19 research outputs found

    Synergistic Gene Expression Signature Observed in TK6 Cells upon Co-Exposure to UVC-Irradiation and Protein Kinase C-Activating Tumor Promoters

    No full text
    <div><p>Activation of stress response pathways in the tumor microenvironment can promote the development of cancer. However, little is known about the synergistic tumor promoting effects of stress response pathways simultaneously induced in the tumor microenvironment. Therefore, the purpose of this study was to establish gene expression signatures representing the interaction of pathways deregulated by tumor promoting agents and pathways induced by DNA damage. Human lymphoblastoid TK6 cells were pretreated with the protein kinase C activating tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) and exposed to UVC-irradiation. The time and dose-responsive effects of the co-treatment were captured with RNA-sequencing (RNA-seq) in two separate experiments. TK6 cells exposed to both TPA and UVC had significantly more genes differentially regulated than the theoretical sum of genes induced by either stress alone, thus indicating a synergistic effect on global gene expression patterns. Further analysis revealed that TPA+UVC co-exposure caused synergistic perturbation of specific genes associated with p53, AP-1 and inflammatory pathways important in carcinogenesis. The 17 gene signature derived from this model was confirmed with other PKC-activating tumor promoters including phorbol-12,13-dibutyrate, sapintoxin D, mezerein, (-)-Indolactam V and resiniferonol 9,13,14-ortho-phenylacetate (ROPA) with quantitative real-time PCR (QPCR). Here we show a novel gene signature that may represent a synergistic interaction in the tumor microenvironment that is relevant to the mechanisms of chemical induced tumor promotion.</p></div

    Pathway enrichment of TPA+UVC gene signature.

    No full text
    <p>Enrichment of signaling and inflammatory pathways connected by at least one gene in the TPA+UVC gene signature is represented (ConsensusPathDB). The node size is based on number of genes represented in each pathway gene set. The color is determined by statistical enrichment value (darker red = lower p value). The edge thickness represents the total number of genes shared between each pathway with the edge color representing the number of genes in the gene signature shared between each pathway (darker red = more genes). The most significantly enriched pathways were TNFα, TGFβ, IFNγ, p53 and AP-1.</p

    Overlap of the signaling pathways enriched in the dose-dependent and synergistic genes induced by TPA+UVC co-treatment.

    No full text
    <p>Overlap of the signaling pathways enriched in the dose-dependent and synergistic genes induced by TPA+UVC co-treatment.</p

    TPA+UVC 8-hour gene signature.

    No full text
    <p>(A) A 90 gene signature was derived by determining genes that were significantly altered compared to either stress alone in the time-course experiment (experiment #1) at 8-hours and also expressed in a TPA dose-responsive trend in experiment #2. (B) Visualization of the 90 gene signature based on fold-change in the dose-response experiment revealed the increasing or decreasing expression trends for each gene (each series represented by individual gene in signature) as the concentration of TPA increased from 0.2 nM to 1.0 nM.</p

    Network analysis of TPA+UVC gene signature.

    No full text
    <p>STRING analysis revealed key sub-network clusters and potential gene level interactions connected to <i>p53</i>, <i>TGFβ</i>, <i>TNF and JUN</i>. Colors represent different subnetworks based on K-means clustering. Edge thickness is representative of confidence in interaction based on database mining, experimental evidence and text mining.</p

    Phenotypically anchored TPA+UVC genes based on synergistic expression, dose-dependency and sustained activation.

    No full text
    <p>Phenotypically anchored TPA+UVC genes based on synergistic expression, dose-dependency and sustained activation.</p

    Sustained seventeen gene signature through 24 hours.

    No full text
    <p>Seventeen genes in TPA+UVC gene signature were significantly altered (fold-change ±2 and FDR <0.05) compared to UVC or TPA alone at both 8 and 24 hours.</p

    Gene set analysis workflow.

    No full text
    <p>Two separate experiments were conducted to determine the time- (experiment #1) and dose-responsive (experiment #2) gene expression patterns in the TPA+UVC co-treated cells. We filtered the gene set through an analysis workflow in order to uncover a synergistic, dose-responsive and reproducible gene signature associated with TPA+UVC exposure. Using several open-source analysis tools, we were able to describe different levels of biological complexity in the data. (1) First, differential expression analysis of TPA, UVC and the TPA+UVC treated cells versus the untreated control was analyzed for significant up or down regulation of biological processes (DAVID) at 4, 8 and 24 hours. Then, differential expression was determined for the TPA+UVC co-treated cells using TPA-alone or UVC-alone treated cells as the basis for comparison (i.e. the control samples). In this manner, we were able to determine the synergistically regulated genes in the TPA+UVC treated cells compared to either stress alone. (2) These synergistic genes were further analyzed to determine the canonical pathways significantly enhanced by TPA+UVC using gene set enrichment (MolSigDB). The synergistically regulated genes in experiment #1 (time-course) that were also dose-responsive in experiment #2 were analyzed for (3) pathway level (ConsensusPathDB) and (4) gene level interactions (STRING). (5) The genes found to be sustained (up to 24 hours) in the synergistic manner, in experiment #1, were considered the key gene signature that is specially enhanced by the combined treatment to TPA+UVC.</p

    Validation of seventeen gene signature with other PKC-activating tumor promoters.

    No full text
    <p>TK6 cells were treated with other PKC-activating tumor promoters including PDBu, SPd, Mez, IndV and ROPA and exposed to UVC-irradiation to verify the 17 gene signature observed with RNA-sequencing. Gene expression was observed with QPCR. Most of the 17 genes had synergistic expression patterns in the co-treated cells (green bar). The fold-change of the UVC-alone (grey bar) and PKC-activator alone (red bar) are stacked to represent the theoretical additive response. One way ANOVA with Bonferroni post-hoc analysis was conducted (p<0.05) to determine statistical significance of the co-treated cells compared to either stress alone.</p
    corecore