Age-related epigenetic drift in the pathogenesis of MDS and AML - PubMed (original) (raw)

doi: 10.1101/gr.157529.113. Epub 2014 Jan 10.

Sheryl M Gough, Naoko Watanabe-Okochi, Yue Lu, Nianxiang Zhang, Ryan J Castoro, Marcos R H Estecio, Jaroslav Jelinek, Shoudan Liang, Toshio Kitamura, Peter D Aplan, Jean-Pierre J Issa

Affiliations

Shinji Maegawa et al. Genome Res. 2014 Apr.

Abstract

The myelodysplastic syndrome (MDS) is a clonal hematologic disorder that frequently evolves to acute myeloid leukemia (AML). Its pathogenesis remains unclear, but mutations in epigenetic modifiers are common and the disease often responds to DNA methylation inhibitors. We analyzed DNA methylation in the bone marrow and spleen in two mouse models of MDS/AML, the NUP98-HOXD13 (NHD13) mouse and the RUNX1 mutant mouse model. Methylation array analysis showed an average of 512/3445 (14.9%) genes hypermethylated in NHD13 MDS, and 331 (9.6%) genes hypermethylated in RUNX1 MDS. Thirty-two percent of genes in common between the two models (2/3 NHD13 mice and 2/3 RUNX1 mice) were also hypermethylated in at least two of 19 human MDS samples. Detailed analysis of 41 genes in mice showed progressive drift in DNA methylation from young to old normal bone marrow and spleen; to MDS, where we detected accelerated age-related methylation; and finally to AML, which markedly extends DNA methylation abnormalities. Most of these genes showed similar patterns in human MDS and AML. Repeat element hypomethylation was rare in MDS but marked the transition to AML in some cases. Our data show consistency in patterns of aberrant DNA methylation in human and mouse MDS and suggest that epigenetically, MDS displays an accelerated aging phenotype.

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Figures

Figure 1.

Figure 1.

MCAM analysis in mouse MDS models. (A) R-I plot of the probes with FDR at 5% and a fold change greater than two for MCAM. An R-I plot displays the log2(R/G) ratio for each element on the array as a function of the log10(R × G) product intensities and can reveal systematic intensity-dependent effects in the measured log2 (ratio) values. The red and blue spots indicate probes hypermethylated and hypomethylated in diseased samples, respectively. (B) Hierarchical clustering analysis of mouse MCAM. Heat-map analysis showing the MCAM results in six model mice. Red, yellow, and blue correspond to hypermethylated, nonchanged, and hypomethylated loci, respectively. For clarity we excluded probes that were unchanged in all samples. (C) Venn diagram of individual differences of hyper- and hypomethylated genes in NHD13 mice analyzed by MCAM. Each circle represents one individual. (D) Venn diagram of mutational differences of hyper- and hypomethylated genes in RUNX1 mice analyzed by MCAM. Each circle represents one individual. (E) Venn diagram of hyper- and hypomethylated genes overlapped between NHD13 and RUNX1 mice analyzed by MCAM. Each circle represents a genotype.

Figure 2.

Figure 2.

DNA methylation profiles by bisulfite pyrosequencing analysis. (A) DNA methylation analysis in MDS mice. The percentages of methylated cytosines in the samples as obtained from pyrosequencing analysis. Each dot corresponds to one animal. We show here data on Grm7, Hand2, Hoxc12, Klf14, and Sox11. The other 33 hypermethylated genes are shown in Supplemental Figures S1 and S2. The averaged data were derived from the methylation data of 38 genes prone to hypermethylation. The bar in the graphs represents the median. (B) Methylation profiles of hypermethylated genes with age in mouse bone marrow and spleen. Association of the averaged percentages of methylated cytosines in the samples as obtained from pyrosequencing (_y_-axis) with age (_x_-axis) for significant genes.

Figure 3.

Figure 3.

Hierarchical clustering analysis of methylation markers in mouse. (A) Hierarchical clustering analysis in bone marrow. Green to red cells indicate the range of methylation percentage from 0 to 95.3. The color codes for mouse strain, tissues, age, and diagnosis are listed on the left side. Orange arrowheads indicate samples for MCAM with number of methylated genes by MCAM. (B) Hierarchical clustering analysis in spleen.

Figure 4.

Figure 4.

DNA methylation analyses in humans. (A) Hierarchical clustering analysis of human MCAM. Heat-map analysis showing the MCAM results in 19 MDS patients. Red, yellow, and blue correspond to hypermethylated, nonchanged, and hypomethylated loci, respectively. All probes that were unchanged in all samples were excluded from the analysis. The bar graph on the left shows the methylation percentage of LINE-1 by pyrosequencing analysis. Red-colored boxes on the right side represent the CIMP-positive case defined by MCAM assay. (B) DNA methylation profiles by DREAM analysis in human cord blood, adult blood, MDS, and AML patients. The percentages of methylated cytosines in the samples as obtained from DREAM analysis. Each dot corresponds to one individual. We show here data on HOXC12, SOX11, and ESPNL. The averaged data were derived from the methylation data of 26 hypermethylated genes listed in Supplemental Table S14. The bar in the graphs represents the median.

Figure 5.

Figure 5.

Methylation analysis of repetitive elements in mouse. (A) Methylation profiles of LINE-1, SINE B1, and major satellite DNA by pyrosequencing analysis. (B) Association of the methylation percentages between LINE-1 (_y_-axis), SINE B1 (_x_-axis), and major satellite DNA (_x_-axis) in all samples. Sample codes are on the right. The Spearman test was used to determine correlations, with significance set at P < 0.05. R represents a measure of the linear relationship between two variables, and varies from −1 to +1.

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