Disease progression and accompanying global DNA methylation in the PU.1 mouse model. (A) Representative histological sections of mouse forelegs showing BM of PU.1-wt and PU.1-kd animals of different disease stages (preleukemic stage, BM blasts <20%; early leukemic stage with residual non-malignant hematopoiesis, BM blasts between 20% and 50%; late leukemic stage with full blown AML, BM blasts >50%). Sections were stained with hematoxylin and eosin; 400× original magnification. (B) PCA based on normalized relative probe intensities between PU.1-kd versus PU.1-wt animals. In total, 88,358 array probes per sample were analyzed. Principal component (PC)1 explains the largest variances of the entire data set and implicates diversification of the DNA methylation patterns in late leukemic stage animals. (C) Circos plot showing the hypermethylated probes of the three disease stages (preleukemic, early leukemic, late leukemic). The outer circle indicates the G-banded mouse chromosomes, the differently colored lines in the inner circles represent hypermethylated probes of the three stages. (D) Percentage of hyper- and hypomethylated probes (DMPs) in the different disease stages (preleukemic, early leukemic, late leukemic). SAM was performed to identify the DMPs. Out of 88,358 probes, 20,787 were aberrantly methylated in at least one disease stage. (E) Venn diagrams showing unique and common hyper- and hypomethylated probes in different disease stages.