This article has been updated to correct Boundless' Series A financing from $6 million in May 2019 to $46 million in June 2019, and to reflect that Sophia Genetics is developing the Echo test for Boundless, not commercializing it.
NEW YORK – Boundless Bio is targeting a newly recognized mechanism driving tumor heterogeneity and drug resistance — extrachromosomal oncogene amplification — to treat genomically driven cancers that do not respond to targeted therapies.
Extrachromosomal DNA (ecDNA) was first observed in the 1960s, but it's not until recently that researchers have uncovered the role these small, free-floating loops of DNA play in amplifying oncogenic driver genes in cancer cells.
Cancer-driver point mutations like KRAS G12C, BRAF V600E, or EGFR L858R are found on chromosomal DNA and promote cancer through constitutive activation of a growth factor. "Those are genomically locked alterations," Boundless CEO Zachary Hornby said. "Whatever that error is, it's locked on the chromosomes and it doesn't change from cell to cell. That's why if you can successfully drug it, that impacts every cell and ultimately shrinks the tumor."
In contrast, ecDNAs are typically wild-type copies of cancer-driver genes that form a circular closed loop, have broken away from the chromosome, and are present in high numbers in the cell. They represent a type of DNA damage and are generally found in cells that have lost DNA damage repair mechanisms like p53. However, they are also an evolutionary mechanism, allowing cells to rapidly adapt in times of need. As an example, Hornby said, "when weeds are treated with the weedkiller RoundUp, eventually some weeds become resistant, and the way they do that is by using ecDNA to amplify resistance to RoundUp."
Oncogenic driver genes in the form of ecDNA can replicate, leading to "massive" amplification, Hornby said. "Those [circular DNAs] are being constantly transcribed by the cellular transcription machinery," he explained. "Not only are there more copies of the gene, but they're more highly expressed, and therefore far more oncogenic in nature."
In addition to expressing large amounts of the cancer-driver gene product, Hornby said ecDNAs have turned out to be one of the principal causes of tumor heterogeneity, giving cancer cells the ability to evade drugs and develop resistance. "If every cell in the tumor is exactly the same, and you can figure out its Achilles heel, then you just treat that Achilles heel and the whole tumor dies," Hornby said. "But with tumor heterogeneity, when each cell looks a little bit different than the one next to it, it's like you're fighting a million beasts at once."
Hornby estimated that ecDNA occurs in between 15 percent and 30 percent of tumors, more commonly in cancers such as sarcoma, glioblastoma, ovarian cancer, and esophageal cancer, and less commonly in some hematologic malignancies. Patients with ecDNA in their tumors do not respond to targeted therapies and have no standard-of-care therapies tailored to oncogene amplifications, he added. These patients also have worse survival, worse outcomes, and more aggressive tumors than those without ecDNA in their tumors.
Although the obvious approach might appear to be targeting the amplified genes on the ecDNA, tumor heterogeneity gets in the way. "One cancer cell might encode one gene on that circle, and the next one might encode a different one," Hornby said. "If you try to target what's on the circle, it actually won't be an effective approach because you'll only kill some of the cells and the other ones will survive."
Instead, Boundless is going after the cellular machinery that allows cells with oncogenes amplified via ecDNA to function. The company's strategy has been to look for liabilities that accompany the cancer cells' reliance on ecDNA and target those specifically, while sparing normal cells without ecDNA.
This work is rooted in Boundless' founding in 2018. It was then that Ben Cravatt, a biologist at Scripps Research Institute, introduced Paul Mischel to ARCH Venture Partners. Mischel, who is currently vice chair of research and a professor of pathology at Stanford University, was then at the University of California, San Diego, and had published multiple foundational papers on ecDNA and oncogene amplification.
Mischel and Cravatt assembled a team comprising other leaders in the field of ecDNA from UCSD and Stanford, and in 2019, the company hired Hornby as CEO. Hornby had previously held executive- and director-level roles at several biotech companies including Fate Therapeutics and Halozyme Therapeutics, and he played a leading role in developing Rozlytrek (entrectinib) at Ignyta. That TRK inhibitor was approved in the US in 2019 for treating solid tumors with NTRK gene fusions and ROS1-positive metastatic non-small cell lung cancer.
