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The Utah startup is pioneering patient-specific 3D cell culture and AI to help fight cancer and bring anticancer drugs to clinical success.

Known Medicine is using machine learning to cure cancer

The Utah startup is pioneering patient-specific 3D cell culture and AI to help fight cancer and bring anticancer drugs to clinical success.

According to statistics from the National Cancer Institute, one in five men and one in six women in the United States are likely to die from cancer during their lifetime. 

This year alone, the American Cancer Society estimates we’re in for a rough ride. In 2023, more than 1.9 million new cancer cases are expected to be diagnosed in the U.S., and nearly 610,000 are expected to die from cancer in the U.S. (about 1,670 deaths per day). Only heart disease outranks cancer, making cancer the second most common cause of death in the nation.

These chilling statistics make it clear why something must be done to save more lives from this hydra of a disease. 

The founders of Known Medicine couldn’t agree more. In 2020, the team launched the startup as a company dedicated to expediting the development of cancer treatments. As explained on its website, Known Medicine’s “machine learning-based sensitivity assay, paired with -omics data, allows [the company] to identify predictive biomarkers and the most likely responders for any new drug.”

Put in simpler terms, Katie-Rose Skelly, co-founder and CTO of Known Medicine, says the company is essentially trying to find out beforehand which patients will respond to which drug. This can help pharmaceutical companies design better clinical trials and improve the drug’s chances for success. 

To conduct its research, Known Medicine works closely with about 10 different cancer research centers that provide samples from patients who have authorized their use for research. The company breaks these tissue samples down into thousands of microtumors and doses each microtumor with a panel of over 100 drugs to see what works for each individual patient. The drugs include some that have already been approved, some that have failed previous clinical trials, some that pharmaceutical partners are interested in and some that Known Medicine might consider for in-licensing.

The Known Medicine team is currently working toward its first peer-reviewed journal publication, which will essentially provide proof of concept for the innovative work the company is doing. “What we’ll be able to show is that we can look at the patient that donated the tissue, see what drug they were given, see how they responded and identify whether that matches what we would have expected,” Skelly says. 

In other words, the initial publication will prove that Known Medicine can replicate patient responses and that its microtumors are a faithful representation of what the patient’s cells will do in the body.

From there, Known Medicine’s goal will be to aid in the drug development process. Skelly explains that most drugs currently fail in clinical trials, with just 3.4 percent of oncology drugs making it to market. This is often due to ineffective patient population selection. 

“If you try running a new anticancer drug on 100 patients, maybe 20 or 30 respond well—better than they would have to any other drug,” Skelly says. “But if you can’t identify that 20 percent to 30 percent upfront, your drug is going to fail clinical trials.”

Known Medicine’s platform will enable drug companies to identify trial candidates that are more likely to respond to their drugs. “We can look at what kind of genetic signatures [patients] have, what kind of RNA expression levels they have,” Skelly says. “We can see if there is anything they can use to separate the patients who will respond from the patients who won’t and only enroll the people who will respond in the clinical trials.”

The concept for the company came as a collaboration between Skelly and Dr. Andrea Mazzocchi, who serves as the company’s CEO. The co-founders initially met by chance—Skelly was working as a data scientist at Recursion, a Utah-based drug discovery digital biology company. Mazzocchi was pursuing her doctorate degree at Wake Forest and happened to be dating Skelly’s best friend at Recursion. 

Looking ahead, Skelly says Known Medicine hopes to be part of the solution to the current one-size-fits-all approach. Only 50 percent of late-stage cancer patients benefit from their first treatment, which she likened to throwing a dart and seeing if it hits.

“Andrea was doing her Ph.D., working in a lot of the web lab techniques, doing the tumor breakdown, creating the microenvironment that represents enough of the patient’s actual body to make sure the cells behave the same,” Skelly says. “She was talking about starting a company, and at the same time, I had learned a ton as an AI-for-drug-discovery data scientist, looking at huge sets of biological data, getting insights, understanding how to run a platform like that.”

The two decided to start Known Medicine and applied to Y Combinator the same day that Mazzocchi was defending her doctoral thesis, which also happened to be the same day the country shut down due to the outbreak of Covid. Despite the turbulent external environment, things have progressed quickly for the startup.

In addition to Y Combinator, Known Medicine was accepted to the Altitude Lab incubator, a collaboration between Recursion and the University of Utah. “We were able to get free lab space which was critical at that point, and raise our initial round of funding,” Skelly says. “We’ve since moved into a larger space in Research Park and grown the team to a little over a dozen people.” Skelly was also recently named on the Forbes 30 Under 30 list in the Healthcare category. 

As women in biotechnology, Skelly acknowledges she and Mazzocchi have been fortunate. Industry statistics indicate that only 23 percent of biotech CEOs are female. Skelly says that when she attends programming-specific meet-ups, she’s often in the extreme minority, and sometimes she’s the only female in the room. She says the same holds true for Mazzocchi, as she often appears as the only woman on an event panel.  

That said, Skelly applauds the Utah community for being especially supportive of Known Medicine. “It’s pretty phenomenal to be able to start a business here as two female founders,” Skelly says. She credits local industry leaders like Chris Gibson, CEO of Recursion, who are proactive in pushing for inclusion, helping give underserved groups more visibility in Utah’s life sciences space.

Looking ahead, Skelly says Known Medicine hopes to be part of the solution to the current one-size-fits-all approach. Only 50 percent of late-stage cancer patients benefit from their first treatment, which she likened to throwing a dart and seeing if it hits. 

“It feels insane to test drugs on people with a coin-flip chance of success,” Skelly says. “The way of the future is driving care that’s based on individuals rather than hoping something works for a wide swath of the population. But how we will get there is still uncertain. There’s the possibility of using a technology like ours to do direct patient-specific selection. There’s also the possibility of developing biomarkers that are a lot better at indicating which treatments will be more effective.”

Regardless of how we arrive at the future of cancer treatment, let’s just hope we get there soon.  

“It’s hard to meet someone who doesn’t have a connection with cancer,” Skelly says. “Whether it’s family or friends, it touches all of us. So you’re able to tap into such a community where I know we have employees who are incredibly driven and talented who could be working elsewhere for a lot more money, who are dedicated to our mission.”