The study reveals how ecDNA fragments trigger gene amplification to create drug resistance in cancer

Researchers led by San Diego member Ludwig Don Cleveland and Peter Campbell of Sanger Center have solved the mystery of how free-floating circular DNA fragments, found almost exclusively in cancer cells, trigger gene amplification to create resistance to drugs in cancer.

The research was published December 23 in the journal Nature, provides new insights into how cancers develop to adapt to a changing environment and suggests ways to reduce drug resistance by combining therapies.

Drug resistance is the most problematic part of cancer therapy. Were it not for drug resistance, many cancer patients would have survived. “

Ofer Shoshani, the first author of the study, a postdoctoral researcher at Cleveland Laboratory, Ludwig Institute for Cancer Research

Extrachromosomal DNA (ecDNA) are various circular units of non-chromosome DNA that pack genomic DNA in the cell nucleus. ecDNA can contain many copies of cancer genes that help tumor growth and survival.

Understanding the biology and origins of ecDNA took hold after a team led by Ludwig member San Diego Paul Mischel and his colleague Vineet Bafna of the University of California, San Diego School of Medicine first reported in 2017 that it is in nearly half of all species tumor and that it plays a major role in the growth and diversity of cancer cells.

In a new study, Shoshani, Cleveland, Campbell, and colleagues show that chromotrips, chromosome fragmentation, and their reassembly in a mixed order initiate ecDNA formation.

Chromotrips was first described in 2011 by the team led by Campbell. Scientists at the time speculated that chromosomal fragmentation could produce circulating DNA clips to create ecDNA, but this has not been proven so far.

“What we were able to show is the link between chromosome breakage and ecDNA formation,” Cleveland said. The team also showed that ecDNA itself can undergo successive rounds of chromotripsy to produce rearranged ecDNAs that provide even greater drug resistance.

“We’ve watched these parts evolve over time as they break and break,” Cleveland said. “This means that if an ecDNA fragment acquires a gene encoding a product that directly opposes an anticancer drug, it can create it more and more, leading to drug resistance. We have now established this in three different cell lines forming methotrexate resistance and in biopsies. patients with human colon and bowel cancer who are resisting BRAF therapy.

Although chromotrips occur naturally in cancer cells, researchers have found that it can also be induced by chemotherapeutic drugs such as methotrexate, which kill cells that divide by damaging their DNA. Moreover, the particular type of DNA damage that these drugs cause — by breaking both strands of the DNA double helix — provides an opening for ecDNA to reintegrate into chromosomes.

“We show that when we break a chromosome, these ecDNAs tend to jump into the fracture and seal them, serving almost as a‘ DNA glue ’,” Shoshani said.Therefore, some of the very drugs used to treat cancer can also trigger drug resistance by generating double-stranded DNA breaks.

The researchers found that such ecDNA production can be stopped by combining chemotherapeutic drugs with molecules that prevent the closure of DNA fragments created by chromosomal fragmentation into circles. Shoshani has shown that, when applied together to cancer cells, this strategy inhibits the production of ecDNA and reduces the occurrence of drug resistance.

“This means that an approach in which we combine DNA repair inhibitors with drugs such as methotrexate or vemurafenib could potentially prevent the initiation of drug resistance in cancer patients and improve clinical outcomes,” Shoshani said.

Cleveland added, “I think the field has accepted that combination therapy will be a way for us to generate better outcomes for cancer patients, but here’s a concrete example of what types of combinations need to be tested.”


Ludwig Institute for Cancer Research