Expanding CRISPR toolkit may render patent fight moot

University of California, Berkeley, scientists have found entirely new classes of Cas proteins, the enzymes responsible for snipping DNA in the CRISPR gene-editing system. The discovery expands the ever-growing CRISPR toolbox and creates a new wrinkle in the ongoing patent dispute between Berkeley and the Broad Institute of Harvard University and MIT over the gene-editing technology.

Geomicrobiologist Jillian F. Banfield led the Berkeley team, which scoured 155 million genes from microbes that cannot be grown in labs to find the Cas proteins. These microbes live in places as varied as groundwater, acidic drainage from mines, and the intestines of infants. In addition to finding new Cas9 proteins, the researchers also discovered entirely new classes of Cas enzymes, dubbed CasX and CasY (Nature 2016, DOI: 10.1038/nature21059).

Because Cas proteins are large, it’s challenging to deliver them into cells for gene-editing purposes. The newly discovered CasX enzymes, however, are among the smallest Cas proteins known, potentially a key advantage over other Cas variants, including the Cas9 protein that’s used by almost everyone working with CRISPR today. Cas9 is part of microbes’ immune systems, found in the pathogenic Streptococcus pyogenes and many other species. “There is just an incredible diversity of microbial life out there,” Banfield says. And the CasX and CasY discovery “is a beautiful example of the kinds of valuable things that can be found.”

Banfield partnered with Jennifer A. Doudna’s lab at UC Berkeley to demonstrate CasX and CasY’s potential for gene-editing in bacterial cells. Doudna, a cocreator of the CRISPR/Cas tool along with Max Planck Institute for Infection Biology’s Emmanuelle M. Charpentier, is currently embroiled in a patent dispute with the Broad Institute over who holds the licenses to CRISPR systems specifically using Cas9. The Berkeley researchers recently filed a patent application related to the newly reported CasX and CasY enzymes. Because these variants are different enough from Cas9, they could give Doudna and colleagues a cushion if they lose the ongoing patent fight.

The timing of the Berkeley team’s Nature report on CasX and CasY is impeccable. Last Friday, several companies, including CRISPR Therapeutics, Intellia Therapeutics, and Caribou Biosciences—which are all tied to either Doudna or Charpentier—formalized an alliance to share, protect, and enforce their intellectual property. On Monday, the Broad-associated Editas Medicine retaliated and announced its own agreement with five universities, licensing “advanced forms of Cas9,” as well as a previously reported Cas9 alternative enzyme named Cpf1.

Jacob S. Sherkow of New York Law School says that in retrospect, knowledge of CasX and CasY likely fueled the cross-licensing agreements. “That is the piece of the jigsaw puzzle we were missing earlier this week” when the last of the deals took place, Sherkow says. “It cannot be coincidence.”

“It is possible that all of the companies involved in CRISPR technologies could avoid being ‘losers’ in the patent dispute by just using different versions” of Cas proteins, says Knut J. Egelie of the Norwegian University of Science & Technology. Alternatives to Cas9—the class of enzyme specified in patents from Berkeley and the Broad institute—“will level out the game and make the patent interference decision less important,” he adds.

Sherkow notes that Berkeley will have a year from the date it filed its provisional patent on the new Cas variants to add claims detailing how to specifically use the CasX and CasY system in all kinds of cells.

In the meantime, Banfield says her lab and Doudna’s will be carrying out gene-editing tests with the new enzymes in cells beyond bacteria, and her lab will continue exploring the mysterious genomes of difficult-to-cultivate microbes.