SAN FRANCISCO—CRISPR is regularly in the news these days as scientists seek to determine the extent—and accuracy—of its gene-editing abilities. But soon enough it could be making headlines not in relation to editing genomes, but rather as a new approach to diagnosis.
Mammoth Biosciences is developing what it says is the world’s first CRISPR-based disease detection platform. Thanks to a recent exclusive licensing deal with the University of California, Berkeley, Mammoth now has Cas14 to add to that platform. Lucas Harrington and Jennifer Doudna, co-founders of Mammoth, were part of the UC Berkeley team that discovered Cas14, which is the smallest CRISPR protein discovered so far. A paper on Cas14 was published in Science in October under the title “Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.”
Mammoth Biosciences’ goal is to develop an easy, affordable point-of-care diagnostic test that can enable rapid, simultaneous detection of several conditions in real time. The company is only a year old, having launched in April 2018, and has raised nearly $25 million to date.
Most often, CRISPR is used for genome editing to target select genetic sequences to be removed or altered. Trevor Martin, co-founder and CEO of Mammoth Biosciences, likens the “traditional” approach to using CRISPR as an editor or word processing tool, while Mammoth sees the system as a “biology search engine.”
“In diagnostics, we program our CRISPR proteins so that they bind to nucleic acid sequences, but in this case, instead of being sequences we want to edit, they’re sequences that are unique to whatever we want to detect. So for malaria, tuberculosis, dengue, Zika or whatever it is, you can bioinformatically say ‘this 20-base pair sequence is unique to this species.’ That’s how you program the protein. So then the CRISPR protein will go and bind to that sequence,” Martin explains.
“Then what happens is that we have these special proteins that are not Cas9, because Cas9 really can only just cut the sequence that you tell it to bind to, and that’s not terribly useful for diagnostics. Our proteins do what Cas9 does, but they do something else—they have this additional second functionality, which is conditional on having bound and successfully cut their target,” he continues. “When the CRISPR system successfully binds to that nucleic acid, it’ll cut that, and what happens that’s really useful for diagnostics is these proteins have a switch that’s activated. They flip this switch where they become these prolific collateral cutters—they start cutting everything in the solution. And that allows us to put these little reporter molecules in that light up when they’re cut, so that way we can breed out the signal, [and] the solution starts lighting up on successful activation.”
With this latest addition, Mammoth holds exclusive commercialization rights to Cas12, Cas13 and Cas14, which have applications for double-stranded DNA, single-stranded RNA recognition and single-stranded DNA, respectively.
“[Cas14] actually has a bunch of properties that make it a very unique and application-enabling protein. One of the key features on the diagnostic side that’s exciting is it targets the ‘untargetable,’” Martin tells DDNews. “CRISPR proteins are these programmable enzymes that, when you give them what’s called a guide RNA, they then bind to the complement of that guide RNA, and that’s how you tell it to bind to this nucleic acid that’s for malaria, or this other nucleic acid that is representative of tuberculosis. And it’s programmable, but there are some caveats with proteins like Cas9 or Cas12 where there’s a bit of restraint on what types of nucleic acid you can target—maybe they need a GTAC sequence, or an AT sequence, so there are some rules basically that constrain what you can have these proteins bind to.
“The exciting thing about Cas14 is that it doesn’t have these rules, and that’s exciting because it means that especially in applications where you need to get it exactly in the right spot, like in oncology—maybe you’re detecting a single snip, and you’re trying to see what the genotype is for that snip; you can’t just put it anywhere in a hundred base pair region.”
The addition of Cas14 is a huge boon for the company for other reasons, according to Martin. With it, the company can target “any nucleic acid you want, at any location,” he remarks, adding that “Cas14 is the most diverse family of CRISPR enzymes that’s ever been discovered, and that means there’s potential for this family of enzymes to have lots of interesting functions that we haven’t even characterized yet.”
And the enthusiasm for this newly completed toolbox extends beyond Mammoth, as Martin tells DDNews that the company has been approached by several companies that are hoping to explore the potential of CRISPR-based diagnostics.
“We’ve had many companies reach out, and we’ve actually signed our first round of partnerships with really exciting partners. I can’t reveal the names, but we’re definitely excited to work with them on the system, and we’re still open to partners that are excited by the potential of this system and what it can do,” he adds.