DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development

Abstract

Background: Osteosarcomas commonly arise during the bone growth and remodeling in puberty, making it plausible to infer the involvement of epigenetic alterations in their development. Procedure: We investigated DNA methylation and related genetic variants in 28 primary osteosarcomas aiming to identify deregulated driver pathways. Methylation and genomic data was obtained using the Illumina HM450K beadchips and the TruSight One sequencing panel, respectively. Results: Aberrant DNA methylation was spread throughout the osteosarcomas genomes. We identified 3,146 differentially methylated CpGs comparing osteosarcomas and bone tissue samples, with high methylation heterogeneity, global hypomethylation and focal hypermethylation at CpG islands. Differentially methylated regions (DMR) were detected in 585 loci (319 hypomethylated and 266 hypermethylated), mapped to the promoter regions of 350 genes. These DMR-genes were enriched for biological processes related to skeletal system morphogenesis, proliferation, inflammatory response and signal transduction. Six tumor suppressor genes harbored deletions or promoter hypermethylation ( DLEC1, GJB2, HIC1, MIR149, PAX6, WNT5A), and four oncogenes presented gains or hypomethylation ( ASPSCR1, NOTCH4, PRDM16, RUNX3). Our analysis also revealed hypomethylation at 6p22, a region that contains several histone genes. DNMT3B gain was found to be a recurrent copy number change in osteosarcomas, providing a possible explanation for the observed phenotype of CpG island hypermethylation. Conclusions: While the detected open-sea hypomethylation likely contributes to the well-known osteosarcoma genomic instability, enriched CpG island hypermethylation suggests an underlying mechanism possibly driven by overexpression of DNMT3B likely resulting in silencing of tumor suppressors and DNA repair genes.