DNA methylation and hydroxymethylation patterns in acute myeloid leukemia patients with mutations in DNMT3A and IDH1/2 and their combinations

Article type: Research Article

Authors: Šestáková, Šárka^a | Krejčík, Zdeněk^a | Folta, Adam^b | Cerovská, Ela^a | Šálek, Cyril^a | Merkerová, Michaela Dostálová^a | Pecherková, Pavla^a | Ráčil, Zdeněk^{b; c} | Mayer, Jiří^{b; c} | Cetkovský, Petr^a | Remešová, Hana^{a; *}

Affiliations: [a] Institute of Hematology and Blood Transfusion, Prague, Czech Republic | [b] Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic | [c] Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic

Correspondence: [*] Corresponding author: Hana Remešová, Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic. Tel.: +420 221 977 231; E-mail: hana.remesova@uhkt.cz.

Abstract: BACKGROUND: Aberrant epigenetic patterns are a hallmark of acute myeloid leukemia (AML). Mutations in profound epigenetic regulators DNMT3A and IDH1/2 often occur concurrently in AML. OBJECTIVES: The aim was to analyze DNA methylation, hydroxymethylation and mRNA expression profiles in AML with mutations in DNMT3A and IDH1/2 (individually and in combinations). METHODS: Infinium MethylationEPIC BeadChip (Illumina) covering 850,000 CpGs was utilized. The validation of hydroxy-/methylation data was done by pyrosequencing. HumanHT-12 v4 Expression BeadChip (Illumina) was used for expression examination. RESULTS: Hierarchical clustering analysis of DNA hydroxy-/methylation data revealed clusters corresponding to DNMT3A and IDH1/2 mutations and CD34+ healthy controls. Samples with concurrent presence of DNMT3A and IDH1/2 mutations displayed mixed DNA hydroxy-/methylation profile with preferential clustering to healthy controls. Numbers and levels of DNA hydroxymethylation were low. Uniformly hypermethylated loci in AML patients with IDH1/2 mutations were enriched for immune response and apoptosis related genes, among which hypermethylation of granzyme B (GZMB) was found to be associated with inferior overall survival of AML patients (P= 0.035). CONCLUSIONS: Distinct molecular background results in specific DNA hydroxy-/methylation profiles in AML. Site-specific DNA hydroxymethylation changes are much less frequent in AML pathogenesis compared to DNA methylation. Methylation levels of enhancer located upstream GZMB gene might contribute to AML prognostication models.

Keywords: AML, DNMT3A and IDH1/2 mutations, methylation, hydroxymethylation, GZMB, CHFR

DOI: 10.3233/CBM-182176

Journal: Cancer Biomarkers, vol. 25, no. 1, pp. 43-51, 2019