Functional profiling in yeast with the benzene metabolites hydroquinone, catechol and 1,2,4-benzenetriol
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE45116 | GEO | 2013/03/13
SECONDARY ACCESSION(S): PRJNA192912
REPOSITORIES: GEO
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Project description:Benzene is a ubiquitous environmental contaminant and is widely used in industry. Exposure to benzene causes a number of serious health problems, including blood disorders and leukemia. Benzene undergoes complex metabolism in humans, making mechanistic determination of benzene toxicity difficult. We used a functional genomics approach to identify the genes that modulate the cellular toxicity of three of the phenolic metabolites of benzene, hydroquinone (HQ), catechol (CAT) and 1,2,4-benzenetriol (BT), in the model eukaryote Saccharomyces cerevisiae. Benzene metabolites generate oxidative and cytoskeletal stress, and tolerance requires correct regulation of iron homeostasis and the vacuolar ATPase. We have identified a conserved bZIP transcription factor, Yap3p, as important for a HQ-specific response pathway, as well as two genes that encode putative NAD(P)H:quinone oxidoreductases, PST2 and YCP4. Many of the yeast genes identified have human orthologs that may modulate human benzene toxicity in a similar manner and could play a role in benzene exposure-related disease. Genome-Wide Functional Profiling Reveals Genes Required for Tolerance to Benzene Metabolites in Yeast. PLoS ONE 2011, 6(8):e24205 - PMID: 21912624. Pools of homozygous diploid deletion mutants (n = 4,607 strains) were grown in rich media (YPD) at 3 concentrations of hydroquinone (HQ), catechol (CAT) and 1,2,4-benzenetriol (BT) for 5 and 15 generations (5g, 15g). Each strain has a deletion in a different gene. In each strain, the gene was replaced by a deletion cassette containing a antibiotic resistance gene and two BARCODES, up and down tags (Please see Giaever et al, 2002, Nature). These tags in the DNA are specific to each strain. We pool all deletion strains and grow them under a selective condition; extract DNA; amplify barcodes using universal primers and hybridize to arrays containing complemetary sequences to the up and down tags. In this way, we can look at growth of each of the strains. Our strategy is to analyze separately the up and down tags. Therefore, for each array (CEL file), we generate two data files, one for all ups and another one for all downs. In these files, the list of genes are the same but the data come from different set of probes, up or down. The values are log2 averages of replicate probes for the same tag. These pre processed files were used to identify strains with differential growth in benzene metabolites by comparing to the control arrays.
2013-03-13 | E-GEOD-45116 | biostudies-arrayexpress
Project description:1,2,4-Benzenetriol (BTO), sourced from the carbohydrate-derived platform chemical 5-hydroxylmethylfurfural (HMF), is an interesting starting point for the synthesis of various biobased aromatic products. However, BTO readily undergoes dimerization and other reactions under mild conditions, making analysis and isolation challenging. To both control and utilize the reactivity of BTO to produce biobased building blocks, its reactivity needs to be better understood. Here it was found that specific BTO aromatic C-H bonds are reactive toward deuterium exchange with D2O, which appears pronounced under acidic conditions at room temperature and can lead to the selective formation of BTO with an aromatic ring that contains one or two deuterium atoms, the first at the five and the second at the three position. By exposure to air, it was shown that BTO forms a 5,5'-linked BTO dimer [1,1'-biphenyl]-2,2',4,4',5,5'-hexaol (1) and subsequently a hydroxyquinone containing dimeric structure 2',4,4',5'-tetrahydroxy-[1,1'-biphenyl]-2,5-dione (2). Additionally, condensed dimer dibenzo[b,d]furan-2,3,7,8-tetraol (3) can be relatively easily accessed. The controlled formation of these symmetric and asymmetric multifunctional dimers illustrates diverse possibilities for BTO to be converted to valuable biobased aromatic compounds. Deuterium exchange was attributed to electrophilic aromatic substitution because this reactivity was found to be independent of oxygen and acid mediated. On the contrary, the dimerization was dependent on the presence of oxygen and thus likely involves radical intermediates. Thus this report overall displays different accessible reaction pathways for BTO that can be exploited for the production of BTO-derived compounds.
