RRBS and the Epigenetic Effects of Steroids in ALL

Acute lymphoblastic leukaemia (ALL) is a malignant proliferation of immature lymphocytes, mainly occurring in childhood. The pathogenesis of the disease is characterised by multiple molecular abnormalities, including aberrant gene expression and abnormal patterns of DNA methylation. This project focussed on DNA methylation, the presence of methyl groups on the 5’ position of cytosine residues, which has a profound effect on gene expression and regulation. This project investigated the possibility that glucocorticoid drugs, used in the treatment of ALL, may induce changes in DNA methylation patterns in ALL cells, as part of their more global effects on gene expression. This hypothesis was based on previous reports of changes in DNA methylation in response to glucocorticoid exposure in non-ALL cells, in particular rat hepatoma cells. The ALL cell-line, NALM-6, was chosen to culture model ALL cell populations, and cells were exposed to the glucocorticoid dexamethasone and compared to unexposed cells. The massively parallel bisulphite sequencing technique Reduced Representation Bisulphite Sequencing (RRBS) was used to compare the DNA methylation patterns of glucocorticoid-exposed and unexposed cells across the genome. The RRBS results were then analysed statistically, using generalised estimating equations. The statistical analysis of the RRBS results found 281 areas of the genome with significant differences in methylation between the dexamethasone-exposed and unexposed NALM-6 cells. However, these differences could not be validated using a separate biochemical technique, Sequenom MassArray. Therefore, we cannot definitively conclude that reproducible changes in DNA methylation patterns occur in response to dexamethasone exposure