Similar Datasets
Project description:Human monocytes exposed to lentivirus expressing shRNA against ETV3 or ETV6 during differentiation
2022-10-05 | GSE188982 | GEO
Project description:To determine the protein partners of ETV6, we expressed ETV6 and HA-tagged ETV6 in Reh pre-B leukemic cells. Anti-HA magnetic beads were used for affinity purification of ETV6-HA (and ETV6 control) from the nuclear and cytoplasmic fraction. Following purification on-beads digest and LC-MS/MS experiments were performed at the Proteomics platform of the CHU de Quebec Research Center, Quebec, Canada.
2022-01-26 | PXD031001 | Pride
Project description:Background: Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies. Notably, the t(12;21) translocation leading to an ETV6-AML1 fusion gene is the most common genetic alteration found in childhood acute lymphoblastic leukemia. Moreover, most of these patients also lack ETV6 expression, suggesting a tumor suppressor function. Results: To gain insights on ETV6 DNA-binding specificity and genome wide transcriptional regulation capacities, we performed chromatin immunoprecipitation experiments coupled to deep sequencing in a t(12;21)-positive pre-B leukemic cell line. This strategy led to high quality ETV6-bound regions. ETV6 binding is mostly cell type-specific as only few regions are shared with other blood cell subtypes. Peaks localization and motif enrichment analyses revealed a unique binding profile that is associated with the presence of the ETV6-AML1 fusion product. Conclusions: We described the first ETV6 binding map in the t(12;21) background. This study highlighted the complex and unique interplay between ETV6 and ETV6-AML1 and underscored the highly regulated mechanisms of ETV6 binding. ETV6 inactivation observed in this context could induce specific transcriptional changes promoting leukemic transformation.
2017-11-15 | GSE102785 | GEO
Project description:Exparession profiling of ETV6-NCOA2 at different stages of disease dEmpty vectorelopment: CD34 cord blood cells transduced with ETV6-NCOA2-GFP or with empty vector-GFP, CD34 cord blood cells transduced with ETV6-NCOA2-NGFR or ETV6-NCOA2-NGFR + NOTCH1-L1601PdP-GFP and transplanted in NSGS mice, and ETV6-NCOA2 patient derived xenografts.
2022-05-16 | GSE161702 | GEO
Project description:ETV6::FRK is a rare kinase-related fusion gene which was identified only in AML but not in ALL. Herein, we firstly identified ETV6::FRK fusion gene in a patient with pediatric B-ALL. Because FRK is Src family tyrosine kinase, we performed functional analysis of ETV6::FRK to establish molecular targeting therapy. Our case with B-ALL was refractory to conventional chemotherapy and received allogeneic bone marrow transplantation following administration of blinatumomab. Cytogenetic analysis demonstrated 46,XY,t(6;12)(q21;p13) and target capture mRNA sequencing revealed ETV6::FRK. Ba/F3 cells expressing ETV6::FRK generated by retroviral transduction (Ba/F3-ETV6::FRK) and analyzed for IL-3 independent growth. Gene expression analysis using whole transcriptome sequencing and gene set enrichment analysis (GSEA) was performed for comprehensive analysis of gene expression profile related to ETV6::FRK. It was also analyzed whether dasatinib, which is Src-kinase inhibitor, suppressed the growth of Ba/F3-ETV6::FRK in vitro and in vivo. Ba/F3-ETV6::FRK proliferated without IL-3, suggesting ETV6::FRK had proliferation activity. Western blot revealed that constitutive phosphorylation of tyrosine residue of ETV6::FRK and STAT3/STAT5, suggesting constitutive activation of FRK-STAT3/STAT5 pathway. GSEA of oncogenic gene sets (C6) from the GSEA Molecular Signatures Database revealed that, compared with control cells, Ba/F3-ETV6::FRK cells were enriched for up-regulation of SNF5 target genes and down-regulation of RB target genes involved in cell cycle regulation. In vitro killing assay showed that dasatinib killed efficiently Ba/F3-ETV6::FRK. Dasatinib also suppressed the growth of Ba/F3-ETV6::FRK in vivo and extended the survival time of the xenografted NSG mice. These findings suggest that activation of FRK-STAT3/STAT5 pathway contributes aberrant growth promotion of Ba/F3-ETV6::FRK. Our study demonstrated that dasatinib might be effective for the patient with B-ALL harboring ETV6::FRK.
