Cracking the code of DNA circles in cancer

Stanford Medicine-led team uncovers potential therapy.

ecDNA catapults into spotlight.

A trio of research papers from Stanford Medicine researchers and their international collaborators transforms scientists’ understanding of how small DNA circles — until recently dismissed as inconsequential — are major drivers of many types of human cancers.

The papers, to be published simultaneously in Nature on Nov. 6, detail the prevalence and prognostic impact of the circles, called ecDNA for extrachromosomal DNA, in nearly 15,000 human cancers; highlight a novel mode of inheritance that overthrows a fundamental law of genetics; and describe an anti-cancer therapy targeting the circles that is already in clinical trials.

The team, jointly known as eDyNAmiC, are a group of international experts led by professor of pathology Paul Mischel, MD. In 2022, Mischel and the eDyNAmiC team were awarded a $25 million grant from the Cancer Grand Challenges initiative to learn more about the circles. Cancer Grand Challenges, a research initiative co-founded by Cancer Research UK and the National Cancer Institute in the United States, supports a global community of interdisciplinary, world-class research teams to take on cancer’s toughest challenges.

“We’re in the midst of a completely new understanding of a common and aggressive mechanism that drives cancer,” said Mischel, who holds the Fortinet Founders Professorship. “Each paper alone is noteworthy, and taken together they represent a major inflection point in how we view cancer initiation and evolution.” Mischel is also an institute scholar at Stanford Medicine’s Sarafan ChEM-H.

Mischel is co-senior author of each of the three papers; Howard Chang, MD, PhD, professor of dermatology and genetics, the Virginia and D.K. Ludwig Professor in Cancer Research and a Howard Hughes Medical Institute investigator, is the co-senior author of two of the three papers and a co-author on the third paper.

Those featured circles, ecDNAs, are small and often contain a few genes on their circular DNA. Frequently, these genes are cancer-associated genes called oncogenes. When a cancer cell contains multiple oncogene-encoding ecDNAs, they can supercharge the cell’s growth and allow it to evade internal checkpoints meant to regulate cell division. The ecDNAs also sometimes encode genes for proteins that can tamp down the immune system’s response to a developing cancer — further advantaging tumor growth.

Greater prevalence than previously thought

Until recently, it was believed that only about 2% of tumors contained meaningful amounts of ecDNA. But in 2017, research in Mischel’s lab showed that the small circles were widespread and likely to play a critical role in human cancers. In 2023, Mischel and Chang further showed that their presence jumpstarts a cancerous transformation in precancerous cells.

In the first of the three papers, of which Chang is a co-author and Mischel is a co-senior author, researchers in the United Kingdom built on Mischel’s 2017 finding by analyzing the prevalence of ecDNA in nearly 15,000 cancer patients and 39 tumor types. They found that 17.1% of tumors contained ecDNA, that ecDNA was more prevalent after targeted therapy or cytotoxic treatments like chemotherapy, and that the presence of ecDNA was associated with metastasis and poorer overall survival.

The researchers also showed that the circles can contain not just cancer-driving oncogenes and genes that modulate the immune response, but also that others can contain only DNA sequences called enhancers that drive the expression of genes on other circles by linking two or more ecDNAs together.

“This was kind of a heretical idea,” Chang said. “The ecDNAs with enhancer elements don’t confer any benefit to the cell on their own; they have to work with other ecDNAs to spur cancer cell growth. If looked at through a conventional lens, the presence of ecDNAs that solely encode enhancers wouldn’t seem to be a problem. But the teamwork and physical connection between different types of circles is actually very important in cancer development.”

“This study is a tour de force of data gathering and analysis,” Mischel said. “We learned critical lessons about which cancer patients are affected and what genes or DNA sequences are found in ecDNAs. We identified the genetic backgrounds and mutational signatures that give us clues as to how cancers originate and thrive.”

Mischel and Chang are the co-senior authors of the second paper that studied how the ecDNA circles are segregated into daughter cells when cancer cells divide. Typically, ecDNAs segregate randomly during cell division. As a result, some new cells could have many ecDNAs while their sister cells had none. This kind of genetic roll of the dice increases the odds that at least some population of cells in the tumor will have the right combination of ecDNAs to evade environmental or drug challenges and contributes to the development of drug resistance.

Chang and Mischel and their colleagues showed that this concept is still true, to a point. But they found that, unlike chromosomes, ecDNA transcription — the process of copying DNA sequences into RNA instructions that are then used to make proteins — continues unabated during cell division. As a result, ecDNAs working in tandem remain interconnected during cell division and segregate together as multi-circle units to daughter cells.

