Lastly, our work underscores the role of negative regulators of receptor RTKs in cellular utilization of these receptors and should be taken into consideration for drug response evaluation of any molecular targeted therapies to other RTKs. Epigenetic changes are increasingly recognised as a major characteristic of many human diseases. Almost all CpG dinucleotides are methylated, except those located in CpG islands, which lack DNA methylation setting them apart from bulk genomic DNA. Aberrant methylation of CGIs in or near the promoter region of tumour suppressor genes represents one of the most consistent hallmarks of human cancers and these TSGs are often silenced in haematopoietic malignancies. Thus, CGI methylation represents an ideal candidate for diagnostic and prognostic cancer markers. Myelodysplastic syndromes comprise a heterogeneous group of bone marrow disorders affecting mainly elderly patients. A number of gene mutations and cytogenetic changes have been implicated in the pathogenesis of MDS, including mutations of RAS, TP53 and RUNX1, and more recently ASXL1, c-CBL, DNMT3A, IDH1/2, TET2, and EZH2. Nevertheless, these genetic abnormalities do not fully explain the pathogenesis of MDS because they are also commonly found in other myeloid malignancies and roughly 20% of MDS patients have no known genetic mutation. On the other hand, hypermethylation of specific genes, such as p15, E-cadherin, ER, MYOD1, and HIC1, have been noted, and whole genome studies have revealed that MDS patients contain aberrant DNA methylation in thousands of genes compared to normal haematopoietic progenitor cells. The process of cytosine methylation is reversible and may be altered by biochemical and biological manipulation, making it an attractive target for therapeutic intervention. Epigenetic therapy with hypomethylating drugs is now the standard of care for MDS. Two prominent examples are the cytosine analogs 5-azacytidine and 2′-deoxy-5-azacytidine. These are potent inhibitors of DNA methyltransferases and have been approved for MDS treatment. Recent efforts have focused on lowering the dosage of azacytidine and decitabine to reduce toxicity. However, the effect of low-dose treatment on the MDS methylome is still unclear. In this report, we have determined concentrations of AZA and DAC that allow prolonged treatment in a leukemic cell model, and have determined how this affects global CGI methylation using a microarray approach. Our results show that the methylome was selectively demethylated by lowdose treatments and that gene-body CGIs were more resistant to this process. We also provide evidence that prolonged lowdose AZA and DAC treatment is sustainably effective in modifying the epigenome. We next examined the correlation between expression and methylation levels. We performed transcriptome analyses for both mock and drug AB1010 VEGFR/PDGFR inhibitor treated SKM-1 cells. The level of methylation in individual islands was summarised by the mean log2-ratios, and these were plotted against expression levels. Since individual genes can overlap multiple CGIs we divided the CGIs into classes depending on their overlap with gene features as described above and made separate plots for each class. In the control cells, a clear anticorrelation between gene expression and methylation was observed for CGIs overlapping promoter elements. This correlation was stronger for promoter CGIs with low CG content, which may be due to the general paucity of highly methylated high CG density CGIs. The data also suggested that relationships between expression levels and DNA methylation exist at non-promoter CGIs. However, these relationships were not as robust with Nutlin-3 observations depending on the summary statistics used, and apparently restricted to subsets of islands within each 
class rather than generally true for the full set of islands. Interestingly, this anti-correlation was lost or markedly reduced in AZA and DAC treated cells. However, expression levels within AZA and DAC treated cells were still anti-correlated against promoter methylation levels in control cells. This strongly suggests that promoter CGI demethylation was not generally sufficient to modify expression patterns, and emphasizes the roles of other means of maintaining cell state. Although a correlation between CGI demethylation and upregulation of gene expression was not generally observed, we identified a small number of genes where expression appeared to change following demethylation.