NEW YORK – Mammoth Biosciences is taking a lead role in a US government-funded, public-private effort to develop multi-pathogen detection platforms based on CRISPR gene editing technology, demonstrating the firm's CRISPR enzyme detection and engineering prowess and underscoring the general flexibility of the approach for infectious disease diagnostics.
The project, funded through a $36.7 million contract from the Defense Advanced Research Projects Agency's (DARPA) Detect It with Gene Editing Technologies (DIGET) program, aims to create a disposable point-of-care device for the detection of at least 10 pathogens, and a massively multiplexed device for the detection of at least 1,000 targets.
Contract research organization MRIGlobal will serve as the primary contractor, with other participating organizations serving as subcontractors with very specific to-do lists. Mammoth will act as one of the primary subcontractors — Cofounder and Chief Technology Officer Janice Chen will lead the team as a co-principal investigator alongside MRIGlobal's Richard Winegar and Julie Lucas, and the company's CRISPR-based DETECTR disease detection platform will be used to help develop the project's technology.
DARPA launched the DIGET program at the end of 2019 to create diagnostic and biosurveillance systems that can keep pace with disease outbreaks and support decision-making at the time and place of need, while taking advantage of advances in gene editing technologies.
Both the point-of-care diagnostic and the massively multiplexed device created under this contract must be simple to operate, low-cost, and rapidly reconfigurable, DARPA said. The disposable point-of-care device will also need to improve the speed and efficacy of triage and treatment, and enhance the standard of care for the military and public health domains in austere environments.
As for the multiplex device, the agency is looking for a diagnostic that can detect threats early, assess disease severity, and improve situational awareness. This platform will also have to provide actionable data for biosurveillance efforts, such as characterizing known and emergent pathogens to inform the deployment of countermeasures.
One of those threats is SARS-CoV-2. Although Chen was not at liberty to disclose all the targets the partners are considering for the panel, she confirmed that the virus currently causing a pandemic will be part of it. The researchers are also considering the different SARS-CoV-2 variants that have recently emerged, and which seem to be more infectious and have, so far, proven to be a challenge to track.
"The reality is that we have these variants that have been identified and we're still trying to understand the clinical significance. And I think that this is not the last time we'll hear about new variants that emerge from this virus or other viruses," Chen said. "That's where actually DARPA is really forward thinking in the way that they've designed this contract and the goals of the program, which is really to leverage the flexibility in designing new CRISPR probes, for instance, to be able to handle these emerging threats and being able to … rapidly program new CRISPR detection enzymes to handle these new variants and new mutations."
Indeed, the programmability of CRISPR is what made so many researchers and companies turn to the technology as a platform for developing SARS-CoV-2 diagnostics in 2020. In this case, Chen said, it will allow the researchers to rapidly design new guides to go after new variants, whether for diagnostic purposes or for biosurveillance.
The researchers are also hoping to create a platform that can be deployed rapidly if new, potentially pandemic-causing viruses emerge. One of DARPA's goals is to develop a full pipeline, from new target identification all the way through the test development, Chen noted.
"Part of the program is actually funding the development of in silico tools. You can think of it as the CRISPR software, where you try to design new guides to go after new disease targets or new infectious disease pathogens," she said. "And the goal is that within 24 hours, you're actually able to configure a test that would be able to run on these platforms."
There are also several other partners involved, whose participation is critical to making this project work. Mammoth is responsible for the CRISPR chemistry, the novel CRISPR detection enzymes, and the design of the guides, as well as helping to design the ultra-low-cost, disposable format device. Draper, IDbyDNA, the University of California, San Francisco, and Toolbox Medical Innovations are all contributing their technology and expertise.
Specifically, Draper — a multidisciplinary engineering and science company — is largely responsible for engineering the massively multiplexed device, Chen said, "so looking at the extreme of what you could do with CRISPR."
The researchers at UCSF will be charged with identifying differential biomarkers that indicate the severity of the diseases conferred by the pathogens on the panel. They'll be providing input on the clinical significance of target selection for the CRISPR guide, Chen noted. Indeed, Mammoth and UCSF are familiar with each other's capabilities in this area. In April 2020, UCSF's Charles Chiu and Chen worked together to develop a CRISPR-based SARS-CoV-2 diagnostic assay that can be run in 30 to 45 minutes with the same sensitivity and specificity as qRT-PCR tests.
In its own statement, IDbyDNA said it will contribute its pathogen database and algorithms to the project. Chen also said that the company will help to develop software and algorithms for interpreting data from the massively multiplexed device.
"As you can imagine, looking at that level of target detection, it's really [important] to be able to pull out the critical information, to actually have decision-making information," she added.
And Toolbox will play a role in the later stages of the project, managing the clinical studies that will be use to seek regulatory clearance for the devices.
It's still very early in the project's timeline, so it's too early to say what format the point-of-care test will take, for example, or which CRISPR enzymes the researchers will use. The paper-based pregnancy test is a good example of a simple, user-friendly test that's been cited several times as the best way to move CRISPR-based testing into the home, but while lateral flow-based tests have served a critical need as far as being cheap, easy to operate, and deployable in the field, they also suffer compared to the gold standard molecular testing in their performance, Chen said.
The goal, she noted, would be to modify CRISPR to fit into that type of format while still delivering high sensitivity and specificity.
Likewise, the researchers haven't yet decided which enzymes they want to use. Mammoth holds several exclusive licenses from the University of California, Berkeley for unique enzymes such as Cas14 and Casɸ, but part of the DARPA contract also involves developing completely new enzymes as well, Chen said.
She also noted that investing in innovation will be the significant step in helping Mammoth and its partners deliver on the program goals. "There are a lot of tools that we have already in-house, but we also want to push it to the next level and be able to identify even better detection enzymes as well," she said.