Novel Method of Identifying DNA Methylation Fingerprint of Acute Myeloid Leukaemia

2017 ◽  
pp. 189-196
Author(s):  
Agnieszka Cecotka ◽  
Joanna Polanska
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Novel Method ◽  
Acute Myeloid

scholarly journals Identification of aberrant DNA methylation in pediatric acute myeloid leukaemia by multiplex methylation sensitive PCR

2016 ◽  
Vol 27 ◽  
pp. vi323 ◽  
Author(s):  
V. Rudenko ◽  
S. Kazakova ◽  
A. Tanas ◽  
A. Popa ◽  
V. Nemirovchenko ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Aberrant Dna Methylation ◽  
Acute Myeloid

scholarly journals DNA methylation analysis ofALOX12andGSTM1in acute myeloid leukaemia identifies prognostically significant groups

2012 ◽  
Vol 159 (2) ◽  
pp. 182-190 ◽  
Author(s):  
Robert S. Ohgami ◽  
Lisa Ma ◽  
Li Ren ◽  
Olga K. Weinberg ◽  
Mahesh Seetharam ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Methylation Analysis ◽  
Dna Methylation Analysis ◽  
Acute Myeloid

CBFβ/MYH11 Hypomethylation Signature In Patients With Acute Myeloid Leukaemia

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3774-3774
Author(s):  
Hana Hajkova ◽  
Markus H.-Y. Fritz ◽  
Jiri Schwarz ◽  
Jana Markova ◽  
Martin Vostry ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Clustering Analysis ◽  
Bisulfite Pyrosequencing ◽  
Molecular Abnormalities ◽  
Cross Experiment ◽  
Genomic Regions ◽  
Acute Myeloid ◽  
Control Samples

Abstract It has been shown that changes in DNA methylation pattern in patients with acute myeloid leukaemia (AML) may both reflect specific molecular abnormalities or characterize a group of patients without a known molecular aberration. Studying genes that are epigenetically deregulated in different groups of patients may contribute to a more detailed understanding of pathways involved in leukemic transformation. For 15 samples (14 AMLs of diverse clinical and genetic background and pool of CD34+ control samples) SureSelectXT Human Methyl-Seq system (Agilent) was used to interrogate DNA methylation of selected regions (84 megabases in total) of their genomes. Targeted bisulfite libraries were run on a HiSeqTM2000 sequencer (Illumina) using 105 bp paired-end sequencing reads. Methylation status of candidate regions was verified using 454 bisulfite pyrosequencing (Roche). The expression levels of selected genes were assessed with TaqMan Gene Expression Assays (Applied Biosystems). Targeted methylation data was correlated with previously obtained whole-genome bisulfite (WGBS) data for the cross-experiment (WGBS/target enrichment) samples (n=3), taking into account positions with minimal coverage of 10. There was a strong positive correlation (R≥0.97) for all three samples. Pairwise Pearson correlations were computed for all (targeted and WGBS) samples and formed the basis of a hierarchical clustering analysis. The cross-experiment replicates clustered together. From the clinical and molecular characteristics, only CBFβ/MYH11+ patients (n=2) clustered together in all clustering analysis performed (using CpG in/out CGIs or all CpG regardless of location). None of the other molecular abnormalities (i.e. DNMT3A mutations, MLL translocations, NPM1 mutations, FTL3/ITDs and CEPBα mutations) formed clusters. We did not observe any effect of clinical status of AML (de novo, secondary AML with dysplastic changes or relapsed AML). Based on this observation, we extracted genomic regions being uniquely differentially methylated for CBFβ/MYH11+ patients. There was a clear tendency towards hypomethylation in 125 regions out of 182 (69%) displaying lower DNA methylation levels compared to CD34+ pool of controls. All CBFβ/MYH11 differentially methylated regions (DMRs) were uploaded to GREAT (http://bejerano.stanford.edu/great/public/html) and enrichment for genes described as upregulated in inv(16) AML (CBFβ/MYH11+) was seen (reported in Valk et al., NEJM 2004, ID: VALK_AML_CLUSTER_9). This enrichment set comprised 10 genomic regions assigned for 6 genes – MN1, SPARC, ST18, DHRS3, FAM171A and BAHCC1.MN1, SPARC, ST18 and DHRS3 – were chosen for hypomethylation verification by 454 bisulfite pyrosequencing. Altogether 11 CBFβ/MYH11+ (inv(16)), 11 non-inv(16) AML M4, 6 other AML subtypes and 5 healthy control samples were examined by 454 pyrosequencing. Average levels of DNA methylation for selected regions were significantly lower for inv(16) versus non-inv(16) AML M4, other AML subtypes and healthy controls (P<0.0001). The 454 results support our theory about site specific CBFβ/MYH11 hypomethylation signature. MN1 gene was overexpressed in 82% of inv(16) AML versus 42% of non-inv(16) patients (χ2 test, P=0.009). Interestingly, MN1 overexpression in non-inv(16) patients was not accompanied with MN1 hypomethylation suggesting different mechanisms of gene deregulation in various AML subtypes. We found a new hypomethylation signature in CBFβ/MYH11+ patients. The described hypomethylated regions were assigned to genes known as being overexpressed in inv(16) patients. As for MN1 gene, we can speculate that different mechanism responsible for its overexpression in inv(16) versus non-inv(16) patients may explain discrepancy between its negative prognostic value in cytogenetically normal AML patients and generally good outcome of inv(16) patients. This study was supported by the project (Ministry of Health, Czech Republic) for conceptual development of research organization (00023736, IHBT) and was a part of the COST Action BM0801 (EuGESMA). Disclosures: No relevant conflicts of interest to declare.

