Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity

Mitigating effect of pomegranate peel extract against the furan induced testicular injury by apoptosis, steroidogenic enzymes and oxidative stress

Furan is generated in a wide array of heat-treated foods through thermal degradation, leading to severe impairments in the male reproductive system. The main objective of this study was to investigate the potential of pomegranate peel extract (PGPE) in mitigating testicular dysfunctions induced by furan. Male rats were categorized into four groups: control/untreated, PGPE, furan, and PGPE + furan group. The study results revealed that furan-treated rats exhibited significantly elevated aminotransferase and phosphatase activity, and also generated increased oxidative stress, and reduced antioxidative stress protein activity. Additionally, protein content levels (ALT, AST, ALP, and ACP) and activities of steroidogenic Leydig cell hydroxysteroid dehydrogenase (3β-HSD and 17β-HSD) enzymes were significantly decreased. Significant variations in testicular parameters, apoptotic genes (Bcl-2, P53, and Caspase3), inflammatory and anti-inflammatory cytokines (IL1β, IL10), male sex hormones follicle-stimulating hormone (FSH), luteinizing hormone (LH), testosterone, and sperm quality were also observed. Furthermore, testicular histological abnormalities were confirmed by biochemical and molecular modifications. Notably, PGPE pre-treated furan-intoxicated animals exhibited significant improvements in most of the assessed parameters compared to furan-treated groups. In conclusion, PGPE presents essential preventive measures and a novel pharmacological potential therapy against furan-induced testicular injury.

Potential implications of vouacapan compounds for insecticidal activity: an in silico study

BACKGROUND

From the fruits and seeds of the species of Pterodon, it is possible to obtain two main products: the essential oil and oleoresin. In oleoresin, numerous vouacapan compounds have been demonstrated to have biological potential, including insecticidal activity.

OBJECTIVE

In silico studies were performed to identify potential candidates for natural insecticides among the vouacapans present in the genus Pterodon.

MATERIALS AND METHODS

Molecular docking and molecular dynamics studies were performed to analyze the interaction of vouacapan compounds with acetylcholinesterase of Drosophila melanogaster. Pharmacokinetic parameters regarding physicochemical properties, plasma protein binding, and activity in the central nervous system were evaluated. The toxicological properties of the selected molecules were predicted using Malathion as the reference compound.

RESULTS

6α,7β-dimethoxivouacapan-17-ene (15) showed a high number of interactions and scores in molecular docking studies. This result suggests that this compound exhibits an inhibitory activity of the enzyme acetylcholinesterase. Regarding physicochemical properties, this compound showed the best results, besides presenting low cutaneous permeability values, suggesting null absorption. Molecular dynamics studies demonstrated few conformational changes in the structure of the complex formed by compound 4 and acetylcholinesterase enzyme throughout the simulation time.

CONCLUSION

It was determined that compound 4 (vouacapan 6α,7β,17β,19-tetraol) is an excellent candidate for usage as a natural insecticide.

Effects of endocrine disruptor furan on reproductive physiology of Sprague Dawley rats: An F1 Extended One-Generation Reproductive Toxicity Study (EOGRTS)

The present study investigated the reproductive toxicity of furan in an Extended One-Generation Reproductive Toxicity Study in rats. Sprague Dawley F0 weaning rats (30 per sex per group) were exposed to furan orally at 0, 1, 2.5, 5, and 10 mg kg^-1 for 10 weeks (males) and 2 weeks (females) and then mated. Results of F0 indicated that in the furan-treated groups (5 mg kg^-1 and 10 mg kg^-1), body weight (bw) gain decreased during prebreed and gestational period while increased during lactation periods. F0 animals prebreeding exposure resulted in head tilt and foot splay at 10 mg kg^-1. Number of live pups at birth were decreased (p < 0.001) at 10 mg kg^-1. At postnatal day (PND) 70, a significant (p = 0.03) decrease in testosterone levels of male rats and estrogen levels of female rats (p = 0.05) was observed in 10 mg kg^-1 furan-treated group in F1 generation. Luteinizing hormone, follicle-stimulating hormone, and progesterone levels were also reduced, but their reduction was not statistically significant in all groups. In higher dose furan group (10 mg kg^-1), testicular and ovarian weights were reduced in F1 generation at PND 70, with decreased daily sperm production (p = 0.01) and disturbed estrous cyclicity (p < 0.01). Some histopathological changes were also observed in testis and ovaries in groups whose parents were previously exposed to 10 mg kg^-1 bw of furan group. Based on the above results, it is suggested that exposure to food-based contaminant furan induced remarkable changes in the F0 (parental stage) and F1 (offspring, pubertal, and adult stage) generations of Sprague Dawley rats.

