Researchers engineer a tool to dismantle cancer's RNA-built growth hubs

In a city, coworking hubs bring people and ideas together. Inside cancer cells, similar hubs form-but instead of fueling progress, they supercharge disease. That's what researchers at the Texas A&M University Health Science Center (Texas A&M Health) have discovered inside the cells of a rare and aggressive kidney cancer.

Their new study, published in Nature Communications, shows how RNA-normally just a messenger-gets hijacked to build liquid-like "droplet hubs" in the nucleus. These hubs act as command centers, switching on growth-promoting genes. But the team didn't stop at observing this-they created a molecular switch to dissolve the hubs on demand, cutting off the cancer's growth at its source.

RNA as a construction worker

The cancer they're investigating, called translocation renal cell carcinoma (tRCC), affects children and young adults and currently has almost no effective therapies. It is caused by TFE3 oncofusions-hybrid genes formed when chromosomes swap and fuse in the wrong places.

Until now, how these fusion proteins drove such aggressive tumors remained unclear. The Texas A&M team found that these fusions enlist RNA as structural scaffolds. Unlike their traditional role as passive messengers, these RNAs now actively assemble droplets, known as condensates, that cluster key molecules together. These droplets become transcriptional hubs-hotspots that switch on cancer-promoting genes.

"RNA itself is not just a passive messenger, but an active player that helps build these condensates," said Yun Huang, PhD, professor at the Texas A&M Health Institute of Biosciences and Technology and senior author.

The researchers also discovered that an RNA-binding protein called PSPC1 acts as a stabilizer, reinforcing the droplets and making them even more powerful engines for tumor growth.

How they cracked the code

To untangle this hidden process, the team leaned on some of today's most advanced tools in molecular biology:

• CRISPR gene editing to "tag" fusion proteins in patient-derived cancer cells, letting them track exactly where these proteins go.
• SLAM-seq, a next-generation sequencing method that measures newly made RNA, showing which genes are switched on or off as the droplets form.
• CUT&Tag and RIP-seq to map where the fusion proteins bind DNA and RNA, revealing their precise targets.
• Proteomics to catalog the proteins pulled into the droplets-pinpointing PSPC1 as a key partner.

By layering these techniques, the researchers built the clearest picture yet of how TFE3 oncofusions hijack RNA to build cancer's growth hubs.

Dissolving the hubs that drive tumors

Discovery alone wasn't enough. The team wanted to know: If the droplets are cancer's engine, can we shut them down?

To test this, they engineered a nanobody-based chemogenetic tool-essentially a designer molecular switch. Here's how it works:

• A nanobody (a miniature antibody fragment) is fused with a dissolver protein.
• The nanobody locks onto the cancer-driving fusion proteins.
• When activated by a chemical trigger, the dissolver melts the droplets, breaking the hubs apart.

The result? Tumor growth ground to a halt in both lab-grown cancer cells and mouse models.

"This is exciting because tRCC has very few effective treatment options today," said Yubin Zhou, MD, PhD, professor and director of the Center for Translational Cancer Research. "Targeting condensate formation gives us a brand-new angle to attack the cancer, one that traditional drugs have not addressed. It opens the door to therapies that are much more precise and potentially less toxic."

Beyond tRCC: A blueprint for new therapies

For the research team, the most powerful part of the study wasn't just watching RNA build these hubs but seeing that they could be dismantled.

"By mapping how these fusion proteins interact with RNA and other cellular partners, we are not only explaining why this cancer is so aggressive but also revealing weak spots that can be therapeutically exploited," said Lei Guo, PhD, research assistant professor at the Institute of Biosciences and Technology.

Because many pediatric cancers are also driven by fusion proteins, the implications extend far beyond tRCC. A tool that can dissolve these condensates could represent a general strategy to cut off cancer's engine rooms at the source.

Why this matters

tRCC makes up nearly 30% of renal cancers in children and adolescents, but for patients and families, treatment options are limited and outcomes are often poor. This research not only explains how the cancer organizes its growth machinery but also offers a tangible way to stop it.

This research highlights the power of fundamental science to generate new hope for young patients facing devastating diseases."

Yun Huang, PhD, Professor, Institute of Biosciences and Technology, Texas A&M Health

Just like cutting power to a coworking hub halts all the activity inside, dissolving cancer's "droplet hubs" could shut down its ability to grow. By showing how RNA actively builds these hubs-and by designing a way to dismantle their scaffolding-Texas A&M Health scientists have uncovered both a weakness and a new path toward treating one of the toughest childhood cancers.