This is a schematic of the RNA-binding region of Rbfox2, shown in grey, attached to part of its natural RNA target, depicted in orange, green, blue, and red. [Yu Chen, Fan Yang, Gabriele Varani/University of Washington]
This is a schematic of the RNA-binding region of Rbfox2, shown in grey, attached to part of its natural RNA target, depicted in orange, green, blue, and red. [Yu Chen, Fan Yang, Gabriele Varani/University of Washington]

A team of researchers from the University of Washington (UW) and the University of Trento in Italy says it has engineered a protein to repress a specific cancer-promoting message within cells. The investigators published their study (“Targeted Inhibition of Oncogenic miR-21 Maturation with Designed RNA-Binding Proteins”) this week in Nature Chemical Biology.

The novel approach to protein design could also be modified to target other cellular messages and functions, said senior author and UW chemistry professor Gabriele Varani, Ph.D. “What we show here is a proving ground—a process to determine how to make the correct changes to proteins.”

For their approach, Dr. Varani and his team modified a human protein called Rbfox2, which occurs naturally in cells and binds to microRNAs (miRNAs). These small RNA molecules adjust gene expression levels in cells like a dimmer switch. Dr. Varani's group sought to engineer Rbfox2 to bind itself to a specific miRNA called miR-21, which is present in high levels in many tumors, increases the expression of cancer-promoting genes, and decreases cancer suppressors. If a protein like Rbfox2 could bind to miR-21, the researchers hypothesized, it could repress miR-21's tumor growth effects. 

But for this approach to be successful, the protein must bind to miR-21 and no other miRNA. Luckily, all RNA molecules, including miRNAs, have an inherent property that imbues them with specificity. They consist of a chain of chemical “letters,” each with a unique order or sequence. To date, no other research team had ever successfully altered a protein to bind to miRNAs.

“That is because our knowledge of protein structure is much better than our knowledge of RNA structure,” said Dr. Varani. “We historically lacked key information about how RNA folds up and how proteins bind RNA at the atomic level.” 

UW researchers relied on high-quality data on Rbfox2's structure to understand, down to single atoms, how it binds to the unique sequence of “letters” in its natural RNA targets. Then they predicted how Rbfox2's sequence would have to change to make it bind to miR-21 instead. Elegantly altering just four carefully selected amino acids made Rbfox2 shift its attachment preference to miR-21, preventing the miRNA from passing along its tumor-promoting message.

The UW team spent several years proving this, because they had to test each change individually and in combination. They also had to make sure that the modified Rbfox2 protein would bind strongly to miR-21 but not other miRNAs. miRNAs have many functions in cells, thus it would be counterproductive to repress miR-21 while disrupting other normal miRNA-mediated functions.

The researchers also engineered a second protein that should clear miR-21 from cells entirely. They did this by grafting the regions of Rbfox2 that bound to miR-21 onto a separate protein called Dicer, which normally chops RNAs into small chunks and generates functional miRNAs. But the hybrid Rbfox2-Dicer protein displayed a specific affinity to slice miR-21 into oblivion. 

Dr. Varini and his team believe that Rbfox2 could be redesigned to bind to miRNA targets other than miR-21. There are thousands of miRNAs to choose from, and many have been implicated in diseases. The key to realizing this potential would be in streamlining and automating the painstaking methods the team used to model Rbfox2's atomic-level interactions with RNA.

“This method relies on knowledge of high-quality structures,” said Dr. Varani. “That allowed us to see which alterations would change binding to the miRNA target.”

Not only would these be useful laboratory tools to study miRNA functions, but they could, in time, form the basis of new therapies to treat disease.








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