RNA-Seq and ATAC-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation
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ABSTRACT:
PROVIDER: PRJNA362635 | ENA |
REPOSITORIES: ENA
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Project description:We report differential gene expression in the human AML cell line NB4 that can be partially differentiated into neutrophil granulocytes by 1µM ATRA for 2d or the vehicle DMSO only ((mock))
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Project description:NB4 is an APL derived cell line, carrying the t(15;17) translocation and expressing the PML/RARa fusion protein. Still, an important question that remains to be addressed is whether PML/RARa target genes are transcriptionally suppressed in primary APL cells and re-activated in all-trans retinoic acid (ATRA) treated NB4 cells. Gene expression of NB4 cells treated with ATRA at different time points were analyzed.
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Project description:We report differential chromatin accessiblity in the human AML cell line NB4 that can be partially differentiated into neutrophil granulocytes by 1µM ATRA for 2d or the vehicle DMSO only ((mock))
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Project description:NB4 is an APL derived cell line, carrying the t(15;17) translocation and expressing the PML/RARa fusion protein. Still, an important question that remains to be addressed is whether PML/RARa target genes are transcriptionally suppressed in primary APL cells and re-activated in all-trans retinoic acid (ATRA) treated NB4 cells. Gene expression of NB4 cells treated with ATRA at different time points were analyzed. Experiment Overall Design: 6 samples at various times. No replicats.
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Project description:Treatment of acute promyelocytic leukemia (APL) with all-trans-retinoic acid (ATRA) results in terminal differentiation of leukemic cells toward neutrophil granulocytes. Administration of ATRA leads to massive changes in gene expression, including down-regulation of cell proliferation-related genes and induction of genes involved in immune function. One of the most induced genes in APL NB4 cells is transglutaminase 2 (TG2). RNAi-mediated stable silencing of TG2 in NB4 cells (TG2-KD NB4) coupled with whole genome microarray analysis revealed that TG2 is involved in the expression of a large number of ATRA-regulated genes. The affected genes participate in granulocyte functions and their silencing lead to reduced adhesive, migratory and phagocytic capacity of neutrophils and less superoxide production. The expression of genes related to cell cycle control also changed, suggesting that TG2 regulates myeloid cell differentiation. CC chemokines CCL2, 3, 22, 24 and cytokines IL1B and IL8 involved in the development of differentiation syndrome (DS) are expressed at significantly lower levels in TG2-KD NB4 cells than in wild-type NB4 cells upon ATRA treatment. Based on our results, we propose that reduced expression of TG2 in differentiating APL cells may suppress effector functions of neutrophil granulocytes and attenuate the ATRA-induced inflammatory phenotype of DS. We used microarrays to detail the global program of gene expression underlying ATRA-induced differentiation of TG2 knockout NB4 cells. TG2 knockout NB4 cells were differentiated for 48 and 72 hours in the presence of ATRA and their gene expression profiles were compared to the wild-type cells at the same time points. Undifferentiated wild-type and TG2 knockout NB4 cells were used as untreated controls. Three biological replicates each.
2010-12-01 | E-GEOD-23702 | biostudies-arrayexpress
Project description:Treatment of acute promyelocytic leukemia (APL) with all-trans-retinoic acid (ATRA) results in terminal differentiation of leukemic cells toward neutrophil granulocytes. Administration of ATRA leads to massive changes in gene expression, including down-regulation of cell proliferation-related genes and induction of genes involved in immune function. One of the most induced genes in APL NB4 cells is transglutaminase 2 (TG2). RNAi-mediated stable silencing of TG2 in NB4 cells (TG2-KD NB4) coupled with whole genome microarray analysis revealed that TG2 is involved in the expression of a large number of ATRA-regulated genes. The affected genes participate in granulocyte functions and their silencing lead to reduced adhesive, migratory and phagocytic capacity of neutrophils and less superoxide production. The expression of genes related to cell cycle control also changed, suggesting that TG2 regulates myeloid cell differentiation. CC chemokines CCL2, 3, 22, 24 and cytokines IL1B and IL8 involved in the development of differentiation syndrome (DS) are expressed at significantly lower levels in TG2-KD NB4 cells than in wild-type NB4 cells upon ATRA treatment. Based on our results, we propose that reduced expression of TG2 in differentiating APL cells may suppress effector functions of neutrophil granulocytes and attenuate the ATRA-induced inflammatory phenotype of DS.
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Project description:The acute promyelocytic leukemia-derived cell line, NB4, was grown at 37°C in 5% CO2 in an RPMI medium supplemented with 2 mM L-glutamine and 10% decomplemented fetal calf serum. Cells were cultured for 48 h with or without 1 μM All-trans retinoic acid (ATRA). Duplicates of 3 independent experiments were analyzed.
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Project description:Cutaneous T-cell lymphoma (CTCL) is a highly heterogeneous non-Hodgkin lymphoma.While retinoids analog including ATRA have been used to treat CTCLs for decades, their mechanism of action and the role of RA-RARα signaling remain poorly understood.Thus,we treated CTCL cells with ATRA.In parallel, we treated acute promyelocytic leukemia (APL) cell line NB4 with ATRA followed by RNA-seq analysis.Total RNA was prepared from biological duplicate plates of cells and subjected to bulk RNAseq. 150-bp paired-end sequencing was performed on the BGISEQ-500.
2024-04-01 | GSE262586 | GEO
Project description:RNA-Seq in SMARCD2 k/d NB4 cells with/without ATRA differentiation
| PRJNA362639 | ENA
Project description:ATRA was identified as a Pin1 inhibitor via fluorescence polarization-based high throughput screening. We performed microarray expression profiling to demonstrate the similarity between ATRA and Pin1 KD at the genome-wide level APL NB4 cells in response to ATRRA or inducible Pin1 knockdown for 3 days were collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to validate in genome-wide level whether similarity occurred between ATRA and Pin1 knockdown-treated NB4 cells.
2015-04-12 | E-GEOD-63059 | biostudies-arrayexpress