5-hydroxymethylcytosine in HPV(+) and HPV(-) oral and oropharyngeal cancers

 描述(申请人提供)：人乳头瘤病毒(HPV)诱导的口腔和口咽鳞状细胞癌(OC/OP SCCs)与吸烟相关的分子机制不同，导致对治疗的反应不同，HPV阳性肿瘤的患者预后好于HPV阴性肿瘤患者。我们和其他人已经证明，HPV(+)和HPV(-)肿瘤之间存在特定部位和全球范围的DNA甲基化差异。5-羟甲基胞嘧啶(5HmC)曾经被认为是去甲基化过程中的一个短暂步骤，现在已知在多种癌症中具有功能后果的异常，但尚未在OC/OP SCC中进行研究。鉴于5hmC也可能在口腔和口咽肿瘤中发挥作用，我们建议研究5hmC及其与DNA甲基化的相互作用，以及这些相互作用如何转化为HPV(+)和HPV(-)OC/OP SCC中基因表达的功能变化。这项提案的目标1的目标将是通过对目前一组OC/OP SCC冷冻肿瘤和匹配的对照进行全基因组5hmC深度测序，确定5hmC参与HPV(+)和HPV(-)肿瘤的程度和形式。在目标2中，我们将把5hmC数据与全基因组亚硫酸氢盐测序数据(不区分5hmC和5mC标记)、通过RNA-SEQ测量的转录数据以及同一肿瘤的拷贝数变异数据相结合，以确定DNA甲基化(5mC)和5hmC去调控如何影响OC/OP SCC的转录编程及其与临床结果的关系。为了帮助实现我们的目标，我们将开发一种生物信息学方法和工具，用于同时分析和解释5mC和5hmC深度测序数据。

 DESCRIPTION (provided by applicant): Differences in molecular mechanisms between human papillomavirus (HPV)-induced oral cavity and oropharyngeal squamous cell carcinomas (OC/OP SCCs) and those associated with tobacco use lead to different responses to therapy, with patients having HPV-positive tumors having a better prognosis than those with HPV-negative tumors. We and others have shown that site-specific and global differences in DNA methylation exist between HPV(+) and HPV(-) tumors. 5-hydroxymethylcytosine (5hmC), once thought of as simply a transient step in the demethylation process, is now known to be aberrant with functional consequences in multiple cancers, however it has not yet been studied in OC/OP SCCs. Given suggestive evidence that 5hmC may also play a role in oral and oropharyngeal tumors, we propose to study 5hmC, its interactions with DNA methylation, and how these translate to functional changes in gene expression in HPV(+) and HPV(-) OC/OP SCCs. The goal of Aim 1 of this proposal will be to determine the extent and form of 5hmC involvement in HPV(+) and HPV(-) tumors by performing whole-genome 5hmC deep sequencing on a current set of OC/OP SCC frozen tumors and matched controls. In Aim 2, we will integrate the 5hmC data with whole-genome bisulfite sequencing data (which does not distinguish between 5hmC and 5mC marks), transcriptomics data measured via RNA-seq, and copy number variation data on the same tumors to determine how DNA methylation (5mC) and 5hmC deregulation affect the transcriptional programming in OC/OP SCCs and their relationship with clinical outcome. To help accomplish our goals, we will develop a bioinformatics method and tool for concurrent analysis and interpretation of 5mC and 5hmC deep sequencing data.