The WIRED Guide to Crispr

[Karlston]

The WIRED Guide to Crispr

Everything you need to know about how scientists can repurpose a bacterial immune system to alter DNA, making everything from cheap insulin to extra starchy corn.

 

 

IN THE EARLY days of gene editing, biologists had a molecular tool kit that was somewhat akin to a printing press. Which is to say, altering DNA was a messy, labor-intensive process of loading genes onto viruses bound for target cells. It involved more than a fair amount of finger-crossing. Today, scientists have the genetic equivalent of Microsoft Word, and they are beginning to edit DNA almost as easily as software engineers modify code. The precipitating event? Call it the Great Crispr Quake of 2012.

 

If you’re asking “What’s Crispr?” the short answer is that it’s a revolutionary new class of molecular tool that scientists can use to precisely target and cut any kind of genetic material. Crispr systems are the fastest, easiest, and cheapest methods scientists have ever had to manipulate the code of life in any organism on Earth, humans included. It is, simply, the first technology truly capable of changing the fundamental chemistry of who we are.

 

The long answer is that Crispr stands for Clustered Regularly Interspaced Palindromic Repeats. A Crispr system consists of a protein with sequence-snipping capabilities and a genetic GPS guide. Such systems naturally evolved across the bacterial kingdom as a way to remember and defend against invading viruses. But researchers recently discovered they could repurpose that primordial immune system to precisely alter genomes, setting off a billion-dollar boom in DNA hacking.

 

Every industry is throwing mad money at Crispr—pharma, agriculture, energy, materials manufacturing, you name it. Even the weed guys want in. Companies are using it to make climate-change-fighting crops, biofuel-oozing algae, self-terminating mosquitoes—and, yes, potential Covid-19 treatments. Academic researchers have almost universally adopted Crispr to more deeply understand the biology of their model organisms. Supporting this biohacking bonanza is an increasingly crowded Crispr backend supply chain: businesses building gene-editor design tools and shipping synthetic guide RNAs or pre-Crispr’d cell lines to these companies’ doors. So far, though, very few Crispr-enhanced products have made it into the hands of actual consumers. In their place, hyperbolic headlines have bugled society’s greatest hopes and fears for the technology, from saving near-extinct species to igniting a superbaby arms race.

 

In November 2018, a Chinese scientist named He Jiankui stunned the world with claims that he had Crispr’d the first humans in an experiment fraught with ethical violations. The fast-unfolding scandal roused the world’s scientists and government officials to address the now-urgent need to figure out how to regulate such a powerful technology. Crispr may have delivered designer children faster than anyone thought possible. But it’s still a long way from ending disease or hunger or climate change. Maybe it never will. Crispr is, however, already beginning to reshape the physical world around us in much less radical ways, one base pair at a time.

 

The History of Crispr

 

It all started with yogurt. To make it, dairy producers have long employed the help of Streptococcus thermophilus, bacteria that gobble up the lactose in milk and poop out lactic acid. It wasn’t until 2005, though, that a young microbiologist named Rodolphe Barrangou discovered that S. thermophilus contained odd chunks of repeating DNA sequences—Crisprs—and that those sequences were keeping it safe from the viruses that can attack it and result in spoilage. (If the thermophilus is gone, nastier bacteria can move in and feed off the lactose, ruining the product.)

 

Before long, DuPont bought the Danish company that Barrangou worked for and began using strains carrying this naturally occurring Crispr to protect all of its yogurt and cheese cultures. Since DuPont owns about 50 percent of the global dairy culture market, you’ve probably already eaten Crispr-optimized cheese on your pizza.

 

All the while, gene sequencing costs were plummeting and research scientists around the world were assembling the genomes of bacteria. As they did, they found Crisprs everywhere—more than half of the bacterial kingdom turned out to have them. Oftentimes those sequences were flanked by a set of genes coding for a class of strand-cutting enzymes called endonucleases. Scientists suspected they were involved in this primitive immune system, but how, exactly?

