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GenomicsA biochemical basis for toggling enhancers from the active to poised state in B cells
BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacety...
ORGANISM(S): Homo sapiens 
2013-08-05 | E-GEOD-29282 | biostudies-arrayexpress
TranscriptomicsGene expression data of BCR-ABL1 transformed B cell precursors from BCL6 wild-type and BCL6 knockout mice
To elucidate the mechanism of BCL6-mediated pre-B cell survival signaling, we investigated the gene expression pattern in BCR-ABL1-transformed BCL6+/+ and BCL6-/- B cell precursors. Pharmacological inhibition of BCR-ABL1 was performed with the BCR-ABL1 kinase inhibitor STI571 (Imatinib). BCR-ABL1 t...
ORGANISM(S): Mus musculus 
2010-05-27 | E-GEOD-20987 | biostudies-arrayexpress
TranscriptomicsThe BCL6 RD2 domain governs commitment of activated B-cells to form germinal centers
Our data demonstrated that Bcl6 directly binds and represses trafficking receptors S1pr1 and Grp183 by recruiting Hdac2 through the RD2 domain. Deregulation of these genes impairs B-cell migration and may contribute to the Germinal Center failure in Bcl6RD2MUT mice. RNAseq was performed in endogeno...
ORGANISM(S): Homo sapiens 
2014-09-14 | E-GEOD-58365 | biostudies-arrayexpress
GenomicsInduction of sarcomas by mutant IDH2
More than 50% of patients with chondrosarcomas exhibit gain-of-function mutations in either isocitrate dehydrogenase 1 (IDH1) or IDH2. In this study, we performed genome-wide CpG methylation sequencing of chondrosarcoma biopsies and found that IDH mutations were associated with DNA hypermethylation ...
ORGANISM(S): Homo sapiens 
2013-10-21 | E-GEOD-50539 | biostudies-arrayexpress
GenomicsIntegrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia [ChIP-seq]
Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. We performed DNA methylation (HELP array) and gene expression profiling in 215 samples of adult B-lineage acute lymphoblastic leukemia (ALL) and 12 normal preB samples. Adult B-lin...
ORGANISM(S): Homo sapiens 
2012-11-27 | E-GEOD-38403 | biostudies-arrayexpress
TranscriptomicsEZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation
The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and h...
ORGANISM(S): Homo sapiens 
2013-05-13 | E-GEOD-45982 | biostudies-arrayexpress
GenomicsA Stable Transcription Factor Complex Nucleated by Dimeric AML1-ETO Controls Leukaemogenesis
AML1-ETO, a fusion protein generated by the t(8;21) translocation in acute myeloid leukemia, is a transcription factor implicated in both gene repression and activation. We now show that, in leukemic cells, AML1-ETO resides in and functions through a stable protein complex (AETFC) that contains seve...
ORGANISM(S): Homo sapiens 
2013-06-20 | E-GEOD-43834 | biostudies-arrayexpress
GenomicsOncogene-Mediated Alterations in Chromatin Conformation
Emerging evidence suggests that chromatin adopts a non-random three-dimensional (3D) topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how on...
ORGANISM(S): Homo sapiens 
2012-05-23 | E-GEOD-37752 | biostudies-arrayexpress
TranscriptomicsGene expression data of interleukin-7-dependent and BCR-ABL1-transformed pre-B cells
This analysis focused on identifying factors that protect pre-B cells against DNA double strand break (DSB)-mediated DNA damage stress during pre-B cell differentiation. Differentiation of pre-B cells including immunoglobulin light chain gene recombination were performed by withdrawal of interleuki...
ORGANISM(S): Mus musculus 
2010-05-27 | E-GEOD-21664 | biostudies-arrayexpress
TranscriptomicsIntegrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype [186 samples]
Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of lim...
ORGANISM(S): Homo sapiens 
2013-06-27 | E-GEOD-38295 | biostudies-arrayexpress
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