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The role of TFEB in retinoid induced differentiation of NB4 APL leukemic cells (shTFEB)

ABSTRACT: We report the use of RNAseq to determine the role of the TFEB transcription factor in all-trans retinoic acid induced differentiation of NB4 acute promyelocytic leukemia (APL) cells. We used lentiviral mediated shRNA approaches to functionally deplete TFEB in NB4 cells and compared the transcriptomes of wild type, scramble control shRNA and shTFEB knockdown cells treated with ethanol (control) versus all-trans retinoic acid for 72 hours.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53258 | GEO | 2019/09/01

REPOSITORIES: GEO

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Retinoid induced differentiation of NB4 APL leukemic cells

Project description:We report the use of RNAseq to determine genomewide transcriptional changes induced by all-trans retinoic acid differentiation of NB4 acute promyelocytic leukemia (APL) cells.

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Expression profiling of ATRA treated NB4 cells

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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Transcription profiling of human ATRA treated NB4 cells

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Transcription profiling of human promyelocytic NB4 cells treated with all-trans retinoic acid

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Expression data from NB4 control shRNA cells and NB4 TRIB3 shRNA cells

Project description:To identify the top 20 up-regulated genes in NB4 TRIB3 shRNA cells in comparison with NB4 control shRNA cells, we examined the microarray gene expression profile of these groups above. Despite the fact that combined therapy of all-trans retinoic acid (ATRA) with arsenic trioxide (ATO) or chemotherapy dramatically improves the prognosis of patients with acute promyelocytic leukemia (APL), these regimens can cause systemic infections and secondary leukemias. Here we report that expression of the pseudokinase Tribble 3 (TRIB3) associates positively with APL progression and therapeutic resistance. The elevated TRIB3 expression promotes APL by interacting with PML-RARa and suppressing its sumoylation, ubiquitylation and degradation. This represses PML nuclear body assembly, p53-mediated senescence, cell differentiation, and supports cellular self-renewal. Genetically inhibiting Trib3 expression or disturbing the TRIB3/PML-RARa interaction produces potent therapeutic efficacy against APL and has synergic anti-APL effects when used in combination with ATRA or ATO by promoting PML-RARa degradation and PML expression. Our study provides new insight into APL pathogenesis and a new therapeutic option against APL.

2017-05-12 | GSE95637 | GEO

Long Intergenic Non-Coding RNA HOTAIRM1 Regulates Cell Cycle Progression During Myeloid Maturation in NB4 Promyelocytic Leukemia Cells

Project description:HOTAIRM1 is a long intergenic non-coding RNA located in the human HOXA gene cluster, with gene expression highly specific for maturing myeloid cells, particularly during all-trans retinoic acid (ATRA) induction of granolopoiesis in NB4, a human t(15;17) acute promyelocytic leukemia (APL) cell line. We sought to assess the impact of HOTAIR knockdown on the global programme of gene expression underlying the granulocytic maturing process in NB4 cells. The knockdown of HOTAIRM1 resulted in a less differentiated expression profile in the NB4 cells after 4 days of ATRA-induced granulocytic differentiation, with retained expression of many otherwise ATRA-suppressed cell cycle and DNA replication genes, as well as abated induction of cell surface leukocyte activation and defense response genes. The shRNA expressing vector targeting the HOTAIRM1 transcript and the control vector expressing scrambled shRNA sequence were generated based on the pLKO.3G vector backbone (Addgene). The stable cell lines derived from NB4 cells transfected with lentiviral vectors were selected by FACS sorting of GFP selection marker positive cells and isolation of single cell derived clones on soft agar plates. Biologically duplicated total RNA samples were prepared from HOTAIRM1 knockdown and the scrambled shRNA expressing control cells, plus one total RNA from each of wild type NB4 cells and HOTAIRM1 knockdown (by a different shRNA construct) cells, before and after 96 hours of ATRA (0.5 uM) induced granulocytic differentiation.

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Transcription profiling by array of ATRA- and control-treated NB4 leukemia cells

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Proteome dynamics of HL-60, NB4, and K562 cells under the ATRA treatment

Project description:Searching for new strategies of acute myeloid leukemia (AML) treatment is of particular interest. Cell lines, e. g. HL-60 and NB4, represent model systems to study molecular features of leukemic cells. The all-trans-retinoic acid (ATRA) has proven itself to be an effective treatment for one of AML subtypes, i.e., acute promyelocytic leukemia (APL). At the same time, ATRA causes granulocytic differentiation of non-APL leukemic cells in vitro. Combination of new therapeutics with ATRA could improve efficiency of treatment. Studying the proteome perturbation in leukemic cells under the ATRA treatment allows to determine potential regulatory molecules that could be affected pharmacologically. Thus, the TMT-based proteomic profiles of HL-60, NB4, and K562 cell lines under the ATRA treatment were obtained at 0, 3, 12, 24, and 72 h after the ATRA treatment.

2024-06-23 | PXD050317 | Pride

Long Intergenic Non-Coding RNA HOTAIRM1 Regulates Cell Cycle Progression During Myeloid Maturation in NB4 Promyelocytic Leukemia Cells

2014-04-30 | GSE49516 | GEO

Gene expression profiling of ATRA-differentiated wild-type and TG2 knockout NB4 cells

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

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