Investigating effects of epigenetic modulation in acute myeloid leukaemia

Lund, K., Cole, J., McBryan, T., Copland, M. and Adams, P. (2014) Investigating effects of epigenetic modulation in acute myeloid leukaemia. Lancet, 383(Supl 1), S70. (doi: 10.1016/S0140-6736(14)60333-0) (PMID:19345831) (PMCID:PMC2866651)

Abstract

Background: Acute myeloid leukaemia (AML) is one of the commonest haemopoietic cancers; despite intensive clinical trial developments there has been little change in survival over the past 20 years. A major focus of research is the identification of less toxic regimens that offer the possibility of response above that of supportive care. Epigenetic therapies, such as the DNA methyltransferase inhibitor azacitidine, offer a novel approach to the treatment of this disease. Despite increasing use in the clinic, the mechansim by which azacitidine regulates gene transcription remains unclear—in particular, whether induction of gene expression change is directly methylation-dependent or secondary to indirect downstream effects. We aimed to investigate the genome-wide effects of azacitidine on DNA methylation and gene transcription in vitro. Methods: Using an acute leukaemia cell line (OCI-AML3), we compared methylation and gene expression in OCI-AML3 cells treated with and without azacitidine. For the best possible comparison, we used whole genome bisulfite sequencing and RNA-Seq. Using these data, we aimed to identify the molecular variables that determine a gene's responsiveness to azacitidine. Findings: We found that a low dose of azacitidine, which resulted in DNA hypomethylation but was not toxic enough to acutely arrest DNA synthesis and cell proliferation, induced widespread methylation loss, of about 50%, across the genome. This demethylation was uniform, rather than selectively targeted, across all genomic features. Hence, the absolute loss of methylation was proportional to the starting density of methylation in a given region of the genome. Azacitidine induced significant gene expression change in 3·4% of all genes with both losses and gains of gene expression (false discovery rate <0·05). We found no evidence that azacitidine-induced hypomethylation at CpG islands was preferentially associated with upregulation of gene expression. However, at genes undergoing significant changes in expression (either increased or decreased expression), low CpG island methylation in untreated cells weakly correlated with altered transcription (r2=−0·252, p=1·46 × 10−14). In line with this finding, a high level of gene expression in untreated cells also correlated with azacitidine-induced alteration in gene expression. Neither of these variables was specifically associated with either upregulation or downregulation of gene expression. Interpretation: We found an inconsistency between the widespread extent of DNA methylation loss and the limited gene expression changes in this model. Therefore, the simple view that DNA methyltransferase inhibitor-induced demethylation at CpG island promoters is primarily responsible for reactivation of previously silenced genes could be an oversimplification. We conclude that azacitidine interacts with other, as yet uncharacterised, factors that contribute to transcriptional changes in hypomethylated CpG island containing genes. This observation provides a clinical rationale for the combination of DNA methyltransferase inhibitors with other epigenetic agents whose function could be synergistically exploited to modify the transcriptional profile of the leukaemia genome.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cole, Mr John and Adams, Professor Peter and Lund, Dr Kirstin and Copland, Professor Mhairi
• Authors: Lund, K., Cole, J., McBryan, T., Copland, M., and Adams, P.
• College/School: College of Medical Veterinary and Life Sciences > School of Cancer Sciences; College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Lancet
• Publisher: Elsevier
• ISSN: 0140-6736
• ISSN (Online): 1474-547X