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DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical, biological and genetic features

ABSTRACT: DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical, biological and genetic features

PROVIDER: PRJNA415143 | ENA |

REPOSITORIES: ENA

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DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical, biological and genetic features

Project description:Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. Epigenetic abnormalities are frequent in CMML, including mutations in DNA methylation and histone-modifying enzymes, but the methylation profile is not well characterized in these patients. In this study we performed DNA methylation microarrays in 65 CMML patients and 10 healthy controls. Differential methylation analysis between patients and controls allowed us to identify abnormalities in DNA methylation including hypermethylated genes, large genome regions with aberrant DNA methylation and altered cellular pathways. Hierarchical cluster analysis identified two main clusters that associated with the clinical, biological and genetic features of patients. Group 1 was enriched in patients that presented with adverse clinical and biological characteristics and that had a poorer overall survival and progression free survival. In addition, significant differences in DNA methylation was observed between patients with low risk and intermediate/high risk karyotypes and between TET2 mutant and wild-type patients. These results demonstrate that DNA methylation is altered in CMML and is associated with distinct biological and clinical features. Furthermore, these results may provide a useful basis for identifying new therapeutic targets.

2017-11-17 | GSE105420 | GEO

DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical, biological and genetic features.

Project description:Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions. Differential methylation analysis between patients and controls allowed us to identify abnormalities in DNA methylation, including hypermethylation of specific genes and large genome regions with aberrant DNA methylation. Unsupervised hierarchical cluster analysis identified two main clusters that associated with the clinical, biological, and genetic features of patients. Group 1 was enriched in patients with adverse clinical and biological characteristics and poorer overall and progression-free survival. In addition, significant differences in DNA methylation were observed between patients with low risk and intermediate/high risk karyotypes and between TET2 mutant and wild type patients. Taken together, our results demonstrate that altered DNA methylation patterns reflect the CMML disease state and allow to identify patient groups with distinct clinical features.

| S-EPMC5837079 | biostudies-literature

Transcriptome of chronic myelomonocytic leukemia

Project description:We report the gene expression of human chronic myelomonocytic leukemia by performing whole transcriptome shotgun sequencing of peripheral blood mononuclear cells of patients with chronic myelomonocytic leukemia.

2020-08-14 | GSE156209 | GEO

Transcriptome of chronic myelomonocytic leukemia

Project description:Transcriptome of chronic myelomonocytic leukemia

| PRJNA657050 | ENA

Transcriptome of ASXL1-mutant and ASXL1-wildtype chronic myelomonocytic leukemia

Project description:We report the gene expression of human chronic myelomonocytic leukemia by performing whole transcriptome shotgun sequencing of bone marrow mononuclear cells of patients with chronic myelomonocytic leukemia.

2022-02-21 | GSE159543 | GEO

Affymetrix SNP array data for chronic myelomonocytic leukemia samples

Project description:Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic disorder with heterogeneous clinical, morphological and genetic characteristics. Clonal cytogenetic abnormalities are found in 20-30% of patients with CMML. Patients with low risk cytogenetic features (normal karyotype and isolated loss of Y chromosome) account for approximately 80% of CMML patients and often fall into the low risk categories of CMML prognostic scores. SNP-A were performed in 82 CMML patients with low risk karyotypes and uninformative results for conventional G-banding cytogenetics (CC).

2015-12-01 | GSE67460 | GEO

Epigenome of ASXL1-mutant and ASXL1-wildtype chronic myelomonocytic leukemia

Project description:We report the chromatin characteristics of human chronic myelomonocytic leukemia by performing chromatin immunoprecipitation sequencing of histone modifications (ChIP-seq), immunoprecipitation sequencing of (hydroxy-)methylated residues (DIP-seq), and transposase accessibility sequencing (ATAC-seq) of bone marrow mononuclear cells of patients with chronic myelomonocytic leukemia.

2022-02-21 | GSE159886 | GEO

Four subgroups by gene expression profile correlate with biological and clinical features in colorectal cancer.

Project description:(Purpose) Biological classification of colorectal cancer (CRC) can help to understand its heterogeneous background. The purpose of this study is to classify CRC based on gene expression profiles using formalin-fixed paraffin-embedded (FFPE) samples and to correlate subgroups of CRC with biological features and clinical outcomes. (Results) CRC was clustered into four subgroups by unsupervised hierarchical clustering method. These subgroups show different biological and clinical features. (Conclusion) Gene expression profiles of CRC using FFPE samples distinguish four subgroups that had different biological features and clinical outcomes. These subgroups may explain heterogeneity of CRC and be useful biomarker for clinical.

2014-01-01 | GSE33193 | GEO

Methylation and chromatin abnormalities in chronic myelomonocytic leukemia.

Project description:In this study, institutional IRB approval was obtained and peripheral blood and bone marrow samples on patients with chronic myelomonocytic leukemia were collected. On the samples, we performed chromatin immuno-precipitation and next generation sequencing to assess histone modifications and epigenetic changes associated with proliferative and dysplastic phenotypes.

2020-08-18 | GSE156377 | GEO

RNA-sequencing of Chronic Myelomonocytic Leukemia and healthy donors bone marrow samples

Project description:RNA-seq of bone marrow samples of chronic myelomonocytic leukemia (CMML) patients and healthy donors to identify the molecular DNA repair pathways involved in CMML pathogenic

2020-08-07 | GSE102312 | GEO

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