chain locus Germline gene editing Goat Myostatin gene knockout Prion protein gene knockout Beta-lactoglobulin gene knockout Increased muscle growth Elimination of prion protein Elimination of milk allergen Pig CD163 gene knockout PRRS Virus Resistance Interspecies RELA allele substitution African Swine Fever Resistance Myostatin gene knockout Increased muscle yield Sheep Myostatin gene knockout Increased muscle yield Van Eenennaam, A. L Genetic Modification of Food Animals. Current Opinion in Biotechnology. 44: Animal Genomics and Biotechnology Education

28 What problem are we trying to solve? PRRS virus affects millions of pigs globally, annual cost to industry is $600 million in US, >$1 billion in Europe Holtkamp et al Geneedited pigs are protected from porcine reproductive and respiratory syndrome virus (PRRSV). Nature Biotechnology 34:20-2.

29 What is the problem we are trying to solve? Need to manually remove horns from dairy calves to protect human handlers and other animals Carlson DF, Lancto CA, Zang B, Kim E-S, Walton M, et al Production of hornless dairy cattle from genome-edited cell lines. Nat Biotech 34:

31 Will gene editing be a trigger for regulatory oversight? Yes/No/Maybe The Cartagena Protocol defines Living modified organism to mean any living organism that possesses a novel combination of genetic material obtained through the use of modern biotechnology "Modern biotechnology" means the application of: a. In vitro nucleic acid techniques, including recombinant deoxyribonucleic acid (DNA) and direct injection of nucleic acid into cells or organelles, or b. Fusion of cells beyond the taxonomic family, that overcome natural physiological reproductive or recombination barriers and that are not techniques used in traditional breeding and selection

32 Editing may or may not introduce rdna and it may or may not be transgenic Meganuclease Zinc finger TALENs CRISPR/Cas9 Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotech 2014;32: Animal Genomics and Biotechnology Education

Aleksandra Domanović and Spencer Lowell http://www.fda.

33 2017 FDA draft guidance considers all gene edited animals whose genomes have been altered intentionally to be drugs Image by Aleksandra Domanović and Spencer Lowell

34 Previously, FDA used the term genetically engineered to refer to animals containing recombinant DNA constructs. The new guidance #187 uses the phrase animals whose genomes have been altered intentionally

35 Are Gene Edited Polled Calves Novel? Naturally-occurring bovine allele at polled locus What is the new animal drug in this case? Am I a drug or a bull? Tan et al Efficient nonmeiotic allele introgression in livestock using custom endonucleases. PNAS 110:

36 Does it make sense to regulate polled dairy calves differently to polled beef calves? Carroll D, Van Eenennaam AL, Taylor JF, Seger J, Voytas DF Regulate genomeedited products, not genome editing itself. Nat Biotech 34: 477-9

Use of gene editing to introduce a naturally-occurring polled allele into Holstein cattle versus selective breeding Attribute Polled Holstein through gene editing Polled Holstein through

37 Use of gene editing to introduce a naturally-occurring polled allele into Holstein cattle versus selective breeding Attribute Polled Holstein through gene editing Polled Holstein through introgression Phenotype: No horns YES YES Mutation uniquely detectable NO NO Food safety concerns associated with phenotype # generations taken to achieve polled >15/16 Holstein NO ONE (FAST) NO MANY (SLOW) Linkage drag? NO YES Improved animal welfare YES YES Regulated? Likely to happen Depends on definition of regulated article Not if takes years and costs millions of dollars NO NO

38 Animal breeders intentionally selected for this natural alteration of the myostatin gene in Belgium Blue Animal Genomics and Biotechnology Education

39 Gene editing of myostatin to obtain double muscle Nellore cattle same sequence Belgian Blue alteration. Only the precise, intentional alteration would be a drug? Proudfoot C, et al Genome edited sheep and cattle. Transgenic Res Feb;24(1):

Many animal breeding goals, including genetically engineered and gene edited

animal well-being, efficiency and reduced environmental footprint Comments on

a new animal drug can be submitted until June 19 th, 2017 Speak up scientists

40 Many animal breeding goals, including genetically engineered and gene edited animals, have the potential to address sustainability goals including improved animal well-being, efficiency and reduced environmental footprint Comments on the revised FDA Draft Guidance #187 regulating intentional gene alterations as a new animal drug can be submitted until June 19 th, 2017 Speak up scientists be a #Force for Science

41 Parting thoughts Regulatory processes should be proportional to risk and consistent across products that have equivalent levels of risk. Regulations based on how products are made are inconsistent with science-based risk assessment unless there is something inherently risky about the process, as compared to existing methods GE animal regulatory burdens are disproportionately high and are associated with unaccountable delay and considerable uncertainty. These regulatory burdens are not justified by scientific evidence or experience Currently regulatory language is insane human intention is not associated with risk, and regulating every SNP as a drug ignores the very real plasticity of genomes which are constantly undergoing spontaneous de novo mutations (aka genetic variation and evolution) Given the importance of enabling safe innovation in breeding, there is an urgent need to ensure a science-based, risk-driven regulatory framework for the use of gene editing in agricultural breeding programs.

42 Thanks for inviting me! My laboratory receives public funding support from the National Institute of Food and Agriculture and the Biotechnology Risk Assessment Grant (BRAG) program, U.S. Department of Agriculture, under award numbers , , and Animal Genomics and Biotechnology Education

Innovation in Agricultural Science

Innovation in Agricultural Science Alison Van Eenennaam, Ph.D. Cooperative Extension Specialist Animal Biotechnology and Genomics Department of Animal Science University of California, Davis, USA Email: