Lim Annette M, Wong Nicholas C, Pidsley Ruth, Zotenko Elena, Corry June, Dobrovic Alexander, Clark Susan J, Rischin Danny, Solomon Benjamin
Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Ave, Nedlands, Western Australia 6009 Australia.
The University of Western Australia, Perth, Australia.
Clin Epigenetics. 2016 Jul 18;8:74. doi: 10.1186/s13148-016-0235-0. eCollection 2016.
DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 109 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. Data pre-processing, quality control and analysis were performed using R packages. Probes mapping to SNPs, sex chromosomes and unreliable probes were accounted for prior to downstream analyses. The relationship between methylation and patient survival was examined using both agnostic approaches and feature selection. The cohort was enlarged by incorporation of 331 The Cancer Genome Atlas (TCGA) HNSCC samples, which included 91 TCGA OTSCC samples with HM450K and survival data available.
Given the use of FFPE-derived DNA, we defined different cohorts for separate analyses. Overall, similar results were found between cohorts. With an unsupervised approach, no distinct hypermethylated group of samples was identified and nor was a prognostic methylation profile identified. The use of multiple downstream feature selection approaches, including a linear models for microarray data (LIMMA), centroid feature selection (CFS), and recursive feature elimination (RFE) support vector machines, similarly failed to identify a significant methylation signature informative for patient prognosis or any clinicopathological data available. Furthermore, we were unable to confirm the prognostic methylation profiles or specific prognostic loci reported within the literature for HNSCC.
With genome-scale assessment of DNA methylation using HM450K in one of the largest OTSCC cohorts to date, we were unable to identify a hypermethylated group of tumours or a prognostic methylation signature. This suggests that either DNA methylation in isolation is not likely to be of prognostic value or larger cohorts are required to identify such a biomarker for OTSCC.
据报道，异质性头颈部鳞状细胞癌（HNSCC）队列的DNA甲基化谱可预测患者预后。我们研究了在单一统一亚部位——舌部的肿瘤组织中是否能找到预后性DNA甲基化谱。使用Illumina HumanMethylation450K（HM450K）芯片检测了来自单一机构的109份经过全面注释的舌鳞状细胞癌（OTSCC）福尔马林固定石蜡包埋（FFPE）样本的甲基化状态。使用R包进行数据预处理、质量控制和分析。在下游分析之前考虑了映射到单核苷酸多态性（SNP）、性染色体的探针以及不可靠的探针。使用无先验假设方法和特征选择来研究甲基化与患者生存之间的关系。通过纳入331份癌症基因组图谱（TCGA）HNSCC样本扩大了队列，其中包括91份有HM450K和生存数据的TCGA OTSCC样本。
鉴于使用了FFPE衍生的DNA，我们定义了不同队列进行单独分析。总体而言，各队列之间发现了相似的结果。采用无监督方法时，未识别出明显的高甲基化样本组，也未识别出预后性甲基化谱。使用多种下游特征选择方法，包括微阵列数据线性模型（LIMMA）、质心特征选择（CFS）和递归特征消除（RFE）支持向量机，同样未能识别出对患者预后或任何可用临床病理数据有意义的显著甲基化特征。此外，我们无法证实文献中报道的HNSCC预后性甲基化谱或特定预后位点。
在迄今为止最大的OTSCC队列之一中使用HM450K对DNA甲基化进行全基因组评估时，我们未能识别出高甲基化肿瘤组或预后性甲基化特征。这表明单独的DNA甲基化不太可能具有预后价值，或者需要更大的队列来识别OTSCC的此类生物标志物。
