Altered Gene Expression in the Bone Marrow Microenvironment of Myelodysplastic Syndromes

Abstract

Introduction: Myelodysplastic syndromes (MDS) are a group of heterogenous diseases characterized by ineffective hematopoiesis and variable degree of increase in blasts with multiple evolutionary stages. Molecular pathogenesis of MDS has been extensively studied, while the molecular change of the MDS bone marrow (BM) microenvironment is rarely known. In this study, we performed cDNA microarray with BM mesenchymal cells of non-hematopoietic origin, and analyzed the differential gene expression in MDS BM microenvironment. Materials and Methods: Primary culture of adherent cell layers (considered as mesenchymal cells) was performed using BM hematopoietic cells obtained from 7 adult normal controls and 7 MDS patients (3 RCMD, 3 RAEB-1 and 1 RAEB-2). cDNA microarray analysis was performed using humanHT-12 expression v.4 bead array (Illumina, San Diego, CA, USA). Data were analyzed using Illumina GenomeStudio v2009.2 (Illumina), and genes with fold change > 1.5 or < – 1.5, p < 0.05 and FDR < 0.05 were considered as differentially expressed genes. Using Ingenuity Pathway Analysis (Ingenuity Systems, www.ingenuity.com) and Cytoscape (www.cytoscape.org), we figured out the gene networks with clinical significance. Results: A total of 669 genes were differentially expressed in MDS (RCMD + RAEB) BM mesenchymal cells – 246 overexpressed and 423 underexpressed. Interferon stimulated genes (ISGs) were consistently overexpressed. Disturbances in genes related with ECM and cytoskeleton composition, transcriptional regulation, ERK-GTPase pathway, PI3K pathway and NFkB pathway were notable. A total of 683 genes and 740 genes were differentially expressed in RCMD BM mesenchymal cells and RAEB BM mesenchymal cells compared with normal. Among them, only 48 genes were in common. Genes related with ECM and cytoskeleton composition and transcriptional regulation were altered in RCMD BM mesenchymal cells, while ISGs and apoptosis related genes were altered in RAEB BM mesenchymal cells. In direct comparison between RCMD and RAEB BM mesenchymal cells, 368 genes were differentially expressed – 86 overexpressed and 282 underexpressed. The dysregulation of cell cycle genes was notable. The differentially expressed genes generated hierarchical clustering which does not clearly separate MDS and normal BM mesenchymal cells, or RCMD and RAEB BM mesenchymal cells. Conclusion and Discussion: Our study provided an overview of altered gene expression of BM microenvironment in adult MDS. The overexpression of ISGs is considered to be the result of the increased level of inflammatory cytokines including interferon-γ in MDS. The alterations in the other pathways probably cause disturbance in normal supportive activity of BM microenvironment, and promote the apoptosis of MDS hematopoietic cells. Only a small portion of genes were commonly observed as differentially expressed genes in RCMD and RAEB BM microenvironment, suggesting that different genetic pathways are involved in the development of RCMD and RAEB, and the alteration in gene expression in BM microenvironment is important in the progression of MDS. Nevertheless, the gene expression profile itself does not clearly distinguish the BM microenvironment of MDS from that of normal, or RAEB from RCMD, probably because BM microenvironment reflect the characteristics of MDS that it is not overt leukemic status or it is a disease of heterogeneity.