The prognostic value of a seven-lncRNA signature in patients with esophageal squamous cell carcinoma: a lncRNA expression analysis

Abstract

Background: Long non-coding RNAs (lncRNAs) have been reported to be prognostic biomarkers in many types of cancer. We aimed to identify a lncRNA signature that can predict the prognosis in patients with esophageal squamous cell carcinoma (ESCC).

Methods: Using a custom microarray, we retrospectively analyzed lncRNA expression profiles in 141 samples of ESCC and 81 paired non-cancer specimens from Sun Yat-Sen University Cancer Center (Guangzhou, China), which were used as a training cohort to identify a signature associated with clinical outcomes. Then we conducted quantitative RT-PCR in another 103 samples of ESCC from the same cancer center as an independent cohort to verify the signature.

Results: Microarray analysis showed that there were 338 lncRNAs significantly differentially expressed between ESCC and non-cancer esophagus tissues in the training cohort. From these differentially expressed lncRNAs, we found 16 lncRNAs associated with overall survival (OS) of ESCC patients using Cox regression analysis. Then a 7-lncRNA signature for predicting survival was identified from the 16 lncRNAs, which classified ESCC patients into high-risk and low-risk groups. Patients with high-risk have shorter OS (HR: 3.555, 95% CI 2.195-5.757, p < 0.001) and disease-free survival (DFS) (HR: 2.537, 95% CI 1.646-3.909, p < 0.001) when compared with patients with low-risk in the training cohort. In the independent cohort, the 7 lncRNAs were detected by qRT-PCR and used to compute risk score for the patients. The result indicates that patients with high risk also have significantly worse OS (HR = 2.662, 95% CI 1.588-4.464, p < 0.001) and DFS (HR 2.389, 95% CI 1.447-3.946, p < 0.001). The univariate and multivariate Cox regression analyses indicate that the signature is an independent factor for predicting survival of patients with ESCC. Combination of the signature and TNM staging was more powerful in predicting OS than TNM staging alone in both the training (AUC: 0.772 vs 0.681, p = 0.002) and independent cohorts (AUC: 0.772 vs 0.660, p = 0.003).

Conclusions: The 7-lncRNA signature is a potential prognostic biomarker in patients with ESCC and may help in treatment decision when combined with the TNM staging system.

Keywords: Esophageal cancer; Expression profile; Survival; TNM stage; lncRNA.

Fig. 1

The 7-lncRNA signature is associated with survivals of ESCC patients in the training and independent cohorts. The risk score was calculated for each patient according to the 7-lncRNA signature and the patients were divided into a high- or low-risk group based on their risk score. Then Kaplan–Meier survival analysis was performed on the patients. a Overall survival (OS) curves of 141 patients with high-risk or low-risk in the training cohort. b Disease-free survival (DFS) curves of 141 patients in the training cohort. c OS curves of 103 patients with high-risk or low-risk in the independent cohort. d DFS curves of 103 patients with high-risk or low-risk in the independent cohort. Note: in the Kaplan–Meier survival curves, the survival time unit is months

Fig. 2

The 7-lncRNA signature can predict distinct survivals of ESCC patients with same TNM stage in the training cohort. The patients with same stage (II or III) were defined as high- or low-risk by the 7-lncRNA signature risk score and then analyzed with Kaplan–Meier survival curves. a Overall survival (OS) curves of 73 patients with high-risk or low-risk in the cases with TNM stage II in the training cohort. b Disease-free survival (DFS) curves in 73 patients with high-risk or low-risk in the cases with TNM stage II in the training cohort. c OS curves in 59 patients with high-risk or low-risk in the cases with TNM stage III in the training cohort. d DFS curves in 59 patients with high-risk or low-risk in the cases with TNM stage II in the training cohort. Note: in the Kaplan–Meier survival curves, the survival time unit is months

Fig. 3

The 7-lncRNA signature improves survival prediction of TNM staging system in ESCC patients. The ESCC patients were defined as low-, moderate- and high-risk by the combination model of 7-lncRNA signature and TNM staging system, and then the survivals of these patients were analyzed with Kaplan–Meier curves and compared with the survivals predicted by TNM staging system. a Overall survival (OS) of patients with TNM stage II or III in the training cohort; b OS of patients with low-, moderate- or high-risk score in the training cohort. c OS of patients with TNM stage II or III in the independent cohort; d OS of patients with low-, moderate- or high-risk score in the independent cohort; e OS of patients with TNM stage II or III in the combination of two cohorts. f OS of patients with low-, moderate- or high-risk score in combination of two cohorts. In the Kaplan–Meier survival curves, the survival time unit is months

Fig. 4

Comparisons of the performances of survival predictions made by the 7-lncRNA signature, TNM stage and combined model of the signature and TNM stage. The performances of survival predictions made by the three methods were compared using receiver operating characteristic (ROC) analysis. a ROC curves of the 7-lncRNA signature, TNM stage and combined model for overall survival (OS) prediction in the training cohort. b ROC curves of the three methods for disease-free survival (DFS) prediction in the training cohort. c ROC curves of the three methods for OS prediction in the independent cohort. d ROC curves of the three methods for DFS prediction in the independent cohort

Fig. 5

The 7-lncRNA signature is likely to correlate with tumour-associated biological processes. The target genes are regulated by transcription factors that could be bound by the 7 lncRNAs, and GO enrichment analysis and the KEGG pathway were performed on these genes. a The genes are enriched in the cell processes in GO enrichment analysis. b The genes are involved in the pathways in the KEGG pathway analysis