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Beyond COVID-19, Proof Dx Plans Infectious Disease, Oncology Tests for CRISPR-Based POC System


NEW YORK – Proof Diagnostics recently submitted a CRISPR-based, point-of-care test for SARS-COV-2 to the US Food and Drug Administration for Emergency Use Authorization. If approved, the assay could be the first such test to make it through the gates of the agency. But there are other tests in the Cambridge, Massachusetts-based startup's pipeline, according to management, and COVID-19 is just the first indication.

"We see this as a platform for molecular diagnostics, full stop," CEO Sid Shenai said this week. "We can design chemistries and have numerous chemistries in our company that can go after basically any nucleic acid target, with the same hardware, with the same cartridge, same reader."

Other infectious diseases are on the firm's to-do list, said Shenai, but other indications and applications, such as precision oncology loom. This would be deployed not necessarily using STOPCovid, the CRISPR-based method of detection the firm has in-licensed from the Broad Institute, but would rely on its Proof Lab Test System, a point-of-care instrument.

"We think it's a broad platform technology," said Shenai. "COVID was the accelerant for what we wanted to do, and it's a proof point for what we wanted to do, but it's not obviously the only thing we want to do."

Shenai is one of Proof Diagnostics' four cofounders. He's also a venture partner at Madrona Venture Group in Seattle, and an affiliate researcher at the University of Washington. Feng Zhang, a molecular biologist at the Broad Institute of MIT and Harvard and a developer of CRISPR technology, is another cofounder. He was the scientific innovator behind the development of STOPCovid, which was published on medRxiv in May 2020, and has also been detailed in a white paper by the group. The work was subsequently published in the New England Journal of Medicine in September 2020.

Cofounders Omar Abudayyeh and Jonathan Gootenberg, both McGovern Institute Fellows at MIT, also helped to develop the technology underpinning STOPCovid, Proof Diagnostics' debut assay.

By any metric, Proof Diagnostics' story has moved quickly. The company was founded in May 2020 to commercialize the STOPCovid technology. "They wanted to get it out into the world, and asked if I could help," Shenai said of the firm's beginnings.

At its start, Proof Diagnostics just had the STOPCovid chemistry, but in less than two years, it further developed the assay, and developed the hardware, software, and firmware to support it. The company also raised $45 million to support its efforts from ARCH Venture Partners, F-Prime Capital, and Madrona Venture Group. It has since grown to about 30 people, mostly based in Cambridge, though Shenai leads the firm from Seattle. At first, he noted, the company worked completely online, given COVID-19 restrictions. Shenai didn't even meet most of Proof's staff until the summer of 2021.

"Five to 10 years ago, if you said you could build a product virtually, people would have said, 'No way, you are crazy,' but here we are," remarked Shenai. "I imagine lots of other companies have also done so during the pandemic, so our story is probably not that atypical." Still, he said that Proof Diagnostics has been the result of "long nights in the lab, and long nights on Zoom."

The roots of Proof Diagnostic trace back to the start of the COVID-19 pandemic, when Zhang, Abudayyeh, and Gootenberg published a protocol for detecting SARS-CoV-2 using CRISPR diagnostics. This was followed by the publication of the method on medRxiv. The approach is based on the SHERLOCK (specific high sensitivity enzymatic reporter unlocking) technique pioneered in Zhang's lab, but further developed to avoid the use of fluid handling steps and equipment. The result was STOP (SHERLOCK testing in one pot), which the researchers claimed is comparable to real-time quantitative PCR tests and has a limit of detection of 100 copies of viral genome input in either saliva or nasopharyngeal swabs per reaction. Given the assay's turnaround time of, at the time, 40 minutes, the authors maintained that its STOPCovid approach could "significantly aid test-trace-isolate efforts, especially in low-resource settings."

Proof Diagnostics has innovated on the work published in 2020, with its Proof Lab Test System able to produce a result in as little as 18 minutes, according to the firm. The company has also claimed that its assay is "cost effective" in its PR, but Shenai declined to comment directly on price, only saying that it will be competitive with other point-of-care SARS-CoV-2 tests out on the market.

The portable device at the core of the Proof Lab Test System was developed with help from partners. "We have definitely been able to leverage partnerships with different vendors who have a lot of experience in the space and that is what allowed us to move fast," remarked Shenai. The small, portable device is Bluetooth enabled. The overall system includes the reader, cartridges, a sample collection kit with a swab, and a mobile app that can connect 12 readers at a time. "These are all components of the package submitted for EUA," Shenai said. "Ongoing digital health development is focused on full cloud integration and support services like electronic health record integration via the cloud."

The company also commenced a trial of the test system in February with partners in Washington, Florida, and North Carolina, the data of which is being included in its EUA.

Shenai declined to discuss Proof Diagnostics' interactions with the US regulatory agency, but he said that if authorized the system and test would be "as we understand it, the first CRISPR-based approval by the FDA at a point-of-care or at home setting." While unique, Shenai said that other "relatively novel technologies" have been cleared by the agency in the past, and that Proof Diagnostics is "hopeful the FDA reviews its package favorably."

There are other CRISPR-based tests for SARS-CoV-2 in development, though, including those that are run at the point of care. Researchers at the Wyss Institute for Biologically Inspired Engineering, the Broad Institute, and MIT published a method called miSHERLOCK for the point-of-care detection of the virus that causes COVID-19 in August 2021. 

There is also Sherlock Biosciences, which Zhang also cofounded, and which developed and commercialized a test using the SHERLOCK technology that received Emergency Use Authorization from the FDA in May 2020 for a SARS-CoV-2 assay. Sherlock's test is intended for use in high-volume CLIA laboratories and hospitals, though, and is not a point-of-care test.

Brisbane, California-based Mammoth Biosciences in January received an EUA for a high-throughput, CRISPR-based DETECTR Boost SARS-CoV-2 Reagent Kit. The test runs on Thermo Fisher Scientific's Applied Biosystems 7500 Fast Dx RT-PCR instrument using the Applied Biosystems MicroAmp Fast Optical 96-Well Reaction Plate.

More than just COVID-19

There is a lot more going on at Proof Diagnostics than just its CRISPR-based SARS-CoV-2 assay, though. Shenai said that the company has other chemistries and technologies from other institutions to build its toolbox, and it also has chemistries it has developed internally, as well as those that have gone off patent. All of these can be deployed on its Proof Lab Test System.

"We can make use of all of these to go after diseases that no one else can," Shenai said. "We can mix and match them to design robust assays that are specifically well suited for a particular disease state or a particular sample type, put that in our hardware, and feed that into our overall platform," he added.

Initial opportunities beyond COVID-19 are in testing for other infectious diseases, said Shenai, but precision oncology is also an opportunity. "There are a lot of things our chemistries can do," he said. "We want to get this out into the world and into the point-of-care and home settings."

While the US market is the immediate target for Proof Diagnostics, the company is looking to get its test into other regions in the coming year, as well as to improve its products over time, Shenai said. Getting the platform into lower-resource settings is also on the company's agenda. Shenai, who once worked as a volunteer consultant in Ghana and Swaziland in Africa, an experience that he said taught him to be "scrappy" and self-reliant when it came to solving problems, said lower-resource countries could become markets for Proof Diagnostics' tests.

"Definitely seeing how people live, work, and get healthcare in those communities was very informative for how I think about our business," said Shenai. "One of our hopes is to be able to take our products out to the developing world."