March 18, 2014

The New York Times calls it “a scientific frenzy.” Science magazine dubbed it “red hot”  “The CRISPR Craze.”

It’s been less than two years since Berkeley biochemist Jennifer Doudna reported in Science a startlingly versatile strategy to precisely target and snip out DNA at multiple sites in the cells of microbes, plants and animals.

But since her landmark paper, more than 100 labs have already taken up the new genomic engineering technique to delete, add or suppress genes in fruit flies, mice, zebrafish and other animals widely used to model genetic function in human disease. 

Jennifer Doudna in her lab. Photo: Roy Kaltschmidt

Last year, Doudna and her colleagues showed that this “molecular scissors” approach, known as CRISPR/Cas9, can be used with great precision to selectively disable or add several genes at once in human cells, offering a potent new tool to understand and treat complex genetic diseases. 

Journal articles now appear almost weekly as researchers around the word apply the technique in basic and clinical research. Patents have been filed and licensed, and companies founded last year in Cambridge, London and Berkeley have begun zeroing in on agricultural, industrial and biomedical applications.

“I’ve never experienced anything like the pace of discovery before in my life,” Doudna says of the flurry of experimentation flowing from her 2012 paper co-authored with Emmanuelle Charpentier, now at the Helmholtz Centre for Infection Research in Germany.

The technology combines RNA molecules with an enzyme known as Cas9 to target specific DNA sequences. The enzyme cuts the DNA in a precise location, so that researchers can either knock out the gene’s activity or patch in a healthy gene.

Since every gene’s DNA has an RNA counterpart, virtually any gene can be targeted by using a specific RNA sequence. And since only one type of enzyme is needed, many genes can be edited at the same time. Last year, one researcher successfully modified five genes in experiments with mouse embryonic stem cells. If advanced to human cells, this could greatly boost the promise of therapy for diseases involving multiple genes.

“The CRISPR/Cas9 technology is a complete game changer,” said Jonathan Weissman, professor of cellular and molecular pharmacology at UCSF. “With CRISPR, we can now turn genes off or on at will” to study normal gene function and understand how genetic defects do their damage at the molecular level.

The new approach lies at the heart of the Innovative Genomics Institute (IGI), just announced by UC Berkeley and UCSF to develop genomic analysis to explore disease processes and generate new treatments.  Doudna is the executive director and UCSF’s Jonathan Weissman is co-director of the new Institute.

A time to toast

On her office bookcase, flanked by molecular biology and biochemistry texts, stands a handsome bottle of Veuve Cliquot Brut champagne wrapped in golden ribbon.

“It’s for the Lurie Prize,” she says simply -- the prestigious Lurie Prize in the Biomedical Sciences, awarded last month by the Foundation for the National Institutes of Health in recognition of her discovery and the research leading up to it.

“It’s an honor to be recognized by my colleagues,” she says. “The prize really recognizes so many people who have worked in my lab. An award like this honors a body of work contributed by many researchers.” Doudna is a professor of biophysics, biochemistry and structural biology at Berkeley.

Molecular scissors: A new DNA-editing strategy aims to disable harmful genes and restore normal function. (Video and voiceover: Janet Iwasa.)

Doudna, Charpentier and their colleagues devised the editing strategy by manipulating an immune defense system used by bacteria against viral attack. The surprisingly sophisticated microbial defense was identified less than ten years ago. Researchers discovered that when a bacterium is invaded by a virus, it “saves” a snippet of the viral DNA – called a spacer -- and inserts it into its own DNA.

 

If the microbe encounters the same virus again, it can convert the original viral spacer DNA into RNA. The RNA then essentially guides the Cas9 enzyme to snip the matching stretch of DNA in the new invader, disabling the virus. 

Ultimately, the bacterial genome becomes studded with the spacers from different viruses the microbe has encountered -- a virtual “mug shot” of invaders, as one observer called it.

Doudna began studying the bacteria’s capacity to edit viral genes in 2006, and eventually realized that its specificity might be exploited to cut and paste defective human genes.  In 2012, she and Charpentier teased apart some of the key molecular mechanics of the microbial defense process.

Just a few months later, along with postdoc Martin Jinek, they reported their success developing a streamlined version of the bacterial editing process. It now allows a “single-guide RNA” to escort the Cas9 enzyme to the target gene, where it can be cut to disable it or to insert a healthy gene.

“Here we have a single protein that can be reprogrammed to work with any RNA sequence to edit selected genes,” Doudna explains. “I think that’s why we’re seeing such an explosion. It’s so accessible, inexpensive and it works very efficiently.”

CRISPR/Cas9 is simpler, quicker, more precise and versatile than current genomic engineering techniques  -- a kind of one-stop genomic editing shop.

Doudna calls her team’s discovery “a triumph of basic science.”

“A reporter for 60 Minutes was interviewing me last week and was asking me if I set out to discover a better genomics technology. We were actually studying the bacterial immune system to find out how it works. It was only through the process of discovery – of basic research -- that we found something very useful for genomic engineering.”

Her lab continues to probe the molecular mechanics underlying the bacterial system and to refine the innovations derived from it. She and Berkeley’s Eva Nogales, professor of molecular biology and biochemistry, recently used x-ray crystallography and electron microscopy to determine key structures of the RNA and enzyme that team up in the bacterial gene editing system.

As recently as March 6, in the cover article in Nature, Doudna further clarified how the RNA-enzyme complex recognizes its gene target, providing more detail to help expand the CRISPR technique or improve its efficiency.

Doudna thinks advanced genomic engineering techniques like the one she developed will first aid research and treatment “ex vivo” -- withdrawing diseased cells in human blood, restoring genetic defects and then introducing them back into the patient. Other genomic strategies are already being tested in this way in clinical trials to treat sickle cell anemia and HIV.  

She expects the CRISPR/Cas9 approach to quickly accelerate progress toward treatments.

“I wouldn’t have said this even six months ago, but I think we will see clinical applications with this technology. I’d be honored and excited if our work leads to new treatments to help people’s lives.”

Maybe then she’ll open that bottle of champagne.

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