Gene expression analysis of different B-cell chronic lymphoproliferative disorders
Improved classification of leukemic B-cell lymphoproliferative disorders using a transcriptional and genetic classifier.
Specimen part
View SamplesThis experiment sought to determine the genome-wide interactome of CTCF in human cells. Overall design: PAR-CLIP seq for CTCF was performed in U2OS cells in 2 biological replicates
CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53.
No sample metadata fields
View SamplesDouble Hit Lymphoma (DHL) were treated with the BRD4 inhibitor 100 nM CPI203 for 6h
The BET bromodomain inhibitor CPI203 overcomes resistance to ABT-199 (venetoclax) by downregulation of BFL-1/A1 in in vitro and in vivo models of MYC+/BCL2+ double hit lymphoma.
Specimen part, Cell line, Subject
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Expression of MALT1 oncogene in hematopoietic stem/progenitor cells recapitulates the pathogenesis of human lymphoma in mice.
Specimen part, Disease
View SamplesAttempts at modeling chromosomal translocations involving MALT1 gene, hallmarks of human mucosa-associated lymphoid tissue (MALT) lymphoma, have failed to reproduce the disease in mice. Here we describe a transgenic model in which MALT1 expression was targeted to mouse hematopoietic stem/progenitor cells. In Sca1-MALT1 mice, MALT1 deregulation activated the NF-kappaB pathway in Sca1+ cells, promoting selective B-cell differentiation and mature lymphocyte accumulation in extranodal tissues, progressively leading to the development of clonal B-cell lymphomas. These tumors recapitulated the histopathological features of human MALT lymphomas, presenting typical lymphoepithelial lesions and plasmacytic differentiation. Transcriptional profiling of Sca1-MALT1 murine lymphomas revealed overlapping molecular signatures with human MALT lymphomas, including MALT1-mediated NF-kappaB activation, pro-inflammatory signaling and XBP1-induced plasmacytic differentiation. Moreover, murine Malt1 showed proteolytic activity by cleaving Bcl10 in Sca1-MALT1 lymphomas. Our novel technological approach has allowed modeling human MALT lymphoma in mice, which represent unique tools study MALT lymphoma biology and evaluate anti-MALT1 therapies.
Expression of MALT1 oncogene in hematopoietic stem/progenitor cells recapitulates the pathogenesis of human lymphoma in mice.
Specimen part, Disease
View SamplesComparison of gene expression profiling analysis of bone marrow isolated CD34+ cells from patients with MALT lymphoma vs. healthy individuals revealed a large number of differentially expressed genes that included NF-kB target genes, genes involved in inflamatory signalling and immunoglobulin genes, suggesting an early lymphoid B-cell priming.
Expression of MALT1 oncogene in hematopoietic stem/progenitor cells recapitulates the pathogenesis of human lymphoma in mice.
Specimen part, Disease, Disease stage
View SamplesAttempts at modeling chromosomal translocations involving MALT1 gene, hallmarks of human mucosa-associated lymphoid tissue (MALT) lymphoma, have failed to reproduce the disease in mice. Here we describe a transgenic model in which MALT1 expression was targeted to mouse hematopoietic stem/progenitor cells. In Sca1-MALT1 mice, MALT1 deregulation activated the NF-kappaB pathway in Sca1+ cells, promoting selective B-cell differentiation and mature lymphocyte accumulation in extranodal tissues, progressively leading to the development of clonal B-cell lymphomas. These tumors recapitulated the histopathological features of human MALT lymphomas, presenting typical lymphoepithelial lesions and plasmacytic differentiation. Transcriptional profiling of Sca1-MALT1 murine lymphomas revealed overlapping molecular signatures with human MALT lymphomas, including MALT1-mediated NFkappaB activation, pro-inflammatory signaling and XBP1-induced plasmacytic differentiation. Moreover, murine Malt1 showed proteolytic activity by cleaving Bcl10 in Sca1-MALT1 lymphomas. Our novel technological approach has allowed modeling human MALT lymphoma in mice, which represent unique tools study MALT lymphoma biology and evaluate anti-MALT1 therapies.
Expression of MALT1 oncogene in hematopoietic stem/progenitor cells recapitulates the pathogenesis of human lymphoma in mice.
Specimen part, Disease
View SamplesTreatment of late passage (LP50) LNCaP cells with R1881 (androgen) and AR shRNA identified a gene program controlled by androgen receptor in the absence of androgen.
Hormone depletion-insensitivity of prostate cancer cells is supported by the AR without binding to classical response elements.
Specimen part
View SamplesSignificance of RNA methylation in the context of HIV-1 infection in human T cells Overall design: MeRIP-Seq of Control and HIV-infected MT4 T-Cells
Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells.
No sample metadata fields
View SamplesDuring early development, the correct establishment of the body axes is a critical step. The anterior pole of the mouse embryo is established when Distal Visceral Endoderm (DVE) cells migrate to form the Anterior Visceral Endoderm (AVE). Asymmetrical expression of Lefty1, Cerl and Dkk determines the direction of DVE migration and the future anterior side. Besides being implicated in the establishment of Anterior-Posterior axis the AVE has also been correlated with anterior neural specification. In order to better understand the role of the AVE in these processes, this cell population was isolated using a cerlP-EGFP transgenic mouse line, and a differential screening was performed using Affymetrix GeneChip technology. From this differential screening, 175 genes were found to be upregulated in the AVE, whereas 35 genes were upregulated in the Proximal-posterior sample. Using DAVID, here we characterize the AVE cell population regarding cellular component, molecular function and biological processes. Among the genes that were found to be upregulated in the AVE, several novel genes with expression in the AVE were identified. Four of the identified transcripts displaying high-fold change were further characterized by in situ hybridization in early stages of development in order to validate the screening. From those four selected genes, ADTK1 was chosen to be functionally characterized by targeted inactivation in ES cells. ADTK1 encodes for an unknown serine/threonine kinase. ADTK null mutants present short limbs and defects in the eye and ear. Taken together, these data point to the importance of reporting novel genes present in the AVE.
Identification and functional analysis of novel genes expressed in the Anterior Visceral Endoderm.
Specimen part
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