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The Crispr Quandary, by Jennifer Kahn, The New York Times

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Long-form introduction to CRISPR-Cas9 and its lead scientist Jennifer Doudna.

Hard to believe this technology has been around less than 5 years given how quickly its utility accelerated:

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.

CRISPR-Cas9 seems like a technology worthy of its hype.

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 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.’’

CRISPR is now being used by nearly every genetic-engineering lab in the world.

Genetic engineering has wrought spectacular changes in the years since it was first developed in 1973. By breeding mice to have particular mutations, researchers have been able to explore the roots of diseases including cystic fibrosis and diabetes. It has also opened the door to new hybrids: pest-resistant corn with genes taken from bacteria, for instance, and yeast modified to churn out an antimalarial drug. As of 2014, the market for genetically engineered products was worth almost $2 billion — a number that is expected to double over the next five years.

But despite these advances, the process of altering genes has remained laborious and inexact. Engineering a mouse with a single mutation took a dedicated lab almost two years, and even that was something of a crapshoot. Altered genes frequently ended up in random locations, or else in widely varying numbers — no copies in one cell, a dozen copies in another — often with confounding results. One scientist told me that before Crispr, he had to microinject roughly a million cells in order to get one perfect mutation. With Crispr, he could get the same result using just 10 cells.

And mice were the best case. Other animals were far harder to engineer — weirdly, even rats were difficult — and many couldn’t be altered at all, for reasons nobody really understood. ‘‘There’s a reason the mouse became the model animal for human diseases,’’ notes Tom Cech, director of the University of Colorado’s BioFrontiers Institute and a Nobel laureate. ‘‘Before Crispr, trying to genetically modify any other animal was either impossible, or impossible to do with any kind of precision.’’ And because scientists could alter only a single gene at a time, moreover, they could barely scratch the surface of many disorders, like cardiovascular disease, that were thought to involve multiple, or, in some cases, even dozens of genes. ‘‘What most people don’t realize is how limited we were before Crispr came along,’’ Cech says. ‘‘The tools we had were extremely crude.’’

In the era of Crispr (short for Clustered Regularly Interspaced Short Palindromic Repeats, a reference to the gene’s structure), those limitations are already disappearing. In October, Harvard researchers used Crispr to simultaneously alter 62 genes in pig embryos, creating animals that could, at least in theory, grow human organs for transplant. Uncannily, the tool also seemed to work in nearly every organism, from silkworms to monkeys, and also in every cell type: kidney, heart and those, like T-cells, that researchers had previously struggled to modify. In early November, the biotechnology start-up Editas Medicine announced that it planned to test a Crispr-based gene therapy technique in hopes of curing a rare form of blindness, by deleting part of a gene that controls the eye’s photoreceptor cells. But most researchers believe that Crispr’s biggest impact will be in speeding up the drug pipeline. Drug development currently relies, in part, on genome-wide association studies to identify mutations that people with a certain disease have in common. The problem is that those studies typically turn up hundreds of loosely associated mutations, each of which may or may not actually relate to the disease. (Some of them may be caused by the disease.) Before Crispr, it was so difficult to edit a single gene accurately that researchers had no easy way to test which mutations actually mattered, and thus which ones to target when looking for a cure.

That alone would qualify as a major advance, but Crispr’s reach will almost certainly be far greater — in part because so many industries now rely on genetic engineering. Re­searchers have begun using Crispr to develop better bio­fuels and to create new enzymes for industrial markets, where they’re used in laundry detergents, water treatment and paper milling. In agriculture, companies are using Crispr to make crops more pest- and drought-resistant, without using genes spliced in from other species, like a flounder gene inside a tomato. (DuPont is collaborating with Doudna’s company, Caribou Biosciences, to grow Crispr-edited corn and wheat, which are expected to reach supermarkets within five years.) Livestock breeders can harness it to produce animals with more muscle mass and leaner meat, faster and more predictably than with ordinary crossbreeding. Food conglomerates, including Dannon, are already deploying Crispr to create strains of bacteria that produce more flavorful yogurt; other fermented foods — cheese, bread, pickles — will probably follow.

For researchers studying complicated psychiatric disorders, Crispr may be a particular boon. ‘‘The major roadblock in that whole field has been that mice are just not good models,’’ says Feng Zhang, a biologist at the Broad Institute who pioneered the use of Crispr in human cells. ‘‘They often don’t even have the same brain structures as are affected in those diseases.’’ Zhang and Robert Desimone, director of M.I.T.’s McGovern Institute for Brain Research, are among a number of researchers now hoping to use Crispr to generate primate models for illnesses like autism and schizophrenia, which are thought to involve multiple mutations in a variety of combinations.

Farther afield, researchers are considering how Crispr might be used to eliminate malarial mosquitoes, or target invasive species like Asian carp in the Great Lakes. ‘‘There’s an almost frantic feeling of discovery,’’ one scientist told me. ‘‘Crispr has made so many experiments possible — it’s like standing in a candy store and knowing that you can choose just three things. Meanwhile, there are a thousand more experiments that you wish you could try, if only you had the time.’’ One prominent scientist estimated that Crispr was now being used by nearly every genetic-engineering lab in the world.

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