Why a Promising Breast Cancer Drug Doesn’t Work and How to Improve It

A decade ago, hopes were high when a new class of drugs, BET inhibitors, emerged to treat blood cancers and solid tumors. But since then, the results of numerous clinical trials have painted a much more complex picture, particularly with regard to breast cancer.

Now, a new study published in Nature Structural and Molecular Biology explains why this therapy, which continues to show promise in treating other cancers, is ineffective in treating a common form of breast cancer. “We found that these therapies only block part of the protein that activates oncogenes,” says Robert G. Roeder, the Arnold and Mabel Beckman Professor. “It turns out that’s not enough.”

Tempting targets

Cancer researchers have long focused on a family of four proteins, collectively known as BETs, that are active in many cancer-related genes and pathways. These proteins, and one in particular, known as BRD4, are attractive drug targets because they use the bromodomain (a 110-amino acid segment that gives BET proteins their name) to bind to acetylated histones (proteins that help organize DNA) to act on genes that promote cell survival.

Additionally, in breast cancer, BET proteins trigger an uncontrolled transcription cycle that results in uncontrolled proliferation of cancer cells. Scientists hoped that BET inhibitors designed to block the bromodomain could nip this cycle in the bud.

But clinical trials have repeatedly failed to demonstrate the effectiveness of BET inhibitors, particularly in breast cancers that use estrogen as fuel to grow.

“We had already started studying how this estrogen receptor-positive breast cancer is transcriptionally driven when the first clinical trials of these BET inhibitors failed,” says Sicong Zhang, first author of the paper and a research associate in Roeder’s lab. “There was no explanation for why these trials failed. We wanted to understand what went wrong.”

A better bet

Zhang and Roeder used several advanced techniques to study the role of BET proteins in gene transcription. They first compared the effect of blocking BET proteins with inhibitors, versus completely eliminating them, on gene transcription. They found that cancer-related genes like MYC depend on the BET protein itself, rather than just its bromodomain.

The team also designed BET proteins without a bromodomain to study their behavior. Among the different BET proteins, only BRD4 was able to activate MYC without relying on its bromodomain. When BRD4 was removed from the cells, the BET inhibitors completely killed the cancer cells.

They also found that BRD4 interacts with a protein complex called Mediator, which plays a major role in gene transcription and works directly with estrogen receptors. When Mediator’s function was disrupted, BRD4’s ability to bind to certain regions of genes was significantly reduced. Interestingly, this interaction between BRD4 and Mediator does not depend on the bromodomain, suggesting that BRD4 is recruited to genes in another way.

Using a new method they developed, called MSDC (mass spectrometry with DTME crosslinking), they discovered that BET proteins help RNA polymerase II find its associated elongation factors (SPT5, SPT6, PAF1 complex). These elongation factors work closely with RNA polymerase II to ensure proper transcription. BET proteins can interact with these elongation factors that do not depend on the bromodomain.

In other words, the therapy works as intended: BET inhibitors actually disable BRD4’s bromodomains. This is not enough to completely block the protein’s oncogenic activity.

The results demonstrate the importance of a deeper understanding of BRD4, and Zhang and Roeder are already focused on that goal. “We still don’t have a high-resolution atomic structure of the BRD4-mediator complex,” Roeder says. “That’s now on the agenda.” They are also investigating whether a combination therapy targeting both the BRD4 bromodomain and its various transcriptional backdoors could lead to a better BET inhibitor.

“We know why BET inhibitors failed,” Zhang says. “Now we’re trying to create one that works.”