Cloning Wildlife and Editing their Genes to Protect Them and Us

Elizabeth Ann, the first cloned black-footed ferret. Image courtesy of USFWS Mountain Prairie

Tweaking the genes of wild animals could save endangered species and protect humans from disease. What could possibly go wrong?

On December 10, 2020, Elizabeth Ann made history just by being born. She isn’t a British royal, an American married to a British royal, a movie star’s daughter, or even human for that matter. Elizabeth Ann is a ferret—but perhaps the most famous ferret of all time. 

More specifically, she is the clone of a black-footed ferret named Willa who has been dead for more than 30 years. Elizabeth Ann’s momentous birth marks the first successful cloning of an endangered species native to North America (endangered species like the gaur, or Indian bison, and the mouflon, a wild sheep originally found in Corsica and Sardinia, have been cloned previously). If she can breed successfully, Elizabeth Ann will add valuable genetic diversity to the very small estimated population of around 600 remaining black-footed ferrets, which are all descended from just seven animals. But low genetic diversity isn’t the only thing standing in the way of these ferrets making a comeback. The other major threat is disease. 

Diseases are a huge problem for many endangered species, but, as the previous year has emphasized all too well, diseases that circulate in animals can also have disastrous consequences if they jump to humans. Genetic engineering of animals in the wild might offer us a way to protect not only our furry friends and feathered compadres, but ourselves as well. Although still in the early stages of research, scientists around the world are working on numerous projects to engineer animals to be resistant to diseases that can impact humans as well, including plague, Lyme disease, dengue fever, and Zika. 

Black-footed ferrets like Elizabeth Ann are especially susceptible to plague. While many of us have not given much thought to plague since our medieval history class, the bacterium responsible for this deadly disease—Yersinia pestis—is very much alive and well, circulating in populations of small mammals throughout North and South America, Africa, and Asia. 

“It’s all over the western part of the United States,” says Bridget Baumgartner, a molecular biologist involved in the black-footed ferret conservation project at Revive & Restore, a wildlife organization that promotes the use of biotechnology in conservation. Unlike the black-footed ferret, plague isn’t native to the Americas—scientists think it was introduced a little over one hundred years ago, when the first known outbreak hit San Francisco in 1900. “Because it’s new here, the black-footed ferret succumbs so quickly that they don’t ever develop an immune response to it,” says Baumgartner. 

Right now, conservationists have to individually vaccinate each black-footed ferret against plague. While this is effective for now, it may not be a good solution in the long-run. “It just creates this problem where they’re always going to be dependent on humans for their ability to survive in the wild. And that’s not at all the goal of the program,” Baumgartner says. 

Genetic engineering might be the key to this frankly adorable species’ long-term survival in the wild. 

A picture of a Black-Footed Ferret popping its head out from a hole in the ground.
The black-footed ferret. Image courtesy of USGS

Normally, different flavors of antibodies are made by B cells through a random genetic cut-and-paste process called somatic recombination. If a B cell has antibodies that are useful (i.e. they can bind to an antigen in a vaccine or a pathogen), that B cell gets copied many times over and refined. The immune system is then able to produce lots of the correct type of antibody, helping the body fight off the infection. But sometimes the infection moves faster than the immune system can respond, spelling disaster for the unfortunate person or animal.

Genetic engineering provides a shortcut. Instead of relying on the time-consuming process of B cells multiplying, scientists can insert the genetic code to make an anti-plague antibody into an animals’ DNA and then instruct any cell type to make these antibodies. That way, animals don’t have to wait for a vaccine to develop a large group of cells capable of making an anti-plague antibody—they will be born with a population of cells that are constantly churning out anti-plague antibodies, keeping them protected from the disease. Even better, these genetic instructions would be passed down to the animal’s offspring as well, eliminating the need for further interventions. 

But figuring out exactly how to do this is tricky and with fewer than a thousand black-footed ferrets left in existence, scientists don’t want to troubleshoot the process by practicing on this endangered species. Instead, they’re starting with lab mice, whose genetics are extremely well-studied. “We’ve created a transgenic line of mice that express antibodies against plague in their germline, and can be passed on from generation to generation,” says Baumgartner. Once mouse testing is complete, researchers would also perform testing in the more common domestic ferret to confirm safety and efficacy before implementing this technique in the black-footed ferret.

Baumgartner says that if this genetic engineering is successful, it will not only keep the ferrets from dying of the disease, it will also keep them from transmitting it. While engineering plague resistance in the black-footed ferret is largely for conservation purposes, blocking transmission is an important factor if scientists ever want to apply this technique to other species in order to protect humans. Perhaps in the future, this genetic engineering trick could be applied to other animals that transmit plague to humans (either through bites or via fleas)—like prairie dogs in the United States, black rats in Madagascar, or great gerbils in Kazakhstan. 

Other projects are more directly targeted at reducing human disease by engineering wildlife. Kevin Esvelt, director of the Sculpting Evolution group at MIT, has turned his attention to the white-footed mouse. With their big eyes and fuzzy white bellies, this species might not look dangerous, but in fact, they are an important natural reservoir for Lyme disease bacteria, which sicken an estimated 300,000 Americans every year.

