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E-GEOD-65027 - Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines [methylation]

Released on 15 January 2016, last updated on 24 January 2016
Homo sapiens
Samples (4)
Array (1)
Protocols (6)
Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. The initial lesion is believed to be the relatively benign precursor lesion (ICGNU), from which either highly chemosensitive seminomas or the more aggressive non-seminomas develop. Previous analyses of selected genes have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. However, the genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours’ biology have not yet been established. Here genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data. This demonstrated that the seminoma cells exhibited very little aberrant DNA methylation while non-seminoma cells exhibited very high levels of DNA methylation. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested did indeed play a role in their silencing and many of these genes were also differentially expressed in primary tumours. Through this approach the genes silenced in the various GCT cell lines were identified. Conclusions: Several pluripotency-associated genes, never before implicated in this type of cancer, were identified as a major functional group of silenced genes. Silencing of these factors that normally suppress somatic differentiation might play an important role in the progression to non-seminoma formation. Genomic DNA and RNA was extracted from cell lines representing four subtypes of GCT. RNA was subjected to Affymetric expression array analysis while DNA was bisulfite treated and analysed using Illumina Infinium 450K arrays. Statistical approaches were used to correlate methylation and expression for each gene.
Experiment type
methylation profiling by array 
Benjamin Squibb, Denise Sheer, Dzul A Noor, Jaime Hughes, Janet Shipley, Jennie N Jeyapalan, Matthew Carr, Paul J Scotting, Safiah Alhazmi
Investigation descriptionE-GEOD-65027.idf.txt
Sample and data relationshipE-GEOD-65027.sdrf.txt
Processed data (1)
Additional data (1)
Array designA-GEOD-13534.adf.txt