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A multi-omics approach identifies key hubs associated with cell type-specific responses of airway epithelial cells to staphylococcal alpha-toxin.

Richter E, Harms M, Ventz K, Gierok P, Chilukoti RK, Hildebrandt JP, Mostertz J, Hochgräfe F - PLoS ONE (2015)

Bottom Line: Phosphoproteomics revealed a substantial impact on phosphorylation-dependent signaling in both cell models and highlights alterations in signaling pathways associated with cell-cell and cell-matrix contacts as well as the actin cytoskeleton as key features of early rHla-induced effects.Along comparable changes in down-stream activity of major protein kinases significant differences between both models were found upon rHla-treatment including activation of the epidermal growth factor receptor EGFR and mitogen-activated protein kinases MAPK1/3 signaling in S9 and repression in 16HBE14o- cells.Strikingly, inhibition of the EGFR sensitized S9 cells to Hla indicating that the cellular capacity of activation of the EGFR is a major protective determinant against Hla-mediated cytotoxic effects.

View Article: PubMed Central - PubMed

Affiliation: Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, 17489, Greifswald, Germany.

ABSTRACT
Responsiveness of cells to alpha-toxin (Hla) from Staphylococcus aureus appears to occur in a cell-type dependent manner. Here, we compare two human bronchial epithelial cell lines, i.e. Hla-susceptible 16HBE14o- and Hla-resistant S9 cells, by a quantitative multi-omics strategy for a better understanding of Hla-induced cellular programs. Phosphoproteomics revealed a substantial impact on phosphorylation-dependent signaling in both cell models and highlights alterations in signaling pathways associated with cell-cell and cell-matrix contacts as well as the actin cytoskeleton as key features of early rHla-induced effects. Along comparable changes in down-stream activity of major protein kinases significant differences between both models were found upon rHla-treatment including activation of the epidermal growth factor receptor EGFR and mitogen-activated protein kinases MAPK1/3 signaling in S9 and repression in 16HBE14o- cells. System-wide transcript and protein expression profiling indicate induction of an immediate early response in either model. In addition, EGFR and MAPK1/3-mediated changes in gene expression suggest cellular recovery and survival in S9 cells but cell death in 16HBE14o- cells. Strikingly, inhibition of the EGFR sensitized S9 cells to Hla indicating that the cellular capacity of activation of the EGFR is a major protective determinant against Hla-mediated cytotoxic effects.

No MeSH data available.


Related in: MedlinePlus

DNA-microarray-based transcription profiles of 16HBE14o- and S9 cells under influence of rHla.A. Volcano plots of mRNA expression differences under control conditions and after treatment with rHla in 16HBE14o- and S9 as a function of statistical significance (ANOVA post hoc p≤0.05) and intensity ratio at the level of probe-sets. Probe sets indicating significant higher expression after rHla-treatment are indicated in ruby, probe sets indicating higher expression under control conditions are in cyan, and probe sets with no significant expression differences are in gray. Numbers indicate the number of gene-specific mRNAs increased (ruby) and decreased (cyan) after assigning probe-sets to genes. B. Expression level changes for selected immediate early response genes after rHla treatment of 16HBE14o- (open circles) and S9 (filled circles) cells (***p<0.001; **p<0.01; *p<0.05). C. Top five cellular functions affected after rHla-treatment in the category molecular functions for 16HBE14o- (black bars) and S9 (gray bars) as predicted by IPA Downstream Effects Analysis based on differentially expressed genes. D. Functional trends after rHla-treatment in all categories as predicted by IPA Downstream Effects Analysis based on direction of change of differentially expressed genes (16HBE14o- upper panel, S9 lower panel). The word cloud depicts the frequency of terms by font size and predicted increase in functional activity is shown in ruby and decrease in activity is shown in cyan.
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pone.0122089.g004: DNA-microarray-based transcription profiles of 16HBE14o- and S9 cells under influence of rHla.A. Volcano plots of mRNA expression differences under control conditions and after treatment with rHla in 16HBE14o- and S9 as a function of statistical significance (ANOVA post hoc p≤0.05) and intensity ratio at the level of probe-sets. Probe sets indicating significant higher expression after rHla-treatment are indicated in ruby, probe sets indicating higher expression under control conditions are in cyan, and probe sets with no significant expression differences are in gray. Numbers indicate the number of gene-specific mRNAs increased (ruby) and decreased (cyan) after assigning probe-sets to genes. B. Expression level changes for selected immediate early response genes after rHla treatment of 16HBE14o- (open circles) and S9 (filled circles) cells (***p<0.001; **p<0.01; *p<0.05). C. Top five cellular functions affected after rHla-treatment in the category molecular functions for 16HBE14o- (black bars) and S9 (gray bars) as predicted by IPA Downstream Effects Analysis based on differentially expressed genes. D. Functional trends after rHla-treatment in all categories as predicted by IPA Downstream Effects Analysis based on direction of change of differentially expressed genes (16HBE14o- upper panel, S9 lower panel). The word cloud depicts the frequency of terms by font size and predicted increase in functional activity is shown in ruby and decrease in activity is shown in cyan.

