New enzyme boosts 'CRISPR toolbox' for disease detection

The Mammoth cofounders: Chief Discovery Officer Lucas Harrington, CEO Travis Martin, CTO Ashley Tehranchi, Jennifer Doudna, and Chief Research Officer Janice Chen. (Mammoth Biosciences)

CRISPR is often associated with gene editing and the Cas9 enzyme—commonly referred to as its “scissors”—but the technology could also prove useful in diagnosing disease. Mammoth Biosciences is working on a platform that can detect any biomarker containing DNA or RNA using different enzymes: Cas12 and Cas13. Now, the company is adding to its “CRISPR toolbox” by licensing a new CRISPR enzyme, Cas14, from the University of California, Berkeley.

Mammoth launched last April with technology licensed from the lab of CRISPR pioneer Jennifer Doudna, Ph.D., at Berkeley. Its goal is to create a point-of-care diagnostic tool that can detect multiple diseases for use in hospitals and at home.

So why does it need so many enzymes?

Each CRISPR Cas protein offers different strengths in various applications because of factors like speed, precision, and cost, the company's founders believe. Adding Cas14 to its arsenal allows Mammoth to target single-stranded DNA, as well as double-stranded DNA (Cas12) and single-stranded RNA (Cas13).

Mammoth CEO Trevor Martin thinks of DNA and RNA as the languages of CRISPR and single-stranded or double-stranded DNA and RNA as different dialects. Being able to speak multiple dialects of different languages allows Mammoth to target many different kinds of disease. The company thinks Cas14 could be particularly useful in infectious disease, oncology and genetic mutations.

“Where this comes in useful in diagnostics is that we have different biomarkers for different things,” Martin told FierceBiotechResearch. “Let’s say you want to genotype someone to see what their risk is for some type of cancer, then you’d want to look at double-stranded DNA. If you’re looking at someone’s immune response, or some sort of pathogen, such as malaria, then you probably want to look at RNA... You might even have other things like DNA viruses; in that case, you might want to look at single-stranded DNA.”

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Cas enzymes are not monolithic; each Cas system has its variants. And certain variants may be able to go where others can't. Take existing CRISPR-Cas9 systems. Most of them have sequence restrictions that limit the number of sites on the genome they can target. This is because these systems need a a "protospacer adjacent motif (PAM) sequence" to recognize a particular target on DNA for cutting. Without that sequence, no editing can occur. But last October, a team at the Massachusetts Institute of Technology discovered a new Cas9 enzyme that overcomes this issue and can target more than half of the locations on the genome.

As for Cas14, Martin sees much potential in what “seems to be a very diverse array of proteins within it,” he said. What's more, it looks like Cas14 targets single-stranded DNA without class 2 sequence restrictions, according to a Science study authored by a Berkeley team that includes Mammoth's cofounders. Like the new Cas9 variant discovered at MIT, Cas14 doesn't need PAM to target sequences either, Martin said.

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Since launch, Mammoth has grown the team “substantially” and started multiple partnerships, though Martin couldn’t disclose any names or disease targets yet. He did say that the company has been looking at areas where this technology could make a large impact, such as infectious diseases and “areas in which you need to know a very accurate result quickly and affordably.”

At the moment, the company is building out its diagnostic systems. A CRISPR-based tool could take various forms, from high-volume screens that live in hospital labs to point-of-care tests in a box.

But “the ultimate vision” is to have an at-home test “similar in use and accessibility as a pregnancy test,” Martin said.

When asked if Mammoth would continue looking for new CRISPR systems, Martin said the company is focusing on “characterizing” the systems it already has, but that it wouldn’t ignore brand-new systems. After all, Cas9 was around for a little while before Cas12 and its peers were discovered, he said.