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E-GEOD-21252 - Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: expression of A/T-treated vs. untreated B-cell lines

Status
Released on 5 May 2011, last updated on 18 May 2011
Organism
Homo sapiens
Samples (22)
Array (1)
Protocols (9)
Description
Background Epigenetic changes are involved in the extinction of the B-cell gene expression program of classical Hodgkin lymphoma. However, little is known regarding epigenetic similarities between classical Hodgkin lymphoma and plasma cell myeloma cells, both of which share an extinction of the gene expression program of mature B-cells. Design and methods Global histone H3 acetylation patterns were determined in cell lines derived from classical Hodgkin lymphoma, plasma cell myeloma and B-cell lymphoma by chromatin immunoprecipitation and subsequent hybridization onto promoter tiling arrays. H3K27 trimethylation was analyzed by chromatin immunoprecipitation and real-time DNA-PCR for selected genes. Epigenetic modifications were compared to gene expression data. Results B-cell characteristic genes were hypoacetylated in classical Hodgkin lymphoma and plasma cell myeloma cell lines, as demonstrated by comparison of their histone H3 acetylation patterns to those of B-cell lines. However, the number of genes jointly hyperacetylated and expressed in classical Hodgkin lymphoma and plasma cell myeloma cell lines, such as IFR4/MUM1 and RYBP, is limited. Moreover, H3K27 trimethylation for selected B-cell characteristic genes revealed that this additional epigenetic silencing is much more prevalent in classical Hodgkin lymphoma as compared to plasma cell myeloma. Conclusion Our epigenetic data support the view that classical Hodgkin lymphoma is characterized by an abortive plasma cell differentiation with a down-regulation of B-cell characteristic genes but without activation of most plasma cell typical genes. Combined 5-aza-dC/TSA (A/T) treatment: The diffuse large B-cell lymphoma (DLBCL)-derived cell lines SU-DHL4, SU-DHL6 and HT and the Burkitt lymphoma-derived cell lines Daudi, Namalwa and Raji were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA. RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A). Microarrays were normalized using RMA and differential expression was calculated using moderated t-test. The gene expression profiles of the untreated and treated cell lines (with the exception of HT) were generated in duplicates. Microarray data (CEL files) for AZA/TSA-treated BL-derived cell lines Raji, Daudi and Namalwa were previously published (GEO accession GSE8388).
Experiment type
transcription profiling by array 
Contacts
Anke Ehlers, Anke Sommerfeld, Dido Lenze, Elisabeth Oker, Harald Stein, Maria Joosten, Michael Hummel, Philippe Thomas, Ulf Leser, Volkhard Seitz
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-21252.idf.txt
Sample and data relationshipE-GEOD-21252.sdrf.txt
Raw data (1)E-GEOD-21252.raw.1.zip
Processed data (1)E-GEOD-21252.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-21252.eSet.r
Links