Smoking status, alcohol consumption and HPV infection (acquired through sexual activity) are the predominant risk factors for oropharyngeal cancer and are thought to alter the prognosis of the disease. Here, we conducted single-site and differentially methylated region (DMR) epigenome-wide association studies (EWAS) of these factors, in addition to ∼ 3-year survival, using Illumina Methylation EPIC DNA methylation profiles from whole blood in 409 individuals as part of the Head and Neck 5000 (HN5000) study. Overlapping sites between each factor and survival were then assessed using two-step Mendelian randomization to assess whether methylation at these positions causally affected survival. Using the MethylationEPIC array in an OPC dataset, we found novel CpG associations with smoking, alcohol consumption and ~ 3-year survival. We found no CpG associations below our multiple testing threshold associated with HPV16 E6 serological response (used as a proxy for HPV infection). CpG site associations below our multiple-testing threshold (PBonferroni < 0.05) for both a prognostic factor and survival were observed at four gene regions: SPEG (smoking), GFI1 (smoking), PPT2 (smoking) and KHDC3L (alcohol consumption). Evidence for a causal effect of DNA methylation on survival was only observed in the SPEG gene region (HR per SD increase in methylation score 1.28, 95% CI 1.14 to 1.43, P 2.12 × 10−05). Part of the effect of smoking on survival in those with oropharyngeal cancer may be mediated by methylation at the SPEG gene locus. Replication in data from independent datasets and data from HN5000 with longer follow-up times is needed to confirm these findings.

中文翻译：

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在口咽癌患者的临床队列中识别已确定的预后因素和存活率的表观遗传生物标志物。

吸烟状况、饮酒和 HPV 感染（通过性活动获得）是口咽癌的主要危险因素，被认为会改变疾病的预后。在这里，我们使用来自 409 名个体全血的 Illumina 甲基化 EPIC DNA 甲基化谱作为一部分，对这些因素进行了单位点和差异甲基化区域 (DMR) 表观基因组范围关联研究 (EWAS)，以及 3 年的生存期。头颈 5000 (HN5000) 研究。然后使用两步孟德尔随机化评估每个因素和生存之间的重叠位点，以评估这些位置的甲基化是否会影响生存。在 OPC 数据集中使用 MethylationEPIC 阵列，我们发现了新的 CpG 与吸烟、饮酒和约 3 年生存率的关联。我们没有发现低于我们的多重检测阈值的 CpG 关联与 HPV16 E6 血清学反应（用作 HPV 感染的代表）相关。在四个基因区域观察到低于我们的多重测试阈值（PBonferroni < 0.05）的 CpG 位点关联：SPEG（吸烟）、GFI1（吸烟）、PPT2（吸烟）和 KHDC3L（饮酒）。仅在 SPEG 基因区域中观察到 DNA 甲基化对生存的因果影响的证据（甲基化评分每 SD 增加的 HR 1.28，95% CI 1.14 至 1.43，P 2.12 × 10-05）。吸烟对口咽癌患者生存的部分影响可能是由 SPEG 基因位点的甲基化介导的。需要复制来自独立数据集的数据和来自 HN5000 的具有更长随访时间的数据来确认这些发现。