While ticks are generally blamed for spreading Lyme disease, this is only half the story. Ticks aren’t born carrying Lyme disease bacteria; they pick up the bacteria when they feed on infected small mammals like the white-footed mouse. They can then transmit the bacteria to their next host, sometimes an unfortunate human. While deer are an important food source for the tick, they don’t actually carry the bacteria and—except in cases where it is possible to totally eliminate the deer populations—there is insufficient evidence that reducing deer numbers helps control Lyme disease. 

A picture of Dolly the cloned sheep in a pen.
Dolly, perhaps the most famous of all cloned animals. Colin McPherson / Alamy Stock Photo

That’s why Esvelt and his team are looking for solutions that target the white-footed mouse. The scientists are searching for the most effective antibodies against Lyme disease in white-footed mice. Once they identify these antibodies, they could build instructions for these antibodies into the genome, just like scientists want to do with the black-footed ferret and plague antibodies. The team could then raise lots and lots of mice that constantly produce antibodies against Lyme disease, making them immune to Lyme. These mice could then be released into areas where Lyme disease is prevalent in order to reduce disease transmission.  

Esvelt says that genetic instructions for antibodies that confer Lyme disease protection are already known in humans and in laboratory mice, and acknowledges that it would probably be easier to just take a protective gene from one of these species and put it in a white-footed mouse. But members of the communities in which the mice might be released—Nantucket and Martha’s Vineyard—expressed that they would prefer that white-footed mice were only engineered to have genes from other individuals of their species, not genes from different species. 

Even if it’s more difficult this way, Esvelt says community members should be able to have the final say. “It’s their environment, so it’s their call.”

This is in accordance with research showing that the public is more concerned about transgenic animals (animals with genes from other species) than cisgenic animals (which are genetically modified, but with added genes from the same species). Cisgenic animals may be perceived as more natural, since their genetic structure is one that is technically possible in nature (i.e. it could occur through breeding or natural mutation) and thus may be seen as less problematic. Even if it’s more difficult this way, Esvelt says community members should be able to have the final say. “It’s their environment, so it’s their call.”

Esvelt says that when it comes to ecological engineering, input from the communities that will be affected is extremely important. If scientists develop a new drug, he points out, you can always choose not to take it. But if scientists alter the place where you live by releasing genetically engineered animals, you can’t choose not to be affected by the consequences. 

“If we deny [communities] a voice in what the technology looks like, if we don’t tell them what we’re doing and invite their concerns and criticism and suggestions from the early experimental design stage when it matters, then we’re denying them a voice in decisions intended to affect them; where they won’t be able to opt out,” Esvelt says. 

Although the team plans to start slowly—releasing and analyzing the mice first on uninhabited islands and then on larger islands like Nantucket—the end goal is for Lyme-resistant mice to be implemented on the mainland, potentially greatly reducing the burden of Lyme disease in the United States. 

A very cute photograph of a White-Footed Mouse in a tree.
The white-footed mouse. Rolf Nussbaumer Photography / Alamy Stock Photo

Even further down the line, Esvelt says that lessons learned during this project could also be relevant for other diseases. For example, the white-footed mouse and its close relative the deer mouse both carry and transmit hantavirus to humans, causing severe and often fatal lung infections. Thus, engineering disease resistance in these mice could help protect humans from multiple types of dangerous pathogens.

Of course, no discussion of genetic engineering of wildlife is complete without including the world’s deadliest animal: the mosquito. Because they spread so many types of pathogens—like those that cause Zika, dengue, West Nile, yellow fever, and malaria, just to name a few—mosquitos are responsible for hundreds of thousands of human deaths each year. Omar Akbari, a professor of cell and developmental biology at the University of California, San Diego, wants to engineer a less-deadly mosquito. Among other creatures, Akbari’s lab works with a species of mosquito called Aedes aegypti. Native to Africa, the Aedes aegypti mosquito now thrives on every continent except Antarctica, sowing epidemics of yellow fever, dengue, chikungunya, and Zika, which have caused tremendous amounts of human suffering and death. 

So far, Akbari and his collaborators have created Aedes aegypti mosquitos that are resistant to dengue and Zika virus. But the work doesn’t stop there—Akbari says that these genetic engineering techniques could be applied to other species of mosquitos and other diseases. “I think it can work for many different disease vectors,” Akbari says. “There are a lot of mosquito species on Earth—over 3,500 different species—but there’s really only a handful of them that are transmitting pathogens to us.” By targeting these few species, scientists could have a major global health impact. 

But while genetically engineering wild species could potentially have major benefits for the species themselves and the humans they share an environment with, the scientists working on these projects emphasize that caution is needed. 