scholarly journals Oncogenic Roles and Inhibitors of DNMT1, DNMT3A, and DNMT3B in Acute Myeloid Leukaemia

2019 ◽  
Vol 14 ◽  
pp. 117727191984645 ◽  
Author(s):  
Kah Keng Wong ◽  
Charles H Lawrie ◽  
Tina M Green
Keyword(s):  
Dna Methylation ◽  
Clinical Trials ◽  
Acute Myeloid Leukaemia ◽  
Clinical Response ◽  
Myeloid Leukaemia ◽  
Dna Methyltransferases ◽  
Clinical Settings ◽  
Hypomethylating Agents ◽  
Dnmt Inhibitors ◽  
Acute Myeloid

Epigenetic alteration has been proposed to give rise to numerous classic hallmarks of cancer. Impaired DNA methylation plays a central role in the onset and progression of several types of malignancies, and DNA methylation is mediated by DNA methyltransferases (DNMTs) consisting of DNMT1, DNMT3A, and DNMT3B. DNMTs are frequently implicated in the pathogenesis and aggressiveness of acute myeloid leukaemia (AML) patients. In this review, we describe and discuss the oncogenic roles of DNMT1, DNMT3A, and DNMT3B in AML. The clinical response predictive roles of DNMTs in clinical trials utilising hypomethylating agents (azacitidine and decitabine) in AML patients are presented. Novel hypomethylating agent (guadecitabine) and experimental DNMT inhibitors in AML are also discussed. In summary, hypermethylation of tumour suppressors mediated by DNMT1 or DNMT3B contributes to the progression and severity of AML (except MLL-AF9 and inv(16)(p13;q22) AML for DNMT3B), while mutation affecting DNMT3A represents an early genetic lesion in the pathogenesis of AML. In clinical trials of AML patients, expression of DNMTs is downregulated by hypomethylating agents while the clinical response predictive roles of DNMT biomarkers remain unresolved. Finally, nucleoside hypomethylating agents have continued to show enhanced responses in clinical trials of AML patients, and novel non-nucleoside DNMT inhibitors have demonstrated cytotoxicity against AML cells in pre-clinical settings.

DNA methylation and targeted sequencing of methyltransferases family genes in canine acute myeloid leukaemia, modelling human myeloid leukaemia

2016 ◽  
Vol 15 (3) ◽  
pp. 910-918 ◽  
Author(s):  
I. Bronzini ◽  
L. Aresu ◽  
M. Paganin ◽  
L. Marchioretto ◽  
S. Comazzi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Targeted Sequencing ◽  
Acute Myeloid

Array-based DNA methylation profiling in acute myeloid leukaemia

2011 ◽  
Vol 155 (1) ◽  
pp. 65-72 ◽  
Author(s):  
Stefan Wilop ◽  
Agustín F. Fernandez ◽  
Edgar Jost ◽  
James G. Herman ◽  
Tim H. Brümmendorf ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Dna Methylation Profiling ◽  
Methylation Profiling ◽  
Acute Myeloid

Functional and Molecular Consequences of the Dnmt3aR882H Mutation in Acute Myeloid Leukaemia

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2424-2424 ◽  
Author(s):  
Malgorzata Gozdecka ◽  
Milena M. Mazan ◽  
Vivek Iyer ◽  
Anna Farne ◽  
Eshwar Meduri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Molecular Mechanism ◽  
Histone Modifications ◽  
Dominant Negative Effect ◽  
Integrated Analysis ◽  
Conditional Expression ◽  
Acute Myeloid

