The New York Times, June 3, 2016
Just a few years ago, Crispr was a cipher — something that sounded to most ears like a device for keeping lettuce fresh. Today, Crispr-Cas9 is widely known as a powerful way to edit genes. Scientists are deploying it in promising experiments, and a number of companies are already using it to develop drugs to treat conditions ranging from cancer to sickle-cell anemia.
Yet there is still a lot of misunderstanding around it. Crispr describes a series of DNA sequences discovered in microbes, part of a system to defend against attacking viruses.
Microbes make thousands of forms of Crispr, most of which are just starting to be investigated by scientists. If they can be harnessed, some may bring changes to medicine that we can barely imagine.
On Thursday, in the journal Science, researchers demonstrated just how much is left to discover. They found that an ordinary mouth bacterium makes a form of Crispr that breaks apart not DNA, but RNA — the molecular messenger used by cells to turn genes into proteins.
If scientists can get this process to work in human cells, they may open up a new front in gene engineering, gaining the ability to precisely adjust the proteins in cells, for instance, or to target cancer cells.
“The groundbreaking thing about this work is that it now opens up the RNA world to Crispr,” said Oliver Rackham, a synthetic biologist at the University of Western Australia who was not involved in the study.
Crispr was first discovered in 1987, but it took decades for scientists to figure out that microbes needed the system to recognize DNA from invading viruses and to chop it into pieces, stopping the infection.
In 2012, a team of scientists led by Jennifer Doudna of the University of California, Berkeley, and Emmanuelle Charpentier, then at Umea University in Sweden, discovered how to use this microbial defense as a gene-editing tool that could potentially alter any piece of DNA.
Most of that early work was carried out with Crispr molecules from a species of bacteria that lives in human skin called Streptococcus pyogenes. Once those molecules proved effective at reassembling human DNA, a number of scientists began looking at other species for Crispr systems that might be even better.
Some researchers investigated familiar species that have been studied in labs for decades. But Eugene V. Koonin and his colleagues at the National Center for Biotechnology Information instead scoured databases containing hundreds of millions of genetic sequences for those that resembled Crispr genes.
Once they discovered some candidates, they joined forces with Feng Zhang of M.I.T., who published one of the first studies on using Crispr to edit human DNA. One of the first candidates they looked at came from a species of bacteria that lives in the mouth, known as Leptotrichia shahii.
It had a group of genes that looked like Crispr genes in some ways, but with stark differences. When the researchers equipped bacteria with these genes, which they called C2c2, they found that the organisms gained a defense that had never been seen.
Many viruses do not contain DNA. Instead, their genetic information is encoded in RNA, DNA’s single-stranded cousin, which they use to hijack the genes of their hosts and cause them to make new viruses. Some of these RNA viruses, such as H.I.V. and poliovirus, attack our species. Many others attack bacteria.
Previously discovered Crispr molecules are very good at whacking apart DNA but don’t protect bacteria from an RNA virus. Dr. Zhang and his colleagues discovered that bacteria with C2c2 make molecules that can attack RNA and chop it up, destroying the invaders.
The researchers also found that they could tailor these genes to cut any RNA molecule they wanted. Now they are tinkering with the process to try to get it to work in human cells.
“There could be a lot of cool applications,” Dr. Zhang said. He hopes, for example, that C2c2 molecules could be trained to destroy RNA made only in cancer cells. Those cells would be unable to make essential proteins and die.
While it remains to be seen if these will become useful tools, Dr. Koonin said, the discovery has already revealed something important about the evolutionary history of these microbial defenses.
Some parts of C2c2 genes share a common evolutionary origin with the defense systems seen in other bacterial species. Over billions of years, Dr. Koonin said, evolution has blindly tinkered with these genes in order to generate new ways to protect against viruses.
Exploring this evolution is more productive for now than trying to design gene-editing technology from scratch, Dr. Zhang said. “We’re not quite smart enough yet,” he added.
In fact, some future advances in gene editing may even not be based on Crispr. Microbes have evolved several different lines of defense against viruses, some of which are only now coming to light.
In recent years, for example, scientists have discovered that microbes can use another group of proteins, called Argonautes, to chop up viral DNA. Last month, a team of Chinese researchers announced that they were able to use Argonaute proteins to edit DNA in human cells.
Paul S. Knoepfler, a cell biologist at the University of California, Davis, is taking a wait-and-see attitude about Argonaute proteins, but he said he would not be surprised if they quickly turned out to be yet another powerful gene-editing tool.
“This field seems to move in dog years,” he said. “It feels like seven times faster than real time.”
Copyright 2016 The New York Times Company. Reprinted with permission.