A pro-tumor environment in the cell can encourage a gene to produce an alternative form of RNA that enables cancer to spread, report researchers at the Medical University of South Carolina in the journal Nature Cell Biology.

MUSC researchers determined for the first time how an alternative form of RNA that does not encode a protein is formed and encourages tumors to spread. The finding may explain why certain breast and lung cancers grow and spread.

Two different kinds of RNA interact with each other to promote the growth of cancer. Neither RNA provides the code to make a protein, as many RNAs do. Instead, they push epithelial cells in the lung and breast to form tumors. Understanding how non-coding RNAs such as these work is a key challenge facing biologists around the world, because they could become an important source of new biomarkers and drug targets.

In cells, genes are expressed when DNA is copied to RNA to provide the code for a protein. Right after DNA is copied, the RNA must be cut and assembled into its final form. Sometimes it is cut and assembled in several different ways, in a process known as alternative splicing. These alternative forms of RNA can provide the code for slightly different proteins, but scientists are discovering that many types of RNA do not, instead performing different functions. Cells use different types of RNA to control how much of a given protein is made, which then helps control how cells behave. MicroRNAs, for example, do not provide the code for proteins, but instead home in on those that do and help degrade them.

It is another class, called long non-coding RNAs (lncRNA), that are of particular interest to Philip H. Howe, PhD, chairman of the Department of Biochemistry and Molecular Biology at MUSC and the Hans and Helen Koebig Endowed Chair in Oncology at the MUSC Hollings Cancer Center.

Less is known about this type of RNA than the many others. Howe and his research team found that the RNA that provides the code for a protein called PNUTS can be spliced into its alternative form, an lncRNA that contributes to cancer progression. The PNUTS lncRNA does not encode a protein, but rather soaks up like a sponge a certain microRNA that prevents cells in the lung and breast from becoming more like tumor cells.

Howe’s group connected a number of dots to explain how this happens. First, they found that breast cancer cells had more PNUTS lncRNA content than normal breast cells, which was a good initial sign that the lncRNA could be involved with cancer development. Those cells were also more likely to form tumors that spread.

They next examined a protein that suppresses alternative splicing and that they thought could prevent this lncRNA from forming. Importantly, they knew that TGF-beta, a molecule that is released in large amounts by tumor cells to help them grow and spread, could prevent this suppressive protein from doing its job. In other words, TGF-beta could potentially allow alternate forms of RNA such as lncRNA to be made. Computer models predicted that this would happen, but the researchers ran experiments to confirm their suspicions. In lung and breast cancer cells, specially-designed RNA tracking probes confirmed that when the suppressive protein was removed from those cells, they had more PNUTS lncRNA. When those cells were exposed to TGF-beta over time, the suppressive protein was also blocked, and PNUTS lncRNA was made in increasing amounts.

Yet the group wanted to confirm exactly how PNUTS lncRNA could encourage tumors to form. Additional computer simulations predicted that, based on its genetic sequence, there were seven potential locations on the PNUTS lncRNA where a microRNA called microRNA-205 could bind. This microRNA helps reduce the levels of a protein called ZEB1 that encourages cells to unstick from one another and spread like tumors. As predicted, without those potential binding loca