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E-GEOD-28079 - Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: expression of PCM vs. B-cell lines

Status
Released on 5 May 2011, last updated on 18 May 2011
Organism
Homo sapiens
Samples (9)
Array (1)
Protocols (8)
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. Gene expression analysis of plasma cell myeloma (PCM) and B-cell lines: Microarray data of the B-cell line Namalwa that was published previously by our group (GEO accession number GSE8388) was analyzed together with newly generated data for the B-cell lines SU-DHL4 and SU-DHL6 (duplicates) and three PCM cell lines (L363, U266, LP1). For all cell lines, 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.
Experiment type
transcription profiling by array 
Contacts
Volkhard Seitz <Volkhard.Seitz@charite.de>, Anke Ehlers, Anke Sommerfeld, Dido Lenze, Elisabeth Oker, Harald Stein, Karin Zimmermann, Lora Dimitrova, Maria Joosten, Michael Hummel, Philippe Thomas, Ulf Leser, Ulrike Paul
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-28079.idf.txt
Sample and data relationshipE-GEOD-28079.sdrf.txt
Raw data (1)E-GEOD-28079.raw.1.zip
Processed data (1)E-GEOD-28079.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-28079.eSet.r
Links