Mentions: Hence, we asked if the observed moderate changes in the proteome following rHla-treatment are preceded or accompanied by alterations at the transcriptional level. For this purpose, global transcriptome analyses of rHla-treated S9 and 16HBE14o- cells were performed. Two hours after the addition of rHla, we monitored 205 (S9) and 915 (16HBE14o-) gene-specific probe sets pointing to their corresponding genes with differential expression (Fig. 4A, S3 Table). Probe-set transformation into genes based on Entrez Genes/Unigenes allowed the identification of 44 and 44 genes in S9 cells, and 266 and 318 genes in 16HBE14o- cells that appeared up-regulated and down-regulated under influence of rHla, respectively. From these, 19 genes are transcribed at higher levels in both S9 and 16HBE14o- cells at comparable rates. For example, mRNAs of NR4A members 1 and 2, FOS, IL6, DUSP1, EGR1 and JUN were observed in this group. 25 genes show decreased transcription levels in both cell lines, including GPR21, CCL2, PMEPA1 and SERPINE1. The comparison of the transcriptome and proteome data revealed a number of direct correlations between mRNA and protein expression changes, e.g. down-regulation of plasminogen activator inhibitor PAI1/SERPINE1 (proteome: -1.9, transcriptome: -2.1) and SDC4 (-2.4; -1.3), and up-regulation of Golgi phosphoprotein 3-like protein GLP3L (1.6; 2.5), observed for 16HBE14o- cells and histone H1.2 (HIST1H1C, -1.9; -1.5) in S9 cells.


A multi-omics approach identifies key hubs associated with cell type-specific responses of airway epithelial cells to staphylococcal alpha-toxin.

Richter E, Harms M, Ventz K, Gierok P, Chilukoti RK, Hildebrandt JP, Mostertz J, Hochgräfe F - PLoS ONE (2015)

DNA-microarray-based transcription profiles of 16HBE14o- and S9 cells under influence of rHla.A. Volcano plots of mRNA expression differences under control conditions and after treatment with rHla in 16HBE14o- and S9 as a function of statistical significance (ANOVA post hoc p≤0.05) and intensity ratio at the level of probe-sets. Probe sets indicating significant higher expression after rHla-treatment are indicated in ruby, probe sets indicating higher expression under control conditions are in cyan, and probe sets with no significant expression differences are in gray. Numbers indicate the number of gene-specific mRNAs increased (ruby) and decreased (cyan) after assigning probe-sets to genes. B. Expression level changes for selected immediate early response genes after rHla treatment of 16HBE14o- (open circles) and S9 (filled circles) cells (***p<0.001; **p<0.01; *p<0.05). C. Top five cellular functions affected after rHla-treatment in the category molecular functions for 16HBE14o- (black bars) and S9 (gray bars) as predicted by IPA Downstream Effects Analysis based on differentially expressed genes. D. Functional trends after rHla-treatment in all categories as predicted by IPA Downstream Effects Analysis based on direction of change of differentially expressed genes (16HBE14o- upper panel, S9 lower panel). The word cloud depicts the frequency of terms by font size and predicted increase in functional activity is shown in ruby and decrease in activity is shown in cyan.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4376684&req=5

