Understanding Drug Resistance in Leukemia Cells

BRD4 gene could be exploited in treatment of acute myeloid leukemia.

One of the most promising new agents in cancer treatment are BRD4 inhibitors.

These powerful agents work to stop the most deadly of cancers in its tracks. However, some leukemia cells can evade the deadly effects of BRD4 inhibition, according to a study at the Research Institute of Molecular Pathology (IMP) and Boehringer Ingelheim in Vienna.

Understanding this adaptation process could aid the development of sequential therapies to outsmart resistant leukemia. In recent years, scientists have illustrated a nearly complete map of mutations in cancer.

However, converting these maps into effective treatments proves to be difficult for researchers. The laboratory of Johannes Zuber at the IMP in Vienna used functional genetic screens to search for new ways to attach cancer cells by probing vulnerabilities of the cells in a systematic and unbiased way.

The endpoint is to find genes that cancer cells depend on and exploit these genes for the development of targeted therapies. Zuber and his colleagues found in 2011 that BRD4 is such a gene that could be exploited in acute myeloid leukemia (AML).

This discovery sparked a lot of excitement about BRD4 as a new target for leukemia therapy, and only 4 years later several BRD4 inhibitors have entered clinical trials, some of which have already reported promising results.

Despite this rapid advance, scientists remain in the dark as to why certain cancer cells respond positively to the inhibitors while others are resistant to the medication.

“After discovering a new Achilles’ heel, we often have no clue why cancer cells depend on a certain gene, although this knowledge would be crucial for developing targeted therapies and selecting the right patients,” said Zuber.

Finding an answer to this question proved to be quite challenging in the case of BRD4. Zuber and his team paired up with previous co-workers in the United States and scientists at Boehringer Ingelheim in Vienna to characterize sensitive and resistant cancer cells. The results reveal a new mechanism to how leukemia cells evade their dependency on BRD4.

BRD4 is a known regulator of transcription and controls the activity of hundreds of genes, which are turned off all at once after inhibitor treatment. In leukemia, a gene of particular importance controlled by BRD4 is the MYC oncogene, a gene needed for leukemia cells’ indefinite growth.

Treatment with the BRD4 inhibitors shut off this important cancer gene, and leukemia cells either die or develop into normal blood cells. Zuber and his team performed a genetic screen to better understand why only certain leukemia subtypes are sensitive to BRD4 inhibition.

They found that the loss of the PRC2 complex can render leukemia cells resistant to the inhibitors. With further cell characterization, the team realized that MYC and other BRD4-regulated genes were back on again, meaning the cancerous cells found a way to evade the effects of the BRD4 inhibitors.

The researchers then compared cells that had acquired resistance to leukemia cells that were resistant in the first place. They found that in both cases leukemia cells use very similar pathways to turn critical genes such as MYC back on and escape the deadly effects of BRD4 inhibition.

“It looked as if sensitive leukemia cells just learned what resistant cells already knew,” explained postdoctoral scientists Philipp Rathert, who spearheaded the study together with Mareike Roth, a graduate student in the Zuber laboratory.

An important pathway turned out to be WNT signaling, which is responsible for activating MYC in colon cancer and other cancer subtypes. Using the STARR-seq method developed by Alexander Stark at the IMP, Zuber and his team found that resistant leukemia cells activate MYC through a very small enhancer region that is bound by WNT components and gains activity following BRD4 inhibition.

The team measured WNT signaling markers and found that patient cells with low WNT activity were sensitive to BRD4 inhibitors, while high WNT activity was associated with resistance. This means the team may hold the first “biomarker” in hands for predicting the success of BRD4 inhibitor therapy.

The study revealed the mechanism by which leukemia cells become resistant to BRD4 inhibitors. This “transcriptional plasticity” highlights an emerging mode of drug resistance that is distinct from established resistance mechanisms such as mutations in binding pockets or drug elimination through efflux pumps.

Zuber and his colleagues believe that a better understanding of these adaptation mechanisms will lead to combination therapies that will ultimately outsmart cancer cells.

“We now have learned that cancer cells can adapt to targeted therapies, but their repertoire of escape routes is quite limited,” Zuber said. “A better understanding of the common escape routes will allow us to predict the next effective targeted therapy, so that we are always one step ahead of the cancer cell.”