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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Dexamethasone treatment of 3B4.15 T hybridoma cells

ABSTRACT: Investigation of whole genome gene expression level changes in Mus musculus 3B4.15 T hybridoma cells treated with 1microMolar Dexamethasone compared to mock treated cells. Interleukin-7 receptor alpha (IL-7Rα) is essential for T cell survival and differentiation. Glucocorticoids are potent enhancers of IL-7Rα expression with diverse roles in T cell biology. Here we identify the transcriptional repressor, Growth factor independent-1 (Gfi1), as a novel intermediary in glucocorticoid-induced IL-7Rα upregulation. We found Gfi1 to be a major inhibitory target of dexamethasone by microarray expression profiling of 3B4.15 T-hybridoma cells. Concordantly, retroviral transduction of Gfi1 significantly blunted IL-7Rα upregulation by dexamethasone. To further assess the role of Gfi1 in vivo, we generated bacterial artificial chromosome (BAC) transgenic mice, in which a modified Il7r locus expresses GFP to report Il7r gene transcription. By introducing this BAC reporter transgene into either Gfi1-deficient or Gfi1-transgenic mice, we document in vivo that IL-7Rα transcription is upregulated in the absence of Gfi1 and downregulated when Gfi1 is overexpressed. Strikingly, the in vivo regulatory role of Gfi1 was specific for CD8+, and not CD4+ T cells or immature thymocytes. These results identify Gfi1 as a specific transcriptional repressor of the Il7r gene in CD8 T lymphocytes in vivo. A six chip study using total RNA recovered from three separate flasks of mock treated 3B4.15 cells and three separate flasks of Dexamethasone treated 3B4.15 cells . Each chip measures the expression level of 44170 target genes

ORGANISM(S): Mus musculus

SUBMITTER: Batu Erman

PROVIDER: E-GEOD-39296 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dexamethasone treatment of 3B4.15 T hybridoma cells

Project description:Investigation of whole genome gene expression level changes in Mus musculus 3B4.15 T hybridoma cells treated with 1microMolar Dexamethasone compared to mock treated cells. Interleukin-7 receptor alpha (IL-7Rα) is essential for T cell survival and differentiation. Glucocorticoids are potent enhancers of IL-7Rα expression with diverse roles in T cell biology. Here we identify the transcriptional repressor, Growth factor independent-1 (Gfi1), as a novel intermediary in glucocorticoid-induced IL-7Rα upregulation. We found Gfi1 to be a major inhibitory target of dexamethasone by microarray expression profiling of 3B4.15 T-hybridoma cells. Concordantly, retroviral transduction of Gfi1 significantly blunted IL-7Rα upregulation by dexamethasone. To further assess the role of Gfi1 in vivo, we generated bacterial artificial chromosome (BAC) transgenic mice, in which a modified Il7r locus expresses GFP to report Il7r gene transcription. By introducing this BAC reporter transgene into either Gfi1-deficient or Gfi1-transgenic mice, we document in vivo that IL-7Rα transcription is upregulated in the absence of Gfi1 and downregulated when Gfi1 is overexpressed. Strikingly, the in vivo regulatory role of Gfi1 was specific for CD8+, and not CD4+ T cells or immature thymocytes. These results identify Gfi1 as a specific transcriptional repressor of the Il7r gene in CD8 T lymphocytes in vivo.

2012-07-13 | GSE39296 | GEO

Development of gene expression signatures on immunity for bursal peptide BPP-II

Project description:To further elucidate the mechanism of BPP-II on immunity on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BPP-II treatment in a mouse derived hybridoma culture system. Hybridoma cell was treated ex vivo, and robust normalization of the data identified 2478 differentially expressed probe sets exhibiting minimum 1.5-fold changes that distinguished between BPP-II and control samples. Various pathwayswere significantly impacted by BPP-II treatment, and gene Ontology annotations show changes in the expression of molecules involved in immune and immunocyte related cellular processes. Expression of 8 genes (MS4A2M-oM-<M-^LCD86M-oM-<M-^LCD80M-oM-<M-^L FasM-oM-<M-^LCDKN2AM-oM-<M-^LCBLC, FGF21 and Fyn) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns. BPP-II induced gene expression in hybridoma cell was measured at 4 hours after exposure to doses of 0ug/ml and 0.2ug/ml. Two independent experiments were performed using different cells for each experiment.