pone.0122089.g004: DNA-microarray-based transcription profiles of 16HBE14o- and S9 cells under influence of rHla.A. Volcano plots of mRNA expression differences under control conditions and after treatment with rHla in 16HBE14o- and S9 as a function of statistical significance (ANOVA post hoc p≤0.05) and intensity ratio at the level of probe-sets. Probe sets indicating significant higher expression after rHla-treatment are indicated in ruby, probe sets indicating higher expression under control conditions are in cyan, and probe sets with no significant expression differences are in gray. Numbers indicate the number of gene-specific mRNAs increased (ruby) and decreased (cyan) after assigning probe-sets to genes. B. Expression level changes for selected immediate early response genes after rHla treatment of 16HBE14o- (open circles) and S9 (filled circles) cells (***p<0.001; **p<0.01; *p<0.05). C. Top five cellular functions affected after rHla-treatment in the category molecular functions for 16HBE14o- (black bars) and S9 (gray bars) as predicted by IPA Downstream Effects Analysis based on differentially expressed genes. D. Functional trends after rHla-treatment in all categories as predicted by IPA Downstream Effects Analysis based on direction of change of differentially expressed genes (16HBE14o- upper panel, S9 lower panel). The word cloud depicts the frequency of terms by font size and predicted increase in functional activity is shown in ruby and decrease in activity is shown in cyan.
Mentions: Hence, we asked if the observed moderate changes in the proteome following rHla-treatment are preceded or accompanied by alterations at the transcriptional level. For this purpose, global transcriptome analyses of rHla-treated S9 and 16HBE14o- cells were performed. Two hours after the addition of rHla, we monitored 205 (S9) and 915 (16HBE14o-) gene-specific probe sets pointing to their corresponding genes with differential expression (Fig. 4A, S3 Table). Probe-set transformation into genes based on Entrez Genes/Unigenes allowed the identification of 44 and 44 genes in S9 cells, and 266 and 318 genes in 16HBE14o- cells that appeared up-regulated and down-regulated under influence of rHla, respectively. From these, 19 genes are transcribed at higher levels in both S9 and 16HBE14o- cells at comparable rates. For example, mRNAs of NR4A members 1 and 2, FOS, IL6, DUSP1, EGR1 and JUN were observed in this group. 25 genes show decreased transcription levels in both cell lines, including GPR21, CCL2, PMEPA1 and SERPINE1. The comparison of the transcriptome and proteome data revealed a number of direct correlations between mRNA and protein expression changes, e.g. down-regulation of plasminogen activator inhibitor PAI1/SERPINE1 (proteome: -1.9, transcriptome: -2.1) and SDC4 (-2.4; -1.3), and up-regulation of Golgi phosphoprotein 3-like protein GLP3L (1.6; 2.5), observed for 16HBE14o- cells and histone H1.2 (HIST1H1C, -1.9; -1.5) in S9 cells.

Bottom Line: Phosphoproteomics revealed a substantial impact on phosphorylation-dependent signaling in both cell models and highlights alterations in signaling pathways associated with cell-cell and cell-matrix contacts as well as the actin cytoskeleton as key features of early rHla-induced effects.Along comparable changes in down-stream activity of major protein kinases significant differences between both models were found upon rHla-treatment including activation of the epidermal growth factor receptor EGFR and mitogen-activated protein kinases MAPK1/3 signaling in S9 and repression in 16HBE14o- cells.Strikingly, inhibition of the EGFR sensitized S9 cells to Hla indicating that the cellular capacity of activation of the EGFR is a major protective determinant against Hla-mediated cytotoxic effects.

View Article: PubMed Central - PubMed

Affiliation: Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, 17489, Greifswald, Germany.

ABSTRACT
Responsiveness of cells to alpha-toxin (Hla) from Staphylococcus aureus appears to occur in a cell-type dependent manner. Here, we compare two human bronchial epithelial cell lines, i.e. Hla-susceptible 16HBE14o- and Hla-resistant S9 cells, by a quantitative multi-omics strategy for a better understanding of Hla-induced cellular programs. Phosphoproteomics revealed a substantial impact on phosphorylation-dependent signaling in both cell models and highlights alterations in signaling pathways associated with cell-cell and cell-matrix contacts as well as the actin cytoskeleton as key features of early rHla-induced effects. Along comparable changes in down-stream activity of major protein kinases significant differences between both models were found upon rHla-treatment including activation of the epidermal growth factor receptor EGFR and mitogen-activated protein kinases MAPK1/3 signaling in S9 and repression in 16HBE14o- cells. System-wide transcript and protein expression profiling indicate induction of an immediate early response in either model. In addition, EGFR and MAPK1/3-mediated changes in gene expression suggest cellular recovery and survival in S9 cells but cell death in 16HBE14o- cells. Strikingly, inhibition of the EGFR sensitized S9 cells to Hla indicating that the cellular capacity of activation of the EGFR is a major protective determinant against Hla-mediated cytotoxic effects.

No MeSH data available.


Related in: MedlinePlus