 

The key insight came from a particularly nasty bug—the one that causes strep throat. Its Crispr system made two RNA sequences that attached to a clam-shaped endonuclease called Cas9. Like a genetic GPS, those sequences directed the enzyme to a strand of DNA complementary to the RNA sequences. When it got there, Cas9 changed shape, grabbing the DNA and slicing it in two. The molecular biologists who made this discovery—Jennifer Doudna and Emmanuelle Charpentier—demonstrated Crispr’s programmable cutting on circular stretches of DNA floating in test tubes. They published their work in Science in 2012, but not before patenting the technology as a tool for genetic engineering. If you just switch out the RNA guide, you can send Cas9 anywhere—to the gene that causes Huntington’s disease, say, and snip it out. Crispr, they realized, would be a molecular biologist’s warp drive.

 

Six months later, a molecular biologist at the Broad Institute of MIT and Harvard named Feng Zhang published a paper in Science showing that Crispr-Cas9 could edit human cells, too. In fact, with the right genetic guides, you can Crispr pretty much anything. That meant it might be put to work on next-generation medicines that could do things like erase genetic defects and supercharge the body’s natural defenses against cancer. And that meant big money.

 

Perhaps predictably, a patent battle ensued—one that is still going on today. Crispr’s early pioneers founded three companies with exclusive licenses to exploit Crispr/Cas9 to cure human diseases; one of them began its first human trials in early 2019. Uncertainty over who will ultimately own the technology has done little to slow the appetite for all things Crispr. If anything, it unleashed a flood of interest in developing competing and adjacent tools that promise to further refine and expand Crispr’s already ample potential.

 

Many of the field’s founding luminaries have also formed, or are currently advising, companies working to lower the cost and labor associated with gene editing, to make it accessible to everyone. But in November 2018, at least some of them got a lesson in what democratization of Crispr really looks like.

 

On the eve of the Second International Summit on Human Gene Editing, news broke that a Chinese scientist named He Jiankui, who was scheduled to speak at the meeting, had been recruiting couples in an effort to create the first Crispr’d babies. Hours later, He Jiankui himself posted five slickly produced promotional videos to YouTube claiming to have already done so: “Two beautiful little Chinese girls, Lulu and Nana, came crying into the world as healthy as any other babies a few weeks ago.” The only difference was that the twins had been injected with Crispr when they were still embryos, in an effort to eliminate a gene called CCR5 and make them resistant to HIV. In a presentation to the summit a few days later, He provided further evidence of his experiment, which he appears to have conducted largely in secret, and revealed that a second pregnancy was underway. Buried in the pages of his clinical paperwork were notes that indicated He had ordered his Crispr components from US biotech companies, in violation of their “research use only” policies.

 

These firms joined the scientific community’s chorus of disgust, outrage, and near-unanimous condemnation of He’s work. Jennifer Doudna said she was “horrified,” Feng Zhang called for an immediate moratorium on the implantation of gene-edited embryos, and more than 100 Chinese scientists signed a letter decrying the study as “crazy.” Within days, He had been fired from his university post and all his research activities were suspended. A subsequent investigation by government authorities found that He violated Chinese law, and he is now serving a three-year prison sentence.

 

And as new revelations keep trickling in, policymakers are scrambling to lay down some ground rules for this new Crispr-baby world. In the aftermath of the He debacle, China formed a new national ethics committee with broad authority over all high-risk medical biotechnologies. It will be tasked with enforcing the country’s new clinical research guidelines, released in February. The World Health Organization has assembled a panel to develop global standards for governments to follow. Late last year, the Russian government cited the advice of this panel when it barred a Russian scientist from creating Crispr babies.

 

Under current US regulations, the Food and Drug Administration is banned from considering any studies that would start a pregnancy with embryos that have been genetically modified. But that language has to be renewed every year by Congress—and, last year, the language was briefly dropped before it was ultimately restored. Given the implausibility of a global consensus on how to move the technology forward responsibly, the task will likely fall to individual nations, and it seems unlikely that every country will institute equally strict regulations.

 

But scientists who hope to move forward with modifying future generations of humans may have more to worry about than just politics. Three separate teams have just demonstrated that Crispr can have catastrophic, unintended effects—like deleting huge chunks of DNA—when used to genetically modify human embryos. While these results have not yet been peer reviewed, they suggest that scientists have a long way to go before they can edit human embryos safely, not to mention ethically.

