A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma links altered methylation with tumor characteristics

Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes and have a higher incidence of regional failure. Additionally, there is a rising incidence of oral tongue cancer among younger population. Studies on functional DNA methylation changes linked with altered gene expression are important towards understanding of tumor development and metastasis. Such studies may provide insights into biomarkers linked with viral infection, tumor metastasis and patient survival in OTSCC. We performed genome-wide methylation analysis of tumors (<i>N</i> = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA methylation signature identified genes near 16 different differentially methylated regions (DMRs), which were validated using data from the cancer genome atlas (TCGA) cohort. In our cohort, hypermethylation of the microRNA <i>MiR-10B</i> was significantly associated with the differential expression of its target genes <i>NR4A3</i> and <i>BCL2L11</i> (<i>P</i> = 0.0125 and <i>P</i> = 0.014 respectively), which was inversely correlated with disease-free survival (<i>P</i> = 9E-15 and <i>P </i>= 2E-15 respectively) in patients. We found differential methylation in <i>FUT3</i>,<i> TRIM5</i>, <i>TSPAN7</i>,<i> MAP3K8,</i> <i>RPS6KA2, SLC9A9 </i>and<i> NPAS3</i> genes to be predictive of certain clinical and epidemiological parameters. <b>Implications</b>: Our study identified a functional minimal methylation signature in oral tongue tumors and linked various signatures with risk habits, clinical and epidemiological parameters. Down-regulation of <i>NR4A3 </i>and its correlation with patient survival makes it a potential target for therapeutic intervention in oral tongue tumors. Data from the current study are deposited in the NCBI Geo database (Accession number GSE75540).口腔舌鳞状细胞癌（Oral tongue squamous cell carcinomas, OTSCC）属于头颈区域一类均质性侵袭性肿瘤，早期即可发生淋巴结转移，区域复发率更高。此外，年轻人群中口腔舌癌的发病率呈逐年上升趋势。研究与基因表达异常相关的功能性DNA甲基化变化，对于阐明肿瘤发生与转移机制具有重要意义。此类研究或可为口腔舌鳞状细胞癌中与病毒感染、肿瘤转移及患者生存相关的生物标志物提供新的研究思路。本研究对52例肿瘤样本（*N*=52）开展全基因组甲基化分析，并将甲基化异常与差异基因表达进行关联分析。本研究鉴定得到的最小肿瘤特异性DNA甲基化特征涵盖16个不同差异甲基化区域（Differentially Methylated Regions, DMRs）附近的基因，并通过癌症基因组图谱（The Cancer Genome Atlas, TCGA）队列数据完成验证。在本研究队列中，微小RNA miR-10B的高甲基化与其靶基因NR4A3和BCL2L11的差异表达显著相关（分别为*P*=0.0125和*P*=0.014），且二者均与患者无病生存期呈负相关（分别为*P*=9E-15和*P*=2E-15）。本研究发现，FUT3、TRIM5、TSPAN7、MAP3K8、RPS6KA2、SLC9A9及NPAS3基因的甲基化异常可预测部分临床及流行病学参数。**研究意义**：本研究在口腔舌肿瘤中鉴定出功能性最小甲基化特征，并将多种特征与风险暴露习惯、临床及流行病学参数相关联。NR4A3的下调及其与患者生存的相关性使其成为口腔舌肿瘤治疗干预的潜在靶点。本研究的相关数据已提交至美国国家生物技术信息中心基因表达综合数据库（National Center for Biotechnology Information Gene Expression Omnibus, NCBI GEO），登录号为GSE75540。