Abstract The de novo DNA Methyltransferase 3A (DNMT3A) gene is one of the most commonly mutated gene in acute myeloid leukaemia with a normal karyotype (AML-NK). Approximately two thirds of mutations are heterozygous and affect codon R882, located within the methytransferase domain. Also, we and others have shown that these mutations occur in a significant proportion of haematologically normal people and behave as leukaemia-initiating changes. DNMT3A mediates the transfer of a methyl group from s-adenosylmethionine (SAM) to the 5' carbon of cytosine residues at CpG dinucleotides. The DNMT3A protein domains bind to unmethylated H3K4, a repressive histone mark, as well as the H3K36Me3 mark associated with active transcription. DNA methylation is linked to histone modifications and DNMT3A binds to class I and II histone deacetylases (HDAC) and histone methyltransferases (HMT), such as SETDB1 and G9a, as well components of Polycomb repressive complex 2 (PRC2). DNMT3AR882H has been reported to exert a dominant-negative effect on wild type (WT) DNMT3A, with a significant reduction of its enzymatic activity. In AML samples, the R882 mutation correlates with global hypomethylation, particularly at CpG islands, shores and promoters, although some promoter hypermethylation has also been reported. However, the molecular mechanism, through which DNMT3AR882H alters methylation to drives leukaemia, remains unknown. In order to understand the molecular and functional consequences of the DNMT3AR882H mutation in leukaemogenesis we developed a mouse model (Dnmt3afloxR882H/+), whereby targeting of the Dnmt3a allele does not inactivate the native locus. This allows conditional expression of the mutant protein within haematopoietic stem and progenitor cells that have developed in the presence of normal levels of Dnmt3a. Dnmt3afloxR882H/+ mice were crossed with mice carrying an interferon-inducible Cre recombinase allele (Mx1-Cre). Upon Cre induction with pIpC the endogenous Dnmt3a exon 23 (last exon), was efficiently replaced by the human exon 23 carrying the R882H mutation. This was confirmed at both the DNA and the RNA level. In order to investigate the molecular effects of Dnmt3aR882H, we analysed pre-leukaemic haematopoietic cells (in mice 5-6 weeks post Cre-induction). We observed that Dnmt3aR882H/+ mutant bone marrow (BM) cells had markedly enhanced self-renewal potential as manifested by increased serial replating in cytokine supplemented methylcellulose media in comparison to WT mice. We next examined the relative haemopoietic reconstitution efficiency of Dnmt3aR882H/+ BM cells in a competitive setting. Dnmt3aR882H/+ BM (CD45.2) cells were mixed with WT competitor BM (CD45.1) cells at a ratio of 1:2 and transplanted into lethally irradiated recipient mice (CD45.1/45.2). The analysis of blood chimerism in recipients indicated an increased contribution from Dnmt3aR882H/+ in comparison to WT cells, indicating the enhanced ability of Dnmt3aR882H/+ BM cells to engraft and reconstitute recipient mice. Currently, we are addressing the role of Dnmt3aR882H in the spontaneous leukaemia development alone as well as in rational combinations with other mutations present in human AML. Additionally, to elucidate the molecular mechanism underlying the striking haematopoietic phenotypes ofDnmt3aR882H/+ we have performed analyses of DNA methylation and hydroxymethylation patterns in the haematopoietic progenitor compartment (lineage negative cell population) of Dnmt3aR882H/+ and WT mice, using reduced representation oxidative bisulfite sequencing (RRoxBS) in the pre-leukaemic setting. Moreover, due to cross-talk between Dnmt3a mediated DNA methylation and other chromatin states, we have analysed Dnmt3aR882H-associated changes in histone tail modifications, using ChIP-Seq. As the DNA and histone modifications associated with Dnmt3aR882H are likely to lead to alter global gene expression, we also performed RNAseq analysis in Dnmt3aR882H/+ and WT mice. Currently, we are conducting an integrated analysis, coupling DNA and histone modifications to aberrant gene expression and Dnmt3aR882H-dependent phenotypes. We predict that this work will provide a detailed understanding of the molecular and cellular effects of DNMT3A-R882H and in so doing reveal rational therapeutic approaches for patients with this common and aggressive subtype of AML. Disclosures No relevant conflicts of interest to declare.

The acute myeloid leukaemia market

2019 ◽  
Vol 19 (4) ◽  
pp. 233-234
Author(s):  
Jorrit Schaefer ◽  
Sorcha Cassidy ◽  
Rachel M. Webster
Keyword(s):  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Acute Myeloid
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