| S-EPMC6369680 | biostudies-literature
Project description:Benzene is a ubiquitous environmental pollutant abundant in household products, petrochemicals and cigarette smoke. Benzene is a well-known carcinogen in humans and experimental animals; however, little is known about the cardiovascular toxicity of benzene. Recent population-based studies indicate that benzene exposure is associated with an increased risk for heart failure. Nonetheless, it is unclear whether benzene exposure is sufficient to induce and/or exacerbate heart failure. We examined the effects of benzene (50 ppm, 6 h/day, 5 days/week, 6 weeks) or HEPA-filtered air exposure on transverse aortic constriction (TAC)-induced pressure overload in male C57BL/6J mice. Our data show that benzene exposure had no effect on cardiac function in the Sham group; however, it significantly compromised cardiac function as depicted by a significant decrease in fractional shortening and ejection fraction, as compared with TAC/Air-exposed mice. RNA-seq analysis of the cardiac tissue from the TAC/benzene-exposed mice showed a significant increase in several genes associated with adhesion molecules, cell-cell adhesion, inflammation, and stress response. In particular, neutrophils were implicated in our unbiased analyzes. Indeed, immunofluorescence studies showed that TAC/benzene exposure promotes infiltration of CD11b+/S100A8+/myeloperoxidase+-positive neutrophils in the hearts by 3-fold. In vitro, the benzene metabolites, hydroquinone and catechol, induced the expression of P-selectin in cardiac microvascular endothelial cells by 5-fold and increased the adhesion of neutrophils to these endothelial cells by 1.5-2.0-fold. Benzene metabolite-induced adhesion of neutrophils to the endothelial cells was attenuated by anti-P-selectin antibody. Together, these data suggest that benzene exacerbates heart failure by promoting endothelial activation and neutrophil recruitment.
2021-12-30 | GSE192643 | GEO
Project description:5-Hydroxymethylfurfural (HMF) is a platform chemical that can be produced from renewable carbohydrate sources. HMF can be converted to 1,2,4-benzenetriol (BTO) which after catalytic hydrodeoxygenation provides a route to cyclohexanone and cyclohexanol. This mixture, known as KA oil, is an important feedstock for polymeric products such as nylons which use benzene as feedstock that is obtained from the BTX fraction produced in oil refineries. Therefore, the conversion of HMF to BTO provides a renewable, alternative route toward products such as nylons. However, BTO is usually considered an undesired byproduct in HMF synthesis and is only obtained in small amounts. Here, we show that Lewis acid catalysts can be utilized for the selective conversion of HMF to BTO in subsuper critical water. Overall, up to 54 mol % yield of BTO was achieved at 89% HMF conversion using ZnCl2. ZnCl2 and similarly effective Zn(OTf)2 and Fe(OTf)2 are known as relatively soft Lewis acids. Other Lewis acid like Hf(OTf)4 and Sc(OTf)3 gave increased selectivity toward levulinic acid (up to 33 mol %) instead of BTO, a well-known HMF derivative typically obtained by acid catalysis. Catalytic hydrodeoxygenation of BTO toward cyclohexanone in water was achieved in up to 45% yield using 5 wt % Pd on Al2O3 combined with AlCl3 or Al(OTf)3 as catalysts. Additionally, a mild selective oxygen induced dimerization pathway of BTO to 2,2',4,4',5,5'-hexahydroxybiphenyl (5,5'-BTO dimer) was identified.
| S-EPMC5871338 | biostudies-literature
Project description:In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for human health risk assessment purposes. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles in human TK6 cells exposed to 28 well-known compounds, and it comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl]benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival (RS) and increases in apoptosis. A strong significant increase in micronucleus induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were less than 2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only induces a small increase in MN, this response is sufficient to induce a cellular DNA damage response that is likely relevant for risk assessment. Benchmark dose modeling revealed that BT is much more potent than DO; the BT benchmark dose for MN induction was similar to that of benzo[a]pyrene, (BaP: a genotoxic carcinogen), which was used as a positive control. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.
