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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Pbx1-d Induces T cell Activation and a Decreased Apoptosis in Response to Retinoic Acids (RA)

ABSTRACT: The hypothesis was tested that the Pbx1-d isoform was responsible for the Sle1a.1 phenotypes in CD4+ T cells. Jurkat T cells were transfected with a lentiviral construct expressing Pbx1-d-GFP or control RFP. Pbx1-d over-expression reduced the percentage of late apoptotic cells in response to anti-CD3 and anti-CD28 stimulation as compared with control-Lin28-transfected cells. Overall, these data demonstrate that over-expression of Pbx1-d results in an activated/inflammatory phenotype and in a defective response to RA in Jurkat T cells, strongly suggesting that the increased expression of Pbx1-d is responsible for the Sle1a.1 phenotypes. Jurkat T cells (5 x 105 cells/ml) were transfected with an lentiviral (LV) vector expressing either control (RFP or Lin28) or Pbx1-d-GFP. Total RNA was extracted from GFP+ or RFP+ FACS-sorted Jurkat T cells transfected LV-GFP-Pbx1-d or LV-RFP, as well as non-transfected cells in 4 independent transfections per group.

ORGANISM(S): Homo sapiens

SUBMITTER: Igor Dozmorov

PROVIDER: E-GEOD-22799 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Pbx1-d Induces T cell Activation and a Decreased Apoptosis in Response to Retinoic Acids (RA)

Project description:The hypothesis was tested that the Pbx1-d isoform was responsible for the Sle1a.1 phenotypes in CD4+ T cells. Jurkat T cells were transfected with a lentiviral construct expressing Pbx1-d-GFP or control RFP. Pbx1-d over-expression reduced the percentage of late apoptotic cells in response to anti-CD3 and anti-CD28 stimulation as compared with control-Lin28-transfected cells. Overall, these data demonstrate that over-expression of Pbx1-d results in an activated/inflammatory phenotype and in a defective response to RA in Jurkat T cells, strongly suggesting that the increased expression of Pbx1-d is responsible for the Sle1a.1 phenotypes.

2010-07-07 | GSE22799 | GEO

The Legionella protein VpdC is a ubiquitin-activated phospholipase effector

Project description:The goal of this project was to identify the host factor(s) required for allosteric activation of the phospholipase VpdC from the intracellular pathogen Legionella pneumophila. For that reason, we performed co-precipitation analyses from lysate of transiently transfected HEK293T cells producing either Red Fluorescent Protein (RFP)-tagged VpdC(257-884) or RFP-VpdC(257-610) as bait.

2023-06-12 | PXD037059 | Pride

RIME against PBX1 protein in P19.6 mouse embryonal carcinoma cells treated for 48 hours with all-trans retinoic acid

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2017-04-03 | PXD006158 | Pride

Gene expression analyses of HB9-GFP D2 mMN cultures following Pbx1 exon 7 inclusion

Project description:PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. We define those exons controlled by PTBP1 in ESCs and NPCs by RNA-seq analysis after PTBP1 depletion and PTBP1 crosslinking-immunoprecipitation. We find that PTBP1 represses Pbx1 exon 7 and the expression of its neuronal isoform Pbx1a in ESC. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of specific neuronal genes including known Pbx1 targets. Thus PTBP1 controls the activity of Pbx1 and suppresses its neuronal transcriptional program prior to differentiation. HB9-GFP mESC were transiently transfected with Cas9 and guide RNA sequences to generate heterozygous deletions at the Pbx1 intron 6 locus (Pbx1 I6 +/-). Wild type and (n=3) or Pbx1 I6 +/- (n=5) clones were differentiated in MN media. Samples were harvested at Day 2 of differentiation, and poly-A RNA was isolated for RNA-sequencing and gene expression analyses.

2016-07-03 | E-GEOD-70883 | biostudies-arrayexpress

Transcription factor profiling of T cells containing stably integrated or transiently transfected HTLV-1 LTR.

Project description:Transcription factor profiling of T cells containing stably integrated or transiently transfected HTLV-1 LTR. Nuclear extract from one million stably or transiently transfected Jurkat (CD4 T cell) cell line was extracted and labeled with TransSignal Probe mix (Panomics) and then hybridized to the array.

