title: Epigenetic genome-wide analysis identifies BEX1 as a candidate tumour suppressor gene in paediatric intracranial ependymoma.
abstract: Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of gene inactivation in cancer. To identify targets of epigenetic silencing in paediatric intracranial ependymoma, we used a pharmacological unmasking approach through treatment of 3 ependymoma short-term cell cultures with the demethylating agent 5-Aza-2'-deoxycytidine followed by global expression microarray analysis. We identified 55 candidate epigenetically silenced genes, which are involved in the regulation of apoptosis, Wnt signalling, p53 and cell differentiation. The methylation status of 26 of these genes was further determined by combined bisulfite restriction analysis (COBRA) and genomic sequencing in a cohort of 40 ependymoma samples. The most frequently methylated genes were BEX1 (27/40 cases), BAI2 (20/40), CCND2 (18/40), and CDKN2A (14/40). A high correlation between promoter hypermethylation and decreased gene expression levels was established by real-time quantitative PCR, suggesting the involvement of these genes in ependymoma tumourigenesis. Furthermore, ectopic expression of brain-expressed X-linked 1 (BEX1) in paediatric ependymoma short-term cell cultures significantly suppressed cell proliferation and colony formation. These data suggest that promoter hypermethylation contributes to silencing of target genes in paediatric intracranial ependymoma. Epigenetic inactivation of BEX1 supports its role as a candidate tumour suppressor gene in intracranial ependymoma, and a potential target for novel therapies for ependymoma in children.
authors: Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK. Electronic address: A.Karakoula@wlv.ac.uk.
authors: Katherine
authors: K
authors: Karakoula
authors: Neural Development Unit, Birth Defects Research Centre, UCL Institute of Child Health, University College London, London WC1E 6BT, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
authors: Thomas S
authors: TS
authors: Jacques
authors: Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
authors: Kim P
authors: KP
authors: Phipps
authors: Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
authors: William
authors: W
authors: Harkness
authors: Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
authors: Dominic
authors: D
authors: Thompson
authors: Division of Neuropathology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4399, USA.
authors: Brian N
authors: BN
authors: Harding
authors: Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK.
authors: John L
authors: JL
authors: Darling
authors: Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK.
authors: Tracy J
authors: TJ
authors: Warr
mesh_terms: D001932:Brain Neoplasms / Q000235:genetics*; D002478:Cells, Cultured; D002648:Child; D019175:DNA Methylation; D004806:Ependymoma / Q000235:genetics*; D044127:Epigenesis, Genetic; D015972:Gene Expression Regulation, Neoplastic; D016147:Genes, Tumor Suppressor; D055106:Genome-Wide Association Study; D006801:Humans; D009419:Nerve Tissue Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D060888:Real-Time Polymerase Chain Reaction; D014162:Transfection
chemical_list: C469586:BEX1 protein, human; D009419:Nerve Tissue Proteins
keywords: 5-Aza-dC; BEX1; DNA methylation; Paediatric ependymoma; Pharmacological unmasking