Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of mouse cytotoxic T lymphocyte cell line CTLL-2 treated with interleukin-2

ABSTRACT: The cytokine IL-2 determines T cell fate by controlling T cell proliferation and differentiation, but the expression files of IL-2 regulated genes are not defined; Using Affymetrix mouse genome array and mouse T cell line CTLL-2, we analyzed the expression profiles of IL-2 regulated genes over 10 time points in 24 hours after IL-2 treatment. A total of 2,813 genes were differentially expressed (>=2-fold change) at least at one time point in response to IL-2 stimulation. Clustering analyses showed that these genes consist of 9 clusters, suggesting that the IL-2 regulated genes in mouse T cells have 9 expression patterns. These genes involve in many biological processes, including immune response, signal transduction, apoptosis, cell cycle, transcription, transport, biosynthesis and various metabolisms. Two supplementary tables are linked to this series:; Table 1: IL-2 responsive genes over the first 24 hours post-stimulation; Table 2: Newly identified IL-2 regulated genes function in a variety of biological processes Experiment Overall Design: Murine cytotoxic T lymphocyte cell line CTLL-2, derived from a C57BL/6 mouse, is an IL-2 dependent cell line. Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours (No IL-2 stimulation, T0, 5 reps). After adding human rIL-2 (100 U/mL, Chiron, IL-2 stimulation), cells were collected at time point 0.5, 1, 2, 4, 6, 8, 10, 12, 16 and 24 hours, at least 3 biological replicates were carried out for each time point.Total RNA were extracted from the cells and was hybridized on Affymetrix GeneChip Mouse Genome 430 2.0 Array.

ORGANISM(S): Mus musculus

SUBMITTER: Zhaoduo Zhang

PROVIDER: E-GEOD-6085 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of expression patterns of IL-2-responsive genes in the murine T cell line CTLL-2.

Zhang Zhaoduo Z Martino Anthony A Faulon Jean-Loup JL

Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research 20071201 12

Interleukin-2 (IL-2) influences T cell proliferation and differentiation through regulation of a number of genes. Many such genes are known, yet their expression profiles have remained elusive. Using Affymetrix mouse genome arrays and the mouse T cell line CTLL-2, we studied the transcriptional response to IL-2 stimulation. A total of 2813 genes (represented by 3838 probes) showed > or =2-fold changes in expression level at one or more time points (10 were analyzed) during the first 24 h poststi ...[more]

PMID: 18184039

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Project description:Molecular mechanisms of cell cycle exit are poorly understood. A group of genes required for cell cycle exit and maintenance of cell quiescence in human fibroblasts following serum deprivation has been recently identified. Studies on lymphocytes following growth factor deprivation-induced cell cycle exit have predominantly focused on the initiation of apoptosis. A set of genes involved in lymphocyte quiescence have also been identified among genes highly expressed in resting lymphocytes and down-regulated after cell activation. In our study, proliferating IL-2-dependent human T cells were forced to exit cell cycle by growth factor withdrawal, and their gene expression profiles were examined. The differential gene expression analysis was performed in primary and immortalized IL-2-dependent T lymphocytes. Cell samples were collected directly from the IL-2-containing cultures and 8-hrs following IL-2 withdrawal, before apoptosis could be evidenced by the Annexin-V staining. The three primary T lymphoblast cell populations were obtained from the peripheral blood mononuclear cells (PBMC) stimulated for 24h by wheat germ agglutinin and cultured in the presence of IL-2 up to 4-8 population doublings. As shown by the cell surface analysis, these populations were composed of T cells exclusively. Samples of these cell populations were subsequently analyzed as biological replicates. Two spontaneously immortalized IL-2-dependent T cell lines were derived from normal spleen and from PBMC derived from Nijmegen Breakage Syndrome patient. Gene expression was assessed by the Affymetrix microarray HG-U133 2.0 Plus that detects 38,500 genes. The expression of a selected number of genes was verified by the qRT-PCR method. We have identified a set of 53 genes that we called a Ã¢??T lymphocyte cell cycle exit signatureÃ¢??, comprised of 13 up-regulated and 40 down-regulated genes. Genes linked to transcription, cell cycle, cell growth, proliferation and differentiation, cell adhesion and immune functions were found to be overrepresented among the differentially expressed, before and after IL-2 deprivation. Among those, PIM1, BCL2, IL-8, HBEGF, DUSP6, OSM, CISH, SOCS2, SOCS3, LIF and IL13 were down-regulated and RPS24, SQSTM1, TMEM1, LRRC8D, ECOP, YY1AP1, C1orf63, ASAH1, SLC25A46 and MIA3 were up-regulated. Identification of genes involved in cell cycle exit and quiescence, may provide new insights into the mechanisms of tissue repair and regeneration as well as of cancer development. Experiment Overall Design: Cell sources and cell sample preparation. Experiment Overall Design: Samples of three primary, IL-2-dependent T lymphoblast cell lines, derived from three healthy donors (j, 43, 6) were collected from IL-2-containing culture and 8-hrs following IL-2 withdrawal (three pairs, each sample was analyzed once = 6 samples). Experiment Overall Design: The two spontaneously immortalized IL-2-dependent T cell lines were derived from normal spleen (line5) and from PBMC derived from a Nijmegen Breakage Syndrome patient (S9). Samples of the two immortalized cell lines were collected in three biological replicates each, from the cultures with and without IL-2 (2 x 2 x 3 = 12 samples).

Dataset Information

Transcription profiling of mouse cytotoxic T lymphocyte cell line CTLL-2 treated with interleukin-2

Publications

Identification of expression patterns of IL-2-responsive genes in the murine T cell line CTLL-2.

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