Genome-wide methylation analysis in HPV(-) and HPV(+) squamous cell carcinoma cell lines

HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. To assess the genome-wide methylation changes in HPV(+) and HPV(-) tumors, we analyzed DNA methylation and expression patterns in two HPV(+) and two HPV(-) cell lines. HPV(+) tumors have overall higher DNA methylation in genic and LINE1 regions than HPV(-) tumors, and polycomb repressive complex 2 (PRC2) targets tend to be much more highly methylated in HPV(+) cells. MeDIP-ChIP performed with GenPathway using 4mg of DNA. Cell lines analyzed: UM-SCC-4, UM-SCC-47, UM-SCC-74A, and CaSki. Methylated DNA was compared to mock-immunoprecipitated input DNA. The BED files with "HPVpos" in the name contain the regions more highly methylated in the HPV(+) samples, and the BED files with "HPVneg" in the name contain the regions more highly methylated in the HPV(-) samples.