The study shows how ecDNA fragments drive gene amplification to create drug resistance in cancer

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

The research published December 23 in the journal natureprovides new insights into how cancers evolve to adapt to changing environments and suggests ways to reduce drug resistance through the combination of therapies.

Drug resistance is the most problematic part of cancer therapy. Without drug resistance, many cancer patients would survive. “

Ofer Shoshani, first author of the study, postdoctoral fellow in Cleveland’s laboratory, Ludwig Institute for Cancer Research

Extrachromosomal DNAs (ecDNA) are different circular DNA units that are not associated with chromosomes and that package genomic DNA in the cell nucleus. ecDNA can contain many copies of cancer genes that promote tumor growth and survival.

Understanding the biology and origins of ecDNA became urgent after a team led by Ludwig San Diego member Paul Mischel and colleague Vineet Bafna of the University of California’s San Diego School of Medicine first reported that it was in almost tumor types occur in half of all cases and that it plays an important role in the growth and diversity of cancer cells.

In the new study, Shoshani, Cleveland, Campbell, and colleagues show that chromothripsis, the breakage of chromosomes and their assembly in mixed order, initiate ecDNA formation.

Chromothripsis was first described in 2011 by a team led by Campbell. At the time, scientists hypothesized that chromosome destruction could produce bits of DNA that circulate to form ecDNA. However, this has not yet been proven.

“What we were able to show is the link between chromosome destruction and the formation of ecDNA,” said Cleveland. The team also showed that ecDNA can itself go through successive rounds of chromothripsis to yield rearranged ecDNAs that offer even higher drug resistance.

“We watched these pieces evolve over time as they were shattered and re-shattered,” Cleveland said. “That means if an ecDNA fragment acquires a gene that codes for a product that directly counteracts a cancer drug, it can always make more of it, leading to drug resistance. We have now found this in three different cell lines, one Resistance to methotrexate and in biopsies from human colon cancer patients who develop resistance to BRAF therapy. “

While chromothripsis occurs naturally in cancer cells, the researchers found that it can also be induced by chemotherapy drugs like methotrexate, which kill dividing cells by damaging their DNA. In addition, the particular type of DNA damage these drugs cause – breaking both strands of the DNA double helix – provides an opening for ecDNA to reintegrate into chromosomes.

“We show that when a chromosome breaks, these ecDNAs tend to jump into the break and seal it, which acts almost like a ‘DNA glue’,” Shoshani said. Therefore, some of the drugs used to treat cancer could also increase drug resistance by creating double-stranded DNA breaks.

The researchers found that such ecDNA formation can be stopped by pairing chemotherapy drugs with molecules that prevent the DNA fragments created by chromosome breakdown from closing and forming circles. Shoshani showed that this strategy, when used together on cancer cells, inhibits ecDNA formation and reduces the incidence of drug resistance.

“This means that an approach where we combine DNA repair inhibitors with drugs like methotrexate or vemurafenib can potentially prevent drug-resistance in cancer patients and improve clinical outcomes,” Shoshani said.

Cleveland added, “I think the field has accepted that combination therapy can produce better outcomes for cancer patients. However, here is a specific example of what types of combinations should be tested.”


Ludwig Institute for Cancer Research