2017-10-16 | GSE95188 | GEO
Project description:In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for human health risk assessment purposes. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles in human TK6 cells exposed to 28 well-known compounds, and it comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl]benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival (RS) and increases in apoptosis. A strong significant increase in micronucleus induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were less than 2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only induces a small increase in MN, this response is sufficient to induce a cellular DNA damage response that is likely relevant for risk assessment. Benchmark dose modeling revealed that BT is much more potent than DO; the BT benchmark dose for MN induction was similar to that of benzo[a]pyrene, (BaP: a genotoxic carcinogen), which was used as a positive control. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.
2017-10-16 | GSE95187 | GEO
Project description:To reveal the gene expression profile changes after exposure to BT, one of benzene metabolites, with or without ABAH, a myeloperoxidase (MPO) inhibitor, and to elucidate how MPO is involved in myelotoxicity of BT, we performed microarray analysis. HL-60 cells suspended in RPMI 1640 containing with 10% of heat-inactivated FBS at 4×10^5/ mL were incubated with or without BT (50 μM) at 37℃ for one or 4 hours. For MPO inhibition experiment, HL-60 (4×10^5 cells/ mL) were pretreatment with 100 μM of ABAH in RPMI 1640/10% of heat-inactivated FBS at 37℃ for 24 hours. Media was then replaced with new media containing the regent plus BT (50 μM) and incubate at 37℃ for one or 4 hours. Unexposed HL-60 cells were used as controls. To validate the microarray results, we selected 22 genes and conducted a real-time PCR.
2013-12-01 | GSE50805 | GEO
Project description:To reveal the gene expression profile changes after exposure to BT, one of benzene metabolites, with or without ABAH, a myeloperoxidase (MPO) inhibitor, and to elucidate how MPO is involved in myelotoxicity of BT, we performed microarray analysis. HL-60 cells suspended in RPMI 1640 containing with 10% of heat-inactivated FBS at 4×10^5/ mL were incubated with or without BT (50 μM) at 37℃ for one or 4 hours. For MPO inhibition experiment, HL-60 (4×10^5 cells/ mL) were pretreatment with 100 μM of ABAH in RPMI 1640/10% of heat-inactivated FBS at 37℃ for 24 hours. Media was then replaced with new media containing the regent plus BT (50 μM) and incubate at 37℃ for one or 4 hours. Unexposed HL-60 cells were used as controls. To validate the microarray results, we selected 22 genes and conducted a real-time PCR. Gene expression alteration induced by 50 μM of BT in HL-60 cells, with or without ABAH, was measured at 1 and 4 hours after exposure to it. Three independent experiments were performed at each time (1 or 4 hours).
2013-12-01 | E-GEOD-50805 | biostudies-arrayexpress
Project description:Benzene, a natural component of petroleum products, is a known hematotoxic and leukemogenic agent. The haematotoxic effect and excess leukemia has been reported below 1 ppm, an exposure level previously considered not to cause any health effects. Gene expression studies suggest that benzene affects genes involved in AML and immune response pathways in a supra-linear manner, and at exposure levels as low as 0.1 ppm benzene. An increased risk of haematopoietic malignancies and altered gene expression also at exposure below 1 ppm is compatible with the emerging knowledge of a non-linear metabolism of benzene, favouring production of a greater proportion of toxic metabolites in subjects exposed to benzene concentrations below 1 ppm than in heavily exposed workers. In the present study, we investigated whether workers found to have a dose-dependent decline in relevant immune cells after benzene-exposure deviated from the unexposed referents in global gene expression changes in whole blood samples, and whether any pathways or genes previously reported in similar low-dose gene expression studies were differentially affected. The study population comprised eight benzene-exposed petroleum workers and five referents deemed unexposed to benzene recruited from the catering section on the same offshore installation (for sampling strategy, see sampling protocol). The two groups significantly differed in age. The dataset was therefore balanced for age by excluding workers at age <35 and >55 in the data modelling to identify significant genes.
2017-10-19 | E-MTAB-5331 | biostudies-arrayexpress