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| Status |
Public on Sep 28, 2012 |
| Title |
Methylation profiling of Low-Risk Myelodysplastic Syndromes (MDSs) |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Genome-wide expression and methylation profiling identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes (MDSs).
Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. Gene expression and methylation status were measured using high-density microarrays. A total of 552 differentially methylated CpG loci were identified as being present in low-risk MDS; hypermethylated genes were more frequent than hypomethylated genes. In addition, mRNA expression profiling identified 1005 genes that significantly differed between low-risk MDS and the control group. Integrative analysis of the epigenetic and expression profiles revealed that 66.7% of the hypermethylated genes were underexpressed in low-risk MDS cases. Gene network analysis revealed molecular mechanisms associated with the low-risk MDS group, including altered apoptosis pathways. The two key apoptotic genes BCL2 and ETS1 were identified as silenced genes. In addition, the immune response and micro RNA biogenesis were affected by the hypermethylation and underexpression of IL27RA and DICER1. Our integrative analysis revealed that aberrant epigenetic regulation is a hallmark of low-risk MDS patients and could have a central role in these diseases.
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| Overall design |
Low-risk MDS patients and age-matched controls without haematological malignancies were included in the study. Mononuclear cells were isolated from bone marrow samples of low-risk MDS patients and controls by density gradient (Ficoll). A cohort of 18 patients with low-risk MDS and seven controls were included in a simultaneous integrative study of methylation (using Methylated CpG Island Amplification and Microarrays, MCAM) and expression (using Affymetrix microarrays HG-U133 Plus 2), while the whole series was used as a control group of expression data.
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| Contributor(s) |
Del Rey M, O’Hagan K, Dellett M, Aibar S, Colyer HA, Alonso M, Diez-Campelo M, Armstrong RN, Sharpe DJ, Gutierrez NC, García J, DeLasRivas J, Mills KI, Hernández-Rivas JM |
| Citation(s) |
22936014 |
| Submission date |
Sep 28, 2012 |
| Last update date |
Sep 28, 2012 |
| Contact name |
Javier De Las Rivas |
| E-mail(s) |
jrivas@usal.es
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| Phone |
34 923 294819
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| Organization name |
Cancer Research Center (CiC-IBMCC)
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| Department |
CSIC and University of Salamanca
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| Lab |
Bioinformatics and Functional Genomics
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| Street address |
Campus Miguel de Unamuno
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| City |
Salamanca |
| ZIP/Postal code |
37001 |
| Country |
Spain |
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| Platforms (1) |
| GPL2040 |
UHN Human CpG 12K Array (HCGI12K) |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE41216 |
Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes. |
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| Relations |
| BioProject |
PRJNA176194 |
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