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Differentially expressed long non-coding RNAs and mRNAs in plasma of clear cell renal cell carcinoma patients based on microarray and bioinformatic analysis

ABSTRACT: Differentially expressed long non-coding RNAs and mRNAs in plasma of clear cell renal cell carcinoma patients based on microarray and bioinformatic analysis

PROVIDER: PRJNA633809 | ENA |

REPOSITORIES: ENA

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Project description:Objective: The diagnostic roles of long non-coding RNAs (lncRNAs) in clear cell renal cell carcinoma (ccRCC) are still not well defined. We aimed to identify differentially expressed lncRNAs and mRNAs in plasma of ccRCC patients and health controls systematically. Methods: Expression profile of lncRNAs and mRNAs in plasma from ccRCC patients and healthy controls was analyzed by microarray assay. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway based approaches were used to investigate biological functions and signaling pathways affected by the differentially expressed mRNAs. SOCS2-AS1 was selected for validation using Real-Time PCR. The differentially expressed genes were further compared with E-MTAB-1830 datasets by Venn and NetworkAnalyst website. The expression level and overall survival (OS) of differentially expressed mRNAs were analyzed in GEPIA and ULCAN website. Results: Compared with healthy controls, a total of 3,664 differentially expressed lncRNAs were revealed by heatmap and volcano-plot, including up-regulation in 1,511 and down-regulation in 2,153 (fold change ≥ 2 and P < 0.05), respectively. And differential expression was noticed in 2,268 mRNAs, including up-regulation in 932 mRNAs and down-regulation in 1,336 mRNAs, respectively (fold change ≥ 2 and P < 0.05). Pathways analysis based on deregulated mRNAs were mainly involved in melanogenesis and Hippo signaling pathway (P < 0.05). The expression of SOCS2-AS1 was down in ccRCC plasma and tissues, as well as in cell lines, which was the same as the results of lncRNA microarray. Compared with the E-MTAB-1830 gene expression profiles, we identified 18 lncRNAs, and 87 mRNAs were differently expressed in both plasma and neoplastic tissues of ccRCC. Ten mRNAs (EPB41L4B, CCND1, GGT1, CGNL1, CYSLTR1, PLAUR, UGT3A1, PROM2, MUC12, and PCK1) were correlated with the overall survival (OS) rate in ccRCC patients based on the GEPIA and ULCAN website.Conclusions: We first reported differentially expressed lncRNAs in ccRCC patient and healthy control systemically. Combined with the published dataset, we identified several differentially expressed lncRNAs and mRNAs which might to be diagnostic or prognostic markers. The biological functions of those lncRNAs and mRNAs should be further validated. Taken together, this study provided the basis for future treatment of ccRCC and novel insights into cancer biology.

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Differentially expressed long non-coding RNAs and mRNAs in plasma of clear cell renal cell carcinoma patients based on microarray and bioinformatic analysis

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