Microarray analysis of gene expression in CD4+CD8+ double pos (DP) thymocytes upon depletion of Ubiquitin specific protease 8
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE55517 | GEO | 2014/03/04
SECONDARY ACCESSION(S): PRJNA239829
REPOSITORIES: GEO
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Project description:T-cell-specific deletion of USP8 (USP8ffCD4Cre) revealed that USP8 is required for thymocyte transition to the CD4+ and CD8+ single positive (SP) stages. To evaluate underlying mechanisms, gene expression profilling was performed in CD4+CD8+ double pos thymocytes derived from control (USP8ff and USP8ffCD4Cre) mice. Microarray analysis of two groups of USP8fl/fl and USP8fl/flCD4Cre thymocytes. Material from two mice was combined for each group (eight mice in total).
2014-03-04 | E-GEOD-55517 | biostudies-arrayexpress
Project description:H2A.Z ChIP-Seq in CD4/CD8 DP thymocytes
2017-02-07 | GSE87529 | GEO
Project description:T cell-specific deletion of PTEN induces premalignancy in CD4+ CD8+ (DP) immature T cells in the thymus, which progresses to the development of mature CD4+ T cell lymphomas in the lymph nodes and spleen. As part of a screen to identify factors that inhibit progression to malignancy, we compared miRNA expression in premalignant PTEN-deficient DP thymocytes versus wild-type controls.
2014-04-12 | GSE56759 | GEO
Project description:T cell-specific deletion of PTEN induces premalignancy in CD4+ CD8+ (DP) immature T cells in the thymus, which progresses to the development of mature CD4+ T cell lymphomas in the lymph nodes and spleen. As part of a screen to identify factors that inhibit progression to malignancy, we compared miRNA expression in premalignant PTEN-deficient DP thymocytes versus wild-type controls. DP thymocytes were collected by cell sorting from three 9-week-old, premalignant T cell-specific PTEN-deficient mice (tPTEN-/-) and three littermate controls. miRNA expression was assessed relative to a reference pool generated from an equal mixture of all samples.
2014-04-12 | E-GEOD-56759 | biostudies-arrayexpress
Project description:Notch1 signaling is an important regulator of cell fate in early stages of T cell development. Because Notch receptors can function redundantly, we sought an approach for inhibiting all endogenous Notch signaling in thymocytes. Upon ligand engagement, Notch receptors undergo two successive proteolytic cleavages, the second involving a Presenilin (PS) containing complex with -secretase activity that releases a small intracellular fragment of Notch. This activated form of Notch (NotchIC) translocates from the membrane to the nucleus, where it acts as a transcription factor, inducing the expression of multiple target genes . Since Presenilins are required for the activation of all four mammalian forms of Notch, we generated mice with deletions of both Presenilin1 and Presenilin2 genes, the only genes encoding Presenilin in the mouse genome. To target Notch inactivation specifically to developing T cells, we introduced Cd4-Cre to mediate Presenilin gene deletion in a tissue- and stage-specific manner. Direct target genes of Notch signaling are largely unknown, and are likely to be cell lineage and stage specific. Therefore in order to identify potential Notch target genes , we compared RNA of thymocytes at the CD4+CD8+ stage of development from H-2b transgenic 5CC7 TCR/ RAG2-deficient / Presenilin1flox/flox /PS2-/- mice, with and without Cd4-Cre. Thymocyte single cell suspensions were generated using 100 µm nylon mesh (PGC Scientifics). DP thymocytes were isolated from RAG2° control or PS1/2° 5CC7 TCR H2bb mice by magnetic bead separation on anti-CD4 coated microbeads (Miltenyi Biotec.). Total RNA was isolated using TRIzol according to manufacturer's instructions (Invitrogen). After quantification and checking for integrity, 1 µg of RNA was subjected to linear amplification. The resulting aRNA was labeled by reverse transcription via Cy5-dCTP incorporation and Cy3-dCTP incorporation. The fluorescent labeled probes were subsequently combined and hybridized on topic-defined PIQORTM Immunology Microarrays Mouse Antisense.
2007-09-14 | E-GEOD-6590 | biostudies-arrayexpress
Project description:Sustained Ca2+ entry into CD4+CD8+ double-positive thymocytes is required for positive selection. We identified a voltage-gated Na+ channel (VGSC), essential for positive selection of CD4+ T cells. Pharmacological inhibition of VGSC activity inhibited sustained Ca2+ influx induced by positive-selecting ligands and in vitro positive selection of CD4+ but not CD8+ T cells. In vivo shRNA knockdown of Scn5a specifically inhibited positive selection of CD4+ T cells. Ectopic expression of VGSC in peripheral AND CD4+ T cells bestowed the ability to respond to a positively selecting ligand, directly demonstrating VGSC expression was responsible for increased sensitivity. Thus active VGSCs in thymocytes provides a mechanism by which a weak positive selecting signal can induce sustained Ca2+ signals required for CD4+ T cell development.
