CRISPR can wipe out entire species

By Jackson Ryan

Charles Darwin had no idea what a gene was. If we dropped the father of evolution into 2019, the idea that humans can willfully alter the genes of an entire species would surely seem like wizardry to him. 

But CRISPR gene drives -- a new, inconceivably powerful technique that forces genes to spread through a population -- have the ability to do just that. Gene drives allow us to hone the blunt edges of natural selection for our own purposes, potentially preventing the spread of disease or eradicating invasive pests. 

Yet as with any science performed at the frontier of our knowledge, we are still coming to terms with how powerful CRISPR gene drives might be. Playing the game of genomes means we may, in the future, choose which species live and which die -- a near-unbelievable capability that scientists and ethicists agree presents us with unique moral, social and ethical challenges.

Charles Darwin

Charles Darwin established the principles of evolutionary theory, but he lived in a time before we understood genes. 

Hulton Archive/Elliott & Fry/Getty Images

But first, let's talk about genetic engineering. 

Humans have been interfering with genetics for millennia. We domesticated dogs, we bred gigantic chickens. But during the 20th century, we learned genes were made of DNA and we created tools that allow us to tinker with them. By the 1970s, that had opened up a new field of research.

Over the next 40 years, genetic engineering became commonplace for scientists. It hasn't been easy. Successfully inserting or deleting genes required time, high-level expertise and a big wallet. But in 2012, with the discovery of CRISPR, genetic engineering became cheaper, faster and more efficient.

Now scientists possess a robust molecular tool that can reliably alter genes in almost any organism. It was touted as a revolution in 2013 -- and it has been, enabling genetic modification of crops, potential new cancer treatments, refining antibiotics and new ways to create animal models of disease.

And CRISPR is being turned against some of the biggest ecological problems in the world by combining it with a "gene drive," a powerful genetic engineering tool used to spread genes through an entire population. Within just five years, CRISPR gene drive technology has gone from pioneering idea to impending reality.

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In London, a team of researchers is trying to perfect a drive that could wipe out entire populations of the malaria-carrying Anopheles mosquito, combating a disease that according to the World Health Organization kills almost half a million people every year. Meanwhile, in Australia, a scourge of poisonous cane toads hop their way across the continent, endangering native species. Researchers hope to render their toxins inert and control their spread, giving the natural flora and fauna a chance to bounce back.

A world without malaria. A planet without invasive species. 

With gene drives, we can tame evolution. 

Real monsters

For 80,000 years, one particular monster has terrorized human beings. 

It is known as Plasmodium, a single-celled parasite that infects the liver and bloodstream. It causes malaria, a disease that can be fatal, particularly in children. The parasite hides in oxygen-carrying red blood cells and multiplies, eventually exploding out of the cell, destroying it in the process. 

In 2016, the disease infected 216 million people, killing 445,000. Over 90 percent of those cases occurred in Africa, and 70 percent of deaths occurred in children under five. 

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Children are particularly vulnerable to malarial infection. In 2015, almost 303,000 African children died before their fifth birthday, according to the WHO.

Chip Somodevilla/Getty Images

To infect humans, Plasmodium relies on the female Anopheles mosquito. The parasite dwells inside the mosquito and is transferred to humans when a mosquito plunges her needlelike mouth into the skin. 

Scientists reasoned that to target malaria, you could target the mosquito, preventing it from transporting the parasite through the population. Early attempts to control malaria via genetic engineering centered on producing "transgenic" Anopheles mosquitoes -- introducing DNA from other organisms into their genome that would help prevent the parasite's spread. 

There were successes in the lab, with studies showing transgenic organisms could be created with genes that inactivated Plasmodium or stopped its development altogether. However, by adding the extra genes, scientists had made the lab-grown insects weak and less likely to survive in the wild. That prevents them from spreading their antimalaria genes because they die out too quickly, before they have the opportunity to breed. 

How could scientists overcome this problem? 

Nature, as is so often the case, provided an answer. 

The origin of changing species

The power to change a species begins with sex. 

Genes exist in pairs. When two organisms mate, they hand down one copy each to their offspring. They don't choose which gene gets inherited. It's a genetic coin-toss: Each gene has a 50 percent chance of being passed down. 