2011-04-19 | E-GEOD-28696 | biostudies-arrayexpress

Development of gene expression signatures on immunity for bursal peptide BSP-II

Project description:To further elucidate the mechanism of BSP-II on immunity on the broad molecular level, we have employed whole genome microarray expression profiling as a discovery platform to examine gene expression patterns during BSP-II treatment in a mouse derived hybridoma culture system. Hybridoma cell was treated ex vivo, and robust normalization of the data identified 1279 differentially expressed probe sets exhibiting minimum 1.5-fold changes that distinguished between BSP-II and control samples. Various pathwayswere significantly impacted by BSP-II treatment, and gene Ontology annotations show changes in the expression of molecules involved in immune and immunocyte related cellular processes. Expression of nine genes (MS4A2, CD3D, FGF21, CD80, PTPRC, NFATC4, IL2RB, Fas and LAT) from this signature was quantified in the RNA samples by QRT-PCR, confirming low variability between the predicted response patterns. BSP-II induced gene expression in hybridoma cell was measured at 4 hours after exposure to doses of 0ug/ml and 5ug/ml. Two independent experiments were performed using different cells for each experiment.

2011-02-17 | E-GEOD-27340 | biostudies-arrayexpress

Context-specific regulation of monocyte surface IL7R expression and soluble receptor secretion by a common autoimmune risk allele

Project description:IL-7 is a key factor in T-cell immunity and IL7R polymorphisms are implicated in autoimmune pathogenesis. IL7R mRNA is induced in stimulated monocytes in a genetically determined manner. Here we show monocyte surface and soluble IL7R (sIL7R) protein are markedly expressed in response to lipopolysaccharide (LPS). Flow cytometry of synovial fluid-derived monocytes from patients with spondyloarthritis showed an enlarged subset of IL7R+ monocytes. Single-cell RNA sequencing of ex-vivo derived monocytes from the synovial fluid and blood of patients revealed that IL7R+ monocytes at the inflammatory site have a unique transcriptional profile that markedly overlaps that induced by IL-7 in-vitro and shows similarity to the previously described ‘Mono4’ subset. These data demonstrate disease-associated genetic variants at IL7R specifically impact monocyte surface IL7R and sIL7R following innate immune stimulation, suggesting a previously unappreciated key role for monocytes in IL-7 pathway biology and IL7R-associated diseases.

2019-08-12 | E-MTAB-8207 | biostudies-arrayexpress

Specification of innate type-2 lymphocytes by the transcriptional determinant Gfi1

Project description:Innate type-2 lymphoid cells (ILC2s) function in immune responses against helminth parasites and are implicated in allergic inflammation and asthma. ILC2s are activated by the epithelial-derived cytokines IL-33 and IL-25 and are major sources of the type-2 cytokines IL-5 and IL-13. We show that the transcription factor Gfi1 promotes the generation of ILC2s and controls their responsiveness during Nippostrongylus brasiliensis infection as well as IL-33- or IL-25-instigated inflammation. Gfi1 directly activates Il1rl1, which encodes the IL-33 receptor. IL- 33 signaling upregulates Gfi1, thereby constituting a positive feedback loop that enables rapid and robust expansion of ILC2s in response to IL-33 signaling. Loss of Gfi1 in activated ILC2s results in an unusual effector state involving derepression of the IL-17 inflammatory program and co-expression of IL-13 with IL-17. ChIPseq reveals key Gfi1 targeted genes that are activated or repressed to maintain ILC2 identity. We propose that Gfi1 functions as a shared determinant within innate and adaptive immune cells to specify type-2 responses, while actively repressing the IL-17 effector state. ILC2s (~3 x 10^7 cells) were sorted from the MLN of IL-25-treated mice. Chromatin fragments bound by Gfi1 were subject to ChIP using Gfi1 antibodies and followed by high-throughput sequencing.

