TCGA based integrated genomic analyses of ceRNA network and novel subtypes revealing potential biomarkers for the prognosis and target therapy of tongue squamous cell carcinoma

Abstract

Objectives The study aimed to investigate the ceRNA network in biological development of Tongue Squamous Cell Carcinoma (TSCC) and to identify novel molecular subtypes of TSCC to screen potential biomarkers for target therapy and prognosis by using integrated genomic analysis based on The Cancer Genome Atlas (TCGA) database. Material and methods Data on gene expressions were downloaded from TCGA and GEO database. Differentially expressed RNAs(DERNAs) were shown by DESeq2 package in R. Functional enrichment analysis of DEmRNAs was performed using clusterprofilers in R. PPI network was established by referring to String website. Survival analysis of DERNAs was carried out by survival package in R. Interactions among mRNAs, miRNAs and lncRNAs were obtained from Starbase v3.0 and used to construct ceRNA network. Consensus Cluster Plus package was applied to identify molecular subtypes. All key genes were validated by comparing them with GEO microarray data. Statistical analyses of clinical features among different subtypes were performed using SPSS 22.0. Results A total of 2907 mRNAs (1366 up-regulated and 1541 down-regulated), 191miRNAs (98 upregulated and 93 down-regulated) and 1831 lncRNAs (1151 up-regulated and 680 downregulated) were identified from tumor and normal tissues. A ceRNA network was successfully constructed and 15 DEmRNAs, 1 DEmiRNA, 2 DElncRNAs associated with prognosis were employed. Furthermore, we firstly identified 2 molecular subtypes, basal and differentiated, and found that differentiated subtype consumed less alcohol and was related to a better overall survival. Conclusion The study constructed a ceRNA network and identified molecular subtypes of TSCC, and our findings provided a novel insight into this intractable cancer and potential therapeutic targets and prognostic indicators.