If a distribution center fails to consign rejects to the disposal bin, the rejects can pile up and disrupt the flow of satisfactory goods—whether the flow is in an Amazon warehouse or a living cell. Unfortunately, in a living cell, the accumulation of reject proteins can be as obscure as it is devastating. Dozens of diseases have been attributed to the buildup of reject proteins, or misfolded proteins, and the mechanisms behind the molecular backups are seldom as obvious as a stalled forklift or stuck conveyor belt.

In one of these diseases, a proteinopathy called mucin-1 kidney disease (MKD), the addition of a single letter in the gene for the mucin-1 protein can lead to the production of MUC1-fs, a truncated, misfolded version of mucin-1. It accumulates in kidney cells, killing them. Eventually, MKD culminates in kidney failure.

To learn more about MKD, researchers from the Broad Institute and Brigham and Women’s Hospital conducted a series of on-site inspections. The researchers, led by physician scientist Anna Greka, MD, PhD, examined human kidney cells, kidney organoids, and animal models of MKD. In every instance, the researchers focused on a cellular shipping network called the secretory pathway, which delivers proteins either to the cell surface or one of the cell’s protein-disposal systems.

Greka and colleagues found that in kidney cells glutted with MUC1-fs, the cells’ failure to remove the misfolded protein could be traced to a specific molecular step in the secretory pathway—the packing of MUC1-fs into vesicles containing a cargo receptor called TMED9. Trapped in the TMED9-enriched vesicles, MUC1-fs fails to reach the lysosome, a sort of recycling bin for faulty proteins.

Remarkably, Greka and colleagues also determined that TMED9 could be induced to let go of MUC1-fs, which would then make its way to the lysosome for destruction. TMED9, the scientists observed, loosens its grip on MUC1-fs when it binds to BRD4780, which is a small molecule from a compound library called the Broad Drug Repurposing Hub.

BRD4780 is a failed blood pressure drug. It could, however, help relieve some of the pressure imposed by misfolded proteins. That is, it could be a starting point for developing new medicines for MKD and several other toxic proteinopathies, for which no treatments are currently available.

Details about the newly discovered MKD mechanism and a potential treatment approach appeared July 25 in the journal Cell, in an article titled, “Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy.” In this article, the scientists showed that:

  • Mutant MUC1-fs is toxic to kidney cells by accumulating in TMED9-enriched vesicles.
  • BRD4780 binds cargo receptor TMED9, releases MUC1-fs, and re-routes it to lysosome.
  • MUC1-fs is cleared from kidneys of knockin mice and patient kidney organoids.

The effect of BRD4780, the article’s authors indicated, was “phenocopied by TMED9 deletion.” That is, the effect was also achieved when the scientists used CRISPR to knock out the TMED9 gene.

MKD proteinopathy reversed by redirecting misfolded MUC1-fs proteins to lysosome. [Dvela-Levitt M, et al., Cell, 2019]

“Our findings reveal BRD4780 as a promising lead for the treatment of MKD and other toxic proteinopathies,” the article’s authors concluded. “Generally, we elucidate a novel mechanism for the entrapment of misfolded proteins by cargo receptors and a strategy for their release and anterograde trafficking to the lysosome.”

MKD is a rare, inherited disease. In 2013, the genetic root of MKD (which was previously called medullary cystic kidney disease, or MCKD) was tracked down by a team led by Broad president and founding director Eric Lander and institute member and program in medical and population genetics co-director Mark Daly.

This work, which led to the identification of MUC1-fs, was extended in the current study, which sifted through the Broad Drug Repurposing Hub’s library to find any drug-like compounds that might be capable of clearing MUC1-fs from cells. Greka and colleagues found that the compound called BRD4780, eliminated MUC1-fs, left normal MUC1 untouched, and prevented kidney cells with the MKD mutation from dying.

“This is completely new biology,” Greka said. “We did not know that a cargo receptor like TMED9 could block and ultimately interfere with the destruction of a misfolded protein. And the question became, is the same biology at work in other conditions caused by a build-up of misfolded proteins?”

More than 50 diseases are considered toxic proteinopathies, including retinitis pigmentosa (RP, an inherited form of blindness where the retina degenerates) and UMOD-associated kidney disease (UKD, another rare genetic kidney disorder). Greka and her colleagues reasoned that similar problems with the secretory pathway might be to blame in at least a few of these diseases.

In in vitro experiments, the researchers saw that BRD4780 could reduce misfolded protein levels and increase cell survival in RP and UKD cells. Greka and her colleagues estimate that drugs similar to BRD4780 might reverse roughly 20 diseases where misfolded proteins become trapped early in the secretory pathway.

“Many of these disorders may tie back to the same mechanism,” Greka suggested. “Our next step is to develop a deeper understanding of cargo receptors [and] why they stop misfolded proteins from being eliminated as they should—and to figure out exactly how to develop drugs to counter them.”

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