Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma

Systems biology approaches can help understand pathogenesis of complex human diseases like cancers for identification of potential new therapeutic targets. Here in this study, we performed genome-wide screening for mRNA and lncRNA profiles in esophageal cancer to identify the novel cancer-related mRNA and lncRNA in esophageal squamous cell carcinoma (ESCC). We identified 3000 up-regulated/2517 down-regulated mRNAs and 402 up-regulated/741 down-regulated lncRNAs. Further functional analysis revealed differentially expressed genes (DEGs) of mRNA and lncRNA are related to different pathways. mRNA pathways are mainly involved in cell cycles while lncRNA pathways are for regulation and metabolic procession. Differentially expressed mRNAs/lncRNAs were validated with qPCR. At last, mRNA and lncRNA co-expression network were built and highly-connected networks were identified, which may provide a mechanism of mRNA expression regulation by lncRNA. To our knowledge, this is the first study to explore the co-expression networks and the lncRNA-mRNA networks could be therapeutic targets for ESCC treatments. we performed genome-wide screening for mRNA and lncRNA profiles in 7 pairs (S1 nomal S2 Tumor, S1 and S2 paired, S3 normal S4 tumor, S3 and S4 paired, etc.) of esophageal cancer and normal tissues to identify the novel cancer-related mRNA and lncRNA in ESCC. Then we build a co-expression network for all of these mRNA and lncRNA to build the relationship between mRNA and lncRNA.