Use of methylation profiling to identify significant differentially methylated genes in bone marrow mesenchymal stromal cells from acute myeloid leukemia

Abstract

The present study aimed to characterize the epigenetic architecture by studying the DNA methylation signature in bone marrow mesenchymal stem cells (BM‑MSCs) from patients with acute myeloid leukemia (AML). Microarray dataset GSE79695 was downloaded from the Gene Expression Omnibus database. Differentially methylated sites and differentially methylated CpG islands were identified in BM‑MSC samples from patients with AML compared with controls. MicroRNAs (miRs) encoding genes covering differentially methylated sites were found and the regulation network was constructed. Pathway enrichment analysis of hypermethylated genes and hypomethylated genes was performed, followed by protein‑protein interaction (PPI) network construction. Moreover, the identified differentially methylated genes were compared with the leukemia‑related marker/therapeutic genes from the literature. Overall, 228 hypermethylated CpG site probes covering 183 gene symbols and 523 hypomethylated CpG sites probes covering 362 gene symbols were identified in the BM‑MSCs from AML patients. Furthermore, 4 genes with CpG island hypermethylation were identified, including peptidase M20 domain containing 1 (PM20D1). The hsa‑miR‑596‑encoding gene MIR596 was found to be hypermethylated and the regulation network based on hsa‑miR‑596 and its targets (such as cytochrome P450 family 1 subfamily B member 1) was constructed. Hypermethylated and hypomethylated genes were enriched in different Kyoto Encyclopedia of Genes and Genomes pathways, including 'hsa05221: Acute myeloid leukemia' and 'hsa05220: Chronic myeloid leukemia', which the hypomethylated gene mitogen‑activated protein kinase 3 (MAPK3) was involved in. In addition, MAPK3, lysine demethylase 2B and RAP1A, member of RAS oncogene family were hubs in the PPI network of methylated genes. In conclusion, PM20D1 with hypermethylation of CpG islands may be associated with the energy expenditure of patients with AML. Furthermore, the aberrantly hypermethylated miR‑159‑encoding gene MIR159 may be a potential biomarker of AML.

Figure 1

Heat map of DMRs and differentially methylated CpG islands. (A) Heat map of DMRs. Rows indicate different samples, while columns represent CpG site probes. (B) Heat map of differentially methylated CpG islands. DMRs, differentially methylated regions; AML, acute myeloid leukemia.

Figure 2

Regulation network based on the hsa-miR-596 and differentially methylated target genes. Red nodes indicate hypermethylated genes and green nodes represent hypomethylated genes. miR, microRNA.

Figure 3

Kyoto Encyclopedia of Genes and Genomes pathways for the hypomethylated genes.

Figure 4

Protein-protein interaction network of aberrantly methylated genes. Node sizes correspond to the degree value. Red nodes indicate hypermethylated genes and green nodes indicate hypomethylated genes.