Dataset Information

The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma.

ABSTRACT: Long noncoding RNAs (lncRNAs) are pervasively transcribed and play a key role in tumorigenesis. The aim of the study was to determine the lncRNA expression profile in astrocytomas and to assess its potential clinical value. We performed a three-step analysis to establish the lncRNA profile for astrocytoma: a) the lncRNA expression was examined on 3 astrocytomas as well as 3 NATs (normal adjacent tissues) using the lncRNA microarray; b) the top-hits were validated in 40 astrocytomas (WHO grade II-IV) by quantitative real time-PCR (qRT-PCR); c) the hits with significant differences were re-evaluated using qRT-PCR in 90 astrocytomas. Finally, 7 lncRNAs were found to have a significantly different expression profile in astrocytoma samples compared to the NAT samples. Unsupervised clustering analysis further revealed the potential of the 7-lncRNA profile to differentiate between tumors and NAT samples. The upregulation of ENST00000545440 and NR_002809 was associated with advanced clinical stages of astrocytoma. Using Kaplan-Meier survival analysis, we showed that the low expression of BC002811 or XLOC_010967, or the high expression of NR_002809 was significantly associated with poor patient survival. Moreover, Cox proportional hazard regression analysis revealed that this prognostic impact was independent of other clinicopathological factors. Our results indicate that the lncRNA profile may be a potential prognostic biomarker for the prediction of post-surgical outcomes.

SUBMITTER: Zhi F

PROVIDER: S-EPMC4529097 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma.

Zhi Feng F Wang Qiang Q Xue Lian L Shao Naiyuan N Wang Rong R Deng Danni D Wang Suinuan S Xia Xiwei X Yang Yilin Y

PloS one 20150807 8

Long noncoding RNAs (lncRNAs) are pervasively transcribed and play a key role in tumorigenesis. The aim of the study was to determine the lncRNA expression profile in astrocytomas and to assess its potential clinical value. We performed a three-step analysis to establish the lncRNA profile for astrocytoma: a) the lncRNA expression was examined on 3 astrocytomas as well as 3 NATs (normal adjacent tissues) using the lncRNA microarray; b) the top-hits were validated in 40 astrocytomas (WHO grade II ...[more]

PMID: 26252651

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Project description:The aim of the present study was to identify long non-coding RNA (lncRNA)-based prognostic biomarkers in papillary renal cell carcinoma (pRCC). lncRNA expression data and corresponding clinical data from patients with pRCC were obtained from The Cancer Genome Atlas. R software and packages were used for data analysis. Univariate Cox regression analysis and least absolute shrinkage and selection operator regression were performed to identify key lncRNAs, which were then used to construct a prognostic model using multivariate Cox regression analysis. Patients were divided into high- and low-risk groups, and Kaplan-Meier (KM) survival curves and time-dependent receiver operating characteristic (ROC) curves were plotted. The C-index was calculated to estimate the model's prognostic power. The hazard ratio (HR), 95% confidence interval (CI), and statistical significance of each key lncRNA were also calculated by multivariate Cox regression. Based on the result of the multivariate Cox regression analysis, KM survival plots were plotted for each significantly associated lncRNA. The subcellular locations of the prognostic biomarkers were predicted using lncRNAMap and lncLocator. A total of 17 lncRNA signatures were identified as key lncRNAs. Overall survival rate was significantly higher in the low-risk group compared with the high-risk group. The areas under the ROC curve were 0.93 (3-year ROC) and 0.902 (5-year ROC), and the C-index was 0.915. A forest plot was used to illustrate the HR and 95% CI of key lncRNAs. KM survival analysis revealed the prognostic significance of two protective biomarkers, AC024022.1 and GAS6-AS1, and three adverse biomarkers, AC087379.2, AL352984.1, and AL499627.1. It was predicted that AC024022.1 and AC087379.2 may be located in the cytoplasm and GAS6-AS1 may be located in the cytosol. The present study may contribute to the management of pRCC and serve as a foundation for further investigations into the underlying mechanism of tumorigenesis and progression of pRCC.

Dataset Information

The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma.

Publications

The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma.

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