In June of that same year, the fledgling Boundless raised $46 million in a Series A financing round, and with it licensed foundational technology from Mischel and the other scientific founders at UCSD and Stanford and began laboratory operations to develop a platform, dubbed Spyglass, for identifying therapeutic vulnerabilities in ecDNA. In subsequent years, the company was able to raise more funds: $105 million in a Series B financing in April 2021 and $100 million in a Series C financing in May 2023.
Spyglass uses a library of 100 different tumor models, both ecDNA-positive and ecDNA-negative, representing various tissues and oncogenes. Boundless researchers conducted a series of screens of the library to identify targets which, when knocked down, were lethal to the ecDNA-positive models but not the ecDNA-negative models.
Hornby said that the screens turned up dozens of candidate targets that they then attempted to validate by determining whether they consistently killed ecDNA-positive cells only across different tumor types and amplified oncogenic drivers. There were "about a half-dozen" targets, Hornby said, which researchers successfully validated as "bona fide ecDNA essential targets." The targets identified by the Spyglass platform centered on three main strategies for targeting ecDNA — ecDNA replication stress, ecDNA assembly and repair, and ecDNA inheritance. The company is going after four ecDNA targets with small molecule oral drug compounds.
Boundless also developed a diagnostic technique called Echo that uses standard sequencing data to detect ecDNA. Hornby said part of the company's strategy is not to slow down or complicate the patient's diagnostic work-up by adding a new test but rather to take advantage of sequencing data for the tumor that is already being routinely generated. Echo uses an algorithm that interprets the sequencing data in such a way that it can detect the presence of circular DNA in tumor cells. "If we can detect [circular DNA], we can determine which genes are encoded on it and how many copies" there are, said Hornby.
After initially developing a prototype, Boundless partnered with Sophia Genetics to commercialize the test. Sophia has been developing validated software based on that algorithm "over the past eight months," which Hornby said Boundless intends to deploy at clinical trial sites and eventually commercialize with diagnostic partners.
Boundless' lead program is BBI-355, a checkpoint kinase 1 (CHK1) inhibitor. CHK1 mitigates DNA replication stress resulting from ecDNA oncogene amplification. When CHK1 is inhibited, cancer cells can no longer self-regulate, leading to cell death. In preclinical studies, BBI-355 was synthetically lethal to ecDNA-enabled oncogene amplified cancer. In oncogene-amplified mouse tumor xenograft models, treatment with BBI-355 resulted in growth inhibition and tumor regression.
Hornby said they saw a strong, consistent effect of BBI-355 against oncogene-amplified cancers in xenograft models of a range of tumor types including colorectal cancer, sarcoma, lung cancer, and neuroblastoma. "We saw tumor growth inhibition across multiple models," Hornby said. "In some cases, we saw single-agent tumor regression, especially shrinking of the tumor," he said. This was seen consistently across different oncogenic drivers including EGFR, MET, CDK4, and FGFR2, which, when encoded on ecDNA, were effectively targeted by BBI-335.
The company is currently evaluating BBI-355 in the POTENTIATE Phase I/II trial. In that study, approximately 47 patients with locally advanced or metastatic non-resectable solid tumors that test positive for ecDNA are receiving BBI-355 as a single agent or in combination with other therapies. The primary goal in POTENTIATE is to identify a maximum tolerated dose and a recommended Phase II dose. Boundless researchers will also monitor anti-tumor activity of BBI-355 until disease progression or death as a secondary endpoint.
Boundless also has investigational new drug application-enabling studies underway for a second compound, BBI-825. That drug targets the ecDNA assembly and repair machinery by inhibiting an essential rate-limiting enzyme. As with BBI-355, in preclinical studies the company has observed anti-tumor activity in multiple tumor types with different oncogenic drivers. "We're eager to bring that forward and see if it plays out in the clinic, as well," said Hornby.
Hornby seemed confident that Boundless is developing a new class of drugs targeting oncogene amplifications that would not compete with treatments already on the market targeting those individual oncogenes. He underscored that the drugs produced by Boundless' Spyglass platform are gene agnostic, meaning they do not target the specific gene carried by the ecDNA but rather target the cellular machinery related to production of ecDNA.
Additionally, while many therapies have been approved targeting specific gene alterations, there are no therapies approved yet for amplified wild-type genes. For example, "a patient with an EGFR amplification, no matter what the tumor type, does not have access to an EGFR inhibitor," Hornby said. "If they have these amplifications, they usually will have received either chemotherapy or possibly a checkpoint inhibitor. Beyond that, there are not a lot of options for these patients."