Identification of alternative splicing events regulated by the oncogenic factor SRSF1 in lung cancer
de Miguel, Fernando J * Sharma, Ravi Datta * Pajares, Maria Jose Montuenga, Luis M × Rubio, Angel Pio, Ruben #
Cancer Research vol:74 issue:4 pages:1105-15
Abnormal alternative splicing has been associated with cancer. Genome-wide microarrays can be used to detect differential splicing events. In this study, we have developed ExonPointer, an algorithm that uses data from exon and junction probes to identify annotated cassette exons. We used the algorithm to profile differential splicing events in lung adenocarcinoma A549 cells after down-regulation of the oncogenic serine/arginine-rich splicing factor 1 (SRSF1). Data were generated using Agilent and Affymetrix microarray platforms. The PCR-based validation rate of the top 20 ranked genes was 60% and 100%, respectively. Functional enrichment analyses found a substantial number of splicing events in genes related to RNA metabolism. These analyses also identified genes associated with cancer and developmental and hereditary disorders, as well as biological processes such as cell division, apoptosis and proliferation. Most of the top 20 ranked genes were validated in other adenocarcinoma and squamous cell lung cancer cells, with validation rates of 80-95% and 70-75%, respectively. Moreover, the analysis allowed us to identify four genes, ATP11C, IQCB1, TUBD1, PRRC2C, with a significantly different pattern of alternative splicing in primary non-small cell lung tumors compared to normal lung tissue. In the case of PRRC2C (proline-rich coiled-coil 2C), SRSF1 down-regulation led to the skipping of an exon overexpressed in primary lung tumors. Specific siRNA down-regulation of the exon-containing variant significantly reduced cell growth. In conclusion, using a novel analytical tool, we have identified new splicing events regulated by the oncogenic splicing factor SRSF1 in lung cancer.