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A two‐CpG‐based prognostic signature for oral squamous cell carcinoma overall survival
Author(s) -
Chen Yanping,
Hei Naiheng,
Zhao Jianguang,
Peng Shixiong,
Yang Kaicheng,
Chen He,
Cui Zifeng,
Jin Linyu,
Sun Ran,
Guo Jingxin
Publication year - 2019
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.28182
Subject(s) - cpg site , methylation , dna methylation , proportional hazards model , gene , biology , biomarker , survival analysis , oncology , cancer , basal cell , cancer research , medicine , gene expression , genetics
Oral squamous cell carcinoma (OSCC) represents one of the most common head and neck cancer that with dire prognosis due partly to the lack of reliable prognostic biomarker. Here, we aimed to develop a CpG site–based prognostic signature through which we could accurately predict overall survival (OS) of patients with OSCC. We obtained OSCC‐related DNA methylation and gene expression data sets from the public accessible Gene Expression Omnibus. Correlations between methylation level of CpG sites and OS of patients with OSCC were assessed by univariate Cox regression analysis followed by robust likelihood‐based survival analysis on those CpG sites with permutation P < 0.05 for further screening the optimal CpG sites for OSCC OS prediction based on the risk score formula that composed of the methylation level of optimal CpG sites weighted by their regression coefficients. Besides, differential expression genes (DEGs) and differential methylation genes (DMGs) in OSCC samples compared with normal samples were obtained and shared genes were considered as vital genes in OSCC tumorgenesis and progression. As a result, two CpG sites including cg17892178 and cg17378966 that located in NID2 and IDO1, respectively, were identified as the optimal prognostic signatures for OSCC OS. In addition, 12 overlapping genes between DEGs and DMGs that closely associated with inflammation or blood and tissue development–related biological processes were obtained. In conclusions, this study should provide valuable signatures for OSCC diagnosis and treatment.