A new take on peas

“This upends Gregor Mendel’s rule of independent assortment of genes that aren’t physically linked by DNA sequences,” Mischel said, referring to the biologist and Augustinian friar who first described how traits are inherited during his studies of pea plants in the 1860s. “It’s really stunning and an enormous surprise.”

“Daughter cells that repeatedly inherit particularly advantageous combinations of ecDNA circles should be rare if the segregation of each type of circle is truly random,” Chang said. “But this study showed that we were seeing many more of these ‘jackpot events’ than would be expected. It’s like getting a good hand in poker. Cancer cells that get dealt that good hand over and over have a huge advantage. Now we understand how this happens.”

These jackpot events highlight a weakness in the cancer cells, however. Chang and Mischel and the eDyNAmiC team realized that there is inherent tension between transcription and replication, each of which are carried out by protein machinery that trundles along the DNA strand. When transcription and replication machinery collide, the process stalls and the cell activates internal checkpoints to pause cell division until the conflict is resolved.

The third paper, of which Chang and Mischel are co-senior authors, reports that blocking the activity of an important checkpoint protein called CHK1 causes the death of ecDNA-containing tumor cells grown in the laboratory and causes tumor regression in mice with a gastric tumor fueled by the DNA circles.

“This turns the table on these cancer cells,” Chang said. “They are addicted to this excess transcription; they can’t stop themselves. We made this into a vulnerability that results in their death.”

Currently in trials

The results were promising enough that a CHK1 inhibitor is now in early phase clinical trials for people with certain types of cancers that have multiple copies of oncogenes on ecDNAs.

“These papers represent what can happen when researchers from many different labs come together with a common goal,” Mischel said. “Science is a social endeavor and together, through many avenues of converging data from wildly different sources, we’ve shown that these findings are real and important. We are going to continue exploring the biology of ecDNAs and use that knowledge for the benefit of patients and their families.”

Mischel, Mariam Jamal-Hanjani, MD, PhD, a professor of cancer genomics and metastasis at the Cancer Research UK Lung Cancer Centre of Excellence at University College London Cancer Institute and Charles Swanton, PhD, a deputy clinical director at the Francis Crick Institute are co-senior authors of the paper on the prevalence and impact of ecDNA in nearly 15,000 cancer patients; clinical research fellow Chris Bailey, PhD, and senior bioinformatics scientist Oriol Pich, MD, PhD, of the Francis Crick Institute are co-lead authors. Jamal-Hanjani is also an honorary medical oncology consultant in translational lung oncology with the UCL Hospitals NHS Trust.

Mischel and Chang are co-senior authors of the paper detailing the mechanisms of inheritance of ecDNA; graduate student King Hung; postdoctoral scholar Matthew Jones, PhD; postdoctoral scholar Ivy Tsz-Lo Wong, PhD; and graduate student Ellis Curtis are the lead authors of the study.

Mischel, Chang and Christian Hassig, PhD, chief scientific officer of Boundless Bio, are the senior authors of the paper describing a new therapeutic approach targeting ecDNAs in cancer cells. Postdoctoral scholar Jun Tang, PhD; pathology instructor Natasha Weiser, MD; and postdoctoral scholar Guiping Wang, PhD, are the lead authors of the study.

Mischel and Chang are scientific co-founders of Boundless Bio, a San Diego-based oncology company developing cancer therapeutics based on ecDNA biology. Boundless Bio is the sponsor of a phase 1/2 study of an inhibitor of CHK1 in people with locally advanced or metastatic solid tumors with oncogene amplifications.

Through Cancer Grand Challenges team eDyNAmiC is funded by Cancer Research UK and the National Cancer Institute, with generous support to Cancer Research UK from Emerson Collective and The Kamini and Vindi Banga Family Trust.

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About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit med.stanford.edu.

About Cancer Grand Challenges 

Cancer Grand Challenges supports a global community of interdisciplinary, world-class research teams with awards of up to $25m over five years to come together, think differently and take on cancer’s toughest challenges. Founded by the two largest funders of cancer research in the world – Cancer Research UK and the National Cancer Institute* in the US – and uniting an international community of partners, Cancer Grand Challenges.

Journal: Nature
DOI: 10.1038/s41586-024-07861-8
Method of Research: Observational study
Subject of Research: Cells
Article Publication Date: 6-Nov-2024

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