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Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway.

Yang M, Lin X, Rowe A, Rognes T, Eide L, Bjørås M - Sci Rep (2015)

Bottom Line: The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown.In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes.In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Oslo University Hospital and University of Oslo, Norway.

ABSTRACT
The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3), antioxidant genes (PRDX4, PTGS1 and CYGB) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and RPRM) and apoptosis (i.e. CytC and CASP9). We demonstrated that OXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress and increase protein expression of the apoptosis initiator protease CASP9. In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.

No MeSH data available.


Related in: MedlinePlus

Identification of early oxidative stress response genes in control and hOXR1 depleted HeLa cells.(a) The differential expression profile induced by H2O2 in control siRNA (siCon_NT vs siCon_R0h) or hOXR1 siRNA transfected cells (siOXR1_NT vs siOXR1_R0h). The total numbers of up- or down-regulated genes are shown in red or green, respectively. (b) Venn analysis of commonly/uniquely up- or down-regulated genes in control siRNA and hOXR1 siRNA transfected cells. (c) Heatmap showing early oxidative stress response genes identified in control siRNA or hOXR1 siRNA transfected cells. Red: up-regulated genes; green: down-regulatied genes; black: no change; siCon: control siRNA; siOXR1: hOXR1 siRNA; NT: non-treatment; R0h: cells were treated with 0.5 mM H2O2 for1 h without recovery.
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f5: Identification of early oxidative stress response genes in control and hOXR1 depleted HeLa cells.(a) The differential expression profile induced by H2O2 in control siRNA (siCon_NT vs siCon_R0h) or hOXR1 siRNA transfected cells (siOXR1_NT vs siOXR1_R0h). The total numbers of up- or down-regulated genes are shown in red or green, respectively. (b) Venn analysis of commonly/uniquely up- or down-regulated genes in control siRNA and hOXR1 siRNA transfected cells. (c) Heatmap showing early oxidative stress response genes identified in control siRNA or hOXR1 siRNA transfected cells. Red: up-regulated genes; green: down-regulatied genes; black: no change; siCon: control siRNA; siOXR1: hOXR1 siRNA; NT: non-treatment; R0h: cells were treated with 0.5 mM H2O2 for1 h without recovery.

Mentions: Oxidative stress induces transcriptional networks in mammalian cells. For example, exposure of the human liver HepG2 cells to hydrogen peroxide, menadione or tert-butyl hydroperoxide revealed 136 genes that are differentially expressed by all three oxidants as compared to non-treated cells17. In this work we identified 31 differentially expressed early stress response genes (24 up and 7 down) immediately after hydrogen peroxide exposure in control HeLa cells, while 57 genes were differentially regulated (56 up and 1 down) in hOXR1 depleted cells (Fig. 5a). Venn analysis shows that 18 DEGs are commonly regulated in both control and hOXR1 depleted cells, including transcription factors JUN and FOS (Fig. 5b,c), suggesting that hOXR1 is not necessary for up-regulation of this subset of genes during hydrogen peroxide induced stress. However, most of the genes showed a significantly stronger up-regulation in hOXR1 depleted cells as compared to control cells, including FOS, JUN and DUSP1 (dual specificity phosphatase 1) (Figs 4e,f and 5c). Furthermore, a subset of 38 hydrogen peroxide induced genes was only found in hOXR1 depleted cells (Fig. 5b), including IL1A (interleukin 1, alpha), HSPA2 (heat shock 70 kDa protein 2), NR4A1 and SPRY2 (sprouty homolog 2) (Fig. 5c). The proteins encoded by this subset of early stress response genes form a large protein-protein interaction network with thousands of other proteins (Supplementary Fig. S4). Thus, the increased number of early stress response genes in hOXR1 depleted cells suggests an important role for hOXR1 in regulating the early stress response during oxidative stress. GO enrichment analysis of the early stress response genes showed that the top biological processes included the stress response cluster under H2O2 induced oxidative stress in both control and hOXR1 depleted cells. Interestingly, the enriched clusters also included “RNA metabolic processes” and “regulation of transcription” in hOXR1-depleted cells, but not in control cells (Supplementary Table S9). Thus it appears that hOXR1 is crucial for balancing transcriptional networks regulating the oxidative stress response.


Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway.

