Large-scale characterization of alternative splicing in lung cancer

Abstract

At the present time, lung cancer remains the main cause of cancer-related death worldwide. The high mortality rate is due to a late detection of the disease. Lung cancer is normally detected in the late stages when therapies are less effective and therefore the survival is very low. Among many molecular functions investigated in recent times, RNA splicing has proved to be a key process promoting. Splicing is a fundamental step in RNA processing and several studies have described the alteration of the RNA splicing machinery as a novel hallmark of cancer. Our aim in this work was to elucidate the relevance of alternative splicing in lung carcinogenesis. During this research project, we first evaluated two microarray platforms in order to determine which one was more accurate in the identification of differentially spliced events. This approach allowed us to detect novel splicing events regulated by the proto-oncogene SRSF1. Moreover, the application of this technique in primary tumors from patients with non-small cell lung cancer allowed us to detect genes alternatively spliced, and to evaluate their contribution to the malignant features of lung cancer cells. The results obtained during this study clearly suggest that the combination of the GeneSplice microarrays from Affymetrix and the ExonPointer algorithm constitutes a robust method for the identification of novel splicing cassette events in biological samples. This technique allowed us to categorize novel targets of the splicing factor SRSF1. We further showed that some of these events were relevant in clinical samples. We also studied the role of PRRC2C splice variants in tumor progression, confirming that the alternative splicing of this gene has a role in cells proliferation. Thus, these results helped to better understand the participation of SRSF1 in lung cancer biology. Furthermore, we identified several splicing events in primary lung tumors, many of which were not described before. Functional studies of the splice variants permitted us to describe for the first time different roles of ESYT2 isoforms in cytoskeletal and endocytosis dynamics. Finally, we found that many of the lung-cancer associated events were regulated by QKI, a RNA-binding protein that is downregulated and has a prognosis value in lung cancer.