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.
Highlights
Alternative splicing is the process by which different mRNA isoforms are processed from a single primary transcript
We developed the ExonPointer algorithm to identify genome-wide differential alternative splicing events in A549 cells in which the levels of the oncogenic serine/arginine-rich splicing factor 1 (SRSF1) were downregulated with a specific siRNA
The experimental validation rates using data from both Oryzon (Agilent) and GeneSplice (Affymetrix) arrays demonstrated the efficacy of ExonPointer, GeneSplice performed noticeably better
Summary
Alternative splicing is the process by which different mRNA isoforms are processed from a single primary transcript. Estimates indicate that as many as 95% of multiexonic genes are alternatively spliced [1]. In which an exon is either retained or spliced out of the transcript, is the most common alternative splicing event in mammals, and accounts for approximately half of all events [2,3,4]. Alternative splicing has an essential role in the regulation of cell homeostasis. When this process becomes deregulated it can lead to pathologic conditions such as cancer [5,6,7,8]. Deregulation of splicing is often associated with an abnormal expression
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