Assessing the relationship between DNA methylation and gene expression in germ cell tumoursTools Alhazmi, Safiah (2016) Assessing the relationship between DNA methylation and gene expression in germ cell tumours. PhD thesis, University of Nottingham.
AbstractGerm cell tumours (GCTs) are a class of tumours classified histologically into two main types: seminoma and non-seminoma. Prior studies revealed that there is a significant difference in global DNA methylation between those two types, where non-seminomas represent more differentiated cells and exhibit a high level of methylation compared with seminomas that resemble the precursor cells of GCTs. A number of studies have reported that silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the silenced genes and the genomic targets that are methylated in GCTs have not yet been systematically identified. Furthermore, many methylation studies in GCTs do not include the level of gene expression in their investigation. We hypothesized that the methylation of genes might play an important role in gene silencing in GCTs, so the main focus of this thesis was studying the relationship between the gene methylation and gene expression in GCT cell lines representing seminoma and non-seminoma. We analysed genome methylation and gene expression of these cell lines using the Illumina infinium Human Methylome 450 bead chip system and Affymetrix Gene Chip Human Genome U133 Plus 2.0 arrays, respectively. We also compared our results with gene expression data from primary tumours in order to identify which events were shared in primary GCTs tumour. qPCR analysis was carried out after treatment of cells with the demethylation agent, 5-aza-2-deoxycytidine, to confirm that expression of identified genes was regulated by methylation.
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