Developing a HPV-mediated DNA methylation panel in HNSCC

人乳头瘤病毒相关口咽鳞状细胞的分子特征 癌症(OPSCC)在基因上是复杂的，但对个体基因的研究提供了一些有希望的见解 有助于提高癌症存活率和肿瘤进展的变化。然而，目前的商业 通过组织病理学检测肿瘤中的HPV的方法在以下情况下显示出较差的敏感性和特异性 与劳动强度较大的检测HPV RNA的金标准方法相比。我们的研究小组已经 最近开发了一种新的22个CpG基因座小组，其甲基化状态区分于OPSCC和 未发现表达E6/E7癌基因的HPV16感染。这具有潜在的临床意义，因为 检测肿瘤中的HPV16E6/E7RNA与显著提高癌症存活率有关 OPSCC。在这项研究中，我们建议验证宿主DNA甲基化面板并测试新的表观遗传学 可能调节关键效应蛋白的事件，包括转录下游的四个面板基因座 CDKN2A(P16)的起始点，尽管与正常组织相比在肿瘤组织中高度甲基化，但 与细胞基因表达增加有关。在这项研究中，我们建议测试和验证这一点 签名。我们将：1)检验假设HPV面板宿主DNA甲基化状态的变化 改变其相应基因表达的功能后果；2)假设HPV病毒 癌基因E6和E7足以诱导宿主DNA甲基化和相应的基因表达 在HPV面板中看到的变化，包括观察到的CDKN2A的新变化(P16)；以及3)测试 我们的HPV驱动甲基化小组在临床样本中的临床相关性，以确定哪些是最 预测临床结果。结合我们确定的功能和临床相关性的实验， 这项研究将为未来的临床研究奠定基础，以测试HPV特异性甲基化的临床应用 面板。

Molecular characterization of human papillomavirus (HPV) associated oropharyngeal squamous cell carcinomas (OPSCC) is genetically complex but has provided some promising insight into individual genetic changes that contribute to improved cancer survival and tumor progression. However, current commercial methods for detecting HPV in tumors by histopathology have shown poor sensitivity and specificity when compared to the more labor intensive gold standard methods for detecting HPV RNA. Our research group has recently developed a novel 22 CpG loci panel whose methylation status distinguishes between OPSCC with and without HPV16 infections expressing the E6/E7 oncogenes. This has potential clinical relevance as detection of HPV16 E6/E7 RNA in tumors has been associated with significantly improved cancer survival in OPSCC. In this study, we propose to validate this host DNA methylation panel and test the novel epigenetic events that may regulate key effector proteins, including for four panel loci downstream of the transcriptional start site of CDKN2A(p16) that, despite being hypermethylated in tumor compared to normal tissues, are associated with increased expression of the cellular gene. In this study, we propose to test and validate this signature. We will: 1) test the hypothesis that changes in host DNA methylation status of the HPV panel have functional consequences in altering expression of their corresponding genes; 2) the hypothesis that HPV viral oncogenes E6 and E7 are sufficient to induce host DNA methylation and corresponding gene expression changes seen in the HPV panel, including the novel changes observed for CDKN2A(p16); and 3) test the clinical relevance of our HPV-driven methylation panel in clinical samples to determine which are most predictive of clinical outcome. Combined with our experiments establishing functional and clinical relevance, this study will lay the groundwork for future clinical studies to test clinical utility of an HPV-specific methylation panel.