A CRISPR Conversion: Jumping from Gene Editing to Life-Saving Detection During the COVID-19 Crisis
September 2, 2020
A team of San Francisco researchers pull CRISPR technology into the pandemic landscape, launching a new diagnostic that can address needs across a continuum of testing using CRISPR proteins.
As COVID-19 moved from a sidebar story to a headline in a matter of weeks, Janice Chen, Ph.D. and her colleagues, tracked its menacing progression around the world with rapidly growing concern. As chief technology officer of Mammoth Biosciences (San Francisco, CA, USA), Chen knew that the company's diagnostic platform held a solution for faster virus testing. It was simply a matter of digging into the RNA of the novel virus.
Three years before, working as graduate students in the lab of CRISPR pioneer Jennifer A. Doudna, Ph.D., Chen and long-time lab partner Lucas Harrington, Ph.D., uncovered something fantastic in their CRISPR technology research – a different “flavor” of the CRISPR protein from the Cas12 family that had ideal properties for nucleic acid detection. Doudna, Chen and Harrington were captivated by the vision to develop CRISPR-based diagnostics for real-world utility and considered that it might have enough traction to spin out into a company.
“It is an exquisite process that gives us so much control,” says Chen of the programmable technology named DETECTR that emerged from their research. The team first used the tool to identify the genetic code of high-risk HPV types in patient samples, and began pursuing a platform for other rapid and affordable diagnostics. When they formed a collaboration with colleagues from Stanford University, (Stanford, CA, USA), the technology blossomed into Mammoth Biosciences – just as Chen and Harrington earned their Ph.D.s. With Doudna serving as chair of the company's Scientific Advisory Board, Harrington as chief science officer, and co-founder, Trevor Martin, Ph.D., serving as CEO, the team began to find a place for the DETECTR technology in the market.
“The idea that you could use nucleic acid detection and build something that works as simply and quickly as a home pregnancy test, for example, has always been a driving force and motivation behind Mammoth,” Chen explains. The team anticipated some of its first pursuits would include using this technology to detect respiratory viruses like influenza. They didn’t anticipate rapidly researching a whole new virus “in the midst of a worldwide health crisis,” she continues. “It’s gratifying to see diagnostics recognized as playing a critical role.”
The Quest for a SARS-CoV-2 Diagnostic
Mammoth launched development of a SARS-CoV-2 diagnostic just eight months ago in January, collaborating with one of their Scientific Advisory Board members, Charles Chiu, M.D., Ph.D., an infectious disease expert from University of California, San Francisco (UCSF, San Francisco, CA, USA), who was among the primary researchers to study the early cases in California.
“Charles had access to the COVID-19 positive samples from the cruise ship that had docked in Oakland, CA, USA, as well as samples from patients with other viral respiratory infections,” Chen explains, noting that there were fewer than 10 COVID-19 cases in the United States and no official name for the virus or disease at that time. Logging late nights and long hours, the team validated samples, but before they reached the finish line to publish their research, San Francisco shut down.
“I remember we were in the middle of a meeting when a co-worker texted me that the mayor announced the Shelter-In-Place order,” Chen says. “We were fortunate that we had such a head start on the test development. The additional safety protocols we implemented to make certain everyone was safe were necessary, but were a huge challenge to completing our work.” Providing PPE, establishing social distancing guidelines for the lab and shifting schedules to decrease the amount of people working in the same place at one time became the daily drill.
“You can’t exclusively work from home if your work takes place in a lab," says Chen. "In biotech, you still need a good majority of your company to be on site. That’s something that many companies, particularly in life sciences, have to figure out moving forward.”
Chen describes the following weeks of work as “a whirlwind” made possible by many dedicated people. “When our paper published, we were able to demonstrate the test on 83 clinical samples – one of the largest data sets on COVID using CRISPR diagnostics at the time,” she says. The resulting rapid (<40 min), easy-to-implement and accurate CRISPR-Cas12-based lateral flow assay detects SARS-CoV-2 from respiratory swab RNA extracts, achieving a high degree of specificity even for asymptomatic patients. DETECTR provides a visual and faster alternative to RT-PCR assays, with a 95 percent positive predictive agreement and 100 percent negative predictive agreement.
A number of diseases, from cancer to COVID-19, benefit from DETECTR’s early detection and closed loop of privacy. Another valuable aspect of the technology is monitoring host response. “For example, with COVID, we know that patients have all kinds of disease profiles. Some people are asymptomatic, some get dangerously sick and a lot of that comes from how the immune system responds to a certain threat. CRISPR diagnostics could make a difference in this area. You can understand the profiles of how the patient is responding – that’s a future direction I am excited about,” she comments.
Recently, DETECTR received Emergency Use Authorization (EUA) approval from the U.S. Food and Drug Administration (FDA) via UCSF’s CLIA lab – an important milestone in third-party validation of the assay. “The UCSF microbiology lab is now authorized to run the test,” Chen says. “Our hope is that our faster, simpler detection method means you can implement higher throughput to relieve some of the burden of testing shortages to keep up with the volume. Given the unprecedented demand for SARS-CoV-2 testing in centralized labs, we realized it was equally important to use our technology to develop a turnkey solution for high-throughput testing in CLIA laboratories.” In July, Mammoth Biosciences was one of the first seven companies to secure a Phase II contract in the NIH Rapid Acceleration of Diagnostics (RADx) program, a $1.5 billion initiative to develop coronavirus diagnostics with the goal of deploying “millions of tests per week.”
