The Reimand Lab links a DNA untangling protein to cancer mutation hotspots

Protein that untangles DNA also linked to cancer mutation hotspots

A study by researchers at the University of Toronto’s Department of Molecular Genetics reveals how a protein responsible for maintaining DNA structure may also identify regions prone to cancer mutations. 

The study was led by Dr. Jüri Reimand, Associate Professor in the Department of Molecular Genetics at the University of Toronto and Senior Scientist at OICR and also brought together researchers in computational biology, epigenomics, and functional genomics across the Department of Molecular Genetics. 

Published in Nature Communications, the study links the DNA-untangling enzyme called Topoisomerase IIB (TOP2B) to mutation hotspots throughout the genome, identifying hidden, cancer-driving changes in non-coding regions of DNA. 

Within the cell, DNA is constantly bending, looping, and folding as genes turn on and off. These movements can create tension, causing strands to twist or become tangled. To manage this, cells use enzymes called topoisomerases, which briefly cut DNA, allow it to pass through itself, and then repair the break.

In this study, researchers zero in on Topoisomerase IIB (TOP2B), an enzyme that helps relieve this tension.

Although this enzyme works to repair DNA breaks, the research team also found that mutations often occur at the sites where TOP2B interacts with the genome.

“Our evidence shows that where TOP2B interacts with a genome to fix DNA loops, a lot of mutations accumulate in cells,” says Reimand. “The vast majority of these mutations are probably harmless, but we also found dozens of well-known cancer-driving mutations at these sites.”

To investigate this pattern, the researchers created a detailed map of TOP2B binding sites across the genome and compared them with mutation data from more than 6,000 cancer genomes representing many tumour types. 

Many of the mutation hotspots appeared in the non-coding genome, which are large regions of DNA that do not produce proteins but help control how genes are turned on or off. Because these regions are less studied than protein-coding genes, mutations in them have historically been difficult to interpret. 

By focusing on TOP2B binding sites in these regions, the team identified hundreds of candidate mutations that may play a role in cancer-related mutations. One site stood out: a regulatory region near a non-coding RNA gene called RMRP, which had previously been linked to breast cancer. 

Using functional genomics approaches and mouse models, researchers showed that mutations in this regulatory region can start tumour growth and increase cancer aggressiveness. This is direct evidence that changes in non-coding DNA can drive tumour development. 

Co-author Dr. Michael Wilson, Professor in the Department of Molecular Genetics at the University of Toronto and Senior Scientist at SickKids, says the study provides important new information on the biological role of TOP2B. “While TOP2B’s natural function is still being defined, we know that it interacts with some of the most important non-coding genomic regions controlling gene expression and chromosome structure,” says Wilson. 

The findings may also help researchers better understand how certain cancer treatments interact with the genome. Some chemotherapy drugs target topoisomerase enzymes to damage cancer cells by stabilizing temporary DNA breaks. So while these treatments are effective and widely used, the same process can sometimes lead to additional mutations or chromosomal rearrangements. 

Identifying genomic regions where TOP2B activity coincides with mutation hotspots helps pinpoint potential sources of cancer-driving mutations and anticipate how treatments might affect these key processes. 

Dr. Daniel Schramek, Professor in the Department of Molecular Genetics at the University of Toronto and Senior Investigator at the Lunenfeld-Tanenbaum Research Institute, says the work highlights the power of combining large-scale computational analysis with experimental validation. 

“We discovered that mutations in a small regulatory region near the RMRP gene can initiate cancer and make it more aggressive,” says Schramek, who specializes in functional genomics. “Testing more of these sites using advanced CRISPR techniques will likely uncover even more hidden non-coding drivers.” 

The findings offer a new understanding of how the 3D structure of the genome affects mutation locations in cancer. By pinpointing DNA regions that are structurally vital and prone to damage, the study reveals ways to understand cancer development and discover hidden driver mutations. 

This study was funded by the Canadian Institutes for Health Research (CIHR), Ontario Institute for Cancer Research (OICR) and the Terry Fox Research Institute.