Transcriptomic analysis of high-throughput sequencing about circRNA, lncRNA and mRNA in bladder cancer

Abstract An increasing number of studies have revealed that long noncoding RNA (lncRNA) and circular RNA (circRNA) participate in the carcinogenesis and progression of tumors. However, most of these noncoding RNAs are of unknown function or without annotation. We carried out high-throughput sequencing to investigate the differential expression of lncRNAs and circRNAs and their biological functions in four coupled bladder cancer and adjacent noncancerous tissues. We identified significant differentially expressed transcripts and genes and acquired their annotations from the RefSeq and circBase databases, then confirmed the expression of randomly selected RNAs with quantitative real-time PCR. We also constructed a coding-noncoding co-expression (CNC) network and a competing endogenous RNA (ceRNA) network to predict the functions of these RNAs using well-studied protein-coding mRNA. Compared with adjacent tissues, 56 lncRNAs, 34 circRNAs and 467 protein-coding mRNAs were upregulated while 32 lncRNAs, 84 circRNAs and 326 protein-coding mRNAs were downregulated in cancer tissues. Co-expression analysis showed that expression of LINC00885 were correlated with GATA3 expression. The ceRNA network indicated that lncRNA MIR194-2HG , AATBC and circRNA PGM5 could harbor bladder cancer-related microRNA (miRNA) recognition elements. We performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to ascertain the biological function of significantly dysregulated genes. Cell cycle and cell division pathways related to proliferation and apoptosis were obvious in enriched terms. Comprehensive analysis indicated that the dysregulated lncRNAs and circRNAs could participate in the genesis and progression of bladder cancer. Our approach may therefore be valuable for detecting novel transcripts, discovering new biomarkers for bladder cancer and expounding the pathogenic mechanisms of this disease.