Researchers uncover a new role for the BRD4 protein in repairing DNA breaks

November 30, 2022
a man in white lab coat poses in a basic science lab
Dr. David Long's lab members collaborated to uncover a protein's role in fixing DNA double-strand breaks. Photo by Clif Rhodes

A protein that is normally thought of as controlling transcription is actually holding down two jobs, researchers at MUSC Hollings Cancer Center found in a study published earlier this year in Nature Communications.

Using an approach that’s a mix of biochemistry and cell biology, the Long Lab looked at the role of the protein BRD4 in repairing DNA double-strand breaks. What they found, said David Long, Ph.D., is that BRD4 not only controls DNA repair by turning genes on and off, but it also has a direct role in repair by acting as a scaffold and recruiting all of the different workers necessary for repair.

Discovering this second job of BRD4 may explain why some types of therapies that target BRD4 are more effective than others in attacking cancer, Long said.

BRD4 plays an important role in cancer. It regulates transcription of oncogenes that control how cells grow and divide. In some cancers, like ovarian cancer, BRD4 is overexpressed.

“When you get BRD4 overexpression, it can drive cell growth and proliferation. And that’s why BRD4 has become an attractive target for anti-cancer therapy – to stop the cells that are growing out of control,” Long said.

"When you get BRD4 overexpression, it can drive cell growth and proliferation. And that’s why BRD4 has become an attractive target for anti-cancer therapy – to stop the cells that are growing out of control."

David Long, Ph.D.

Unfortunately, BRD4 inhibitors have shown limited effectiveness because cancer cells often develop resistance to treatment, he said. Some newer studies have started looking at combining BRD4 inhibitors with DNA damaging agents. The research from Long’s lab indicates that this strategy may work for a different reason than what was initially assumed. The initial reasoning was that BRD4 helped to turn on transcription of repair genes when DNA was damaged.

"But our work suggests that it's a lot more than that,” Long said. “BRD4 is essentially acting as a repair protein itself. So when cancer cells are treated with both DNA damaging agents and with BRD4 inhibitors, the cells won’t be able to fix the damage and eventually die. We think that this is part of why that strategy works so well and why it should be explored further.”

Long credited then-doctoral student John Barrows, Ph.D., who has since graduated and moved to a postdoctoral position at Kennesaw State University, with developing the method that allowed them to uncover BRD4’s multiple functions.

To understand what a protein is doing, scientists will often remove it from cells and see what changes. But if a protein like BRD4 is doing more than one thing, then it can be hard to figure out how it works. In the case of BRD4, researchers didn’t know whether DNA repair wasn’t happening because BRD4 wasn’t there to turn on transcription of repair genes or because it wasn’t there to do some other task.

Instead, the team developed a cell-free system using the eggs of Xenopus laevis frogs, which were placed in a centrifuge to create an extract or “protein soup.” That meant they could single out the process they wanted to observe by controlling what was added to the extract.

“We thought, ‘OK, we can take BRD4 and just look at what it’s doing in repair. We don't have to worry about cell cycle changes, gene expression going up and down and other things that make it more complicated. We can ask one simple question to see if it really has a direct role during DNA repair,’” Long explained. “And we found out very quickly that it was critical for repairing double strand breaks.”

Long said that BRD4 appears to work the same way in repair that it does in transcription, by acting as a scaffold to recruit the machinery required for each job. His team showed that BRD4 brings in chromatin remodelers, which take histones off the DNA to get them out of the way, as well as resection machinery, which chews back the DNA ends to expose single-stranded DNA needed for repair.

Long said that the next big question is how BRD4 knows whether it should be turning on transcription mode or repair mode because doing both at the same time could cause more problems. He also noted that although BRD4 is greatly overexpressed in some cancers, like ovarian cancer, its function is so fundamental that understanding how it works could prove useful in other diseases. He's also worked with or initiated collaborations with other Hollings Cancer Center researchers who are looking into other aspects of BRD4.

The paper in Nature Communications came together only because of the teamwork of everyone in his lab, he said.

“Most of our lab worked together to put this paper together. It was an exciting project, but it took a lot of work to figure out the mechanism and understand what was really going on.”

This research was supported by the National Institutes of Health (NIH), Grant: R35 GM119512.