Career Development Program
Project Six: Epigenomic Profiling and Biomarker Discovery in HPV+ and HPV-SCC
Maureen A. Sartor, Ph.D.
Specific Aims are:
1. Examine genome-wide histone modification profiles of HPV+ and HPV- SCC cell lines using next generation sequencing (NGS) to determine distinguishing epigenomic histone marks. We will perform ChIP-seq against H3K27me3 and combined H3K4 mono-, di-, and tri-methylation marks in the same four cell lines used in our preliminary studies, as well as in normal mucosal keratinocytes as a control.
2. Perform integrative bioinformatics analyses on the histone modification data together with corresponding data on gene expression profiles and CpG DNA methylation. We will integrate our data to prioritize findings for follow-up, and begin development of novel integrative bioinformatics methods that are aimed at prioritizing functional markers.
3. Confirm key findings on a larger panel of HPV-positive and HPV-negative cell lines. Clinicalprioritized findings based on the integrative analyses will be validated on the larger set of cell lines that we propose to use in our R01.
Squamous cell carcinomas (SCC) of the genital tract and oropharynx can be driven either by infection with high risk human papillomavirusus (HPV) or by classical carcinogenic factors such as tobacco smoke. While the role of HPV in cervical cancer has been known for many years, only recently was its role in oropharyngeal cancer discovered. Given the observed increasing incidence of HPVinduced oral cancers throughout the last two decades, this etiology of a unique subset head and neck cancers cannot be ignored. It has become clear that HPV drives a distinct carcinogenic program compared to that of non-HPV tumors in head and neck SCC (HNSCC), leading to different response rates to therapy. For example, HPV(+) and HPV(-) tumors are opposing with respect to CDKN2A expression, which is lost in nearly all HPV(-) tumors and over-expressed in most HPV(+) tumors (1). These differences likely have substantial ramifications for optimal treatment choice. Indeed, HPV(+) HNSCC patients have a substantial prognostic advantage over HPV(-) HNSCC patients with a history of tobacco use, and those with both tobacco and HPV have an intermediate prognosis . However, despite these findings, thus far tumor HPV status is not used to alter therapeutic management. Further understanding of the molecular mechanisms that drive tumor behavior in HPV(+) versus HPV(-) SCCs is a necessary step towards individualized therapy. We and others have recently observed that the differing mechanisms of carcinogenesis of HPV(+) and HPV(-) tumors are likely much more widespread than what is understood to be the primary genic targets of HPV proteins E6 and E7. Our preliminary data, presented below, point to striking genome-wide epigenetic differences between HPV(+) and HPV(-) SCC. The objective of this proposal is to enhance our preliminary data of genome-wide DNA methylation and gene expression profiles in HPV(+) and HPV(-) SCC cells by examining histone modifications in the same cells, and validating our top findings in a larger panel of cell lines. Our central hypothesis is that integrative analyses of genomewide DNA methylation, histone modifications, and expression profiles will help to elucidate the roles of epigenetics, the stem cell signature and selected mutational events in HPV-induced versus classic carcinogen-induced HNSCC.