Expanding the reach of proteasome inhibitors

By probing the molecular basis of proteasome inhibitor resistance in cancer cells, a Broad-led team finds new vulnerability — and compounds that exploit it.

Susanna M. Hamilton, Broad Communications
Credit: Susanna M. Hamilton, Broad Communications

A research team led by scientists at the Broad Institute has uncovered a molecular workaround that enables cancer cells to withstand an important class of drugs, known as proteasome inhibitors. The team’s findings highlight how drug sensitivity connects to cancer cells' metabolism. The study also suggests that a different drug that has been previously studied in clinical trials may provide a way to overcome resistance to proteasome inhibition by exploiting the cells' metabolic processes.  

“Using a combination of complementary, large-scale technologies, we’ve covered the full spectrum of cell and molecular biology to reveal a fundamental mechanism cells use to cope with proteasome inhibition,” said Peter Tsvetkov, a postdoctoral fellow in the Broad Institute's Cancer Program and corresponding author, along with Cancer Program director Todd Golub, on a paper describing the work in Nature Chemical Biology.

As their name suggests, proteasome inhibitors (PIs) target a key housekeeping apparatus in cells known as the proteasome, which breaks down old or worn out proteins. Drugs that block this recycling process cause proteins to build up within cancer cells, ultimately destroying the cells through a toxic state called proteotoxic stress.

The first PI was approved for clinical use in the United States more than 15 years ago. To date, these drugs are primarily used to treat a blood cancer called multiple myeloma.

“In the pharmaceutical industry, one of the pressing questions about proteasome inhibitors is whether these drugs can be made to work in other tumor types, especially solid tumors,” said Tsvetkov. “But in order to do that, we first need to understand the basic mechanisms that enable cells to adapt to and withstand the proteotoxic stresses these drugs can cause.”

For the last five years, Tsvetkov has worked to dissect the countermeasures cells use to survive proteasome inhibition, first as a postdoctoral fellow in the Whitehead Institute lab of the late Susan Lindquist and later at the Broad Institute under Golub's mentorship. In a paper published two years ago in PNAS, Tsvetkov and his Whitehead colleagues described a change in the structure of the proteasome that can lead to PI resistance across diverse cancer cell lines. Importantly, this change appears in multiple myeloma patients whose tumors do not respond to PI therapy.

Using these earlier findings as a starting point, Tsvetkov and his colleagues searched for genetic signatures that correspond to the PI-resistant state. Surprisingly, the team discovered a signature that suggests the involvement of mitochondria, the cell’s powerhouse. Further studies, including large-scale cell screening using the PRISM method, revealed that a shift in cell metabolism — from a process that takes place in the cell's cytoplasm to one that relies heavily on mitochondria — makes cells PI-resistant.

Tsvetkov, Golub, and their colleagues wondered if they could exploit this metabolic shift. They screened a library of over 4,000 chemical compounds, searching for ones that could transform PI-resistant cells into PI-sensitive ones. The team identified three compounds that could achieve this result: elesclomol and disulfiram, two sulfur-containing compounds with the unusual capability of binding to copper; and navitoclax, a compound already known to enhance the effects of proteasome inhibitors.

Elesclomol, it turns out, was originally developed as a potential cancer treatment. It reached phase 3 clinical trials as part of a combination therapy for patients with metastatic melanoma. However, it failed due to lack of efficacy.

“This drug has previously been in people, which opens up a simpler path to testing it along with proteasome inhibitors,” said Tsvetkov. “This also suggests that other similar molecules with the some of the same characteristics might also be efficacious in this setting.”

Although elesclomol has a history of clinical testing, its mechanism of action was unknown. Tsvetkov and his colleagues, including John Markley at the University of Wisconsin-Madison, determined that elesclomol directly targets a mitochondrial enzyme FDX1. They went on to show that when bound to copper, elesclomol not only blocks FDX1's activity, but is itself also activated by FDX1 to promote an unusual form of cell death that Tsvekov has informally dubbed "cuproptosis."

Bolstered by these initial results, the researchers are now working to explore the various biochemical attributes of elesclomol and related compounds. Their goal is to create a promising proof-of-concept for testing in cancer cell lines and other preclinical models that may one day help expand the clinical reach of proteasome inhibitors.

Support for this work was provided by the National Institute of General Medical Sciences, the National Institute of Neurological Disorders and Stroke, National Cancer Institute, the Multiple Myeloma Research Foundation, the Howard Hughes Medical Institute, and other sources.

Paper(s) cited

Tsvetkov P, et al. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nature Chemical Biology. Online May 27, 2019. DOI: 10.1038/s41589-019-0291-9.