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.
While genetic mutations have long been known to be a major contributor to cancer, epigenetic changes are also now known to play a role. In this proposal, we will study a newly appreciated epigenetic mark called 5-hydroxymethylcytosine (5hmC) in two subtypes of oral cancers. Using advanced bioinformatics methods, we will study the differences in 5hmC between oral tumors caused by the human papillomavirus and those associated with patient tobacco use, and determine how these changes affect the expression of genes and are related to clinical outcomes. 5hmC has not yet been assessed in relation to oral cancers.
| Cavalcante, Raymond G; Patil, Snehal; Park, Yongseok et al. (2017) Integrating DNA Methylation and Hydroxymethylation Data with the Mint Pipeline. Cancer Res 77:e27-e30 |