The Future of Crispr

 

Despite the arrival of Lulu and Nana, Crispr is still mostly a biologist's buzzword. But just as computers evolved from a nerdy, niche tool for math geeks to a ubiquitous, invisible extension of our own bodies, so Crispr will one day weave seamlessly into the fabric of our physical reality. It will simply be the way to solve a problem, if that problem is remotely genetic in nature.

 

Take industrial fermentation, for example. With the help of old-school genetic engineering techniques, scientists have already reprogrammed microbes like E. Coli and brewer’s yeast into factories that can make everything from insulin to ethanol. Crispr will rapidly enlarge the catalog of designer chemicals, molecules, and materials that biorefineries can produce. Self-healing concrete? Fire-resistant, plant-based building materials lighter than aluminum? Fully biodegradable plastics? Crispr not only makes all these possible—it makes it possible to produce them at scale.

 

But we won’t get there with the tools we’ve currently got, which is why researchers are now racing to chart the full expanses of the Crispr universe. At this moment, they’re scouring the globe for obscure bacteria to sequence, and they’re tinkering with the systems that have already been discovered. They’re filing patents on every promising new nuclease they come across, adding to a list that is sure to expand in the coming decade. Each new enzyme will not only advance Crispr’s gene editing powers but also extend its capabilities far beyond DNA manipulation. You see, slicing and dicing isn’t the only interesting thing to do to DNA. Tricked-out new Crispr systems could temporarily toggle genes on and off or surveil the genome to fix mutations as they happen in real time, no snipping required. The first would let scientists treat human diseases where there’s too much or too little of a certain substance—say, insulin—without permanently altering a patient’s DNA. The second could one day prevent diseases like cancer from occurring altogether. The specificity of Crispr, perhaps more than its actual cutting mechanism, will inspire applications we can’t yet imagine.

 

As of now, scientists working on the medical applications of Crispr have already achieved some impressive results with real human impact: Victoria Gray, a 34-year-old woman who has struggled with sickle cell anemia for most of her life, just celebrated a year of being symptom-free. To treat her debilitating illness, researchers extracted some of her stem cells, used Crispr to reprogram them to produce healthy blood cells, and returned them to her body. Scientists are working to treat cancer and HIV with a similar approach and have been able to establish its safety—but not, as of yet, its effectiveness.

 

But none of these trials involved inserting Crispr directly into the patient’s body, because it can be difficult to deliver Crispr to a specific organ or tissue where needles and syringes can’t reach. Though scientists have devised some methods for doing so, these approaches can have potentially harmful consequences: Crispr, when administered in this way, can wreak havoc on portions of the genome where it should never have been in the first place. These unintended modifications, called off-target effects, could theoretically prevent tissues from functioning properly or could jump-start cancers. Figuring out how to limit these off-target effects is a major goal of current Crispr research. And scientists have made some material progress. A team at Johns Hopkins University recently created a light-activated form of Crispr, which can be deactivated to limit its off-target effects. And scientists are experimenting with other approaches for delivering Crispr to particular locations in the body: One individual has even had Crispr injected directly into their retinas in an effort to cure their blindness.

 

Meanwhile, consumers can expect to see the first Crispr-designed foods lining grocery store shelves very soon. Because Crispr doesn’t use plant pathogens to manipulate DNA (the old GMO-generating method), the USDA has given a free regulatory pass to gene-edited crops, which may allow drought-tolerant soybeans and extra-starchy corn to ease into your favorite processed foods without any additional labeling. Specialty fruits and vegetables will likely follow the commodity crops; the reduced regulatory burden and the cheapness of Crispr will allow companies that prioritize consumers’ senses rather than farmers’ bottom lines to enter the market. Already a dozen or so startups have popped up to challenge the Bayer/Monsanto, DowDupont/Pioneers of the world.

 

This democratizing aspect of Crispr-based tech, combined with its nearly limitless commercial possibilities, makes today a great time to be a molecular biologist. Want to make antibiotics that only target bad bugs without wiping out the entire microbiome? Companies are doing that. Want to make paper-based diagnostics that doctors can take into the field to test for diseases like dengue, Zika, and even the novel coronavirus? Research labs and startups are doing that too. And as more tools come online, the backend Crispr ecosystem will continually expand to support, supply, and optimize them.