Careful evaluation of downstream ecological effects is essential. If the genetic engineering causes the species to become more abundant, scientists need to make sure that it doesn’t harm the species that they consume or compete with. If the engineered species becomes less abundant, they need to make sure that doesn’t impact animals that rely on that species for food. Just like plants and animals, pathogens may also fill a newly vacated ecological niche—so if animals no longer host one type of pathogen, scientists need to make sure that a new pathogen won’t swoop in to claim the newly available real estate. 

But ecology is a complex science and even with careful assessment, there may be unforeseen problems and scientists need to have a back-up plan if things go wrong. “It comes down to being able to take it back. So that’s one of the things that’s scariest about it—if we put [a genetically modified species] out in the wild, it’s not like we can just go and get it again,” Baumgartner says. “The safety mechanisms have to be developed in parallel with these genetic interventions.” 

A picture of Prometea, a cloned pony.
Prometea, the world’s first cloned horse. REUTERS / Alamy Stock Photo

Scientists are working on building these safety mechanisms into the animals themselves. If scientists want the genes for disease resistance to spread throughout an animal population, they can use a CRISPR-mediated gene drive—a technique that alters the probability that the gene of interest will be inherited by offspring. While most genes have a 50 percent chance of being inherited by an organism’s babies, scientists can use a gene drive to increase this likelihood—theoretically up to 100 percent. Scientists do this by giving the animal genetic code not only for the disease resistance gene, but also code to build a CRISPR system to cut out the gene they don’t want. The offspring of a modified organism and a wild organism starts out with one copy of the disease resistance gene and one copy of the wild gene. But the CRISPR system it inherited from the modified parent snips out the copy of the wild gene, which gets replaced by the modified, disease resistance gene. This happens every time a modified organism mates, resulting in all the offspring, and the offspring’s offspring, and so on, having two copies of the disease resistance gene.

But once this drive gets going, it could result in this gene spreading to every animal of this species in the entire world, so researchers want to make sure there is a way to hit the brakes. 

Scientists are experimenting with different ways to create gene drives that are self-limiting: drives that can be used to spread a gene throughout a local population but won’t spread indefinitely. One way to do this is to split up the components that the gene drive needs to function. For example, in a split drive, scientists can split the drive into part A and part B and put them in different places on the genome. When an organism has part A and part B, the gene drive functions and all of the animal’s offspring will have the gene of interest—in this case, the gene that makes it resistant to disease. But scientists can also make it costly for an organism to carry part A; maybe part A makes the animal just a little bit less able to survive or reproduce. After several generations, natural selection will eventually eliminate part A from the population. Without part A, the drive no longer functions, and the gene of interest will once again only have a 50 percent chance of being inherited.

Scientists still need to do more testing on the various ways to put the brakes on a gene drive to make sure that they won’t go awry once the animals are released into the wild. Currently, genetic modification is regulated on a country- or continent-level basis, which may be problematic as releasing a gene drive in one country could potentially affect many surrounding countries. In the United States, regulation of genetically modified organisms falls under the Coordinated Framework for Regulation of Biotechnology, which includes the FDA, USDA, and the EPA. Regulation is a contentious subject: Debates at the United Nations have turned into yelling matches and critics have argued that current regulations do not take into account input from local communities, who may be most affected by the release of gene-drive organisms.

Attempts to modify nature will always be haunted by early, carelessly initiated biocontrol efforts—like the introduction of cane toads in Australia or mongooses in Hawaii—that had disastrous consequences for native wildlife. More recent failures have been less spectacularly devastating but still concerning; for example, a fly introduced to eat an invasive weed in Australia also appears to serve as a pollinator for it. In another case, gall flies were introduced to control a different invasive weed in the American West. Unfortunately, the fly larvae turned out to be a great source of nutrition for deer mice. As the deer mouse population increased, so too did the levels of hantavirus, which is carried by mice and can be deadly to humans. Clearly, more exhaustive evaluation of ecosystem effects was warranted in these scenarios. 

Even with careful testing, assessment, and regulation, it’s possible that something could go wrong. The natural world is a complicated place—even within a single square mile, it might not be possible to fully understand the interactions of every species of mammal, reptile, insect, plant, parasite, bacteria, fungus, and virus and how these interactions would respond to changes in the ecosystem.

As scientists and bioethicists have pointed out, many seemingly beneficial genetic changes could have catastrophic consequences. For example, if scientists engineered a species of coral to be resistant to climate change, it might be able to outcompete all of the other coral species on the reef, resulting in a loss of coral biodiversity and negative impacts on other creatures living in the reef ecosystem. Engineering animals to be pathogen-resistant puts new evolutionary pressures on the pathogen, which could cause it to change in dangerous ways: It might become more virulent or evolve the ability to infect different species, ultimately increasing instead of decreasing the burden of human disease. 

However, while there are tangible risks of unforeseen consequences for releasing genetically engineered wildlife, there also could be serious consequences of not implementing these technologies. “If you have a problem like malaria, for example, with no really great solutions,” Akbari says, “you have the risk of people dying if you don’t use the new technology.” Eventually, we’ll need to choose whether to risk altering ecosystems with genetic engineering or risk the lives of humans and endangered species by foregoing it.

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