Prognosis of clear cell renal cell carcinoma (ccRCC) based on a six-lncRNA-based risk score: an investigation based on RNA-sequencing data

Autor: Jiang-hui Zeng, Wei Lu, Liang Liang, Gang Chen, Hui-hua Lan, Xiu-Yun Liang, Xu Zhu
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Zdroj: Journal of Translational Medicine, Vol 17, Iss 1, Pp 1-20 (2019)
Druh dokumentu: article
ISSN: 1479-5876
DOI: 10.1186/s12967-019-2032-y
Popis: Abstract Background The scientific understanding of long non-coding RNAs (lncRNAs) has improved in recent decades. Nevertheless, there has been little research into the role that lncRNAs play in clear cell renal cell carcinoma (ccRCC). More lncRNAs are assumed to influence the progression of ccRCC via their own molecular mechanisms. Methods This study investigated the prognostic significance of differentially expressed lncRNAs by mining high-throughput lncRNA-sequencing data from The Cancer Genome Atlas (TCGA) containing 13,198 lncRNAs from 539 patients. Differentially expressed lncRNAs were assessed using the R packages edgeR and DESeq. The prognostic significance of lncRNAs was measured using univariate Cox proportional hazards regression. ccRCC patients were then categorized into high- and low-score cohorts based on the cumulative distribution curve inflection point the of risk score, which was generated by the multivariate Cox regression model. Samples from the TCGA dataset were divided into training and validation subsets to verify the prognostic risk model. Bioinformatics methods, gene set enrichment analysis, and protein–protein interaction networks, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were subsequently used. Results It was found that the risk score based on 6 novel lncRNAs (CTA-384D8.35, CTD-2263F21.1, LINC01510, RP11-352G9.1, RP11-395B7.2, RP11-426C22.4) exhibited superior prognostic value for ccRCC. Moreover, we categorized the cases into two groups (high-risk and low-risk), and also examined related pathways and genetic differences between them. Kaplan–Meier curves indicated that the median survival time of patients in the high-risk group was 73.5 months, much shorter than that of the low-risk group (112.6 months; P
Databáze: Directory of Open Access Journals
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