Unlocking biotechnology with RNA

May 17, 2022

Imagine if there were drugs that could optimize their dose in real-time, leading to better patient outcomes. Cellular factories that could self-regulate their metabolism, enabling sustainable chemical production. Gene editing tools that could target specific cells, reducing toxic off-target effects. The key to realizing those technological advances, according to University of Washington molecular engineering alums Jason Fontana and David Sparkman-Yager, is RNA.

RNA is a molecule with many functions in the cell, from coding proteins to catalyzing chemical reactions. One type of RNA molecule, called an aptamer, detects molecules with high affinity and specificity, similar to how an antibody binds an antigen. In nature, cells use RNA aptamers like sensors to monitor their environment and respond in real time; for example, they can modulate gene expression as a result of changes in the local concentration of small effector molecules.

If scientists could dictate which molecules RNA aptamers bind to, and how the cell responds, they could engineer biology to solve complex problems.

Fontana and Sparkman-Yager have developed a computational platform that allows them to do just that. Their technology is based on research they conducted for their theses under chemical engineering professor James Carothers, and chemistry professor Jesse Zalatan. In January 2021, they started a company, Wayfinder Biosciences, to apply this platform to everything from sustainable biomanufacturing to targeted therapeutics.

"We've figured out how to design RNA so that we can control how biology responds, on demand, to the molecules we choose," said Fontana, who received his Ph.D. in molecular engineering in 2020. "Basically, we pair RNA aptamers with another piece of RNA that does something useful, such as producing a measurable output like light or activating a guide RNA to induce gene editing, only when the aptamer binds its target."

"By elucidating the quantitative design rules governing how RNA folds and functions, we can identify aptamer-based switches that are likely to work before even going into the lab," said Sparkman-Yager, who also received his Ph.D. in molecular engineering in 2020. "This process is much faster and easier than screening thousands of candidates from a large random sequence pool."

Among the many different applications for this technology, one area Fontana and Sparkman-Yager are currently pursuing is biomanufacturing. Many molecules are colorless and hard to measure, requiring cumbersome and slow analytical methods to quantify. Using their platform, Fontana and Sparkman-Yager can design RNA that emits an easily-measured fluorescent signal upon detecting (and binding to) a specific molecule, effectively allowing the RNA to indirectly measure the concentration of the molecule of interest. The team is engineering such RNA sensors to measure the amount of Human Milk Oligosaccharides (HMOs) the main component of human milk that is missing from the cow's milk used in infant formula within complex mixtures, accelerating biomanufacturing efforts.

Another application Fontana and Sparkman-Yager are particularly excited about is CRISPR. CRISPR-based therapies use what's known as guide RNAs to direct DNA cutting enzymes to remove and repair specific sequences of DNA in the cell. These therapies have come a long way since CRISPR was first used to edit genes in mammalian cells in 2013, but are still hindered by low specificity and off-target effects. The Wayfinder team is working on developing RNA sensors that can turn CRISPR on and off in response to changes in the local environment.

"By combining RNA aptamers with CRISPR guide RNAs we will be able to target CRISPR such that gene editing is only activated when and where it is needed," said Sparkman-Yager. "This will help make CRISPR safer and more cost effective."

Starting a startup

"We're scientists, not business people," said Fontana. "We knew that we would need help launching a company. Luckily, there are many resources on campus that we could take advantage of."

In the spring of 2020, Fontana and Sparkman-Yager participated in the I-Corps program at CoMotion. Funded by the National Science Foundation, the program aims to "accelerate academic research projects that are ready to move toward commercialization."

"The I-Corps program helped us test the viability of our idea by pushing us to talk to potential customers and figure out if the tech we are developing is something that they actually need or want," said Fontana. "This was a really great starting point because the stakes were pretty low. As students exploring a business idea, we found that people were very willing to talk with us and give us honest feedback."

Added Sparkman-Yager, "Our experience in the I-Corps program crystallized for us that there is a market for our technology and that there are real-world problems that we can use our technology to solve. That was a big moment for us."

The team subsequently applied for and received a grant from the Innovation Gap Fund in fall 2020. A partnership between CoMotion and the Washington Research Foundation, the Innovation Gap Fund awards grants to novel projects with promising impact, helping university innovators transition from academic research grants to attracting seed-stage investment. In addition to $50,000 in funds, the program provided the team access to business, IP and technical experts to guide them as they began officially forming their company.

