title: Differences in global DNA methylation of testicular seminoma are not associated with changes in histone modifications, clinical prognosis, BRAF mutations or gene expression.
abstract: Testicular germ cell tumours of young adults are comprised of a heterogeneous group of non-seminomas and a homogeneous group of seminomas. While the majority of seminomas retain a hypo-methylated genome, a small fraction displays a highly methylated genome, resembling hyper-methylated non-seminomas. It is well established from e.g. melanoma, colorectal and thyroid cancer that a methylated phenotype can be correlated to prognosis and can be related to BRAF mutations. In the present study we investigated the global methylation level in 67 seminomas and classified them as hypo-methylated, intermediate, patchy and hyper-methylated, respectively. A selected subset representing each level of DNA methylation and the TCam2 seminoma cell line were subsequently analysed for a range of other epigenetic marks (6 histone marks and 5-hydroxymethylcytosine), the presence of the BRAF V600E de novo mutation, differences in the transcriptome and finally correlated to the clinical outcome. We did not identify any histone marks or hydroxymethylation levels that correlated with the methylation level of the genome. Some histone marks, however, showed a great variation while others were found at the same level in all the investigated seminomas. We did not identify any tumours with the BRAF V600E mutation and transcriptome analysis revealed no significant differences between hypo- and hyper-methylated seminomas. Similarly, no obvious differences in the clinical manifestation of the patients representing hypo- or hyper-methylated seminomas were identified. The level of DNA methylation in testicular seminomas consequently seems secondary to the manifestation of the tumour phenotype.
authors.affiliation: Dept. of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Denmark; International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Denmark.
authors.forename: Louise Holm
authors.initials: LH
authors.lastname: Pedersen
authors.affiliation: Dept. of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Denmark; International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Denmark.
authors.forename: John E
authors.initials: JE
authors.lastname: Nielsen
authors.affiliation: Department of Oncology, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.
authors.forename: Gedske
authors.initials: G
authors.lastname: Daugaard
authors.affiliation: Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.
authors.forename: Thomas V O
authors.initials: TV
authors.lastname: Hansen
authors.affiliation: Dept. of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Denmark; International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Denmark.
authors.forename: Ewa
authors.initials: E
authors.lastname: Rajpert-De Meyts
authors.affiliation: Dept. of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Denmark; International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Denmark. Electronic address: kristian@almstrup.net.
authors.forename: Kristian
authors.initials: K
authors.lastname: Almstrup
mesh_terms: D045744:Cell Line, Tumor; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015870:Gene Expression; D042421:Histone Code; D006801:Humans; D008297:Male; D009154:Mutation; D010641:Phenotype; D011379:Prognosis; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics*; D018239:Seminoma / Q000235:genetics* / Q000473:pathology; D013736:Testicular Neoplasms / Q000235:genetics* / Q000473:pathology; D055815:Young Adult
chemical_list: C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf
keywords: Epigenetics; chromatin; germ cell neoplasms; seminoma