Once brushed aside as a curiosity, extrachromosomal DNA (ecDNA) is now taking centrestage in the complex field of cancer biology. Scientists first discovered it as a small fragment of genetic material in cancer cells 50 years ago. Because it was present in only 1.4% of tumours, they didn’t consider it to be important.
But more sophisticated genomic techniques later revealed their mistake: one study published in 2017 revealed ecDNA is present in nearly 40% of cancer cell lines and in up to 90% of patient-derived brain tumour samples, revealing its pivotal role in cancer biology.
On November 6, three papers were published in the journal Nature by a team called eDyNAmiC — an international collaboration led by Stanford University professor Paul Mischel. The studies explore how ecDNA is formed and contributes to the progression of cancer and drug resistance.
Importantly, the findings also challenge a fundamental law of genetics.
What is ecDNA?
In normal human cells, the nucleus contains 23 pairs of chromosomes that enclose the DNA. There are some natural processes that can damage DNA. For example, in chromothripsis, which occurs in some cancers, the chromosomes are broken and rearranged. Cells can also make mistakes in the DNA when making copies of it to imbue in new cells. Such processes could cause a small part of the DNA to break away from the main chromosome and form a circular structure that floats freely inside the nucleus. This is ecDNA.
One of the three studies was led by eDyNAmiC members Mariam Jamal-Hanjani and Charles Swanton, both professors at University College London. They analysed the mutation patterns in tumours before and after the formation of ecDNA. They identified various environmental factors, including smoking, exposure to certain substances, and genetic mutations, to be triggers of DNA damage that could lead to the formation of ecDNA.
In the same study, the researchers attempted a comprehensive analysis of samples from nearly 15,000 cancer patients from U.K.’s 100,000 Genomes Project, covering 39 tumour types. They validated their findings using a method called fluorescence in-situ hybridisation (or FISH), which specifically looks for certain cancer-related genes in tissue samples.
They found that ecDNA was present in about 17% of tumour samples but more so in liposarcomas, brain tumours, and breast cancers. They also reported that the prevalence of ecDNA rose after treatments like chemotherapy, and correlated with metastasis and worse patient outcomes.
ecDNA and cancer growth
ecDNA present in tumours often contain multiple copies of oncogenes — mutated genes capable of causing cancer — that are required to activate tumour growth. But these oncogenes are not present in chromosomes, where scientists used to believe they lived.
In a study published in 2021 led by another Stanford University professor, Howard Chang, showed that while chromosomal DNA is fixed within specific regions in the cell, ecDNA moves freely and can interact with other ecDNA to form hubs — concentrated zones where oncogenes are expressed more.
Cells transcribe DNA to mRNA to use the latter to manufacture proteins. The 2021 study also found that when cells transcribe ecDNA to mRNA, the process causes specific oncogenes to become four-times more common in the cell than if the DNA came from the chromosomes.
This anomaly has the potential to accelerate the evolution of tumours and help the cancer resist drugs.
An inheritance of loss
Another finding reported in the new studies involves a fundamental shift in scientists’ understanding of genetics.
Typically, when cells divide, they duplicate the chromosomes and distribute it equally among their daughter cells. In this process, researchers have known the genes on the same chromosome are inherited together while those on different chromosomes are distributed independently of one another. This basic genetic principle is called Mendel’s third law of independent assortment (named after Gregor Mendel).
But in the second of the three studies, a team led by Mischel and Chang used single-cell sequencing, imaging, and modelling to report that ecDNA is passed on in clusters to the daughter cells during cell division — a violation of the third law. This clustering gives some cancer cells an advantage because it allows them to enhance gene interactions, support cancer growth, and preserve favourable genetic combinations over multiple life-cycles. The researchers have called this the “jackpot effect”.
This discovery has profound implications. It overturns the idea that gene inheritance is entirely random when the genes are not linked by DNA strands. The researchers also reported that the transcription process — from DNA to RNA — facilitates the coordinated segregation of ecDNA during cell division.
A new vulnerability in cancer cells
But for the new threats posed by ecDNA, the third study uncovered a potential weakness in tumours that relies on ecDNA. The unusual structure of the ecDNA and its interactions with other DNA elements increases the activity of specific genes. This can lead to a conflict between the cellular machinery involved in making RNA and the activity of cancer cells that leads to DNA damage.
Cells respond to this conflict by the heavy use of a protein called CHK1, which helps fix DNA and allows the cell to keep growing. When the researchers used a drug called BBI-2779 that blocks CHK1, they found the drug selectively killed cancer cells with ecDNA, significantly reducing the number of tumours in mice with stomach cancer.
A San Diego-based biotechnology company co-founded by Mischel and Chang, called Boundless Bio, is currently working to translate these discoveries for clinical use. The company’s stated aim is to give patients new treatment options that target vulnerabilities created by ecDNA. This is particularly crucial for patients with ecDNA-driven cancers, such as glioblastoma and ovarian and lung cancers, where current treatments often fall short.
Manjeera Gowravaram has a PhD in RNA biochemistry and works as a freelance science writer.
Published – December 04, 2024 05:30 am IST
