Circular DNA takes center stage in a deadly form of cancer, research shows

A circular form of DNA, known as extrachromosomal DNA, often contains genes that can turbocharge the development of cancer while dampening the immune system’s capacity to cope with the assault.

A new study examines the role of extrachromosomal DNA in the development of esophageal adenocarcinoma, or EAC, a highly lethal cancer. This cancer can progress over time from a common condition known as Barrett’s esophagus. This condition, especially when accompanied by long-term gastroesophageal reflux disease, places patients at heightened risk of cancer.  

Researchers have long struggled to understand the factors causing some patients to advance from Barrett’s esophagus to EAC. In new research in the current issue of the journal Nature, Arizona State University Professor Carlo Maley joins an international team led by Stanford Medicine. Their findings show a strong statistical link between cancer development and the presence of extrachromosomal DNA, revealing that people with this form of DNA in their precancerous cells are 20 to 30 times more likely than others to develop cancer.

The results are important for advancing the understanding of this bewildering and generally fatal illness, but also suggest a dramatic shift in thinking about how cancers evolve over time in the body and successfully evade immune defenses.

By understanding the underlying mechanisms involved in disease progression, researchers hope to identify cancer cell vulnerabilities and develop new therapies to combat intractable cancers.

“When cancer genes pop out of the chromosomes and start replicating as little circles of DNA, they can evolve rapidly,” Maley said. “Understanding this gives us a new signal for predicting which tumors are going to be dangerous and which patients need additional care.”

Maley is director of the Arizona Cancer and Evolution Center, researcher in the Biodesign Center for Biocomputing, Security and Society and professor with the School of Life Sciences.

Carlo Maley

Common condition poses ominous threat

Barrett's esophagus occurs when the normal squamous lining of the esophagus is replaced with columnar tissue, which is more resistant to the damaging effects of stomach acid. This change is typically a result of long-standing gastroesophageal reflux disease, also known as GERD. White men with chronic GERD and who are obese are most at risk for developing Barrett's esophagus.

Regular endoscopic surveillance and appropriate interventions, such as lifestyle modifications, medications or endoscopic procedures, can help reduce the risk of progression from Barrett's esophagus to cancer.

Extrachromosomal DNA refers to any DNA that is not part of the linear chromosomes within a cell nucleus. It is typically found in the form of circular molecules, separate from the main genomic DNA. The most common types of extrachromosomal DNA include plasmids in bacteria, mitochondrial DNA in eukaryotic cells, and circular DNA viruses in both prokaryotic and eukaryotic organisms.

Extrachromosomal DNA has been increasingly recognized for its presence in cancer for several reasons. Cancer-causing genes, known as oncogenes, are often found in extrachromosomal DNA. When such genes are mutated or expressed at high levels, it can result in cancer. The circular structure of extrachromosomal DNA allows it to replicate independently of the main genome, which can lead to increased copy numbers of oncogenes, promoting cancer growth and progression.

Such DNA can enhance tumor heterogeneity, due to its unequal distribution during cell division. This heterogeneity can make it challenging to target and eradicate cancer cells with a single therapy, as different cells may have distinct genetic profiles that impact their response to treatment.

Extrachromosomal DNA can confer resistance to cancer treatments, such as chemotherapy and targeted therapies, through the overexpression of drug-resistant genes. This can lead to the survival and proliferation of resistant cancer cells.

This form of DNA may be transferred between cells, enabling the spread of drug-resistant genes throughout the tumor. This horizontal gene transfer can accelerate tumor evolution, making cancer cells more adaptable to environmental challenges, including therapeutic interventions.

Kickstarting cancer

Previous studies indicated that these circular structures, common in human cancers but seldom seen in healthy cells, mainly emerge late in the disease process, in advanced tumors. This was believed to be the result of an increasing failure of abnormal cells to accurately perform the complex process of DNA replication prior to each cell division.

The new study undermines these conclusions, showing that the circular extrachromosomal DNAs already appear in precancerous cells and apparently act to initiate the transformation to cancer. If new treatments can be developed to block the formation of extrachromosomal DNA in precancerous cells, or blunt their effect, there is hope the cancer could be stopped in its tracks.

Unlocking the role of extrachromosomal DNA in cancer was one of four Cancer Grand Challenges awarded by the National Cancer Institute and Cancer Research UK in 2022. The  program is designed to unite researchers from around the world to address particularly daunting areas of research. Paul Mischel of Stanford, one of six senior authors of the new study, was awarded $25 million to lead the international group to investigate extrachromosomal links to cancer.

Malignant transformation

The researchers explored esophageal tissue samples acquired from frequent biopsies performed on patients with Barrett’s esophagus used to keep close tabs on their condition. The study tracked the prevalence of extrachromosomal DNA, identifying the specific genes they carried. The tissue biopsies came from nearly 300 people with Barrett’s esophagus or esophageal cancer treated at the University of Cambridge and Seattle’s Fred Hutchinson Cancer Center.

The dramatic results showed that extrachromosomal DNA increased 24% to 43% in early- versus late-stage esophageal cancer, highlighting the continual formation of the tell-tale circular DNA during cancer progression. Further, 33% of people with Barrett’s esophagus who went on to develop esophageal cancer had extrachromosomal DNA in their precancerous cells.

The increase in extrachromosomal DNA over the course of the cancer’s progression indicates that the circular DNA forms are highly advantageous to cancer growth. The results showed that the extrachromosomal DNAs also contain immune-modulatory genes, which can blunt the immune system’s ability to identify and respond to cancer.

Ongoing research will help advance the use of extrachromosomal DNAs as targets for cancer diagnosis and drug development, as well as open a new window on the mechanisms of tumor growth.