Chromothripsis could be key to cancer's drug resistance

SAN DIEGO—Researchers have solved the mystery of how free-floating circular DNA fragments, which are found almost exclusively in cancer cells, drive gene amplification to generate drug resistance in cancer.

Dr. Don Cleveland is professor of medicine, neurosciences, and cellular and molecular medicine at University of California San Diego School of Medicine; he also has a lab in the Ludwig Institute for Cancer Research. He and Dr. Peter Campbell of the Wellcome Sanger Institute are co-senior authors of the research, which has been published in Nature. 

The study describes how the process of chromothripsis shatters chromosomes and then reassembles them in shuffled order.

“Drug resistance is the most problematic part of cancer therapy,” noted Dr. Ofer Shoshani, a postdoctoral researcher in Cleveland’s lab and the study’s first author. “If not for drug resistance, many cancer patients would survive.”

Extrachromosomal DNAs (ecDNA) are distinct circular units of DNA, unassociated with chromosomes, which package genomic DNA in the cell’s nucleus. ecDNA can contain many copies of cancer genes that help tumors grow and survive. 

In 2017, a team led by Ludwig San Diego member Paul Mischel and his colleague Vineet Bafna at UC San Diego School of Medicine first reported that ecDNA is found in almost half of all tumor types, and that it plays a major role in the growth and diversity of cancer cells. 

In the new study, Shoshani, Cleveland, Campbell, and colleagues have shown that chromothripsis initiates the formation of ecDNA. The team also proved that ecDNA can undergo successive rounds of chromothripsis to spawn rearranged ecDNAs that provide even higher drug resistance.

“What we were able to show is the link between chromosomal shattering and the formation of ecDNA. We’ve watched these pieces evolve with time as they get shattered and re-shattered. That means if an ecDNA fragment acquires a gene that encodes for a product that directly counters an anticancer drug, it can make more and more of it, leading to drug resistance,” Cleveland said. “We have now established this in three different cell lines forming resistance to methotrexate and in biopsies from human colorectal cancer patients forming resistance to BRAF therapy.”

While chromothripsis occurs naturally in cancer cells, the researchers found that it can also be induced by chemotherapeutic drugs like methotrexate, which kill dividing cells by damaging their DNA. And the kind of DNA damage these drugs cause provides an opening for ecDNA to reintegrate back into chromosomes.

“[W]hen we break a chromosome, these ecDNAs have a tendency to jump into the break and seal them, serving almost like a ‘DNA glue,’” added Shoshani. 

Some of the very drugs used to treat cancers could also be driving drug resistance by generating double-stranded DNA breaks.

The researchers found that this type of ecDNA formation can be halted by pairing chemotherapeutic drugs with molecules that prevent the DNA fragments created by chromosomal shattering from closing to form circles. Shoshani showed that when applied together to cancer cells, this strategy inhibited the formation of ecDNA and reduced the emergence 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 stated.

“I think the field has accepted that combination therapy is how we’re going to generate better outcomes for cancer patients, but here’s a specific example of what kinds of combinations should be tested,” concluded Cleveland.