Combined analysis of DNA methylation and gene expression profiles of osteosarcoma identified several prognosis signatures

Abstract

Osteosarcoma (OS) is a common primary malignancy in children and adolescents with relative high survival rate after chemotherapy. While, the toxicity of chemotherapy and personalized different response to chemotherapy makes it difficult for the selection of therapeutics and improvement of diagnosis. In this study, we conducted a combined analysis of two types of microarray datasets (gene expression and DNA methylation) from the Gene Expression Omnibus (GEO). Differential methylation sites (DMS) were identified by the IMA package and differential expression genes (DEGs) were screened out via the limma package. A total of 11,242 DMS (corresponding to 3080 genes (DMGs)) and 337 DEGs, with 40 overlaps (OS genes) between DEGs and DMGs, were identified. Enriched functions of OS genes were obtained through the Database for Annotation, Visualization and Integrated Discovery (DAVID). The OS genes were mainly enriched in the biological processes related to inflammatory/immune response and Pertussis pathways and Hematopoietic cell lineage pathways. Besides, OS-specific disease network was obtained, and found that UBS and NRF1 were regulated by multiple OS genes. Kaplan Meier analysis of OS genes identified BHMT2, DOCK2, DNALI1 and RIPK3 as significant OS survival-related genes. SEMA3A and PRAME are included in the 40 OS genes and within the top 10 most up-regulated DEGs. Their expression changes were further validated in U2OS osteosarcoma cell lines and hOB normal cell lines through quantitative PCR (qPCR) and consistent result with microarray analysis was obtained. Based on this study, some novel targets were identified for OS, which would be helpful in its early diagnosis and treatment.

Keywords: DNA methylation; GEO; Kaplan Meier; TCGA.