2012-07-01 | GSE38909 | GEO
Project description:Notch1 signaling is an important regulator of cell fate in early stages of T cell development. Because Notch receptors can function redundantly, we sought an approach for inhibiting all endogenous Notch signaling in thymocytes. Upon ligand engagement, Notch receptors undergo two successive proteolytic cleavages, the second involving a Presenilin (PS) containing complex with -secretase activity that releases a small intracellular fragment of Notch. This activated form of Notch (NotchIC) translocates from the membrane to the nucleus, where it acts as a transcription factor, inducing the expression of multiple target genes . Since Presenilins are required for the activation of all four mammalian forms of Notch, we generated mice with deletions of both Presenilin1 and Presenilin2 genes, the only genes encoding Presenilin in the mouse genome. To target Notch inactivation specifically to developing T cells, we introduced Cd4-Cre to mediate Presenilin gene deletion in a tissue- and stage-specific manner. Direct target genes of Notch signaling are largely unknown, and are likely to be cell lineage and stage specific. Therefore in order to identify potential Notch target genes , we compared RNA of thymocytes at the CD4+CD8+ stage of development from H-2b transgenic 5CC7 TCR/ RAG2-deficient / Presenilin1flox/flox /PS2-/- mice, with and without Cd4-Cre. Keywords: presenilin, thymocytes, mouse
2007-09-14 | GSE6590 | GEO
Project description:Sustained Ca2+ entry into CD4+CD8+ double-positive thymocytes is required for positive selection. We identified a voltage-gated Na+ channel (VGSC), essential for positive selection of CD4+ T cells. Pharmacological inhibition of VGSC activity inhibited sustained Ca2+ influx induced by positive-selecting ligands and in vitro positive selection of CD4+ but not CD8+ T cells. In vivo shRNA knockdown of Scn5a specifically inhibited positive selection of CD4+ T cells. Ectopic expression of VGSC in peripheral AND CD4+ T cells bestowed the ability to respond to a positively selecting ligand, directly demonstrating VGSC expression was responsible for increased sensitivity. Thus active VGSCs in thymocytes provides a mechanism by which a weak positive selecting signal can induce sustained Ca2+ signals required for CD4+ T cell development. Pre-selected AND DP thymocytes were stimulated with plate bound peptide-loaded I-Ek Ig dimers. Genes were differentially regulated by positive and negative selection signals. The goal of this study is to identify ion-channel related genes critical for thymic positive selection, given the sustained Ca2+ entry into double positive thymocytes is required for positive selection. Total RNA of pre-selected AND thymocytes stimulated with I-Ek Ig dimers loaded with the positively-selecting peptide gp250, the negatively-selecting agonist peptide MCC, or the non-selecting control peptide Hb were used for the transcriptional profiling analysis. We found 28 genes were differentially down-regulated by MCC stimulation but upregulated by gp250 stimulation. One of them, scn4b, was ion-channel related.
2012-06-30 | E-GEOD-38909 | biostudies-arrayexpress
Project description:To assess the importance of the Wnt pathway during T cell develoment, we generated a mouse line (R26-βcat) in which high levels of active β-catenin are maintained throughout T cell development. Young R26-βcat mice (6-week-old) show a differentiation block at the CD4+CD8+ DP stage. All R26-βcat mice develop T cell leukemias with a DP phenotype at 5-6 months of age. To identify the molecular pathways involved in tumor development, we profiled the global gene expression of transformed and pre-transformed DP cells.
2013-06-21 | GSE48203 | GEO
Project description:The RNase III enzyme dicer is essential for the processing of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from double-stranded RNA precursors. miRNAs and siRNAs regulate chromatin structure, gene transcription, mRNA stability and translation in a wide range of organisms. To provide a model system to explore the role of dicer-generated RNAs in the differentiation of mammalian cells in vivo, we have generated a conditional dicer allele. Deletion of dicer at an early stage of T cell development compromised the survival of αβ lineage cells, while the numbers of γδ-expressing thymocytes were not affected. In developing thymocytes, dicer was not required for the maintenance of transcriptional silencing at pericentromeric satellite sequences (constitutive heterochromatin), the maintenance of cytosine DNA methylation and X chromosome inactivation in female cells (facultative heterochromatin) and the stable shutdown of a developmentally regulated gene (developmentally regulated gene silencing). Most remarkably, given that one-third of mammalian mRNAs are putative miRNA targets, dicer appears to be dispensable for CD4/8 lineage commitment, a process where epigenetic regulation of lineage choice has been well documented. Thus, although dicer appears critical for the development of the early embryo, it may have limited impact on the implementation of lineage-specific gene expression programs. LckCre was used to delete a floxed Dicer1 allele from developing thymocytes (Cobb BS, Nesterova TB, Thompson E, Hertweck A, O'Connor E, Godwin J, Wilson CB, Brockdorff N, Fisher AG, Smale ST and Merkenschlager M. T cell lineage choice and differentiation in the absence of the RNAse III enzyme dicer. J. Exp. Med. 2005 201: 1367-1373). Thymocytes were stained for CD4 and CD8, and double-positive (DP) thymocytes were sorted by flow cytometry. Three biological replicates of Dicer lox/lox control samples and LckCre Dicer lox/lox KO samples were analysed.
2015-01-28 | E-GEOD-57511 | biostudies-arrayexpress