However, some genes are selfish. They use molecular tricks to ensure they're passed down with a greater than 50 percent chance. Breaking the rules of inheritance like this, these selfish genes can survive and spread throughout populations over time, even if they make an organism weaker. 

Scientists have toyed with the possibility of modifying selfish genes to control insect species since the 1960s, but in 2003, Austin Burt, from Imperial College London, penned a seminal paper that first conceptualized the gene drive. 

He suggested that a particular kind of selfish gene could be engineered to deliberately bias inheritance, allowing scientists to edit the genes not just of individuals, but of entire populations. Burt and his colleagues developed the idea over eight years, eventually showing it was possible in 2011 but cautioning there were still "technical hurdles" that needed to be addressed. 

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An illustration of the CRISPR-Cas9 gene editing complex. The Cas9 nuclease protein (white and green) uses a guide RNA (red) sequence to cut DNA (blue) at a complementary site. 

Molekull/Science Photo Library/Getty


But that occurred in a time before a monumental, global upheaval in genetic engineering: the invention of CRISPR/Cas9 (or more simply "CRISPR") in 2012. CRISPR is a powerful genetic engineering tool, often referred to as a "pair of molecular scissors," because of how precisely it can cut and edit genes in almost any species.

And two years later, it would be CRISPR -- and a turtle -- that provided a Boston geneticist with a world-changing idea. 

Walking over a footbridge in the Emerald Necklace, a historic stretch of parks and waterways that curl through Boston, Kevin Esvelt stared into the serene, still water and noticed a turtle, sparking a groundbreaking idea: combining CRISPR with the concept of a gene drive would create an unimaginably powerful genetic engineering tool.

It would create a new type of man-made selfish gene, placing the CRISPR scissors and the instructions where to cut inside an organism's genome. It would also be easier to deploy and more robust than Burt's idea in 2003.

As most of us learned in high school biology, an organism gets one copy of a gene from its mother and one from its father. But if one parent carries the CRISPR gene drive, it can cut out the other parent's gene, and copy the gene drive over in its place. Over many generations, that would allow the gene drive to spread through the gene pool of an entire species. 

The red mosquito contains a CRISPR gene drive. When it mates with a wild mosquito (blue), it hands down the genes necessary to copy the CRISPR gene drive over: an altered gene (eg. one that reduces mosquito fertility), the Cas9 enzyme (the "scissors") and the guide RNA (which tells Cas9 where to cut). Every mosquito born to the original parents will contain a copy of the gene drive.

Amy Kim/Viva Tung


Esvelt's idea went to press in 2014, before his lab had even developed a working CRISPR gene drive. That paper, published in eLife, suggested a number of applications for the technology: eradicating insect-borne diseases such as malaria, sensitizing agricultural pests to pesticides and controlling invasive species.

Applying the technique to a population of malaria-carrying mosquitoes? Well, that might change the world. 

Full collapse 

In September 2018, a research team at Imperial College, London, led by Andrea Crisanti and featuring pioneer Austin Burt, revealed it had generated a CRISPR gene drive that caused a total population collapse in lab-bred Anopheles gambiae mosquitoes.

The researchers targeted a gene known as doublesex, which acts like a gatekeeper that decides whether a mosquito becomes a male or a female. By altering this gene, the team was able to breed female mosquitoes that were infertile and had mouthparts that could not draw blood. In essence, they flipped a genetic switch that caused females to develop more like males.

After starting with 600 mosquitoes, the gene drive spread through the population within 7 to 11 generations, causing a total collapse. The research team had created a similar drive in 2015 targeting a different gene, but it hadn't been as successful in crashing the population because genetic mutations arose over time. This, then, was the most powerful drive yet. 

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Using CRISPR gene drives, researchers were able to flip a genetic switch, making female mosquitoes infertile (copyright: Crisanti Lab/Alekos Simoni)

Crisanti Lab/Alekos Simoni

"The most important and surprising thing is that doublesex can not be changed without altering its function. A lot of mutations were generated, but none were functional," Crisanti explains.  

"Now we're trying to understand if this region is really 'resistance-proof' and if it is, we really have a tool that has the potential to be used in the field -- and solve the problem of malaria."