2013-09-13 | E-GEOD-50806 | biostudies-arrayexpress

Mus musculus

Project description:Dexamethasone treatment of 3B4.15 T hybridoma cells

| PRJNA170507 | ENA

Mouse ILC2 cells from wild-type or Gfi1-KO animals

Project description:Innate type-2 lymphocytes (ILC2s) are a newly described cell type whose biology and contribution to disease are poorly understood. We are interested in investigating the role of the transcription factor Gfi1 in ILC2s, which appear to be a prominent source of IL-5 and IL-13 during type-2 immune responses. We have compelling evidence demonstrating a critical role for Gfi1 in the development and effector state of ILC2s. We would like to elucidate the molecular role of Gfi1 in ILC2s by identifying Gfi1-regulated genes by microarray analysis. Gfi1+/+ or Gfi1GFP/GFP (a GFP cassette has been 'knocked-in' to the Gfi1 locus and thus functions both as a surrogate for Gfi1 promoter activity and as a loss-of-function allele) mice were injected with IL-25 once daily for 4 days. On day 5, ILC2s (Lin-/Sca-1+/ICOS+/CD127+/c-Kit+) were sorted from the mesenteric lymph nodes of Gfi1+/+ (3 mice/sample were pooled together) or Gfi1-/- mice (6 mice/sample were pooled together) and cultured for 6 days in RPMI 1640, 10% FBS, Gln, P/S, 2ME, IL-2 (50ng/ml), IL-7 (10ng/ml), and IL-25 (50ng/ml). Whole RNA was harvested on day 6 via the RNeasy kit (Qiagen).

2013-10-20 | E-GEOD-45621 | biostudies-arrayexpress

Characterizing the interactions between a naturally-primed IgA (mAb 260.8) and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice [array]

Project description:Comparisons of gnotobiotic Rag1-/- mice, with and without subcutaneous 260.8 hybridomas, disclosed that this IgA does not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but does affect bacterial gene expression in ways that are emblematic of a diminished host innate immune response. C57BL/6 wildtype, C57BL/6J Rag1-/- , and C57BL/6J Rag1-/- mice harboring the 260.8 IgA producing hybridoma were colonized for 10 days with Bacteroides thetaiotaomicron VPI-5482.

2015-06-29 | E-GEOD-65455 | biostudies-arrayexpress

IL7R mutational activation can initiate Ph-like and PAX5 P80R precursor B-cell acute lymphoblastic leukemia

Project description:Interleukin-7 receptor α (encoded by IL7R) is essential for lymphoid development. Whether acute lymphoblastic leukemia (ALL)-related IL7R gain-of-function mutations can trigger leukemogenesis remains unclear. Here, we demonstrate that lymphoid-restricted mutant IL7R, expressed at physiological levels in conditional knock-in mice, establishes a pre-leukemia stage in which B-cell precursors display self-renewal ability, initiating precursor B-ALL that resembles PAX5 P80R or Ph-like human leukemia. Full transformation associates with transcriptional upregulation of oncogenes such as Myc or Bcl2, downregulation of tumor suppressors such as Ikzf1 or Arid2, and major IL-7R signaling upregulation (involving both JAK/STAT5 and PI3K/mTOR), required for leukemia cell viability. Accordingly, maximal signaling drives full penetrance and early leukemia onset in homozygous IL7R mutant animals. Notably, we identify 2 transcriptional subgroups in mouse and human Ph-like ALL, and show that dactolisib and sphingosine-kinase inhibitors are novel treatment avenues for IL-7R-related cases. Our model, a unique resource to explore the pathophysiology and therapeutic vulnerabilities of B-ALL, demonstrates that IL7R can initiate this malignancy.

2021-11-02 | PXD017147 | Pride

A novel small compound SH-2251 suppresses Th2 cell-dependent airway inflammation through selective modulation of chromatin status at the Il5 gene locus

Project description:IL-5 is a key cytokine that plays an important role in the development of pathological conditions in chronic allergic inflammation. Identification of a strategy to inhibit IL-5 production is important for establishment of new therapies for allergic inflammation. We found that SH-2251, a novel thioamide-related compound, selectively inhibits the differentiation of IL-5-producing Th2 cells. SH-2251 inhibited the formation of the active histone modifications (H3K4me3, H3K9ac, H3K27ac) at the Il5 gene locus during Th2 cell differentiation. The recruitment of RNA polymerase II and the induction of Th2 cell-specific intergenic transcription between the Rad50 and Il5 gene locus was also inhibited. Furthermore, Th2 cell-driven airway inflammation in mice was suppressed by oral administration of SH-2251. We identified Gfi1 as a downstream target molecule of SH-2251 treatment. The expression of Gfi1 was dramatically decreased in SH-2251-treated Th2 cells. SH-2251-mediated inhibition of the IL-5-producing Th2 cell generation was restored by transduction of Gfi1. Thus, our study unearths SH-2251 as a novel therapeutic candidate for allergic inflammation that selectively inhibits IL-5 production. Gene expression in SH-2251-treated and untreated Th2 cells

2013-04-30 | E-GEOD-42131 | biostudies-arrayexpress

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