 

As some scientists work to apply Crispr to new and surprising biological problems, others are working to generate more powerful, more precise tools for gene editing. Some of these inventions are improvements on the Crispr we know and love: Prime editors, for example, pair Cas9 with reverse transcriptase to make for a tool that can precisely modify bits of DNA. But others leave Crispr aside entirely. This year, researchers designed an entirely new system to edit mitochondrial DNA, which lives apart from the rest of our DNA in our cells and can transmit a number of diseases from mother to child. Like Crispr, this new system takes advantage of bacteria’s natural defense machinery—in this case, a toxin that bacteria can use to kill competing strains. And a startup has spearheaded a technique for inserting long stretches of DNA into the genome, something that is currently beyond Crispr’s capabilities.

 

Crispr and other editing tools are only going to become more powerful, and, when they do, they will rightly invite more scrutiny and probably more regulation. Scientists and regulators are going to have to figure out if it’s OK to wipe out an entire species in the name of conservation and bring other ones back from extinction. They’ll have to wrestle with the possibility that gene editing tools might be used to produce biological weapons of unfathomable destruction. Lulu and Nana have already kindled difficult conversations around the real possibility—or, perhaps, inevitability—of designer babies; when is it acceptable to fix a genetic mutation? What about adding features? Where do you draw the line? Crispr, and all the tools that will one day make up the Crispr universe will undoubtedly force societies—not just scientists—to confront these questions and ponder the oldest one of all; what does it mean to be human?

Learn More:

• Everything You Need To Know About Crispr Gene Editing
  Okay, you get it, Crispr’s a big deal. But now, aren’t you curious to know exactly how it works? You don’t have to be a microbiologist to understand this step-by-step look inside the molecular multitool of the century.

• A Crispr Calf Is Born. It’s Definitely a Boy
  UC Davis scientists spent years editing a sex-determining gene into bovine embryos. In April, Cosmo arrived—the first bull who will be able to sire mostly male offspring. But a close look at his DNA reveals how far the field still has to go.

• First Human-Pig Chimera Is a Step Toward Custom Organs
  Scientists have long been dreaming of xenotransplantation—putting animal organs into people—as a possible solution to the current human organ shortage. But almost all attempts to do so have failed. Here’s how Crispr is bringing new hope to the dream of animal organ farms.

• Scientist who Crispr’d Babies Bucked His Own Ethics Policy
  A Chinese researcher named He Jiankui crossed every bright red ethical line (and probably broke a few laws) to bring the first gene-edited children into the world. Here’s what he got so, so wrong.

• US Biotech Firms Made Crispr Babies Possible
  You heard it here first, even Crispr babies have a global supply chain.

• Here’s the Plan to End Malaria With Crispr-Edited Mosquitoes
  A Bill Gates-backed organization hopes to eradicate malaria in Africa by exterminating the continent’s disease-carrying mosquitoes. But when manipulating the fate of a species, moving slowly is a virtue.

• Process of Elimination
  For decades conservationists have used medieval methods for eradicating invasive island predators like rats. And all those traps and guns and poisons still haven’t gotten the job done. Local species are still under threat of extinction. Now some scientists are turning to Crispr gene drives, a particularly potent genetic tool that could forever transform our power over nature. Emma Marris went to the Galapagos to see how they might work in the wild.

• Crispr'd Cells Show Promise in First US Human Safety TrialUsing genetically-edited cells to supercharge the immune system caused no adverse effects in cancer patients. Now that they know it's safe, scientists' next question is, could it be a cure?

• Easy DNA Editing Will Remake the World. Buckle Up.
  Still haven’t had enough Crispr? Amy Maxmen’s 2015 cover story is the definitive survey of this gene-editing technology; from its humble bacterial beginnings, to the trenches of its ferocious patent battle, to inside the companies already churning toward our Crispr-created future.

Plus! Crispr uploads a galloping horse GIF into a living bacteria and more WIRED gene editing coverage.

 

This guide was last updated on July 30, 2020.

 

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The WIRED Guide to Crispr