Construction of a lncRNA-risk score signature associated with the prognosis of oral squamous cell carcinoma using microarray re-annotation
GE Chun-cheng;HE San-gang;WANG Xi;TONG Guo-yong;XU Jia;Enshi Tujiaand Miao Autonomous Prefecture Center Hospital,Oral Diagnosis and Treatment Center;Oral and Maxillofacial Trauma and Plastic Surgery of Wuhan University Stomatology Hospital;
Objective: To construct alncRNA risk score( lncRNA-RS) model for predicting the prognosis of oral squamous cell carcinoma( OSCC) by using microarray re-annotation pipeline.Methods: Datasets of GSE42743 from GEO and Head and Neck Cancer cohort from TCGA were obtained as training dataset and test dataset,respectively.Gene probes in the training dataset were re-annotated using bioinformatics method,and univariate and multivariate Cox regression analysis were used to establish the lncRNA-RS model asscoiated with OSCC prognosis. Survival curve analysis and multivariate Cox regression were then performed to evaluate the prognostic power of lncRNA-RS for OSCC.Finally,KEGG pathway analysis was conducted to explore the potentially functional mechanisms of lncRNAs in the model.Results: Univariate Cox regression analysis found that 5 lncRNAs were significantly correlated with the prognosis of OSCC( P 0. 001). The lncRNA-RS model was then constructed based on these lncRNAs,and patients were divided into high-risk group( n = 37) and low-risk group( n = 37) according to the median value of lncRNA-RS.Survival curve analysis indicated that compared with high-risk group,the overall survival in low-risk group was significantly longer in both training dataset( P0. 001) and test dataset( P = 0. 022).Multivariate Cox regression showed that lncRNA-RS could independently affect the prognosis of OSCC in either training( HR: 9. 860,95%CI: 4. 289 ～ 22. 667,P0. 001) or test datasets( HR: 2. 259,95%CI: 1. 171 ～ 4. 357,P = 0. 015).The results of KEGG enrichment analysis suggested that these lncRNAs were mainly involved in metabolic pathways,calcium signaling pathway,m TOR signaling pathway and AMPK signaling pathway.Conclusion: Our study has constructed alncRNA-RS model based on 5 lncRNAs,which may be used as a panel biomarker to predict OSCC prognosis and deserves further investigation.