title: Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.
abstract: Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML) we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. Two genes (SPHKAP and DPP6) with significantly methylated promoters were of interest and further analysis of their expression showed them to be repressed in AML. We also demonstrated considerable cytogenetic subtype specificity in the methylomes affecting different genomic features. Significantly distinct patterns of hypomethylation of certain interspersed repeat elements were associated with cytogenetic subtypes. The methylation patterns of members of the SINE family tightly clustered all leukemic patients with an enrichment of Alu repeats with a high CpG density (P<0.0001). We were able to demonstrate significant inverse correlation between intragenic interspersed repeat sequence methylation and gene expression with SINEs showing the strongest inverse correlation (R(2) = 0.7). We conclude that the alterations in DNA methylation that accompany the development of AML affect not only the promoters, but also the non-promoter genomic features, with significant demethylation of certain interspersed repeat DNA elements being associated with AML cytogenetic subtypes. MeDIP-seq data were validated using bisulfite pyrosequencing and the Infinium array.
authors.affiliation: Centre of Haemato-Oncology, Barts Cancer Institute, Barts and the London School of Medicine, Queen Mary University, London, United Kingdom.
authors.forename: Marwa H
authors.initials: MH
authors.lastname: Saied
authors.forename: Jacek
authors.initials: J
authors.lastname: Marzec
authors.forename: Sabah
authors.initials: S
authors.lastname: Khalid
authors.forename: Paul
authors.initials: P
authors.lastname: Smith
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Down
authors.forename: Vardhman K
authors.initials: VK
authors.lastname: Rakyan
authors.forename: Gael
authors.initials: G
authors.lastname: Molloy
authors.forename: Manoj
authors.initials: M
authors.lastname: Raghavan
authors.forename: Silvana
authors.initials: S
authors.lastname: Debernardi
authors.forename: Bryan D
authors.initials: BD
authors.lastname: Young
mesh_terms: D000208:Acute Disease; D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D004152:Dipeptidyl-Peptidases and Tripeptidyl-Peptidases / Q000235:genetics; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D018922:HL-60 Cells; D006801:Humans; D051796:Inhibitor of Differentiation Proteins / Q000235:genetics; D007951:Leukemia, Myeloid / Q000235:genetics*; D009419:Nerve Tissue Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D015221:Potassium Channels / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C490128:ID4 protein, human; D051796:Inhibitor of Differentiation Proteins; D009419:Nerve Tissue Proteins; D015221:Potassium Channels; C466999:SPHKAP protein, human; C503535:DPP6 protein, human; D004152:Dipeptidyl-Peptidases and Tripeptidyl-Peptidases