Characterization of Epigenomic Alterations in HPV16 Head and Neck Squamous Cell Carcinomas

Abstract

Background: Epigenetic changes associated with human papillomavirus (HPV)-driven tumors have been described; however, HPV type-specific alterations are less well understood. We sought tocompareHPV16-specific methylation changes with those in virusunassociated head and neck squamous cell carcinomas (HNSCC). Methods: Within The Cancer Genome Atlas, 59 HPV16 HNSCC, 238 nonviralHNSCC(no detectableHPVor other viruses), and 50 normal head and neck tissues were evaluated. Significant differentially methylated regions (DMR) were selected, and key associated genes were identified. Partial least squares models were generated to predict HPV16 status in additional independent samples. Results: HPV infection in HNSCC is associated with typespecific methylomic profiles. Multiple significant DMRs were identified between HPV16 , nonviral, and normal samples. The most significant differentially methylated genes, SYCP2, MSX2, HLTF, PITX2, and GRAMD4, demonstrated HPV16-associated methylation patterns with corresponding alterations in gene expression. Phylogenetically related HPV types (alpha-9 species; HPV31, HPV33, and HPV35) demonstrated a similar methylation profile to that of HPV16 but differed from those seen in other types, such as HPV18 and 45 (alpha-7). Conclusions: HNSCC linked to HPV16 and types from the same alpha species are associated with a distinct methylation profile. This HPV16-associated methylation pattern is also detected in cervical cancer and testicular germ cell tumors. We present insights into both shared and unique methylation alterations associated with HPV16 tumors and may have implications for understanding the clinical behavior of HPV-associated HNSCC.