Inhibition of miR-9 regulates HuR and DICER1 and blocks Hodgkin Lymphoma tumor outgrowth
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE27529 | GEO | 2012/05/02
SECONDARY ACCESSION(S): PRJNA138539
REPOSITORIES: GEO
Similar Datasets
Project description:An Hodgkin Lymphoma cell line have been treated with an LNA inhibitor for miR-9 or with a scramble LNA to identify miR-9 regulated pathways that could be important for Hodgkin Lymphoma pathogenesis. L428 cells were transfected with a miR-9 LNA inhibitor or a scrambled LNA. Total RNA was harvested 9 hours post-transfection and analyzed on Affymetrix HG-U133 Plus 2.0 human arrays. A total of six arrays were analyzed. For filtering, uninformative genes with the same expression level across all arrays (including non-expressed genes) were removed and the differentially expressed genes, their corresponding p-values and false discovery rates were calculated using limma.
2012-05-01 | E-GEOD-27529 | biostudies-arrayexpress
Project description:A high-resolution time series study of transcriptome dynamics following antimiR--mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line revealed both general and miR-9 specific aspects of the miRNA--mediated post--transcriptional dynamic response.MiR-9 inhibition induced a multiphasic gene response, with an initial direct response at approximately 4 hours and multiple later responses which showed transcription factor enrichments indicative of indirect causally downstream responses, and an overall shift of gene product function from predominantly mRNA processing at early time points to translation at later time points. The full time course used was: 2,4,6,8,10,12,14,16,18,20,22,26,32,40,56,80,112 hours post-miR-9 inhibition. Microarrays were Affymetrix HuGene-10-st-v1. Each LNA-antimiR treated cell sample was matched with an LNA scramble control at each time point. This overall time schedule was divided into two independent biological replicates: one covering early time points (2 hours to 20 hours), and another covering later time points (22 hours to 112 hours).
2015-06-06 | E-GEOD-52710 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE25986: Gene expression profiling of cell lines derived from classical Hodgkin lymphoma GSE25987: Gene expression profiling of Hodgkin lymphoma cell line KMH2: Comparison of CIITA-BX648577 knockdown cultures with non-silencing controls GSE25989: Copy number analysis of Hodgkin lymphoma cell lines KM-H2 and L-428 Refer to individual Series *** This submission represents the microarray gene expression and microarray copy number components of the study
2010-12-11 | E-GEOD-25990 | biostudies-arrayexpress
Project description:Global proteomics profiling of anaplastic large cell lymphoma cell lines DEL, SU-DHL-1 (ALK+), Mac-1, Mac-2A (ALK-) as well as Hodgkin lymphoma cell lines L-428, L-540, L-1236 and HDLM-2.
2022-08-12 | PXD031907 | Pride
Project description:In Burkitt lymphoma (BL), a network consisting of MYC, MYC-repressed miR-150, known miR-150 target MYB and two novel targets of miR-150, ZDHHC11 and ZDHHC11B, has been established. This network plays an important role on the growth of BL cells. Here, we confirmed that MYB, ZDHHC11 and ZDHHC11B are targeted by miR-150 in Hodgkin lymphoma (HL) cell lines too.
2021-11-06 | GSE188310 | GEO
Project 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 Hodgkin lymphoma (cHL) and B-cell lines: Microarray data for three Hodgkin lymphoma cell lines (KM-H2, L1236, L428) and the B-cell line Namalwa that were published previously by our group (GEO accession GSE8388) were analyzed together with newly generated data for the B-cell lines SU-DHL4 and SU-DHL6. 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. The gene expression profiles of the cell lines were generated in duplicates.
2011-05-05 | E-GEOD-21251 | biostudies-arrayexpress
Project 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.
2011-05-05 | GSE21251 | GEO
Project description:Hodgkin lymphoma is derived from germinal center / post-germinal center B cells. Gene expression profilies of the Hodgkin lymphoma cell lines were compared to 5 samples of CD77+ centroblasts derived from reactive tonsils
2012-08-31 | E-GEOD-39132 | biostudies-arrayexpress
Project description:Analysis of differential gene expression in human non-Hodgkin`s lymphoma cell lines and a primary leukaemic tumor sample of large cell anaplastic type in comparison with Hodgkin`s lymphoma cell lines and other non-Hodgkin`s lymphoma samples and non-neoplastic lymphocytes Experiment Overall Design: Samples were analyzed to be compared to publically available data sets
2008-06-13 | E-GEOD-4109 | biostudies-arrayexpress
Project description:Hodgkin lymphoma is derived from germinal center / post-germinal center B cells. To determine differentially expressed genes between Hodgkin Reed Sternberg cells and their presumed cell of origin we investigated the expression profiles of 5 commonly used Hodgkin lymphoma cell lines as compared to reactive germinal centers.
2010-12-11 | E-GEOD-25986 | biostudies-arrayexpress