The War Over Genome Editing Just Got A Lot More Interesting

The cutting circle GETTY IMAGES

IF YOU WANT to drop some real DNA editing knowledge—like, I don’t know, at a party!—here’s a tip. Instead of calling the much hyped precise genome-editing tool CRISPR, call it CRISPR/Cas9. CRISPR, you see, just refers to stretches of repeating DNA that sit near the gene for Cas9, the actual protein that does the DNA editing.

Well, at least for now. Today, gene-editing scientists dropped some curious news: They’ve found a CRISPR system involving a different protein that also edits human DNA, and, in some cases, it may work even better than Cas9.

The discovery comes at a time when CRISPR/Cas9 is sweeping through biology labs. So revolutionary is this new genome editing technique that rival groups, who each claim to have been first to the tech, are bitterly fighting over the CRISPR/Cas9 patent. This new gene-editing protein called Cpf1—and maybe even others yet to be discovered—means that one patent may not be so powerful after all.

And there’s good reason to think more useful CRISPR proteins are out there. CRISPR sequences are a part of primordial immune systems, found in some 40 percent of bacteria and 90 percent of archaea. In a study published today in Cell, Feng Zhang (no relation to this writer) and colleagues trawled through bacterial genomes looking for different versions of Cpf1. They found two, from Acidominococcus and Lachnospiraceae, that can snip DNA when scientists insert them into human cells.

“There are definitely many more defense systems out there, and maybe some of them might even have spectacular applications like with the Cas9 system,” says John van der Oost, a microbiologist at Wageningen University who is a co-author on the paper. “We have the feeling it’s just the tip of the iceberg.”

Zhang and van der Oost’s search was deliberate, but the initial discovery of CRISPR/Cas9 as a gene-editing tool was not. Back in the 1980s, microbiologists saw strange repeating sequences in the DNA of bacteria. Those clustered regularly interspaced short palindromic repeats became CRISPR, and scientists realized they were evidence of an immune system bacteria used to defend against viruses. The spacers between the repeats are in fact snippets of viral genomes, which CRISPR-associated proteins called Cas use as “mug shots” to recognize viruses and shred their DNA.

Many different proteins are associated with CRISPR. But in the early 2010s, Emmanuelle Charpentier, who was studying the flesh-eating bacteria Streptococcus pyogenes, stumbled onto one with special powers. Her bacteria happen to carry Cas9 proteins, which have the remarkable ability to precisely cut DNA based on a RNA guide sequence. In 2012, Charpentier and UC Berkeley biologist Jennifer Doudna published a paper describing the CRISPR/Cas9 system and speculated about its genome editing capabilities. And they filed a patent application. Much more on that patent later.

The Obscure Protein

While Cas9 has driven thousands of lab experiments and millions of dollars in funding for startups trying to capitalize on the technology, Cpf1 has remained relatively obscure. This study drags Cpf1 into the limelight. “It’s a very comparable to Cas9 and it has a few different features which could be quite useful,” says Dana Carroll, a biochemist at the University of Utah.

That’s because Cas9 isn’t perfect, despite its hype as a laser-precise genome editing tool. Cpf1 offers some slight advantages. For example, when it cuts double-stranded DNA, it snips the two strands in slightly different locations, resulting in overhang that molecular biologists call “sticky ends.” Sticky ends can make it easier to insert a snippet of new DNA—say, a different version of a gene—though the Cell paper does not actually show data directly comparing Cas9 and Cpf1 when inserting DNA.

Cpf1 is also physically a smaller protein, so it may be easier to put into human cells. It requires only one RNA molecule instead of two, with Cas9. But it’s not a rival so much as a complementary tool: The two proteins favor binding to different locations in the genome, so together, they might allow more flexibility in where scientist want to cut.

But Cpf1 has implications reaching far outside the lab.

Patent Wars

Not long after Doudna and UC Berkeley filed a patent, the Broad Institute and MIT filed their own patent on behalf of Zhang for the CRISPR/Cas9 system. Zhang had been working on actually showing that CRISPR/Cas9 can edit mammalian genomes in mammalian cells, an application he published in 2013 and says he came up with independently. The Broad’s and MIT’s attorney paid a fee to accelerate their application. Ultimately, the US Patent and Trademark Office awarded the patent to Zhang, MIT, and the Broad Institute. The University of California, obviously unhappy with the decision, filed an application for an interference proceeding to get the USPTO to reconsider. That process is ongoing.

But biotech companies have raced ahead to develop therapeutics and techniques with the system. Feng and Doudna have since licensed their technology to rival companies, Editas and Caribou. Charpentier also cofounded Crispr Therapeutics in Switzerland. Whoever wins the patent dispute will have a monopoly on CRISPR/Cas9 technology, the hottest new thing in biotech.

But with Cfp1, the stakes of that specific patent dispute go down. A lab or company could use Cfp1 without infringing on the CRISPR/Cas9 patent. “It takes power away from whoever the winner is going to be,” says Jacob Sherkow, a professor at New York Law School1 (Zhang has indicated the rights to Cpf1 may not necessarily go to the company he cofounded, Editas.) Whether a CRISPR/Cfp1 system is patentable as a separate invention—Sherkow says it probably is—perhaps isn’t even relevant because its very existence means Cas9 is no longer the only game in town.

And if biologists keep trawling through bacterial genomes, they might find even more proteins to join Cfp1 and Cas9. Who knows what else is hiding in the genomes of microbes?

ORIGINAL: Wired

By SARAH ZHANG

09.25.15