Identification of four prognostic LncRNAs for survival prediction of patients with hepatocellular carcinoma

Abstract

BackgroundAs the fifth most common cancer worldwide, Hepatocellular carcinoma (HCC) is also the third most common cause of cancer-related death in China. Several lncRNAs have been demonstrated to be associated with occurrence and prognosis of HCC. However, identification of prognostic lncRNA signature for HCC with expression profiling data has not been conducted yet.MethodsWith the reuse of public available TCGA data, expression profiles of lncRNA for 371 patients with HCC were obtained and analyzed to find the independent prognostic lncRNA. Based on the expression of lncRNA, we developed a risk score model, which was evaluated by survival analysis and ROC (receiver operating characteristic) curve. Enrichment analysis was performed to predict the possible role of the identified lncRNA in HCC prognosis.ResultsFour lncRNAs (RP11-322E11.5, RP11-150O12.3, AC093609.1, CTC-297N7.9) were found to be significantly and independently associated with survival of HCC patients. We used these four lncRNAs to construct a risk score model, which exhibited a strong ability to distinguish patients with significantly different prognosis (HR = 2.718, 95% CI [2.103–3.514], p = 2.32e−14). Similar results were observed in the subsequent stratification survival analysis for HBV infection status and pathological stage. The ROC curve also implied our risk score as a good indicator for 5-year survival prediction. Furthermore, enrichment analysis revealed that the four signature lncRNAs may be involved in multiple pathways related to tumorigenesis and prognosis.DiscussionOur study recognized four lncRNAs to be significantly associated with prognosis of liver cancer, and could provide novel insights into the potential mechanisms of HCC progression. Additionally, CTC-297N7.9 may influence the downstream TMEM220 gene expression through cis-regualtion. Nevertheless, further well-designed experimental studies are needed to validate our findings.

RNA-Sequencing Data Reveal a Prognostic Four-lncRNA-Based Risk Score for Bladder Urothelial Carcinoma: An in Silico Update

“…BLCA patients were then categorized into low-and high-risk groups based on the median of the newly calculated prognostic risk score [28,29,31,32]. The whole process is presented in Fig.…”

Systematic analyses of a novel lncRNA‐associated signature as the prognostic biomarker for Hepatocellular Carcinoma

“…Wang et al 31 also identified a four-lncRNA signature (RP11-322E11.5, RP11-150O12.3, AC093609.1, CTC-297N7.9) which might be an independent prognostic biomarker for the prediction of HCC patient survival. However, compared with previous study, we used more stringent screening criteria.…”

Identification of Potential Prognostic Long Non-Coding RNA Biomarkers for Predicting Survival in Patients with Hepatocellular Carcinoma

“…Although TCGA database was previously used to analyze lncRNA-related signatures for HCC prognosis, the present study was different in that it investigated the optimum combination of these prognostic lncRNAs using the ''step'' function in the R platform [46]. Therefore, the prognostic signature constructed in the present study is more accurate than that identified in a previous study [46]. In addition, comprehensive survival analysis of the present 13-DEL prognostic signature was performed by developing a nomogram, and stratified and joint effects survival analysis was performed to investigate its potential application.…”

“…He et al, Tang et al and Zang et al used TCGA lncRNA dataset to identify a lncRNA expression-based prognostic signature for assessing the survival of patients with soft-tissue sarcoma, lung cancer, and colorectal adenocarcinoma [36][37][38]. TCGA lncRNA datasets of cutaneous melanoma [39], bladder urothelial carcinoma [40], breast cancer [41], clear cell renal cell carcinoma [42], gastric cancer [43,44], head and neck squamous cell carcinoma [45], and HCC [46] have been used in lncRNA expressionbased prognostic signature investigations by other researchers. These studies used a genome-wide screening method to identify potential prognostic lncRNAs and calculated a risk score based on lncRNA expression.…”