A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes.

AbstractOral tongue squamous cell carcinomas (OTSCCs) 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 in younger populations. Studies on functional DNA methylation changes linked with altered gene expression are critical for understanding the mechanisms underlying tumor development and metastasis. Such studies also provide important insight into biomarkers linked with viral infection, tumor metastasis and patient survival in OTSCC. Therefore, we performed genome-wide methylation analysis of tumors (N = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA 5-methycytosine (5mc) signature identified genes near 16 different differentially methylated regions (DMRs), which were validated using genomic data from The Cancer Genome Atlas (TCGA) cohort. In our cohort, hypermethylation of miR-10b was significantly associated with the differential expression of its target genes NR4A3 and BCL2L11 (P = 0.0125 and P = 0.014 respectively), which was inversely correlated with disease-free survival (P = 9E-15 and P = 2E-15 respectively) in patients. Finally, differential methylation in FUT3, TRIM5, TSPAN7, MAP3K8, RPS6KA2, SLC9A9 and NPAS3 genes was found to be predictive of certain clinical and epidemiological parameters.<b>IMPLICATIONS:</b><br>This study reveals a functional minimal methylation profile in oral tongue tumors with associated risk habits, clinical and epidemiological outcomes. In addition, NR4A3 down-regulation and correlation with patient survival suggests 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).

摘要：口腔舌鳞状细胞癌（Oral tongue squamous cell carcinomas, OTSCCs）是头颈部一类均质性侵袭性肿瘤，具有早期淋巴结转移、区域治疗失败发生率较高的特征。此外，年轻人群中口腔舌癌的发病率呈逐年上升趋势。探究与基因表达改变相关的功能性DNA甲基化（DNA methylation）变化，对于阐明肿瘤发生与转移的潜在分子机制至关重要，同时也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（biomarkers）提供重要见解。为此，我们对52例肿瘤样本开展了全基因组甲基化分析（genome-wide methylation analysis），并将甲基化异常与差异基因表达（differential gene expression）进行关联分析。本研究鉴定得到的最小肿瘤特异性DNA 5-甲基胞嘧啶（5-methycytosine, 5-mC）特征，可定位16个不同差异甲基化区域（differentially methylated regions, DMRs）附近的基因，该特征经癌症基因组图谱（The Cancer Genome Atlas, TCGA）队列的基因组数据验证。在本研究队列中，miR-10b的高甲基化与其靶基因（target genes）NR4A3及BCL2L11的差异表达显著相关（分别为P=0.0125和P=0.014），且该高甲基化与患者的无病生存期（disease-free survival）呈负相关（分别为P=9E-15和P=2E-15）。最后，研究发现FUT3、TRIM5、TSPAN7、MAP3K8、RPS6KA2、SLC9A9及NPAS3基因的差异甲基化可预测部分临床与流行病学参数。<b>研究启示：</b><br>本研究揭示了口腔舌肿瘤中存在与风险相关习惯、临床结局及流行病学特征相关的功能性最小甲基化谱。此外，NR4A3的下调及其与患者生存的关联提示，其可作为口腔舌肿瘤治疗干预的潜在靶点。本研究相关数据已提交至NCBI基因表达综合数据库（GEO），登录号为GSE75540。