On the other end of the testing spectrum, a partnership with GSK Consumer Health announced in May this year will accelerate the development of a handheld, disposable device, one that is analogous to an at-home pregnancy test that can detect nucleic acids with the accuracy of lab-based test. Following approval from an EUA submission planned for the end of this year, the device would first be available in a clinical setting and then later could be sold directly to consumers in a drugstore. The Mammoth team projects that by the time the test is directly available to consumers, the diagnostics kit could be programmed for indications beyond COVID-19, including disease as serious as Ebola or as mundane as strep throat.
“At Mammoth, we’re passionate about diagnostics and how we’ve been using it to tackle the challenges we face today, such as increasing the throughput of testing,” says Chen. “We want to shift the paradigm of ‘I need to go to the doctor’s office for testing’ to the consumer’s home. It will help us detect diseases earlier.”
In the midst of the busiest six months of her life, Chen took time from her schedule to present an overview of the DETECTR technology during the SLAS Transformed virtual event, an interactive video conference focused on 'omics, synthetic biology and genome editing along with applicable implications for the current pandemic. The June event featured 30-minute scientific research presentations, live exhibitor presentations and one-on-one networking opportunities. “SLAS did a great job of pulling in familiar names from the life sciences community,” says Chen. “It’s critical to provide access such as this to people working in this space.”
While she didn’t have any expectations going into her first virtual presentation, Chen says she was surprised by how interested and engaged the participants were during the Q&A session. “Being part of the virtual conference was awesome, and it was incredibly well produced. The SLAS team gave me such good preparation that I was ready for the 20-minutes-worth of questions afterward,” she says with a laugh. She adds that she hopes the participants have many opportunities to recall and expand on the message that CRISPR is a tool with many different applications. “It was inspiring to see how people in the community were trying to learn more and connect with the information.”
Pursuing the Building Blocks of Life
The intricacies of biology always have fascinated Chen, who did her undergraduate work at Johns Hopkins University (Baltimore, MD, USA). “During my time there, I had an opportunity to work in a wet laboratory during an interactive and immersive course called ‘Build-A-Genome’ that was part of a larger, ambitious project led by Jef Boeke, Ph.D. The goal was to synthesize the building blocks of a yeast genome and create it from scratch,” Chen says.
Through that experience, Chen connected to a research lab in Johns Hopkins’s School of Public Health in the department of Biochemistry and Molecular Biology. “The principal investigator, Valeria Culotta, Ph.D., was a highly recommended mentor. She was amazing and gave me an opportunity to learn in a lab as an undergraduate and pursue my own independent research,” Chen says.
Chen also benefited from working with her graduate student mentor, Allen Baron, Ph.D. “My experience there was formative and helped me be excited about biology in a context outside the classroom. Allen was instrumental in helping me understand the scientific method and challenging me to find my own answers instead of getting the information from someone else,” says Chen. “That experience inspired me to take some time to focus on science and research.”
Her interest in yeast biology and metabolism led her to work with Harvard Medical School’s Pamela Silver, Ph.D. Chen enthusiastically describes Silver as a rock star pursuing exciting blue skies projects such as engineering memory in bacteria and designing bacteria to produce biofuels. “We leveraged organisms to get results we wanted,” Chen explains. “After spending that year in Silver’s research lab, I decided to go to graduate school and explore the relationships between protein structure and function. I found that UC Berkeley fit all my criteria and championed basic research.” Chen joined Doudna’s lab in 2014.
“I’ve truly benefitted from training in multiple laboratories led by female PIs. It’s not common for a lot of people,” Chen notes. “As a result, I have been unafraid of taking leadership positions, even in male-dominated fields, because that has been modeled for me successfully.”
As the CRISPR revolution exploded, Chen explored the new technology through protein biochemistry, determining how to reengineer the molecular machines for enhanced features and characterizing activities of newly discovered CRISPR proteins. “There are a lot of details at the atomic level, and some of our time was spent refining questions to ask when we didn’t quite fully understand the mechanisms of these CRISPR nucleases,” Chen explains. Discovering the Cas12 family’s capabilities changed her graduate work and sent her on the pursuits she now follows.
She muses that much of graduate education can be a solo journey dedicated to becoming a subject-matter expert in a certain area, “but building a company is not about you. It’s about building a team and accomplishing goals as a group. That’s something incredibly meaningful to me,” Chen observes.
Working through months on end of a rapidly changing situation requires great determination, and Chen and colleagues remain undaunted in the face of supply shortages, staffing schedule hassles and the summer's spikes in COVID cases around the country. The Mammoth team continues to push toward making the COVID-19 diagnostic available on a large scale.
“If a rapid, single-use disposable diagnostic was easy to create, it would exist already,” Chen notes, adding that she maintains her motivation in a number of ways. For particularly overwhelming days, she heads out for a run – even though it requires a face mask to accomplish. When she begins to wonder about how to navigate long hours, she listens to stories from her husband, Orestes Mavrothalassitis, M.D., an anesthesia resident at UCSF.
“We’re fortunate that he’s not being overwhelmed with COVID cases, but hearing about the clinical experiences and listening to how much impact diagnostics have there is meaningful to me. This keeps driving us forward,” she comments.