Researchers studying a DNA–cutting enzyme with a crucial role in regulating the structure of genes have discovered a broad role for its cutting activity in driving abnormal genetic rearrangements called translocations that cause cancer, including leukemias and solid tumors.

The enzyme, type II topoisomerase, called TOP2, snips the DNA double strand to allow fundamental cellular activities to occur: transcription (converting DNA information into RNA) and replication (copying a DNA double helix into two daughter molecules). TOP2 also rejoins the broken DNA strands that it cuts, but if this process goes wrong, mismatched ends of DNA can give rise to a translocation. The translocation can produce a fusion protein that leads to abnormal white blood cells, the hallmark of leukemia.

A physician–researcher and a biologist specializing in RNA have teamed up to create a novel DNA sequencing tool that identifies specific sites of TOP2 cutting (cleavage) along the entire genome of human leukemia cells. “This tool opens new possibilities to better understand and eventually manipulate TOP2 cutting to prevent the rearrangements that give rise to leukemias,” said study co–leader Carolyn A. Felix, MD, a pediatric oncologist at Children’s Hospital of Philadelphia (CHOP). Felix, who holds the Joshua Kahan Endowed Chair in Pediatric Leukemia Research at CHOP, focuses on infant leukemia as well as treatment–related or secondary leukemia that may occur as a side effect of TOP2–related chemotherapy drugs.

Felix’s team has collaborated for the past several years with a team led by biologist Brian D. Gregory, PhD, of the University of Pennsylvania, who uses genome–wide sequencing to catalog the sites on DNA and RNA molecules that are bound by proteins. “We designed a way to pull down the DNA bound to TOP2, then to break that bond so that only the DNA undergoing cleavage is free to be sequenced at single base–pair precision,” he said. “This enabled us to map, for the first time, topoisomerase cleavage on a genome–wide scale.”

The scientists reported their findings online April 6, 2017, in the journal Genome Research.

“The fact that TOP2 cleavage clusters in the same genomic environment alongside histone marks and transcription regulators implicates the TOP2 enzyme as a prominent orchestrator of DNA remodeling,” said Felix.

Felix added that the findings open possibilities for new clinical approaches. “The better we identify where cleavage occurs across the genome, the better we can understand how the translocations happen. We could use that knowledge to design smarter anticancer drugs to target the TOP2 enzyme that don’t have such a high risk of causing translocations, or we could design drugs to protect sequences in the genome from unwanted cutting.”