Differences in DNA methylation between patients with different molecular features were also explored
Differences in DNA methylation between patients with different molecular features were also explored. and post-translational histone modification, such as in (40-50%) Mouse monoclonal antibody to Annexin VI. Annexin VI belongs to a family of calcium-dependent membrane and phospholipid bindingproteins. Several members of the annexin family have been implicated in membrane-relatedevents along exocytotic and endocytotic pathways. The annexin VI gene is approximately 60 kbplong and contains 26 exons. It encodes a protein of about 68 kDa that consists of eight 68-aminoacid repeats separated by linking sequences of variable lengths. It is highly similar to humanannexins I and II sequences, each of which contain four such repeats. Annexin VI has beenimplicated in mediating the endosome aggregation and vesicle fusion in secreting epitheliaduring exocytosis. Alternatively spliced transcript variants have been described and (5-10%) [5C8]. In cancer, there are complex changes in DNA methylation . Frequently, global DNA demethylation is accompanied by the methylation of CpG islands. In particular, hypermethylation of CpG islands overlapping gene promoters has been associated with the transcriptional silencing of tumor suppressor genes (TSG), leading to clonal advantage of the affected cell . DNA methylation has been widely investigated in hematological neoplasms [10C12]. MDS is characterized by local DNA hypermethylation that increases with disease severity [13C15]. In AML, DNA methylation correlates with specific cytogenetic abnormalities  and the hypermethylation of specific genes such as and has been shown to have an impact on the outcome of MDS and AML patients [13C15]. In CMML, hypermethylation of genes such as and has been reported [16,17]. In addition, a signature of DNA methylation was found to predict the response of CMML patients to hypomethylating agents . It is further clear that mutations correlate with changes in DNA methylation in CMML and other diseases [19C22]. These studies show that DNA methylation plays a role in the pathogenesis of CMML. However, little is known about genome-wide DNA methylation changes and their relevance for disease progression. In this study, we performed DNA methylation microarrays in 64 CMML patients with the aim to investigate the differences in the methylation profile between CMML patients and healthy controls, as well as to evaluate the possible prognostic impact of DNA methylation abnormalities. In addition, we have explored the differences in DNA methylation between patients with different cytogenetic and molecular features. Results Characteristics of CMML patients A total of 64 patients with CMML were included in the study. Median follow-up of living patients was 36 months (range: 5.7 to 83.3 months). Main clinical and biological characteristics of patients are summarized in Table?1. Median age at diagnosis was 71?years and there was a 1.8:1 male:female ratio. According to the FAB criteria , 47 (73%) patients were classified as MD-CMML and 17 (27%) as MP-CMML. Considering the 2008 WHO classification , 46 (72%) cases corresponded to CMML-1 and 18 (28%) to CMML-2. Progression to AML was observed in 25 (39%) patients. Conventional G-banding cytogenetics (CC) was performed at diagnosis and an informative result was obtained in all but one patient. This patient had no chromosomal abnormalities when analyzed by SNP array (SNP-A). According to the CMML-specific cytogenetic risk stratification , ABX-464 most patients (50, 78%) had low risk cytogenetic features: normal karyotype (47) and isolated -Y (3). The rest of cases displayed alterations that corresponded to intermediate (7, 11%) or high risk (7, 11%) groups ABX-464 (Table?1). Targeted deep sequencing of 83 myeloid-related genes had been previously performed on a subset of these patients . The following genes were mutated in 10% of analyzed cases: (34/46, 73%), (26/57, 46%), (21/57, 37%), (13/46, 28%), (8/57, 14%), (6/46, 13%) and (5/46, 11%) (Table?1). Table 1. Main clinical and hematological characteristics of CMML patients at diagnosis (n = 64). 0.05) differentially methylated probes across the series of CMML patients. Each row represents a single probe and each column corresponds to a separate patient. Each probe has been normalized by the mean -value in all samples and the color in the heatmap represents the scaled methylation value. Below is represented in color-code the distribution of the clinical features from the patients (WHO classification, FAB classification, AML progression, CPSS risk groups, and cytogenetic features and gene mutations). White gaps represent missing data. AML: acute myeloid leukemia; CPSS: CMML specific prognostic scoring system; FAB: French-American-British; Int: intermediate; WHO: World Health Organization. Differential methylation between CMML and healthy controls To identify changes in DNA methylation associated with CMML, we compared the DNA methylation patterns between CMML patients (n = 64) and healthy controls (n = 10) by differential methylation analysis. Differentially methylated probes included 1,844 probes hypermethylated and 255 ABX-464 probes hypomethylated in CMML patients compared to controls ( 0.3 methylation ABX-464 difference, clusters tandemly linked on this region (Supplementary Figure?2). Other highly significant DMBs included a region on chromosome 17q24.3-q25.3 that contained genes with several altered sites, such as genes (Supplementary Table?2). Aberrant DNA methylation was also detected in many genes involved in inflammation mediated by chemokine and cytokine signaling pathways.