2022-12-31 | GSE220610 | GEO
Project description:We have carried out global gene expression analysis to clarify the interrelationship between 1,25-dihydroxyvitamin D3 and differentiation-driven gene expression patterns in developing human monocyte-derived dendritic cells. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. This design allows one to identify genes regulated by differentiation and/or 1,25-dihydroxyvitamin D3 in human monocyte-derived dendritic cells. Experiment Overall Design: Human monocytes were obtained from buffy coats from healthy donors by Ficoll gradient centrifugation followed by immunomagnetic cell separation with anti-CD14-conjugated microbeads. Monocytes were cultured in RPMI-1640 supplemented with 10% FBS, 800 U/ml GM-CSF and 500 U/ml IL-4. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. Experiments were performed in biological triplicates representing samples from different donors. 15 samples were processed and hybridized to Human Genome U133 Plus 2.0 Arrays.
2009-02-21 | E-GEOD-13762 | biostudies-arrayexpress
Project description:Monocytes can give rise to multiple highly specialized cell types to perform a wide array of functions, ranging from pathogen phagocytosis to bone resorption. This differentiation is induced by the binding of cytokines to dedicated receptors on the surface of monocytes, which results in the initiation of genetic programs that enable cells to perform their specialized functions. Given their common background, it is not surprising that monocyte-derived cells share abilities and cellular markers, yet their specialized functions require a dedicated set of proteins. In order to dissect the monocyte differentiation process and to define cell type-specific marker proteins, we differentiated circulating monocytes into dendritic cells, M1 and M2 macrophages, and osteoclasts, and assessed their proteomes by quantitative mass spectrometry throughout the differentiation process. Statistical analysis indicated that monocyte differentiation is a linear process characterized by a common core of proteins that is similarly affected among the distinct differentiation paths. Throughout the specialization process a cluster of RNA-binding and processing proteins was downregulated whereas proteins associated to metabolic processes were increased. Analysis of the specialized cells after 10 days of differentiation uncovered existing and putative novel dendritic cell markers. Combined, we here present a comprehensive proteomic analysis of monocyte differentiation uncovering shared and distinct proteomic features of differentiating monocytes and monocyte-derived cells.
2021-09-09 | PXD016245 | Pride
Project description:Human monocytes are a heterogeneous cell population consisting of three subsets: classical CD14++CD16-, intermediate CD14++CD16+ and nonclassical CD14+CD16++ monocytes. Intermediate monocytes contribute to inflammation, and their circulating cell counts are increased in many chronic inflammatory diseases, even though the underlying pathways are poorly characterized. We tested in how far epigenetic mechanisms regulate human monocytes heterogeneity in chronic kidney disease, which is a proinflammatory condition of substantial epidemiological importance. By applying next-generation Methyl-Sequencing (Methyl-Seq) we characterized genome-wide DNA methylation within the three monocyte subsets and analyzed the impact of uremia on DNA methylation in differentiating monocytes. We found that each monocyte subset displays a unique phenotype with regards to DNA methylation. Genes with differentially methylated promoter regions in intermediate monocytes were linked to distinct immunological processes, which is in line with results from recent gene expression analyses. In vitro, uremia induced a dysregulation of DNA methylation in differentiating monocytes which affected several transcription factors important for monocyte differentiation (e.g. FLT3, HDAC1, MNT) and led to enhanced generation of intermediate monocytes. As a potential mediator, the uremic toxin and DNA methylation inhibitor S-Adenosylhomocysteine induced shifts in monocyte subsets in vitro, and associated with monocyte subset counts in vivo. In summary, our data support the concept of monocyte trichotomy and the distinct role of intermediate monocytes in human immunity. The shift in monocyte subsets which occurs in chronic kidney disease, a proinflammatory condition of substantial epidemiological impact, may be induced by the accumulation of specific uremic toxins that mediate epigenetic dysregulation.
2015-10-07 | GSE73788 | GEO
Project description:ETV6-RUNX1 is a first-hit mutation in childhood B cell precursor acute lymphoblastic leukaemia. ETV6-RUNX1 is a fusion protein which inherits the DNA-binding runt domain from RUNX1. Here we performed chromatin precipitation for native RUNX1 and ETV6-RUNX1 using RUNX1 antibodies and specifically for the ETV6-RUNX1 fusion using a V5-tag pull down.
2022-10-31 | E-MTAB-12208 | biostudies-arrayexpress
Project description:Transcriptional effects of ETV6 inactivation in immature T-ALL were investigated by gene expression analysis upon siRNA-mediated knockdown of ETV6 in LOUCY cells, a T-ALL cell line with a transcriptional program highly related to that of immature T-ALLs. Gene Set Enrichment Analysis (GSEA) of the ETV6 knockdown signature showed a significant enrichment in genes characteristically upregulated in ETV6 mutant immature T-ALLs including HOXA13, PRDM16, PTEN and CD33. 4 samples were analyzed: two biological replicates for each experimental group.
2011-11-24 | E-GEOD-33820 | biostudies-arrayexpress