title: Identification of alternative splicing events regulated by the oncogenic factor SRSF1 in lung cancer.
abstract: 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 downregulation of the oncogenic serine/arginine-rich splicing factor 1 (SRSF1). Data were generated using two different microarray platforms. The PCR-based validation rate of the top 20 ranked genes was 60% and 100%. 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 biologic 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% to 95% and 70% to 75%, respectively. Moreover, the analysis allowed us to identify four genes, ATP11C, IQCB1, TUBD1, and proline-rich coiled-coil 2C (PRRC2C), with a significantly different pattern of alternative splicing in primary non-small cell lung tumors compared with normal lung tissue. In the case of PRRC2C, SRSF1 downregulation led to the skipping of an exon overexpressed in primary lung tumors. Specific siRNA downregulation 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.
authors.affiliation: Authors' Affiliations: Division of Oncology, Center for Applied Medical Research (CIMA); Departments of Histology and Pathology and Biochemistry and Genetics, Schools of Science and Medicine, University of Navarra, Pamplona; and CEIT and TECNUN, University of Navarra, San Sebastian, Spain.
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: de Miguel
authors.forename: Ravi D
authors.initials: RD
authors.lastname: Sharma
authors.forename: María J
authors.initials: MJ
authors.lastname: Pajares
authors.forename: Luis M
authors.initials: LM
authors.lastname: Montuenga
authors.forename: Angel
authors.initials: A
authors.lastname: Rubio
authors.forename: Ruben
authors.initials: R
authors.lastname: Pio
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D000077192:Adenocarcinoma of Lung; D017398:Alternative Splicing / Q000187:drug effects / Q000235:genetics*; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D005091:Exons / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D046228:Microarray Analysis; D009687:Nuclear Proteins / Q000037:antagonists & inhibitors / Q000502:physiology*; D034741:RNA, Small Interfering / Q000494:pharmacology; D016601:RNA-Binding Proteins / Q000037:antagonists & inhibitors / Q000502:physiology*; D000068103:Serine-Arginine Splicing Factors
chemical_list: D009687:Nuclear Proteins; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins; D000068103:Serine-Arginine Splicing Factors