Alternative RNA Splicing and Tumor Progression

Catalan Institution for Research and Advanced Studies (ICREA) Research Professor Eduardo Eyras, PhD, of the Computational RNA Biology Group, Pompeu Fabra University of Barcelona, spoke with Cancer Network about the emerging roles of RNA splicing variants in cancer and how they can affect tumor biology for cancer genes even in the absence of DNA-altering mutations.

Cancer Network: Normal alternative splicing allows cells to express multiple RNA and protein isoforms from a single gene. What led your team to study the role of this process in tumor progression? 

Dr. Eyras: At the time, there was already evidence that alternative splicing leads to specific functional changes and can trigger important phenotypic transitions in cells, like differentiation. In parallel with this line of evidence, we and others had observed frequent splicing changes in tumor samples compared to normal samples.

Some people had proposed that these changes were a noisy effect due to the splicing machinery being altered or becoming disarrayed in cancer. If that were true, we should find that the functional impact of those splicing changes should not matter. We would expect to find random [effect] patterns.

To test this, we measured the splicing alterations per patient, to be able to study their functional impacts in each patient. Once we had this information, we could then test whether there were any commonalities in these functional alterations, as well as any similarities with the alterations caused by mutations in the same patients.

Cancer Network: Your team found that some alternative splicing alterations can affect cancer-related proteins even in the absence of gene mutations, correct?

Dr. Eyras: In fact, what we found is that there are similar functional domains that are affected by splicing alterations or by mutations, but these tend to occur in different proteins. Protein functional domains are usually classified into families, according to their sequence and structural similarities. Different proteins may include domains from the same family, and they are generally associated to similar functions. This is experimentally known for some cases, but for most genes we can only predict this by their domain similarities.

We found frequent splicing changes that would deplete domains associated to, among other functions, apoptosis and repressors of signalling. Domains from these families were also frequently found to be mutated in the same tumor types.

However, these domains (either altered through splicing or mutations) occur in different genes and in different patients. This is very interesting, because it supports the notion that there is selection: once the alteration occurs in one patient, the other one is not necessary.

Cancer Network: So your team found a negative correlation between alternative splicing alterations and somatic cancer-driving mutations. Why might that be?

Dr. Eyras: This would support the idea that the splicing alterations are selected by the tumor. Once the alteration occurs in one patient, the other one (a mutation) is not required for the tumor to continue growing. The implication is that some splicing changes recapitulate functional alterations that are favorable to the tumor.

Cancer Network: What are the potential clinical implications of these findings?

Dr. Eyras: By identifying those splicing alterations that show evidence of being important and selected for tumor growth, one could aim to try to revert them.

There are various molecular technologies that can be explored. For instance, antisense oligonucleotides can be used to target specifically these splicing events and revert them to a normal form. Alternatively, multiple small molecule compounds could be screened in cell models of cancer to determine which ones are effective are reverting those patterns.

Additionally, some of the alternative splicing drivers may actually be linked to a mechanism of therapy resistance. This information can be used in the clinic to avoid using a therapy that is not going to be effective and search for an alternative one.

Cancer Network: What’s next?

Dr. Eyras: Most of the studies we are performing with cancer samples show that even though there is a high heterogeneity in the measurable RNA signals, there are converging patterns that reflect important mechanisms in cancer. These patterns are hard to find, as they required the development and use of specialized computational tools. Identifying the important signals among the molecular noise can be crucial for building up knowledge and technology for precision medicine.