How Rearranged Genes Promote Kidney Cancer Progression

In findings from a study led by investigators at the Johns Hopkins Kimmel Cancer Center and the Johns Hopkins Bloomberg School of Public Health, scientists report that they have learned how certain combinations of rearranged genes can promote the progression of a rare type of kidney cancer. The work was supported by the National Institutes of Health.

The researchers demonstrated that proteins made from these rearranged, so-called fusion genes form tiny liquid droplets inside the cell, where they turn on and off other genes that promote cancer growth and spread.

Disrupting these droplets prevents the cancer genes from being activated. Using a similar strategy in patients, they say, could lead to new therapies for a cancer that currently has no standard treatment. The findings of their study were published April 22 in Cell Reports.

“Other cancers, such as Ewing sarcoma and leukemia are caused by fusion genes as well,” says senior author Danfeng “Dani” Cai, Ph.D., assistant professor of biochemistry and molecular biology at the Johns Hopkins Bloomberg School of Public Health. “It’s possible that these fusion genes form similar droplets, or condensates, that regulate genes in these cancers and could react to similar treatment strategies.”

The rare kidney cancer, known as translocation renal cell carcinoma, develops when a chromosome rearranges, swapping a DNA segment that combines the tail end of the TFE3 gene with the beginning of one of several other genes (such as PRCC, NONO and SFPQ). This essentially forms new TFE3 fusion gene versions that code for and make TFE3 fusion proteins not normally found in healthy cells. Scientists have known that these TFE3 fusion proteins cause this rare kidney cancer, but they were not sure how they drove cancer to form.

“There are about 20 fusion partners of TFE3 in translocation renal cell carcinoma, but we mainly focused on the two most common ones (NONO and SFPQ), making up 40% of all TFE3 fusions,” Cai says.

To study how the TFE3 fusion proteins drive cancer progression, Cai and her team attached a glowing tag on the TFE3 fusion proteins in cells from patients with kidney cancer. Through a microscope, they saw that these fusion proteins form dots in the nucleus of the cells, where the cell stores its DNA. They observed these proteins forming liquid “condensates” — concentrated molecules interacting together in a small space performing a specific cell process — something Cai’s laboratory specializes in. Next, the team noted that a marker protein typically found on active genes and another protein that turns on genes also appeared inside these droplets. These findings suggest that TFE3 fusion proteins interact with DNA and may turn on genes.

DNA is condensed and packaged into chromatin in the cell that resembles beads on a string. Where the string is tightly wound around the bead, the genes are turned off, and where there is an open string between beads, the genes can be more easily accessed and turned on.

Cai partnered with Eneda Toska, Ph.D., an assistant professor of oncology at the Johns Hopkins Kimmel Cancer Center, to determine more specifically how the TFE3 fusion proteins interact with DNA, and what genes they regulate.

“We found that these fusion proteins open and close different sites on the chromatin by making chemical modifications,” says Toska. “They bind, regulate and redesign the chromosome landscape, interacting with target genes that promote cell proliferation and movement — functions that cancer needs to grow and spread.”

Finally, the researchers edited out different parts of the TFE3 fusion proteins to see which pieces were important for maintaining the liquid condensate structure. When they removed a small segment that creates a coiled-coil (coil within a coil) shape in the part that connects the TFE3 tail to the other protein component, the TFE3 fusion proteins no longer formed the liquid droplets, and they no longer turned on cancer-promoting genes.

“Individually, all the protein components found in the TFE3 fusions, including full-length TFE3, NONO and SFPQ, are typically involved in the cell machinery that turns on genes to make proteins,” says Cai. “However, we found when in the form of these fusion proteins, they acquire an even stronger ability to control what genes get turned on.”

In future work, the research team hopes to identify other components in the liquid condensates that drive the cancer, which would allow them to screen for drugs or small molecules that can disrupt these structures as ways to potentially treat the cancer.

Reference: So CL, Lee YJ, Vokshi BH, et al. TFE3 fusion oncoprotein condensates drive transcriptional reprogramming and cancer progression in translocation renal cell carcinoma. Cell Rep. 2025;44(4). doi: 10.1016/j.celrep.2025.115539

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