The self-propagating drive proposed by the London lab in September may prove to be the genetic iceberg that sinks an entire species, but there are still vast seas of knowledge to traverse. For Crisanti, work now turns to replicating the tropical conditions in which the Anopheles mosquitoes thrive and examining how the gene drive fares under such conditions. 

The toxic toad 

In the arid northern plains of Australia, an invader slowly hops its way west, across the continent.

The amphibious raider looks like a muscular pancake with legs, bulging shoulders (yes, they have shoulders) and warty bumps all over: the cane toad, Rhinella marinus. 

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Two beautiful, hulking randy trespassers.

Digital Zoo/Getty Images

The biggest toad species in the world, the cane toad is a toxic, randy trespasser. In 1935, a state government-owned sugar industry body introduced the species into Australia's northwest as a biological control measure -- a way to stop cane beetles from damaging their crops. But the toad thrived in the Australian tropics, reproducing quickly and wreaking havoc on the natural ecosystem by competing for food and, with a cocktail of deadly toxins, killing off any predator that might try to eat it.

The toads present a different problem than the Anopheles mosquitoes. They aren't dangerous to humans (unless you should, for whatever reason, decide to lick one) but they cause a great amount of suffering to native fauna and flora. For the past 83 years they've been nearly impossible to contain and have been linked to dwindling numbers of Australia's native lizards, snakes and frogs.

And their lethal secreted toxins, which have helped them spread, may also may end up contributing to their downfall.

Mark Tizard, project lead of genome engineering at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Australia, believes his team can use CRISPR to genetically modify the toad to prevent it from producing the lethal toxins.

"The toad itself isn't lethal until the toxin is squeezed out, and when it's squeezed out it's activated and becomes lethal -- there's an enzyme that does it," Tizard explains.

Where there's an enzyme, there's a gene, and where there's a gene, CRISPR can go to work.

"We've been working on a system to go in and clip out that enzyme. The objective is then that you have a toad that can never make a lethal toxin."

But the toad will still make other toxins -- just not ones that are fatal for any hungry predators (or unsuspecting pets) that might try to eat it. Those toxins won't kill the predator, instead teaching it that the toad is not a great source of food. Tizard calls this a "teacher toad," and suggests it could be released into regions where the toads are likely to invade next, fostering predator-prey interactions naturally and convincing the natural fauna not to eat the toads.

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Ian Waldie/Getty Images

Nuts, bolts, warts and all

At first, it might seem like the CRISPR gene drive is a perfect machine to combat the toad, just like it would be the malaria-carrying mosquito. However, the cane toad provides an example of where the self-propagating gene drives, like the one being developed in London, may be overkill.
 
The drives could wipe out the invasive species, but they aren't always going to be the perfect tool. It comes back to sex.

"It would be really great if we could use a gene drive to knock out the toxin and spread that through the population," Tizard says. However, while the frogs are voracious breeders, they take two to three years to sexually mature, and this "generation interval" is one of the major issues in implementing a gene drive in the warty amphibians. The time frame between birth and sexual maturity would stymie the spread of the gene drive.

"The nuts and bolts of what we we would do with a gene drive in a cane toad aren't absolutely clear yet," Tizard says. 

Esvelt doesn't believe a self-propagating drive should be used to alter invasive species like the toad. Rather, he believes that such a drive is only viable in four specific cases that cause great human or animal suffering: the Anopheles gambiae mosquito, the New World screwworm, whose larvae feed on the tissue of living mammals, and two parasitic worms that cause the majority of schistosomiasis cases, which the WHO estimates affects over 200 million people a year.

But Tizard still hopes that genetic techniques will combat the march of the cane toads -- and still expects to use CRISPR -- acknowledging that, using a gene drive or not, the genetically modified toad will raise a host of social and ethical questions around releasing such a creature into the wild. 

Fielding questions

That a gene drive can self-propagate presents a unique experimental problem: It cannot be trialed in the field. It is impossible to guarantee the engineered organisms will stay in a controlled zone. Once unleashed, it would eventually spread to every organism of the species.

Although the technical mountains of building a drive have mostly been scaled, we have only just begun scaling the ethical, moral and social quandaries looming over this ecosystem-changing technology. It's true that a release of a self-propagating drive may save thousands of lives or protect native species from invasive threats, but it's also true that we can't fully predict the consequences of releasing such a drive into the wild.

