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Curiosity seeker

Cutting + Pasting the Genome

Jennifer Doudna, CRISPR Code Killer

Why you should care

Because a Nobel Prize winner says this breakthough is better than his breakthrough.

Jennifer Doudna has always had an explorer’s spirit. It’s what led the UC Berkeley molecular and cell biology professor to engineer a cheaper, easier way to correct DNA defects. Her game-changing technology takes a mysterious bacterial genetic code and transforms it into a powerful tool for cutting and pasting bits of genetic material – meaning not only could the entire field of gene therapy be revived, but her genome-editing tool could one day be used to treat a range of diseases, from cancer and AIDS to hereditary disorders like Down syndrome and Huntington disease.

That willingness to wander, to maybe even get a little lost, could be how she was able to make a creative break from earlier technologies.

Growing up in rainy Hilo, Hawaii, Doudna used curiosity as her compass. She never planned her weekend hikes, she just went. And just going she always discovered something fascinating. Sometimes she joined a family friend who was a biologist at the University of Hawaii, collecting mushrooms and examining tiny mollusks for his research. Doudna thought the finds were “so cool” that she worked in his lab the summer before college. It was her first taste of scientific research — and she never looked back.

”I wasn’t actively trying to go in any particular direction,” she said. That willingness to wander, to maybe even get a little lost, could be how she was able to make a creative break from earlier genome-editing technologies. Doudna “certainly didn’t set out to discover a genome editing tool by any stretch of the imagination.” It all began with a puzzle she couldn’t resist solving, thanks largely to her father. When Doudna was growing up, the literature professor got her hooked on one of his favorite pastimes — decoding short pieces of encrypted text, or cryptograms.

CRISPRs: Clustered regularly interspaced short palindromic repeats. Or, “weird repetitive RNA sequences tucked in the genomes” of bacteria that play an important role in immunity.

RNA: The molecule that carries out DNA instructions for creating the proteins that drive processes in the body.

In 2005, a colleague presented Doudna with a genetic cryptogram — weird repetitive RNA sequences tucked in the genomes of many of the bacteria she studied. Most scientists weren’t even aware of these so-called CRISPRs, much less their function. But Doudna suspected they hid a crucial purpose.

Sure enough, scientists discovered that CRISPRs played an important role in immunity: they recognize the DNA of viral invaders for the bacteria to chop up and fight off. But how did this search-and-destroy mechanism work? Teaming up with Umea University molecular biologist Emmanuelle Charpentier, Doudna unearthed the first clue when she found that a protein called Cas9 acts like a pair of molecular scissors. A CRISPR RNA fragment hooks up with Cas9 to precisely target the DNA of an invading virus, which it then cuts and destroys.

Here’s where it gets really complicated. Martin Jinek, a postdoctoral researcher in Doudna’s lab, found that Cas9 in bacteria needs two RNA guide strands – this sent the gears in their heads turning. What if they could engineer the system to require only a single, programmable RNA strand? Then biologists could use it to easily target and cut any DNA sequence. Doudna felt “a chill of excitement.” Maybe they could link the two RNA strands into one, and loop it in on itself — mimicking a double-stranded structure. Those chills were warranted: Doudna’s lab and other groups successfully used this simplified CRISPR system to modify genes in bacteria, plant and animal cells.

One early form of CRISPR-based gene therapy could involve editing the genes responsible for blood disorders like sickle-cell anemia in bone marrow cells, growing them into mature blood cells and injecting them back into patients.

Little more than a year after Doudna first described CRISPR in the journal Science, the cut-and-paste technology has yielded promising results in labs around the world. Last month, researchers from the Netherland’s Utrecht institute reported in Cell Stem Cell that CRISPR corrected the gene mutation responsible for cystic fibrosis in stem cells developed from two children with the life-threatening disease. Doudna believes a clinical trial of CRISPR-based gene therapy could begin in less than a decade.

Doudna experienced “many frustrations” getting CRISPR to work in human cells. But she knew if she succeeded, CRISPR would be “a profound discovery” — and maybe even a powerful gene therapy technique.

Scientific Graphic illustration with several different illos within

We knew if the system could be made to work in human cells, it would be a really profound discovery.

“I hope you’re sitting down,” an excited colleague told Doudna in an unexpected phone call. “CRISPR is turning out to be absolutely spectacular in [Harvard geneticist] George Church’s hands.” He had even gotten it to work in human cells. Thrilled, Doudna immediately contacted Church. They shared their results, and both published studies in January 2013 showing that CRISPR can cut, delete and replace genes in human cells. University of Massachusetts biologist Craig Mello, who shared the 2006 Nobel Prize for another genome editing tool, hails Doudna’s CRISPR technique as a “tremendous breakthrough,” even admitting that “in many ways it’s better” than his own technique.

Other techniques can also edit genes at specific DNA regions. But they require scientists to engineer a separate protein for each target site. In contrast, CRISPR only needs the Cas9 protein, allowing it to correct multiple defects at once. Besides being cheaper and easier to use, CRISPR is also much more precise, reducing the risk of off-target modifications introducing dangerous mutations. As a result, it could help revive the gene therapy field, whose early clinical failures — including patient deaths — led some to dismiss it as overhyped.

That doesn’t mean CRISPR is perfect, though. While it’s extremely precise, it occasionally modifies DNA at similar sites elsewhere in the genome instead of the target gene. Understanding and exploiting how Cas9 avoids these close matches “is an active area of investigation,” Doudna said. Still, CRISPR is ”a real game-changer,” Mello told the Independent. “It’s incredibly powerful.”

As for Doudna, she’s still soaking it all in. “It’s been very exciting to see work that started very much as a backwater kind of project, very much basic science, come to such fruition,” she said.

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Meet The Author Melissa Pandika

Melissa Pandika is a lab rat-turned-journalist with eye to all things science, medicine and more. Like? Distance running, snails, late-night Korean BBQ + R&B slow jams.

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