RNA components of the spliceosome are regulatory.

Gene transcription produces pre-messenger RNAs (pre-mRNA) that are composed of exons and introns as the first RNA species. Subsequent splicing consists of the deletion of introns and the specific excision of some of the exons. Depending on the exons excised, different mature mRNAs arising from the same pre-mRNA will be translated into different proteins, allowing one gene to encode several proteins. The spliceosome is the cell machinery that is in charge of all the splicing activity, and thus is central to the regulation of gene expression. RNA splicing typically depends upon both basal and regulatory components. Whereas the basal proteins are necessary for any splicing event, the regulatory elements modulate the process and lead to alternative splicing. However, recent studies suggest that some of the basal components may have regulatory function in pathological conditions. In addition to proteins, the spliceosome is also composed of small nuclear RNAs (snRNAs) that are responsible for splice site recognition and were long thought to be basal elements of the spliceosome. However, it was recently demonstrated that snRNAs are mutated in cancer^{1, 2}. The Bradley lab (Public Health Sciences and Basic Sciences Divisions) hypothesized that these snRNAs may also have regulatory functions and recently published the results of their work in Genome Research³. The study was led by Dr. Heidi Dvinge, who tragically passed away recently . She was a driving force in her field and an early proponent of the now widely accepted hypothesis that RNA splicing factors play a major role in cancer^{4, 5}.

In this recent publication, Dr. Dvinge and colleagues first sought to understand the pattern of expression of these snRNAs throughout a wide range of healthy tissues at different developmental stages. They observed a tremendous variability in snRNA expression depending on the tissue, some of which have specific snRNA signatures. Interestingly, when analyzing breast cancer samples, they noted that triple-negative breast tumors can be isolated from other tumor subtypes and regrouped in subpopulations based on snRNA expression, suggesting that these snRNA have a major role in tumor evolution.

As snRNAs are required for splicing, the authors reasoned that downregulation of snRNAs should lead to widespread failure of splicing (intron retention). However, when knocking down snRNAs in MCF-7 cells (breast cancer cells), most splicing changes affected only one exon. Intron retention was limited to knockdown of some of the snRNAs, but not all of them. These data strongly support Heidi’s hypothesis of regulatory functions for snRNAs.

To assess the physiopathological relevance of their findings, the researchers deep sequenced 136 invasive breast carcinomas and compared the naturally occurring splicing anomalies in those cancers to the splicing errors associated with snRNA knock-down in the MCF-7 cells. Many splicing anomalies were concordant with snRNA expression patterns in these tumor samples.

These results should change how the field thinks of the normal roles of snRNAs in splicing, explained Dr. Bradley: “Heidi’s findings upend the traditional view of spliceosomal RNAs as essential for splicing catalysis, but unimportant for splicing regulation. Her discovery that spliceosomal RNAs regulate splicing in both normal and cancerous tissues is particularly important given the recent discovery that a spliceosomal RNA is recurrently mutated in several cancer types, suggesting that these mutations drive cancer development."

This work was supported by the Seattle Tumor Translational Research program and U.S. Department of Defense Breast Cancer Research Program.

Fred Hutch/UW Cancer Consortium members Drs. Porter and Bradley contributed to this research.

1. Suzuki H. et al. 2019. Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature. 574(7780):707-711. doi: 10.1038/s41586-019-1650-0.
2. Shuai S. et al. 2019. The U1 spliceosomal RNA is recurrently mutated in multiple cancers. Nature. doi: 10.1038/s41586-019-1651-z.
3. Dvinge H, Guenthoer J, Porter PL, Bradley RK. 2019. RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing. Genome Res. 29(10):1591-1604. doi:10.1101/gr.246678.118.
4. Dvinge et al. 2016. RNA splicing factors as oncoproteins and tumour suppressors. Nat Rev Cancer. 16(7):413-30. doi: 10.1038/nrc.2016.51.
5. Dvinge H., Bradley RK. 2015. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 7(1):45. doi: 10.1186/s13073-015-0168-9.