No matter how well-meaning the intentions of scientists, nature is unpredictable. It continues to find ways to outsmart us. 

From the very beginning, Esvelt, who now heads up MIT's Sculpting Evolution group, has championed scientific responsiveness when dealing with gene drive technologies. He believes the technology has such far-reaching effects that the scientific community must engage and interact with the community openly, from the earliest stages of a project.

 Tizard agrees.

"We don't want to fall into the trap of being the clever scientist in their ivory tower who decides on something for everyone," he says. "We need to have everyone involved in the decision making." 

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Rodents, such as rats, are potential targets for gene drive technology. In January 2019, a research team in the US demonstrated a working gene drive in lab mice for the first time.

fotografixx/Getty Images

In June 2018, Esvelt and his associates at MIT published a paper in the journal eLife, highlighting some of the potential risks of introducing self-propagating gene drives into wild populations. Their mathematical modelling showed that "even the least effective drive systems reported to date are likely to be highly invasive."

When the London team revealed it had developed a resistance-free gene drive in September, Esvelt cautioned "success carries a message for those of us working on gene drive in other species: we must use safeguards. Anyone building a potentially invasive gene drive system should be extraordinarily careful to use safeguards beyond simple walls and cages."

One mistake, Esvelt reasons, might not only cripple an ecosystem but also cause social backlash, severely damaging the public's trust in performing responsible science. That could set gene drive research back years, or decades.

And those invasive, genetically modified organisms might cross state lines, adding biological fuel to political fires or unintentionally altering ecosystems they were never intended to be in. 

The game of genomes

Almost every two minutes another child dies of malaria.

Given that damning statistic, should we not act as soon as possible to prevent the disease? If we can eliminate the mosquitoes that carry it -- just a handful of species out of 3,500 -- and prevent those deaths, aren't we obliged to do so? Or are we digging our noses into nature's secret diaries, scrounging around without consent?

"Even without invoking any particular religious beliefs, many think that use of laboratory-based technologies is equivalent to 'interfering' with nature or natural processes, or otherwise going too far, particularly in environmental terms," says Rachel Ankeny, a bioethicist at the University of Adelaide.

And beliefs such as those have seen over 160 environmental advocacy groups call for a global moratorium on development and release of gene drive technologies, believing they pose "significant ecological, cultural and societal threats." In addition, the US Defense Advanced Research Projects Agency (DARPA) has invested $100 million into development of gene drive technology, spurring advocacy groups to fight against further research over fears of militarization.

"Gene drives are a highly risky, unproven experimental technology that will cost millions of dollars to develop and have no guarantee of success," says Louise Sales, emerging-tech project coordinator at Friends of the Earth, which co-signed the call for a moratorium. Although the United Nations rejected those calls last November, it did suggest that "parties and other Governments... apply a cautionary approach" and evaluate gene drive projects on a case-by-case basis. 

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At the 14th Convention on Biological Diversity, the UN rejected calls for a moratorium on gene drive technology.

UN Biodiversity/Twitter

In many ways, scientists working on gene drives, such as Esvelt, Crisanti and Tizard, have been on the front foot from the beginning, building in physical safeguards and working to educate communities about the potential risks and benefits of the technology well before any potential release.

"Those working with gene drives have tended to build ethical considerations into their work from the start, and there have been extensive discussions at global and national levels about appropriate mechanisms for ethical review of these technologies," Ankeny says.

The technology is progressing at such a pace that it's hard for regulatory bodies to keep up. When I spoke to Crisanti in October 2018, he believed that it would be a few years until we had a working gene drive in mammals. But in January, a research team published its work on the first gene drive working in rodents, showing that could bias inheritance in lab mice.

Researchers are doing their best to keep ahead of any ethical dilemmas, by building safeguards into the genetic systems. Esvelt's team has concocted another form of gene drive, known as a "daisy drive," designed to contain the release within a local environment for a limited time, rather than spread indefinitely. In January, a team from Cornell University described another set of safeguards it could build into the drives that would also prevent unintended spread.

So in taming evolution, humanity is now the arbiter of the genetic realm. We've not just entered the game of genomes, we've ascended the throne. And though their release is likely several years away yet, our ability to craft CRISPR machines that drive species extinct or change them forever was something we could not have dreamed about just five years ago. 

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