title: CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia.
abstract: BACKGROUND
  Studying DNA methylation changes in the context of structural rearrangements and point mutations as well as gene expression changes enables the identification of genes that are important for disease onset and progression in different subtypes of acute myeloid leukemia (AML) patients. The aim of this study was to identify differentially methylated genes with potential impact on AML pathogenesis based on the correlation of methylation and expression data.
  
  
  METHODS
  The primary method of studying DNA methylation changes was targeted bisulfite sequencing capturing approximately 84 megabases (Mb) of the genome in 14 diagnostic AML patients and a healthy donors' CD34+ pool. Subsequently, selected DNA methylation changes were confirmed by 454 bisulfite pyrosequencing in a larger cohort of samples. Furthermore, we addressed gene expression by microarray profiling and correlated methylation of regions adjacent to transcription start sites with expression of corresponding genes.
  
  
  RESULTS
  Here, we report a novel hypomethylation pattern, specific to CBFB-MYH11 fusion resulting from inv(16) rearrangement that is associated with genes previously described as upregulated in inv(16) AML. We assume that this hypomethylation and corresponding overexpresion occurs in the genes whose function is important in inv(16) leukemogenesis. Further, by comparing all targeted methylation and microarray expression data, PBX3 differential methylation was found to correlate with its gene expression. PBX3 has been recently shown to be a key interaction partner of HOX genes during leukemogenesis and we revealed higher incidence of relapses in PBX3-overexpressing patients.
  
  
  CONCLUSIONS
  We discovered new genomic regions with aberrant DNA methylation that are associated with expression of genes involved in leukemogenesis. Our results demonstrate the potential of the targeted approach for DNA methylation studies to reveal new regulatory regions.
authors.forename: Hana
authors.initials: H
authors.lastname: Hájková
authors.forename: Markus Hsi-Yang
authors.initials: MH
authors.lastname: Fritz
authors.forename: Cedrik
authors.initials: C
authors.lastname: Haškovec
authors.forename: Jiří
authors.initials: J
authors.lastname: Schwarz
authors.forename: Cyril
authors.initials: C
authors.lastname: Šálek
authors.forename: Jana
authors.initials: J
authors.lastname: Marková
authors.forename: Zdeněk
authors.initials: Z
authors.lastname: Krejčík
authors.forename: Michaela
authors.initials: M
authors.lastname: Dostálová Merkerová
authors.forename: Arnošt
authors.initials: A
authors.lastname: Kostečka
authors.forename: Martin
authors.initials: M
authors.lastname: Vostrý
authors.forename: Ota
authors.initials: O
authors.lastname: Fuchs
authors.forename: Kyra
authors.initials: K
authors.lastname: Michalová
authors.forename: Petr
authors.initials: P
authors.lastname: Cetkovský
authors.forename: Vladimír
authors.initials: V
authors.lastname: Beneš
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D016000:Cluster Analysis; D019175:DNA Methylation / Q000235:genetics*; D005260:Female; D015973:Gene Expression Regulation, Leukemic / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D053208:Kaplan-Meier Estimate; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000401:mortality; D008297:Male; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D011379:Prognosis; D016016:Proportional Hazards Models; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; C095514:CBFbeta-MYH11 fusion protein; D018398:Homeodomain Proteins; D015514:Oncogene Proteins, Fusion; D011518:Proto-Oncogene Proteins; C090466:proto-oncogene protein Pbx3