Said Fontana, "Thanks to these UW programs, we not only met some of our current investors and advisors, but we were also able and prepared to pursue other opportunities beyond campus."

For example, Fontana used part of the $2,500 he received from I-Corps to attend the 2021 Built with Biology conference which brings together investors, engineers, entrepreneurs and others in the synthetic biology community. At the conference, he met someone from IndieBio an accelerator based in San Francisco that supports early-stage biotechnology companies and quickly landed a coveted spot in their 12^th cohort of startups.

"It's a big adjustment to go from conducting research in the lab as a scientist to coming up with a business strategy and meeting with potential investors as a founder," said Fontana. "IndieBio was like an accelerated bootcamp for science entrepreneurs, teaching us how to successfully raise a seed round so that our company can grow, expanding our network through countless introductions and giving us lab space to continue our research."

Last year, the Wayfinder team was also selected to be part of the first ever Seattle cohort of the Creative Destruction Lab (CDL). CDL is a nonprofit organization that runs startup accelerators around the world. In 2021 they launched an accelerator in Seattle, based at the UW's Foster School of Business, for early-stage, science-based technology companies. CDL has a unique format: companies are selected to participate in a series of meetings where company founders pitch CDL mentors in the hopes that they will agree to mentor their company for the duration of the program. If no one volunteers to mentor the company, the company founders are not invited back to the next meeting.

"The CDL program sometimes felt like a game show!" said Sparkman-Yager. "It's been a challenging but really awesome experience. We've met lots of people from the Seattle tech and investing communities, who as mentors, have helped us think about how we can use our technology to change the world in meaningful ways."

Student entrepreneurship

Neither Fontana nor Sparkman-Yager set out to be entrepreneurs when they began pursuing their Ph.D.s, but both jumped at the chance to commercialize their RNA aptamer technology.

“To this day, I am in awe of RNA and excited about programming it to carry out novel functions," said Sparkman-Yager. "As a graduate student, I spent so much time diving deep on this topic that the idea of graduating and moving on to something else felt like a missed opportunity. In starting a company, not only do I get to continue pursuing this work, but I get to hopefully see it reach its full potential."

Fontana and Sparkman-Yager attribute the flexibility of the molecular engineering program and the support of their Ph.D. advisors as integral to the development of Wayfinder's technology.

“As a MolE student I was able to take courses based on what I wanted to learn, not what discipline they were technically tied to, accelerating my research,” said Sparkman-Yager. “I also benefited from James’ mentorship as he allowed me to take on a big research question that no one had an answer for which ultimately led to Wayfinder.”

When asked what advice they have for students interested in becoming entrepreneurs, both Fontana and Sparkman-Yager agreed: don't do it alone.

"Know your strengths and weaknesses and find people who complement them," said Fontana. "This will help you to be competent as an entrepreneur, despite not having extensive experience."

Said Sparkman-Yager, "Don't become an entrepreneur just to be an entrepreneur. To be successful as an entrepreneur, you must be passionate about the technology. People can tell when you're pitching something you don't fully believe in. In my opinion, the right time to become an entrepreneur is when you see science that is not being utilized to its fullest potential and you think you know how to do that."

When it comes to what you should do: take advantage of the resources UW gives you because there are many.

"In addition to the various programs and competitions available to innovators on campus, there is a thriving startup community to tap into," said Fontana. "We've been fortunate to be able to learn from other synthetic biology startups that have emerged from the UW in recent years, such as A-Alpha Bio and Parse Biosciences. The UW is truly a great place to be an innovator."

The future is RNA

Thus far, Fontana and Sparkman-Yager have raised over $1.1 million and are currently in the midst of raising a highly sought-after seed round. In February, the Wayfinder team moved into CoMotion's incubator space in Fluke Hall. They are focused on building out their team hiring a lab manager, research technicians and scientists with expertise in relevant areas with the goal of getting their research capabilities up and running as quickly as possible.

"The Fluke Hall incubator space is not only cost effective, but great for recruiting students and staying connected to the UW community,"said Sparkman-Yager. "Moreover, we're excited to be neighbors with A-Alpha Bio which also has lab space in Fluke.""This technology has so many potential applications, allowing us to tap into, and hopefully help solve, all sorts of challenging problems," said Fontana. "We're looking forward to seeing what the future holds for biotechnology."