Developing a HPV-mediated DNA methylation panel in HNSCC

描述(申请人提供)：人乳头瘤病毒(HPV)相关口咽鳞状细胞癌(OPSCC)的分子特征在遗传上是复杂的，但为有助于提高癌症存活率和肿瘤进展的个体基因变化提供了一些有希望的见解。然而，目前通过组织病理学检测肿瘤中HPV的商业方法与检测HPV RNA的劳动强度较高的金标准方法相比，显示出较差的敏感性和特异性。我们的研究小组最近开发了一个新的22个CpG基因座小组，其甲基化状态区分有无表达E6/E7癌基因的HPV16感染的OPSCC。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OPSCC的癌症存活率有关。在这项研究中，我们建议验证宿主DNA甲基化面板，并测试可能调节关键效应蛋白的新表观遗传学事件，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。在本研究中，我们建议对该签名进行测试和验证。我们将：1)测试假设，即HPV组宿主DNA甲基化状态的变化在改变其相应基因的表达方面具有功能性后果；2)假设HPV病毒癌基因E6和E7足以诱导宿主DNA甲基化和在HPV组中看到的相应基因表达变化，包括观察到的CDKN2A(P16)的新变化；以及3)在临床样本中测试我们的HPV驱动的甲基化小组的临床相关性，以确定哪些是最能预测临床结果的。结合我们建立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，以测试临床 人乳头瘤病毒特异性甲基化小组的效用。

DESCRIPTION (provided by applicant): 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.