title: Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines.
abstract: BACKGROUND
  Originating from Primordial Germ Cells/gonocytes and developing via a precursor lesion called Carcinoma In Situ (CIS), Germ Cell Cancers (GCC) are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS). During physiological germ cell formation/maturation, epigenetic processes guard homeostasis by regulating the accessibility of the DNA to facilitate transcription. Epigenetic deregulation through genetic and environmental parameters (i.e. genvironment) could disrupt embryonic germ cell development, resulting in delayed or blocked maturation. This potentially facilitates the formation of CIS and progression to invasive GCC. Therefore, determining the epigenetic and functional genomic landscape in GCC cell lines could provide insight into the pathophysiology and etiology of GCC and provide guidance for targeted functional experiments.
  
  
  RESULTS
  This study aims at identifying epigenetic footprints in SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in the pathophysiology and etiology of GCC. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data were acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP-sequencing (activating histone modifications (H3K4me3, H3K27ac)). Results indicate known germ cell markers not only to be differentiating between SE and NS at the expression level, but also in the epigenetic landscape.
  
  
  CONCLUSIONS
  The overall similarity between TCam-2/NCCIT support an erased embryonic germ cell arrested in early gonadal development as common cell of origin although the exact developmental stage from which the tumor cells are derived might differ. Indeed, subtle difference in the (integrated) epigenetic and expression profiles indicate TCam-2 to exhibit a more germ cell-like profile, whereas NCCIT shows a more pluripotent phenotype. The results provide insight into the functional genome in GCC cell lines.
authors.affiliation: Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Yvonne G
authors.initials: YG
authors.lastname: van der Zwan
authors.affiliation: Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Martin A
authors.initials: MA
authors.lastname: Rijlaarsdam
authors.affiliation: Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: Rossello
authors.affiliation: Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Notini
authors.affiliation: Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
authors.forename: Suzan
authors.initials: S
authors.lastname: de Boer
authors.affiliation: Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
authors.forename: D Neil
authors.initials: DN
authors.lastname: Watkins
authors.affiliation: Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Ad J M
authors.initials: AJ
authors.lastname: Gillis
authors.affiliation: Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Lambert C J
authors.initials: LC
authors.lastname: Dorssers
authors.affiliation: Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, Australia.
authors.forename: Stefan J
authors.initials: SJ
authors.lastname: White
authors.affiliation: Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Leendert H J
authors.initials: LH
authors.lastname: Looijenga
mesh_terms: D018236:Carcinoma, Embryonal / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D009373:Neoplasms, Germ Cell and Embryonal / Q000235:genetics* / Q000473:pathology; D018239:Seminoma / Q000235:genetics* / Q000473:pathology