PO-358 CELf2 at the core of a prognostic alternative splicing signature in colorectal cancer

Abstract

IntroductionColorectal carcinoma (CRC) is a common malignancy, being the fourth cause of cancer-related deaths worldwide. Dysregulation of alternative splicing (AS) is a molecular hallmark of cancer, having been associated with initiation and development of CRC. However, the global patterns of dysregulation of AS and its association to prognosis in CRC remain largely unexplored.Material and methodsClinically annotated tumour transcriptomes from The Cancer Genome Atlas (TCGA) were analysed in order to identify AS events with prognostic value in CRC. DNA methylation patterns in their vicinity were explored using TCGA methylation array data. A local CRC patient sample cohort and CRC cell lines were used in the experimental validation of the TCGA-derived AS prognostic signatures.Results and discussionsWe revealed a novel gene expression-independent AS signature, with prognostic value additional to that assigned to pathological stage and age, dominated by three AS events in the mRNA complement of CELF2, a gene encoding for RNA-binding proteins and reportedly an onco-suppressor in CRC. Those events relate to the expression of three isoforms with alternative promoter usage and potentially distinct sub-cellular localization and functions in RNA processing, namely AS regulation, mRNA edition and translation inhibition. We corroborated the prognostic value of alterations in CELF2 isoform expression using clinically annotated CRC samples from the local biobank. Further analyses in primary tumour-derived and metastasis-derived colon cancer cell lines confirmed those alterations as markers of increased tumour malignancy. Moreover, analyses of CRC TCGA DNA methylation profiles revealed significant differences in methylation in the vicinity of the three prognostic AS events in CELF2 associated with expression levels of the involved isoforms in matched patients.ConclusionOur analyses suggest that a switch in the relative expression of CELF2 isoforms associates with prognosis in CRC. That switch dominates a gene expression-independent AS signature with prognostic value in CRC, representing a novel biomarker potentially usable in the prospective selection of patients for adjuvant therapy. We hypothesise that modifications in the dynamic balance between nuclear and cytoplasmic activities is the functional link between AS and the CELF2 prognostic value. This may be explained, at least in part, by local epigenetic alterations, given the observed changes in promoter methylation patterns in tumour samples from patients with poorer prognosis.