title: Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma.
abstract: BACKGROUND
  Osteosarcomas are the most common non-haematological primary malignant tumours of bone, and all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies.
  
  
  RESULTS
  The cell lines showed complex patterns of DNA copy number changes, where genomic copy number gains were significantly associated with gene-rich regions and losses with gene-poor regions. By integrating the datasets, 350 genes were identified as having two types of aberrations (gain/over-expression, hypo-methylation/over-expression, loss/under-expression or hyper-methylation/under-expression) using a recurrence threshold of 6/19 (>30%) cell lines. The genes showed in general alterations in either DNA copy number or DNA methylation, both within individual samples and across the sample panel. These 350 genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. The aberrations of three selected genes, CXCL5, DLX5 and RUNX2, were validated in five cell lines and five tumour samples using PCR techniques. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2'-deoxycytidine treatment for four genes tested; AKAP12, CXCL5, EFEMP1 and IL11RA. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for detrimental genes.
  
  
  CONCLUSIONS
  Integrative analysis of genome-wide genetic and epigenetic alterations identified dependencies and relationships between DNA copy number, DNA methylation and mRNA expression in osteosarcomas, contributing to better understanding of osteosarcoma biology.
authors.affiliation: Department of Tumour Biology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
authors.forename: Stine H
authors.initials: SH
authors.lastname: Kresse
authors.forename: Halfdan
authors.initials: H
authors.lastname: Rydbeck
authors.forename: Magne
authors.initials: M
authors.lastname: Skårn
authors.forename: Heidi M
authors.initials: HM
authors.lastname: Namløs
authors.forename: Ana H
authors.initials: AH
authors.lastname: Barragan-Polania
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Cleton-Jansen
authors.forename: Massimo
authors.initials: M
authors.lastname: Serra
authors.forename: Knut
authors.initials: K
authors.lastname: Liestøl
authors.forename: Pancras C W
authors.initials: PC
authors.lastname: Hogendoorn
authors.forename: Eivind
authors.initials: E
authors.lastname: Hovig
authors.forename: Ola
authors.initials: O
authors.lastname: Myklebost
authors.forename: Leonardo A
authors.initials: LA
authors.lastname: Meza-Zepeda
mesh_terms: D001859:Bone Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018628:Gene Dosage; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D055106:Genome-Wide Association Study; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012516:Osteosarcoma / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger