An Edited Gene In A Couple of Days?

One day in March 2011, Emmanuelle Charpentier, a geneticist who was studying flesh-eating bacteria, approached Jennifer Doudna, an award-winning scientist, at a microbiology conference in Puerto Rico. Charpentier, a more junior researcher, hoped to persuade Doudna, the head of a formidably large lab at the University of California, Berkeley, to collaborate. While walking the cobblestone streets of Old San Juan, the two women fell to talking. Charpentier had recently grown interested in a particular gene, known as Crispr, that seemed to help flesh-eating bacteria fight off invasive viruses. By understanding that gene, as well as the protein that enabled it, called Cas9, Charpentier hoped to find a way to cure patients infected with the bacteria by stripping it of its protective immune system.

Among scientists, Doudna is known for her painstaking attention to detail, which she often harnesses to solve problems that other researchers have dismissed as intractable. Charpentier, who is French but works in Sweden and Germany, is livelier and more excitable. But as the pair began discussing the details of the experiment, they quickly hit it off. ‘‘I really liked Emmanuelle,’’ Doudna says. ‘‘I liked her intensity. I can get that way, too, when I’m really focused on a problem. It made me feel that she was a like-minded person.’’

At the time, bacteria were thought to have only a rudimentary immune system, which simply attacked anything unfamiliar on sight. But researchers speculated that Crispr, which stored fragments of virus DNA in serial compartments, might actually be part of a human-style immune system: one that keeps records of past diseases in order to repel them when they reappear. ‘‘That was what was so intriguing,’’ Doudna says. ‘‘What if bacteria have a way to keep track of previous infections, like people do? It was this radical idea.’’

The Crispr Quandary – Is Genetic Engineering Here?

The other thing that made Crispr-Cas9 tantalizing was its ability to direct its protein, Cas9, to precisely snip out a piece of DNA at any point within the genome and then neatly stitch the ends back together. Such effortless editing had a deep appeal: In the lab, the process remained cumbersome. At the time, though, Doudna didn’t think much about Crispr’s potential as a gene-editing tool. Researchers had stumbled on such systems in the past, but struggled to harness them. Nonetheless, she says: ‘‘I had this feeling. You know when you pick up a suspense novel, and read the first chapter, and you get a little chill, and you know, ‘Oh, this is going to be good’? It was like that.’’

Doudna arranged for a postdoctoral researcher, Martin Jinek, to collaborate with Charpentier’s team. After months of experimentation, they determined that Crispr relied on two separate kinds of RNA: a guide, which targeted the Cas9 protein to a particular location, and a tracer, which enabled the protein to cut the DNA. But even then, it wasn’t clear whether Crispr was anything more than a curiosity. Unlike most living things — people, animals, plants — the cells of bacteria have no nucleus, and their RNA and DNA interact in a different way. Because of that, Jinek says, it was hard to say ‘‘whether the system would be portable’’ — whether it would work in anything except bacteria. Going over the problem in Doudna’s office, Jinek began sketching the two RNA molecules on the whiteboard. In their natural form, the two are separate, but Doudna and Jinek believed that it would be possible to combine them into a single tool — one that was more likely to work in a wide range of organisms. ‘‘That was the moment the project went from being ‘This is cool, this is wonky’ to ‘Whoa, this could be transformative,’ ’’ Doudna says.

The tool Doudna ultimately created with her collaborators paired Crispr’s programmable guide RNA with a shortened tracer RNA. Used in combination, the system allowed researchers to target and excise any gene they wanted — or even edit out a single base pair within a gene. (When researchers want to add a gene, they can use Crispr to stitch it between the two cut ends.) Some researchers have compared Crispr to a word processor, capable of effortlessly editing a gene down to the level of a single letter.

Even more surprising was how easy the system was to use. To edit a gene, a scientist simply had to take a strand of guide RNA and include an ‘‘address’’: a short string of letters corresponding to a particular location on the gene. The process was so straightforward, one scientist told me, that a grad student could master it in an hour, and produce an edited gene within a couple of days. ‘‘In the past, it was a student’s entire Ph.D. thesis to change one gene,’’ says Bruce Conklin, a geneticist at the Gladstone Institutes in San Francisco. ‘‘Crispr just knocked that out of the park.’’

Click here to read the entire article.

New York Times – by Jennifer Kahn, November 9, 2015