2011-11-12 | E-GEOD-33628 | biostudies-arrayexpress

Expression data from control and Pbx1-null CMPs and GMPs

Project description:The capacity of the hematopoietic system to promptly respond to peripheral demands relies on adequate pools of progenitors able to transiently proliferate and differentiate in a regulated manner. However, little is known about factors that may restrain progenitor maturation to maintain their reservoirs. In addition to a profound defect in hematopoietic stem cell (HSC) self-renewal, conditional knockout mice for the Pbx1 proto-oncogene have a significant reduction in lineage-restricted progenitors, including common myeloid progenitors (CMPs) and, to a lesser extent, granulocyte-monocyte progenitors (GMPs). Through analysis of purified progenitor proliferation, differentiation capacity and transcriptional profiling, we demonstrate that in the absence of Pbx1 the CMP pool is reduced due to aberrantly rapid myeloid maturation, associated with decreased expression of Meis1 and its targets including Flt3. BM cells were obtained from multiple bones of individual three to five week old Tie2Cre+.Pbx1-/f or Tie2Cre+.Pbx1+/f control mice (4-5 biological replicates/group). CMPs and GMPs were sorted by flow cytometry according to the following markers: Lin-/c-Kit+/Sca-/CD34+/CD16/32int, and Lin-/c-Kit+/Sca-/CD34+/CD16/32high, respectively, prior to RNA extraction.

2013-03-31 | E-GEOD-30028 | biostudies-arrayexpress

Deep sequencing of human naive CD4 T cells identifies miR-34c-5p as a novel regulator of T cell activation and HIV replication

Project description:We generated a model for miR-34c-5p overexpression by transfecting Jurkat T cell line with a pcDNA3 vector containing the pre-miR-34c-5p precursor sequence and selecting for antibiotic resistance to isolate both pools and clones of stably transfected cells (J34c cells), in parallel with control cells transfected with the empty parental vector (JÃ cells). Both pools of stably transfected cells and the derived clonal lines expressed high levels of the miR.

2016-12-21 | E-MTAB-4190 | biostudies-arrayexpress

Genome-wide binding map of the HIV Tat protein to the human genome (gene expression)

Project description:The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome. Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells (Jurkat-Tat cells) using chromatin immunoprecipitation combined with next-generation sequencing. cDNA microarray was used to monitor gene expression changes between Jurkat and Jurkat-Tat cells. Additionally, we compared distribution of H3K9ac near gene promoters between Jurkat and Jurkat-Tat cells using ChIP-chip method and hybridized onto Agilent promoter array. Our data reveal that Tat’s interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle. Agilent gene expression microarray was used to compare gene expression changes between Jurkat T cells and Jurkat T cells expressing HIV-Tat protein (Jurkat-Tat T cells) Expression profiles on Jurkat-Tat cells versus Jurkat cells. ChIP on chip for H3K9ac in Jurkat-Tat versus Jurkat cells. ChIP-seq for HIV-1 Tat protein in Jurkat-Tat cells.

2011-11-06 | E-GEOD-30734 | biostudies-arrayexpress

Gene expression signature of fast and slow cycling intestinal crypt base columnar cell populations

Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary stem cells from small intestine. Using the cell cycle specific expression og the mKi67 gene, we generated a novel Ki67-RFP knock-in allele which identifies dividing cells. Using Lgr5-GFP;Ki67-RFP mice, we isolated CBCs with distinct Wnt signaling levels and cell cycle features, and analyzed their global gene expression pattern using microarrays. We concluded that the cycling Lgr5hi stem cells exit the cell cycle in transition into the secretory lineage. Lgr5med Ki67low intermediate precursors reside in the zone of differentiation, resemble quiescent stem cells and generate the Dll1+ secretory precursors and the label retaining cells. Our findings support the cycling stem cell hypothesis and highlight the heterogeneity of early progenitors during lineage commitment. We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter, and Ki67-TagRFP mice where the RFP is fused to the C-terminus of the endogenous Ki67 gene. RNA was isolated from several FACS sorted cell populations of combinations expressing different levels of GFP and RFP: GFP high RFP high (Lgr5hi Ki67hi), GFP high RFP low (Lgr5hi Ki67low), GFP medium RFP high (Lgr5med Ki67high) and GFP medium RFP low (Lgr5med Ki67low). Purified RNA was processed, hybridized, and scanned according to the manufacturerM-bM-^@M-^Ys protocol and were hybridized on Affymetrix Mouse Gene ST 1.1 arrays).

2014-09-08 | E-GEOD-52813 | biostudies-arrayexpress

CUT&Tag of mouse primary B cells transduced Pbx1 overexpression plasmid.

Project description:We performed the cleavage under targets and tagmentation (Cut & tag) assay followed by sequencing enriched DNA fragments to reveal the direct downstream targets of Pbx1. Firstly, we overexpressed Pbx1b with Pbx1b-IRES-GFP retrovirus in murine peripheral B cells to ensure the yields of DNA fragments. CUT & tag libraries were generated following instructions of the manufacturer’s protocol (Vazyme; cat TD901-01) and the Pbx1 antibody (CST; cat 4342) was used for signal enrichment.

2023-03-26 | E-MTAB-12769 | biostudies-arrayexpress

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