Identification of <i>SYT10</i> as a potential prognostic biomarker in esophageal cancer by comprehensive analysis of a mRNA-pseudogene/lncRNA-miRNA ceRNA network

Abstract

Background: Esophageal carcinoma (ESCA) is often diagnosed at the advanced stages, has a poor survival rate and overall is one of the deadliest cancers world-wide. Recent studies have elaborated the significance of non-coding RNAs such as pseudogenes, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in cancer progression. In this study, we constructed a four-component competing endogenous RNA (ceRNA) network in ECSA and suggested an RNA with prognostic potential. Materials and methods: Expression profiles of mRNAs, pseudogenes, lncRNAs and miRNAs were collected from The Cancer Genome Atlas (TCGA) database. A ceRNA network was then constructed based on the differentiallyexpressed RNAs (DERs). KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) functional analysis and PPI (Protein-Protein Interaction) network analysis was carried out on differentially-expressed (DE) mRNAs of the ceRNA network. Survival analysis was carried out on a selection of RNAs with the highest degree centrality ranks to discover potential prognostic biomarkers. Results: A four-component ceRNA network with 529 nodes and 729 edges was constructed. The most significant GO biological process terms included positive regulation of transcription from RNA polymerase II promoter, negative regulation of transcription from RNA polymerase II promoter and positive regulation of transcription, DNA-templated. The analysis of KEGG pathways showed that DE mRNAs were significantly enriched in pathways such as pathways in cancer, PI3K-Akt signaling pathways and MicroRNAs in cancer. Among the RNAs that were found to be associated with survival, Synaptotagmin 10 (SYT10) had the highest hazard ratio and thus, proved to be a potential prognostic biomarker for ESCA. Conclusion: Our study presented a four-component ceRNA network for ESCA, and identified RNA candidates that were associated with survival of ECSA. Further experimental evaluations and precise validation studies are needed for their clinical significance and roles in the progression of ESCA.