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A three-lncRNA expression signature associated with the prognosis of gastric cancer patients.

ABSTRACT: Long noncoding RNAs (lncRNAs) have emerged as essential players in gene regulation. An ever-increasing number of lncRNAs has been found to be associated with the biogenesis and prognosis of gastric cancer (GC). We aimed to develop an lncRNA signature with prognostic value for survival outcomes of GC. Using an lncRNA mining approach, we analyzed the lncRNA expression profiles of 492 GC patients from the Gene Expression Omnibus (GEO), which consisted of the GSE62254 set (N = 300) and the GSE15459 set (N = 192). The associations between the lncRNAs' expression and survival outcome were evaluated. A set of three lncRNAs (LINC01140, TGFB2-OT1, and RP11-347C12.10) was identified to significantly correlate with overall survival. These lncRNAs were then combined to form a single prognostic signature. Based on this three-lncRNA expression signature, patients in the GSE62254 set were classified into high- and low-risk subgroups with significantly different overall survival (hazard ratio [HR] = 1.93, P < 0.001) and disease-free survival (HR = 1.91, P < 0.001). Good reproducibility for the prognostic value of this lncRNA signature was confirmed in the GSE15459 set. Further analysis showed that the prognostic value of this signature was independent of some clinical characteristics. Gene set enrichment analysis indicated that high-risk scores positively related to several molecular pathways of cancer metastasis. Our results suggest that this innovative lncRNA expression signature may be a useful biomarker for the prognosis of patients with GC based on bioinformatics analysis.

SUBMITTER: Song P

PROVIDER: S-EPMC5463065 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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A three-lncRNA expression signature associated with the prognosis of gastric cancer patients.

Song Peng P Jiang Bo B Liu Zhijian Z Ding Jie J Liu Song S Guan Wenxian W

Cancer medicine 20170426 6

Long noncoding RNAs (lncRNAs) have emerged as essential players in gene regulation. An ever-increasing number of lncRNAs has been found to be associated with the biogenesis and prognosis of gastric cancer (GC). We aimed to develop an lncRNA signature with prognostic value for survival outcomes of GC. Using an lncRNA mining approach, we analyzed the lncRNA expression profiles of 492 GC patients from the Gene Expression Omnibus (GEO), which consisted of the GSE62254 set (N = 300) and the GSE15459 ...[more]

PMID: 28444881

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Project description:Long non-coding RNAs (lncRNAs) are transcripts characterized by >200 nucleotides, without validated protein production. Previous studies have demonstrated that certain lncRNAs have a critical role in the initiation and development of acute myeloid leukemia (AML). In the present study, the subtype‑specific lncRNAs in AML was identified. Following the exclusion of the subtype‑specific lncRNAs, the prognostic value of lncRNAs was investigated and a three‑lncRNA expression‑based risk score [long intergenic non‑protein coding RNA 926, family with sequence similarity 30 member A and LRRC75A antisense RNA 1 (LRRC75A‑AS1)] was developed for AML patient prognosis prediction by analyzing the RNA‑seq data of AML patients from Therapeutically Available Research to Generate Effective Treatments (TARGET) and The Cancer Genome Atlas (TCGA) projects. In the training set obtained from TARGET, patients were divided into poor and favorable prognosis groups by the median risk score. The prognostic effectiveness of this lncRNA risk score was confirmed in the validation set obtained from TCGA by the same cut‑off. Furthermore, the lncRNA risk score was identified as an independent prognostic factor in the multivariate analysis. As further verification of the independent prognostic power of the lncRNA risk score, stratified analysis was performed by a cytogenetics risk group and revealed a consistent result. The prognostic predictive ability of the risk score was compared with the cytogenetics risk group by time‑dependent receiver operating characteristic curves analysis. It was revealed that the combination of the lncRNA risk score and cytogenetics risk group provided a higher prognostic value than a single prognostic factor. The present study also performed co‑expression analysis to predict the potential regulatory mechanisms of these lncRNAs in a cis/trans/competing endogenous RNA manner. The results suggested that LRRC75A‑AS1 was highly associated with the target genes of transcription factors tumor protein 53 and ETS variant 6. Overall, these results highlighted the use of the three‑lncRNA expression‑based risk score as a potential molecular biomarker to predict the prognosis in AML patients.

Dataset Information

A three-lncRNA expression signature associated with the prognosis of gastric cancer patients.

Publications

A three-lncRNA expression signature associated with the prognosis of gastric cancer patients.

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