A powerful gene-editing technology is the biggest game changer to hit biology since PCR. But with its huge potential come pressing concerns.
Three years ago, Bruce Conklin came across a method that made him change the course of his lab.
Conklin, a geneticist at the Gladstone Institutes in San Francisco, California, had been trying to work out how variations in DNA affect various human diseases, but his tools were cumbersome. When he worked with cells from patients, it was hard to know which sequences were important for disease and which were just background noise. And engineering a mutation into cells was expensive and laborious work. “It was a student's entire thesis to change one gene,” he says.
Then, in 2012, he read about a newly published technique1 called CRISPR that would allow researchers to quickly change the DNA of nearly any organism — including humans. Soon after, Conklin abandoned his previous approach to modelling disease and adopted this new one. His lab is now feverishly altering genes associated with various heart conditions. “CRISPR is turning everything on its head,” he says.
The sentiment is widely shared: CRISPR is causing a major upheaval in biomedical research. Unlike other gene-editing methods, it is cheap, quick and easy to use, and it has swept through labs around the world as a result. Researchers hope to use it to adjust human genes to eliminate diseases, create hardier plants, wipe out pathogens and much more besides. “I've seen two huge developments since I've been in science: CRISPR and PCR,” says John Schimenti, a geneticist at Cornell University in Ithaca, New York. Like PCR, the gene-amplification method that revolutionized genetic engineering after its invention in 1985, “CRISPR is impacting the life sciences in so many ways,” he says.
Reporter Kerri Smith investigates the meteoric rise of CRISPR
But although CRISPR has much to offer, some scientists are worried that the field's breakneck pace leaves little time for addressing the ethical and safety concerns such experiments can raise. The problem was thrust into the spotlight in April, when news broke that scientists had used CRISPR to engineer human embryos (see Nature 520, 593–595; 2015). The embryos they used were unable to result in a live birth, but the report2 has generated heated debate over whether and how CRISPR should be used to make heritable changes to the human genome. And there are other concerns. Some scientists want to see more studies that probe whether the technique generates stray and potentially risky genome edits; others worry that edited organisms could disrupt entire ecosystems.
“This power is so easily accessible by labs — you don't need a very expensive piece of equipment and people don't need to get many years of training to do this,” says Stanley Qi, a systems biologist at Stanford University in California. “We should think carefully about how we are going to use that power.”
Biologists have long been able to edit genomes with molecular tools. About ten years ago, they became excited by enzymes called zinc finger nucleases that promised to do this accurately and efficiently. But zinc fingers, which cost US$5,000 or more to order, were not widely adopted because they are difficult to engineer and expensive, says James Haber, a molecular biologist at Brandeis University in Waltham, Massachusetts. CRISPR works differently: it relies on an enzyme called Cas9 that uses a guide RNA molecule to home in on its target DNA, then edits the DNA to disrupt genes or insert desired sequences. Researchers often need to order only the RNA fragment; the other components can be bought off the shelf. Total cost: as little as $30. “That effectively democratized the technology so that everyone is using it,” says Haber. “It's a huge revolution.”
CRISPR methodology is quickly eclipsing zinc finger nucleases and other editing tools (see 'The rise of CRISPR'). For some, that means abandoning techniques they had taken years to perfect. “I'm depressed,” says Bill Skarnes, a geneticist at the Wellcome Trust Sanger Institute in Hinxton, UK, “but I'm also excited.” Skarnes had spent much of his career using a technology introduced in the mid-1980s: inserting DNA into embryonic stem cells and then using those cells to generate genetically modified mice. The technique became a laboratory workhorse, but it was also time-consuming and costly. CRISPR takes a fraction of the time, and Skarnes adopted the technique two years ago.
Publications: Scopus; Patents: The Lens; Funding: NIH RePORTER.
Researchers have traditionally relied heavily on model organisms such as mice and fruit flies, partly because they were the only species that came with a good tool kit for genetic manipulation. Now CRISPR is making it possible to edit genes in many more organisms. In April, for example, researchers at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, reported using CRISPR to study Candida albicans, a fungus that is particularly deadly in people with weakened immune systems, but had been difficult to genetically manipulate in the lab3. Jennifer Doudna, a CRISPR pioneer at the University of California, Berkeley, is keeping a list of CRISPR-altered creatures. So far, she has three dozen entries, including disease-causing parasites called trypanosomes and yeasts used to make biofuels.
Yet the rapid progress has its drawbacks. “People just don't have the time to characterize some of the very basic parameters of the system,” says Bo Huang, a biophysicist at the University of California, San Francisco. “There is a mentality that as long as it works, we don't have to understand how or why it works.” That means that researchers occasionally run up against glitches. Huang and his lab struggled for two months to adapt CRISPR for use in imaging studies. He suspects that the delay would have been shorter had more been known about how to optimize the design of guide RNAs, a basic but important nuance.
By and large, researchers see these gaps as a minor price to pay for a powerful technique. But Doudna has begun to have more serious concerns about safety. Her worries began at a meeting in 2014, when she saw a postdoc present work in which a virus was engineered to carry the CRISPR components into mice. The mice breathed in the virus, allowing the CRISPR system to engineer mutations and create a model for human lung cancer4. Doudna got a chill; a minor mistake in the design of the guide RNA could result in a CRISPR that worked in human lungs as well. “It seemed incredibly scary that you might have students who were working with such a thing,” she says. “It's important for people to appreciate what this technology can do.”