title: Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma.
abstract: BACKGROUND
  Epigenetic mechanisms such as DNA methylation and histone modifications are important regulators of gene expression and are frequently involved in silencing tumor suppressor genes.
  
  
  METHODS
  In order to identify genes that are epigenetically regulated in neuroblastoma tumors, we treated four neuroblastoma cell lines with the demethylating agent 5-Aza-2'-deoxycytidine (5-Aza-dC) either separately or in conjunction with the histone deacetylase inhibitor trichostatin A (TSA). Expression was analyzed using whole-genome expression arrays to identify genes activated by the treatment. These data were then combined with data from genome-wide DNA methylation arrays to identify candidate genes silenced in neuroblastoma due to DNA methylation.
  
  
  RESULTS
  We present eight genes (KRT19, PRKCDBP, SCNN1A, POU2F2, TGFBI, COL1A2, DHRS3 and DUSP23) that are methylated in neuroblastoma, most of them not previously reported as such, some of which also distinguish between biological subsets of neuroblastoma tumors. Differential methylation was observed for the genes SCNN1A (p < 0.001), PRKCDBP (p < 0.001) and KRT19 (p < 0.01). Among these, the mRNA expression of KRT19 and PRKCDBP was significantly lower in patients that have died from the disease compared with patients with no evidence of disease (fold change -8.3, p = 0.01 for KRT19 and fold change -2.4, p = 0.04 for PRKCDBP).
  
  
  CONCLUSIONS
  In our study, a low methylation frequency of SCNN1A, PRKCDBP and KRT19 is significantly associated with favorable outcome in neuroblastoma. It is likely that analysis of specific DNA methylation will be one of several methods in future patient therapy stratification protocols for treatment of childhood neuroblastomas.
authors.affiliation: Department of Clinical Genetics, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden. helena.caren@clingen.gu.se
authors.forename: Helena
authors.initials: H
authors.lastname: Carén
authors.forename: Anna
authors.initials: A
authors.lastname: Djos
authors.forename: Maria
authors.initials: M
authors.lastname: Nethander
authors.forename: Rose-Marie
authors.initials: RM
authors.lastname: Sjöberg
authors.forename: Per
authors.initials: P
authors.lastname: Kogner
authors.forename: Camilla
authors.initials: C
authors.lastname: Enström
authors.forename: Staffan
authors.initials: S
authors.lastname: Nilsson
authors.forename: Tommy
authors.initials: T
authors.lastname: Martinsson
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics; D001932:Brain Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D045744:Cell Line, Tumor; D019175:DNA Methylation; D044127:Epigenesis, Genetic / Q000502:physiology*; D020869:Gene Expression Profiling; D052138:Genes, Neoplasm / Q000235:genetics; D016147:Genes, Tumor Suppressor; D056726:Genetic Association Studies; D006801:Humans; D046228:Microarray Analysis; D009447:Neuroblastoma / Q000175:diagnosis* / Q000235:genetics*; D011379:Prognosis; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor