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Global gene expression changes in human embryonic lung fibroblasts induced by organic extracts from respirable air particles.

Líbalová H, Uhlířová K, Kléma J, Machala M, Šrám RJ, Ciganek M, Topinka J - Part Fibre Toxicol (2012)

Bottom Line: Dose-dependent increases in the number of significantly deregulated transcripts as well as dose-response relationships in the levels of individual transcripts were observed.The transcriptomic data did not differ substantially between the localities, suggesting that the air pollution originating mainly from various sources may have similar biological effects.Other important deregulated pathways in all 4 localities were ABC transporters (involved in the translocation of exogenous and endogenous metabolites across membranes and DNA repair), the Wnt and TGF-β signaling pathways (associated particularly with tumor promotion and progression), Steroid hormone biosynthesis (involved in the endocrine-disrupting activity of chemicals), and Glycerolipid metabolism (pathways involving the lipids with a glycerol backbone including lipid signaling molecules).

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic.

ABSTRACT

Background: Recently, we used cell-free assays to demonstrate the toxic effects of complex mixtures of organic extracts from urban air particles (PM2.5) collected in four localities of the Czech Republic (Ostrava-Bartovice, Ostrava-Poruba, Karvina and Trebon) which differed in the extent and sources of air pollution. To obtain further insight into the biological mechanisms of action of the extractable organic matter (EOM) from ambient air particles, human embryonic lung fibroblasts (HEL12469) were treated with the same four EOMs to assess changes in the genome-wide expression profiles compared to DMSO treated controls.

Method: For this purpose, HEL cells were incubated with subtoxic EOM concentrations of 10, 30, and 60 μg EOM/ml for 24 hours and global gene expression changes were analyzed using human whole genome microarrays (Illumina). The expression of selected genes was verified by quantitative real-time PCR.

Results: Dose-dependent increases in the number of significantly deregulated transcripts as well as dose-response relationships in the levels of individual transcripts were observed. The transcriptomic data did not differ substantially between the localities, suggesting that the air pollution originating mainly from various sources may have similar biological effects. This was further confirmed by the analysis of deregulated pathways and by identification of the most contributing gene modulations. The number of significantly deregulated KEGG pathways, as identified by Goeman's global test, varied, depending on the locality, between 12 to 29. The Metabolism of xenobiotics by cytochrome P450 exhibited the strongest upregulation in all 4 localities and CYP1B1 had a major contribution to the upregulation of this pathway. Other important deregulated pathways in all 4 localities were ABC transporters (involved in the translocation of exogenous and endogenous metabolites across membranes and DNA repair), the Wnt and TGF-β signaling pathways (associated particularly with tumor promotion and progression), Steroid hormone biosynthesis (involved in the endocrine-disrupting activity of chemicals), and Glycerolipid metabolism (pathways involving the lipids with a glycerol backbone including lipid signaling molecules).

Conclusion: The microarray data suggested a prominent role of activation of aryl hydrocarbon receptor-dependent gene expression.

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Related in: MedlinePlus

Venn diagram representing numbers of common and locality-specific deregulated genes following 24-h treatment of HEL cells with 60 μg EOM/ml, relative to DMSO used as a solvent control (adjusted P-value < 0.05, average expression level (AvgExp) > 4, and log2 FC (fold change) > /1/).
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Figure 2: Venn diagram representing numbers of common and locality-specific deregulated genes following 24-h treatment of HEL cells with 60 μg EOM/ml, relative to DMSO used as a solvent control (adjusted P-value < 0.05, average expression level (AvgExp) > 4, and log2 FC (fold change) > /1/).

Mentions: We first identified differential gene expression in each EOM dose from all 4 localities. A full list of deregulated genes is available as Additional file 2. The number of deregulated transcripts with adjusted P-value < 0.05, average expression level (AvgExp) > 4, and log2 FC (fold change) > /1/exhibiting a positive dose response for all 4 localities is shown in Figure 1. More than 1200 transcripts were deregulated at the highest dose of 60 μg EOM/ml for the heavily polluted area of Ostrava-Bartovice, while after the exposure to the extract sample from Ostrava-Poruba (6 km from Ostrava-Bartovice) only about 700 genes were deregulated. Significant overlap of deregulated transcripts was observed between the localities (Figure 2). More than 360 transcripts were deregulated simultaneously in all 4 localities for EOM at the concentration of 60 μg EOM/ml. This number represented approximately 30% of all deregulated genes for Ostrava-Bartovice, 50% for Ostrava-Poruba, 68% for Karvina, and 36% for Trebon sample. Despite this significant overlap, 388 transcripts (32%) were exclusively deregulated in cells treated with EOM (60 μg/ml) from Ostrava-Bartovice, while only 58 (8%), 37 (7%), and 178 (18%) transcripts were deregulated by samples from Ostrava-Poruba, Karvina, and Trebon, respectively.


Global gene expression changes in human embryonic lung fibroblasts induced by organic extracts from respirable air particles.

Líbalová H, Uhlířová K, Kléma J, Machala M, Šrám RJ, Ciganek M, Topinka J - Part Fibre Toxicol (2012)

Venn diagram representing numbers of common and locality-specific deregulated genes following 24-h treatment of HEL cells with 60 μg EOM/ml, relative to DMSO used as a solvent control (adjusted P-value < 0.05, average expression level (AvgExp) > 4, and log2 FC (fold change) > /1/).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3275518&req=5

Figure 2: Venn diagram representing numbers of common and locality-specific deregulated genes following 24-h treatment of HEL cells with 60 μg EOM/ml, relative to DMSO used as a solvent control (adjusted P-value < 0.05, average expression level (AvgExp) > 4, and log2 FC (fold change) > /1/).
Mentions: We first identified differential gene expression in each EOM dose from all 4 localities. A full list of deregulated genes is available as Additional file 2. The number of deregulated transcripts with adjusted P-value < 0.05, average expression level (AvgExp) > 4, and log2 FC (fold change) > /1/exhibiting a positive dose response for all 4 localities is shown in Figure 1. More than 1200 transcripts were deregulated at the highest dose of 60 μg EOM/ml for the heavily polluted area of Ostrava-Bartovice, while after the exposure to the extract sample from Ostrava-Poruba (6 km from Ostrava-Bartovice) only about 700 genes were deregulated. Significant overlap of deregulated transcripts was observed between the localities (Figure 2). More than 360 transcripts were deregulated simultaneously in all 4 localities for EOM at the concentration of 60 μg EOM/ml. This number represented approximately 30% of all deregulated genes for Ostrava-Bartovice, 50% for Ostrava-Poruba, 68% for Karvina, and 36% for Trebon sample. Despite this significant overlap, 388 transcripts (32%) were exclusively deregulated in cells treated with EOM (60 μg/ml) from Ostrava-Bartovice, while only 58 (8%), 37 (7%), and 178 (18%) transcripts were deregulated by samples from Ostrava-Poruba, Karvina, and Trebon, respectively.

Bottom Line: Dose-dependent increases in the number of significantly deregulated transcripts as well as dose-response relationships in the levels of individual transcripts were observed.The transcriptomic data did not differ substantially between the localities, suggesting that the air pollution originating mainly from various sources may have similar biological effects.Other important deregulated pathways in all 4 localities were ABC transporters (involved in the translocation of exogenous and endogenous metabolites across membranes and DNA repair), the Wnt and TGF-β signaling pathways (associated particularly with tumor promotion and progression), Steroid hormone biosynthesis (involved in the endocrine-disrupting activity of chemicals), and Glycerolipid metabolism (pathways involving the lipids with a glycerol backbone including lipid signaling molecules).

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetic Ecotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic.

ABSTRACT

Background: Recently, we used cell-free assays to demonstrate the toxic effects of complex mixtures of organic extracts from urban air particles (PM2.5) collected in four localities of the Czech Republic (Ostrava-Bartovice, Ostrava-Poruba, Karvina and Trebon) which differed in the extent and sources of air pollution. To obtain further insight into the biological mechanisms of action of the extractable organic matter (EOM) from ambient air particles, human embryonic lung fibroblasts (HEL12469) were treated with the same four EOMs to assess changes in the genome-wide expression profiles compared to DMSO treated controls.

Method: For this purpose, HEL cells were incubated with subtoxic EOM concentrations of 10, 30, and 60 μg EOM/ml for 24 hours and global gene expression changes were analyzed using human whole genome microarrays (Illumina). The expression of selected genes was verified by quantitative real-time PCR.

Results: Dose-dependent increases in the number of significantly deregulated transcripts as well as dose-response relationships in the levels of individual transcripts were observed. The transcriptomic data did not differ substantially between the localities, suggesting that the air pollution originating mainly from various sources may have similar biological effects. This was further confirmed by the analysis of deregulated pathways and by identification of the most contributing gene modulations. The number of significantly deregulated KEGG pathways, as identified by Goeman's global test, varied, depending on the locality, between 12 to 29. The Metabolism of xenobiotics by cytochrome P450 exhibited the strongest upregulation in all 4 localities and CYP1B1 had a major contribution to the upregulation of this pathway. Other important deregulated pathways in all 4 localities were ABC transporters (involved in the translocation of exogenous and endogenous metabolites across membranes and DNA repair), the Wnt and TGF-β signaling pathways (associated particularly with tumor promotion and progression), Steroid hormone biosynthesis (involved in the endocrine-disrupting activity of chemicals), and Glycerolipid metabolism (pathways involving the lipids with a glycerol backbone including lipid signaling molecules).

Conclusion: The microarray data suggested a prominent role of activation of aryl hydrocarbon receptor-dependent gene expression.

Show MeSH
Related in: MedlinePlus