Stanford researchers reveal key role of extrachromosomal DNA in cancer

A trio of research papers by Stanford Medicine researchers and their international collaborators is transforming scientists’ understanding of how the small circles of DNA -? until recently dismissed as unimportant -? are key factors in many types of human cancers.

The papers, which will be published simultaneously on Nature on November 6, detailed the prevalence and prognostic impact of the cycles, called ecDNA for extrachromosomal DNA, in nearly 15,000 human cancers. highlight a new mode of inheritance that overturns a fundamental law of genetics. and describe a cycle-targeting cancer therapy already in clinical trials.

The team, collectively known as eDyNAmiC, is a group of international experts led by pathology professor Paul Mischel, MD. In 2022, Mischel and the eDyNAmiC team received a $25 million grant from the Cancer Grand Challenges initiative to learn more about cycles. 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 multidisciplinary, world-class research teams to tackle cancer’s toughest challenges.

“We are 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 on its own is remarkable, and together they represent an important turning point in how we view cancer initiation and progression.” Mischel is also an institute fellow 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 DK Ludwig Professor in Cancer Research and a Howard Hughes Medical Institute investigator, is co-senior author on two of the three papers and co-author on the third paper.

These characterized circles, ecDNA, are small and often contain a few genes in their circular DNA. Often, these genes are cancer-related genes called oncogenes. When a cancer cell contains multiple ecDNAs that encode an oncogene, they can supercharge the cell’s growth and allow it to evade internal checkpoints meant to regulate cell division. EcDNAs also sometimes code for genes for proteins that can dampen the immune system’s response to a growing cancer. further favors tumor growth.

Greater prevalence than previously thought

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

In the first of three papers, of which Chang is a co-author and Mischel is co-senior author, researchers in the UK 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 such as chemotherapy, and that the presence of ecDNA was associated with metastasis and poorer overall survival.

The researchers also showed that circles may contain not only cancer-causing oncogenes and genes that regulate the immune response, but that others may contain only DNA sequences called enhancers that drive gene expression in other circles by connecting two or more ecDNAs. between them. .

This was a somewhat heretical idea. ecDNAs with enhancer elements provide no benefit to the cell by themselves. they must work with other ecDNA to stimulate cancer cell growth. If viewed through a conventional lens, the presence of ecDNA exclusively encoding enhancers would not appear to be a problem. But teamwork and the physical connection between different types of cycles is actually very important for cancer growth.”

Howard Chang, MD, PhD, professor of dermatology and genetics, the Virginia and DK Ludwig Professor in Cancer Research, and a Howard Hughes Medical Institute investigator

“This study is a data collection and analysis tour,” Mischel said. “We have learned critical lessons about which cancer patients are affected and which genes or DNA sequences are found in ecDNA. We have identified the genetic background and mutational signatures that give us clues about how cancers originate and thrive.”

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

Chang and Mischel and their colleagues showed that this idea still holds, to a point. But they found that, unlike chromosomes, the transcription of ecDNA -? the process of copying DNA sequences into RNA instructions that are then used to make proteins – continues unabated during cell division. As a result, the ecDNAs that function in parallel remain intertwined during cell division and segregate together as multicycle units in the daughter cells.

A new take on peas

“This overturns Gregor Mendel’s rule of independent assortment of genes not physically linked to DNA sequences,” Mischel said, referring to the biologist and Augustinian monk who first described how traits are inherited during his studies of pea plants in 1860s. “It is really amazing and a huge surprise.”

“Daughter cells that repeatedly inherit highly advantageous combinations of ecDNA cycles should be rare if the segregation of each cycle type is truly random,” Chang said. “But this study showed that we were seeing a lot more of these ‘jackpot events’ than you might expect. It’s like getting a good hand in poker. Cancer cells that deal that good hand over and over again have a huge advantage. Now we understand how this happens.”

However, these jackpot events highlight a weakness in cancer cells. Chang and Mischel and the eDyNAmiC team realized that there is an inherent tension between transcription and replication, each of which is carried out by protein machinery that moves along the DNA strand. When the transcription and replication machinery conflict, the process stops and the cell activates internal checkpoints to stop 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 cancer cells grown in the lab and causes tumor regression in mice with gastric tumor powered by DNA cycles.

“This turns the table on these cancer cells,” Chang said. “They’re addicted to this over-transcription; they can’t stop themselves. We’ve turned it into a vulnerability that leads to their death.”

Currently in testing

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

“These papers represent what can happen when researchers from many different laboratories come together with a common goal,” Mischel said. “Science is a social endeavor and together, through many avenues of converging data from very different sources, we have shown that these findings are real and important. We will continue to explore the biology of ecDNA and use this knowledge to benefit patients and their families”.

Mischel, Mariam Jamal-Hanjani, MD, PhD, professor of cancer genomics and metastasis at the Cancer Research UK Lung Cancer Center of Excellence at University College London Cancer Institute, and Charles Swanton, PhD, associate 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 researcher 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 UCL Hospitals NHS Trust.

Mischel and Chang are co-senior authors of the paper detailing the mechanisms of ecDNA inheritance. graduate student King Hung; postdoctoral scholar Matthew Jones, PhD; postdoctoral fellow 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 senior authors of the paper that describes a new therapeutic approach that targets ecDNA in cancer cells. Postdoctoral Fellow Jun Tang, PhD; professor of pathology Natasha Weiser, MD; and postdoctoral fellow Guiping Wang, PhD, are lead authors of the study.

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

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