In the past, cancer researchers have mainly focused on targeting genes that are located on the chromosome. But a type of doughnut-shaped DNA that resides outside of the chromosome may give cancer cells their malignant qualities, suggests a team led by scientists at the University of California, San Diego (UCSD) branch of the Ludwig Institute for Cancer Research and Stanford University.
The structure, known as extrachromosomal DNA (ecDNA), is found in abundance in human tumor cells. These circles of DNA change how cancer-driving oncogenes are expressed, and, in so doing, promote cancer growth and play a key role in tumors’ ability to evolve and resist treatments, according to findings published in Nature.
The study’s co-senior author, UCSD's Paul Mischel, Ph.D., has founded a biotech called Boundless Bio to advance treatments aimed at ecDNA. In September, the startup emerged from stealth mode with $46 million in series A funding led by Arch Venture Partners and City Hill Ventures.
The existence of ecDNA has been known for decades. In a 2017 Nature paper, Mischel and colleagues showed that ecDNA could be found in nearly half of human cancers but almost never in normal cells. They also demonstrated that cancer-driving oncogenes usually multiply on ecDNA in a phenomenon known as gene amplification, which is common in cancer cells. However, understanding of the structure of ecDNA and how it affects gene regulation remains limited.
For their new study, Mischel and teammates first confirmed that ecDNA is circular. Its round shape looks very much like plasmid, a small DNA molecule in bacterial cells, which is key in promoting cell survival such as resistance to antibiotics. Turns out, ecDNA’s shape provides similar capabilities.
Gene amplification increases the number of available DNA templates, but are oncogenes on ecDNA actually expressed? The answer is yes, the researchers said.
By using RNA sequencing, the team found that oncogenes on ecDNA are among the most highly expressed genes in cancer genomes, far outpacing the same genes amplified on linear structures. But the sheer volume of DNA is likely not the sole factor in overly aggressive transcription, the researchers hypothesized.
In humans, normal DNA is packed into cell nuclei with clusters of protein complexes. This makes it hard to access and read DNA’s genetic instructions unless aided by enzymes and complicated machinery. That’s why, in many cases, oncogenes on the chromosome never really lead to cancer.
But ecDNA in cancer cells is different. While it’s also wrapped in protein nuclei, it’s highly accessible, with more access points and places where genetic information can be quickly transcribed and expressed. This allows tumor cells to transcribe massive amounts of oncogenes and evolve more quickly in the presence of anticancer drugs, the team suggests.
The researchers also showed that the circular shape of ecDNA pulls genes closer to each other. This allows for new interactions that might be important in controlling gene expression in cancer.
Based on the findings, the team has constructed circular maps of ecDNA which they say might prove valuable in guiding drug discovery.
“By showing that ecDNA is circular, then elucidating its epigenetic organization, we demonstrate something very powerful,” Mischel said in a statement. “This unique shape in human cancer cells is quite unlike normal human DNA. It really shines a new light onto the 3D organization of the screwed-up cancer genome and epigenome, which now provides a mechanistic basis for understanding why certain tumor cells are so aggressive.”
Future research could delve into how ecDNA forms, replicates and moves, Sihan Wu, the study’s first author, said (Chinese) in a post on Zhihu, China’s Quora-like platform. “If the mechanism tumors use to maintain ecDNA homeostasis is identified, we could even develop a universal anti-tumor strategy, namely directly targeting ecDNA,” he said.
In a separate statement, Boundless Bio CEO Zachary Hornby said the biotech will move forward “to develop the first medicines capable of targeting the underlying biology that causes overexpressed oncogenes to develop and perpetuate in tumors that historically have been difficult-to-treat.”