Boundless Bio Inc. emerged Sept. 19 with $46.4 million in funding and a claim to new territory: extrachromosomal DNA.

These short fragments of DNA are rarely found in healthy cells, but they fuel aggressive cancers. CEO Zachary Hornby told the San Diego Business Journal he’s unaware of other drugmakers focused on extrachromosomal DNA, or ecDNA for short.

“That was part of the appeal for me,” said Hornby. “I thought this was a completely new and untapped area of biology.”

Hornby was previously the chief operating officer of Ignyta, a cancer drugmaker that started in San Diego and sold to Roche in 2017 for $1.7 billion. Jonathan Lim, who was the CEO of Ignyta, is the chairman of Boundless Bio.

Drug Resistance

The company has its roots in a team of cancer researchers who in 2017 published a major discovery in the journal Nature. They found ecDNA plays a much greater role in cancer cells and drug resistance than once thought.

Although ecDNA has been recorded in cancer tissues for decades, the researchers showed cancer genes can be found outside our chromosomes in ecDNA. Not only that, ecDNA rapidly replicates — potentially explaining why cancer can resist treatment.

Hornby said historically the drug industry has sought to inhibit certain proteins. But the turn toward ecDNA looks to unlock a new set of drug targets.

“Not only can we focus on the gene and the protein, but we can actually focus on the process by which the gene goes haywire in the first place,” Hornby said.

Boundless Bio didn’t reveal which cancers it wants to treat, only that its programs are in the drug discovery phase.

The $46.4 million Series A financing will help the company find additional tumors linked to ecDNA. Hornby said the company looks to cast a wide net.

“Whenever we find tumors where (ecDNA) is present, irrespective of where in the body the tumor happens to be located, then those will be the candidate cancers for us to try and treat,” Hornby said.

Paul Mischel, a company founder and UC San Diego professor, has led ecDNA research in recent years. At his invitation, researchers who came across ecDNA independently banded together and ended up becoming scientific founders of Boundless Bio.

They are: Vineet Bafna and Prashant Mali of UC San Diego; Howard Chang of Stanford University; Ben Cravatt of Scripps Research; and Roel Verhaak at The Jackson Laboratory.

Hornby said he hasn’t seen anything quite like the collaborative spirit.

“Competing investigators can have an adversarial relationship. It’s the exact opposite here, where everyone is aligned in their interest,” he said.

Boundless Bio has 15 employees. Plans call for the payroll to grow to 20 by end of year, according to Hornby.

The $46.4 million financing was co-led by ARCH Venture Partners and City Hill Ventures. Also participating were Vertex Ventures, GT Healthcare Capital Partners, Boxer Capital of the Tavistock Group, Alexandria Venture Investments and other investors that were not disclosed.