Whole-Genome DNA Methylation Sequencing Reveals Epigenetic Changes in Myelodysplastic Syndromes

Abstract

Epigenetic dysregulation of cancer-associated genes has been identified to contribute to the pathogenesis of myelodysplastic syndromes (MDS). However, few studies have elucidated the whole-genome DNA methylation in the initiation pathogenesis of MDS. Reduced representation bisulfite sequencing was performed in five de novo MDS patients and four controls to investigate epigenetic alterations in MDS pathogenesis. The mean global methylation in five MDS patients showed no significant difference compared with the four controls. In depth, a total of 1,459 differentially methylated fragments, including 759 hypermethylated and 700 hypomethylated fragments, were identified between MDS patients and controls. Targeted bisulfite sequencing further identified that hypermethylation of DLEU7, FOXR1, LEP, and PANX2 were frequent events in an additional cohort of MDS patients. Subsequently, LEP hypermethylation was confirmed by real-time quantitative methylation-specific PCR in an expanded cohort of larger MDS patients. In clinics, LEP hypermethylation tended to be associated with lower bone marrow blasts and was significantly correlated with U2AF1 mutation. Survival analysis indicated that LEP hypermethylation was associated with a markedly longer survival time but was not an independent prognostic biomarker in MDS patients. Functional studies revealed pro-proliferative and anti-apoptotic effects of leptin in the MDS cell line SKM-1, and it was significantly associated with cell growth and death as well as the Toll-like receptor and NF-kappa B signaling pathways. Collectively, our findings demonstrated that whole-genome DNA methylation analysis identified novel epigenetic alterations such as DLEU7, FOXR1, LEP, and PANX2 methylations as frequent events in MDS. Moreover, LEP might play a role in MDS pathogenesis, and LEP hypermethylation was associated with longer survival but not as an independent prognostic biomarker in MDS.

Hypermethylation of GSTM5 and its effect on oxidation in myelodysplastic syndrome

“…Analysis of a human 12K CpG microarray and GeneChips Human Genome U133 Plus 2.0 arrays by del Rey et al revealed 552 differentially methylated CpG loci and 1005 genes that significantly differed between low-risk MDS patients and the control group [23]. Zhou et al performed reduced representation bisulfite sequencing to investigate epigenetic alterations involved in the pathogenesis of MDS, identifying 1459 differentially methylated fragments, including 759 hypermethylated fragments and 700 hypomethylated fragments, between MDS patients and controls [24]. Lee et al applied a whole-genome-wide DNA microarray technique combined with Ingenuity Pathway Analysis to determine differential states of DNA methylation between RAEB and refractory cytopenia with multi-lineage dysplasia and identified 16 increased hypermethylation events specifically in RAEB samples [16].…”

LEP promoter methylation in the initiation and progression of clonal cytopenia of undetermined significance and myelodysplastic syndrome

“…A recently published study demonstrated that LEP promoter hypermethylation in bone marrow MNCs was associated with inferior OS and could serve as an independent prognostic predictor in AML [ 30 ]. However, the same authors reported that LEP hypermethylation in bone marrow MNCs from MDS patients was associated with a longer survival time in MDS but without being an independent prognostic marker [ 29 ]. Our study suggests a worse prognosis in MDS patients with a high LEP promoter methylation at the time of diagnosis.…”

“…The direct role of leptin in the initiation and progression of myeloid neoplasms is controversial and not fully understood. Several studies suggest a proliferative and/or anti-apoptotic effect of leptin on MDS [ 29 ] and AML [ 42 - 44 ] cells in vitro and one study suggests that leptin stimulates leukemic cell growth in vivo by stimulation of angiogenesis [ 45 ]. However, this is contradicted by the low or normal plasma leptin levels reported in several studies [ 34 - 39 ] and the LEP hypermethylation found in MDS patients in our study and reported by others [ 29 ].…”

“…The obesity-regulated gene LEP encodes the hormone leptin that besides regulating appetite and body mass plays a role in proinflammatory immune response, angiogenesis and lipolysis [ 28 ]. Recently, the LEP promoter was reported to be hypermethylated in MDS [ 29 ] and AML [ 30 ] patients. In AML patients, LEP hypermethylation was reported as an independent risk factor for shorter OS [ 30 ].…”

“…In AML patients, LEP hypermethylation was reported as an independent risk factor for shorter OS [ 30 ]. However, in MDS patients, LEP hypermethylation was associated with longer OS but was not an independent prognostic marker [ 29 ].…”