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

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.

Li M ，Liu Y ，Zhang X ，Liu J ，Wang P ... -  《-》

Comprehensive analysis of differentially expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in bladder carcinoma.

Huang M ，Zhong Z ，Lv M ，Shu J ，Tian Q ，Chen J ... -  《Oncotarget》

Comprehensive analysis of the whole coding and non-coding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma.

Recently, accumulating evidence has demonstrated that non-coding RNAs (ncRNAs) play a vital role in oncogenicity. Nevertheless, the regulatory mechanisms and functions remain poorly understood, especially for lncRNAs and circRNAs. In this study, we simultaneously detected, for the first time, the expression profiles of the whole transcriptome, including miRNA, circRNA and lncRNA + mRNA, in five pairs of laryngeal squamous cell carcinoma (LSCC) and matched non-carcinoma tissues by microarrays. Five miRNAs, four circRNAs, three lncRNAs and five mRNAs that were dysregulated were selected to confirm the verification of the microarray data by quantitative real-time PCR (qRT-PCR) in 20 pairs of LSCC samples. We constructed LSCC-related competing endogenous RNA (ceRNA) networks of lncRNAs and circRNAs (circRNA or lncRNA-miRNA-mRNA) respectively. Functional annotation revealed the lncRNA-mediated ceRNA network were enriched for genes involved in the tumor-associated pathways. Hsa_circ_0033988 with the highest degree in the circRNA-mediated ceRNA network was associated with fatty acid degradation, which was responsible for the depletion of fat in tumor-associated cachexia. Finally, to clarify the ncRNA co-regulation mechanism, we constructed a circRNA-lncRNA co-regulated network by integrating the above two networks and identified 9 modules for further study. A subnetwork of module 2 with the most dysregulated microRNAs was extracted to establish the ncRNA-involved TGF-β-associated pathway. In conclusion, our findings provide a high-throughput microarray data of the coding and non-coding RNAs and establish the foundation for further functional research on the ceRNA regulatory mechanism of non-coding RNAs in LSCC.

Zhao R ，Li FQ ，Tian LL ，Shang DS ，Guo Y ，Zhang JR ，Liu M ... -  《-》

High‑throughput sequencing reveals differentially expressed lncRNAs and circRNAs, and their associated functional network, in human hypertrophic scars.

Li M ，Wang J ，Liu D ，Huang H ... -  《-》

Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in mouse germline stem cells.

Li X ，Ao J ，Wu J 《Oncotarget》