Methylome Analysis of HPV-Associated Head and Neck Cancer

Abstract

Objective: A significant proportion of HNSCC is caused by human papillomavirus. Patients diagnosed with this subtype have a significantly better outcome. It is the aim of the UCL Head and Neck Cancer Epigenome Project to generate and analyze comprehensive, genome-wide profiles of epigenetic aberrations in this specific type of human cancer.

Method: Whole-genome DNA methylation (methylome) analysis of 3 HPV positive and 3 HPV negative frozen HNSCC samples (obtained from the UCL Head and Neck Cancer Tissue Bank as part of a larger discovery set) was conducted using methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-Seq).

Results: On average, each sample in the pilot phase generated 2 x 10⁷ sequencing reads and 70% coverage of all CpG sites within the host genome. HPV type 16 was observed in all HPV positive samples and, interestingly, methylated regions of this virus were identified—most notably at genes E1 and L1 (previously shown to have been methylated in cervical cancer). We also detected multiple methylation changes between HPV positive and HPV negative host’s methylomes, of which a significant proportion mapped to genes previously shown to display down-regulated expression in transcriptionally active HPV positive oropharyngeal cancer.

Conclusion: The observed epigenetic differences between the 2 types might explain the different clinical behavior of HPV-associated HNSCC. Although preliminary, these pilot data are encouraging with respect to the possibility of identifying potential diagnostic and prognostic markers, as well as putative therapeutic targets in this subtype of HNSCC.