CRISPR, the Disruptor

Heidi Ledford, Nature, June 3, 2015

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.

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. 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.”

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{snip} 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.”

Andrea Ventura, a cancer researcher at Memorial Sloan Kettering Cancer Center in New York and a lead author of the work, says that his lab carefully considered the safety implications: the guide sequences were designed to target genome regions that were unique to mice, and the virus was disabled such that it could not replicate. He agrees that it is important to anticipate even remote risks. “The guides are not designed to cut the human genome, but you never know,” he says. “It’s not very likely, but it still needs to be considered.”

Editing out disease

Last year, bioengineer Daniel Anderson of the Massachusetts Institute of Technology in Cambridge and his colleagues used CRISPR in mice to correct a mutation associated with a human metabolic disease called tyrosinaemia5. It was the first use of CRISPR to fix a disease-causing mutation in an adult animal–and an important step towards using the technology for gene therapy in humans (see ‘A brief history of CRISPR’).

The idea that CRISPR could accelerate the gene-therapy field is a major source of excitement in scientific and biotechnology circles. But as well as highlighting the potential, Anderson’s study showed how far there is to go. To deliver the Cas9 enzyme and its guide RNA into the target organ, the liver, the team had to pump large volumes of liquid into blood vessels–something that is not generally considered feasible in people. And the experiments corrected the disease-causing mutation in just 0.4% of the cells, which is not enough to have an impact on many diseases.

Over the past two years, a handful of companies have sprung up to develop CRISPR-based gene therapy, and Anderson and others say that the first clinical trials of such a treatment could happen in the next one or two years. Those first trials will probably be scenarios in which the CRISPR components can be injected directly into tissues, such as those in the eye, or in which cells can be removed from the body, engineered in the lab and then put back. For example, blood-forming stem cells might be corrected to treat conditions such as sickle-cell disease or β-thalassaemia. It will be a bigger challenge to deliver the enzyme and guide RNA into many other tissues, but researchers hope that the technique could one day be used to tackle a wider range of genetic diseases.

Yet many scientists caution that there is much to do before CRISPR can be deployed safely and efficiently. Scientists need to increase the efficiency of editing, but at the same time make sure that they do not introduce changes elsewhere in the genome that have consequences for health. “These enzymes will cut in places other than the places you have designed them to cut, and that has lots of implications,” says Haber. “If you’re going to replace somebody’s sickle-cell gene in a stem cell, you’re going to be asked, ‘Well, what other damage might you have done at other sites in the genome?’”

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