Developing a HPV-mediated DNA methylation panel in HNSCC

描述（由申请人提供）：人乳头瘤病毒（HPV）相关口咽鳞状细胞癌（OPSCC）的分子特征在遗传学上很复杂，但对有助于改善癌症生存率和肿瘤进展的个体遗传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的商业方法与用于检测HPV RNA的更劳动密集型的金标准方法相比显示出较差的灵敏度和特异性。我们的研究小组最近开发了一种新的22个CpG位点的面板，其甲基化状态区分OPSCC与HPV 16感染和不表达E6/E7癌基因。这具有潜在的临床相关性，因为肿瘤中HPV 16 E6/E7 RNA的检测与OPSCC中癌症存活率的显著改善相关。在这项研究中，我们建议验证这个宿主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事件，包括转录调控子下游的四个面板基因座。 CDKN 2A（p16）的起始位点，尽管与正常组织相比，其在肿瘤中被高甲基化，但与细胞基因的表达增加相关。在这项研究中，我们建议测试和验证这个签名。我们将：2）HPV病毒致癌基因E6和E7足以诱导宿主DNA甲基化和HPV组中观察到的相应基因表达变化的假设，包括对CDKN 2A（p16）观察到的新变化;和3）测试我们的HPV驱动的甲基化组在临床样品中的临床相关性，以确定哪些最能预测临床结果。结合我们建立功能和临床相关性的实验，本研究将为未来的临床研究奠定基础，以测试临床 HPV特异性甲基化组的效用。

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.