Yang M, Lin X, Rowe A, Rognes T, Eide L, Bjørås M - Sci Rep (2015)

Identification of early oxidative stress response genes in control and hOXR1 depleted HeLa cells.(a) The differential expression profile induced by H2O2 in control siRNA (siCon_NT vs siCon_R0h) or hOXR1 siRNA transfected cells (siOXR1_NT vs siOXR1_R0h). The total numbers of up- or down-regulated genes are shown in red or green, respectively. (b) Venn analysis of commonly/uniquely up- or down-regulated genes in control siRNA and hOXR1 siRNA transfected cells. (c) Heatmap showing early oxidative stress response genes identified in control siRNA or hOXR1 siRNA transfected cells. Red: up-regulated genes; green: down-regulatied genes; black: no change; siCon: control siRNA; siOXR1: hOXR1 siRNA; NT: non-treatment; R0h: cells were treated with 0.5 mM H2O2 for1 h without recovery.
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getmorefigures.php?uid=PMC4663793&req=5

f5: Identification of early oxidative stress response genes in control and hOXR1 depleted HeLa cells.(a) The differential expression profile induced by H2O2 in control siRNA (siCon_NT vs siCon_R0h) or hOXR1 siRNA transfected cells (siOXR1_NT vs siOXR1_R0h). The total numbers of up- or down-regulated genes are shown in red or green, respectively. (b) Venn analysis of commonly/uniquely up- or down-regulated genes in control siRNA and hOXR1 siRNA transfected cells. (c) Heatmap showing early oxidative stress response genes identified in control siRNA or hOXR1 siRNA transfected cells. Red: up-regulated genes; green: down-regulatied genes; black: no change; siCon: control siRNA; siOXR1: hOXR1 siRNA; NT: non-treatment; R0h: cells were treated with 0.5 mM H2O2 for1 h without recovery.
Mentions: Oxidative stress induces transcriptional networks in mammalian cells. For example, exposure of the human liver HepG2 cells to hydrogen peroxide, menadione or tert-butyl hydroperoxide revealed 136 genes that are differentially expressed by all three oxidants as compared to non-treated cells17. In this work we identified 31 differentially expressed early stress response genes (24 up and 7 down) immediately after hydrogen peroxide exposure in control HeLa cells, while 57 genes were differentially regulated (56 up and 1 down) in hOXR1 depleted cells (Fig. 5a). Venn analysis shows that 18 DEGs are commonly regulated in both control and hOXR1 depleted cells, including transcription factors JUN and FOS (Fig. 5b,c), suggesting that hOXR1 is not necessary for up-regulation of this subset of genes during hydrogen peroxide induced stress. However, most of the genes showed a significantly stronger up-regulation in hOXR1 depleted cells as compared to control cells, including FOS, JUN and DUSP1 (dual specificity phosphatase 1) (Figs 4e,f and 5c). Furthermore, a subset of 38 hydrogen peroxide induced genes was only found in hOXR1 depleted cells (Fig. 5b), including IL1A (interleukin 1, alpha), HSPA2 (heat shock 70 kDa protein 2), NR4A1 and SPRY2 (sprouty homolog 2) (Fig. 5c). The proteins encoded by this subset of early stress response genes form a large protein-protein interaction network with thousands of other proteins (Supplementary Fig. S4). Thus, the increased number of early stress response genes in hOXR1 depleted cells suggests an important role for hOXR1 in regulating the early stress response during oxidative stress. GO enrichment analysis of the early stress response genes showed that the top biological processes included the stress response cluster under H2O2 induced oxidative stress in both control and hOXR1 depleted cells. Interestingly, the enriched clusters also included “RNA metabolic processes” and “regulation of transcription” in hOXR1-depleted cells, but not in control cells (Supplementary Table S9). Thus it appears that hOXR1 is crucial for balancing transcriptional networks regulating the oxidative stress response.

Bottom Line: The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown.In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes.In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Oslo University Hospital and University of Oslo, Norway.

ABSTRACT
The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3), antioxidant genes (PRDX4, PTGS1 and CYGB) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and RPRM) and apoptosis (i.e. CytC and CASP9). We demonstrated that OXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress and increase protein expression of the apoptosis initiator protease CASP9. In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.

No MeSH data available.


Related in: MedlinePlus