Extrachromosomal DNA is any DNA that is found outside of the nucleus of a cell. It is also referred to as extranuclear DNA or cytoplasmic DNA. Most DNA in an individual genome is found in chromosomes but DNA found outside of the nucleus also serves important biological functions.
In the evolution of cancer, the most vicious circle may be that perpetrated by circular DNA, which is also known as extrachromosomal DNA (ecDNA). According to a new study, ecDNA is found in nearly half of all types of tumors, and it encodes multiple copies of driver oncogenes, or cancer-driving genes. Worse, driver oncogenes appear to be more harmful in ecDNA than in chromosomal DNA. Driver oncogenes in ecDNA contribute to tumor heterogeneity and drug resistance.
These new findings appeared February 8 in the journal Nature, in an article entitled, “Extrachromosomal Oncogene Amplification Drives Tumour Evolution and Genetic Heterogeneity.” The article indicates that ecDNA, once thought to be rare in tumor cells, is actually very common and seems to play a fundamental role in tumor evolution. The article’s main point—that ecDNA contributes to accelerated evolution in cancer—could lead to new ways to prevent and treat many malignancies.
The Nature paper is based on a study led by an interdisciplinary team led jointly by Paul Mischel, M.D., a member of the Ludwig Institute for Cancer Research, and Vineet Bafna, Ph.D., a professor at the University of California San Diego School of Medicine. The scientists analyzed cells from 17 different types of cancer to explore ecDNA. They also analyzed the structure and function of chromosomes of 2572 dividing cells during metaphase, and they developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis.
“Here we show that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells,” wrote the authors of the Nature paper. “Driver oncogenes were amplified most commonly in ecDNA, thereby increasing transcript level.”
Essentially, the researchers showed that ecDNA plays a far bigger role in the growth, diversity, and drug resistance of cancer cells than the same genes housed on chromosomes in such tumors.
“We’ve discovered something fundamental about how cancers diversify and evolve,” said Mischel. “This is an essential rethinking about what goes wrong with genes in cancer.”
The Nature paper describes how the scientists performed whole-genome sequencing, structural modeling, and cytogenetics to detect, quantify, and analyze ecDNA. They found that ecDNA was present in about 40% of tumor cell lines, but was extremely rare in normal cells. And when the scientists looked specifically at patient-derived models of brain tumors, nearly 90% of these carried ecDNA. The researchers also found that oncogenes are more likely to occur on ecDNA than on chromosomes.
“Mathematical modelling predicted that ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effectively than chromosomal amplification,” the authors added. “We validated these predictions by quantitative analyses of cancer samples and verified their model’s predictions through experiments conducted on tumor samples from patients.”
These studies revealed that tumors are more heterogeneous when oncogenes are amplified on ecDNA instead of on chromosomes, enabling them to more rapidly achieve and maintain high levels of cancer promoting genes.
Unlike chromosomes, ecDNA is parceled out randomly to daughter cells when a tumor cell divides. So, any given cell in a tumor might have no ecDNA in its nucleus, or it might be crammed with ecDNA. And the greater the variation in oncogene copy number, the greater the heterogeneity of cells in a tumor. It is this cellular diversity that makes tumors far more resistant to environmental challenges, most notably drug therapy.
The new work was inspired by a previous study led by Mischel and reported in Science in 2014. In that study, Mischel and colleagues revealed that ecDNA plays a central role in the drug resistance of certain brain tumors.
This finding came as a surprise because, for decades, cancer biologists had focused more on which genes promote cancer rather than where those genes are located. Genomic technologies too evolved along lines that favored this type of analysis. Although a few cancer biologists in the 1960s had described the presence of ecDNA in some tumor cells, they lacked the tools to quantify ecDNA, so the phenomenon had long been considered rare and inconsequential to the development of cancer.
“It occurred to us after we made the observations published in 2014 that maybe ecDNA is a lot more common and consequential than anyone thought,” explained Mischel. “Understanding how tumor cells evolve and how they increase the copy number and variability of their drivers is likely to yield some pretty important clues about the fundamental biology of cancer and how we might be able to target it.”
Mischel his team are now working to unearth the molecular mechanisms involved in the genesis and maintenance of ecDNA and exploring how ecDNA levels change in response to changes in the tumor’s internal environment.