Protective Role of Propolis on Low and High Dose Furan-induced Hepatotoxicity and Oxidative Stress in Rats

INTRODUCTION

The aim of this study was to evaluate potential protective effects of propolis on furan-induced hepatic damage by assessing the levels of malondialdehyde (MDA) and reduced glutathione (GSH), antioxidant enzyme activities, and histopathological changes in the liver.

MATERIAL AND METHODS

Albino Wistar rats were divided into six groups: a control, propolis-treated (100 mg/kg b.w./day), low-dose furan-treated (furan-L group; 2 mg/kg b.w./day), high-dose furan-treated (furan-H group; 16 mg/kg b.w./day), furan-L+propolis treated, and furan-H+propolis treated group. Propolis and furan were applied by gavage; propolis for 8 days, and furan for 20 days in furan-L groups and 10 days in furan-H groups.

RESULTS

While MDA levels were elevated in furan-treated groups, levels of GSH and activities of antioxidant enzymes decreased (p < 0.001). The levels of MDA and GSH and activities of antioxidant enzymes were normal in the furan+propolis groups, especially in the furan-L+propolis group (p < 0.001). While the aspartate transaminase, alanine transaminase, alkaline phosphatase, and lactate pdehydrogenase activities were elevated in the furan-H treated group (p < 0.05 and p < 0.001), they were unchanged in the furan-L treated group. Histopathologically, several lesions were observed in the liver tissues of the furan-treated groups, especially in the higher-dose group. It was determined that these changes were milder in both of the furan+propolis groups.

CONCLUSION

The results indicate that propolis exhibits good hepatoprotective and antioxidant potential against furan-induced hepatocellular damage in rats.

The hepatic innate immune response is lobe-specific in a murine model endotoxemia

The liver plays a central role in the innate immune response to endotoxemia. While previous studies have demonstrated lobe-specific transcriptional responses to various insults, whether this is true in response to endotoxemia is unknown. We sought to assess whether there were significant intra- and inter-lobe differences in the murine hepatic innate immune transcriptional response to endotoxemia. Adult male ICR mice were exposed to i.p. LPS (5 mg/kg, 30 min, 60 min, 5 h) and primary (Tnf, Cxcl1, Nfkbia, Tnfiap3) and secondary (Il6, Nos2) innate immune response gene expression was assessed in the left medial, right medial, left lateral, and right lateral lobes, and the papillary and caudate processes. The expression of all innate immune response genes increased following i.p. LPS challenge. When tested at the early time points (30 and 60 min), the left medial lobe and caudate process consistently demonstrated the highest induction of gene expression. Most inter-lobe differences were attenuated at later time points (5 h). To improve reproducibility of the study of endotoxemia induced by i.p. LPS challenge, inclusion of appropriate methodological details regarding collection of hepatic tissue should be included when reporting scientific results in published manuscripts.

Toward of Safer Phenylbutazone Derivatives by Exploration of Toxicity Mechanism

A drug design for safer phenylbutazone was been explored by reactivity and docking studies involving single electron transfer mechanism, as well as toxicological predictions. Several approaches about its structural properties were performed through quantum chemistry calculations at the B3LYP level of theory, together with the 6-31+G(d,p) basis sets. Molecular orbital and ionization potential were associated to electron donation capacity. The spin densities contribution showed a preferential hydroxylation at the para-positions of phenyl ring when compared to other positions. In addition, on electron abstractions the aromatic hydroxylation has more impact than alkyl hydroxylation. Docking studies indicate that six structures 1, 7, 8 and 13–15 have potential for inhibiting human as well as murine COX-2, due to regions showing similar intermolecular interactions to the observed for the control compounds (indomethacin and refecoxib). Toxicity can be related to aromatic hydroxylation. In accordance to our calculations, the derivatives here proposed are potentially more active as well safer than phenylbutazone and only structures 8 and 13–15 were the most promising. Such results can explain the biological properties of phenylbutazone and support the design of potentially safer candidates.

Furan-induced cardiotoxicity in diabetic rats and protective role of lycopene

The objective of this current study is to search the impacts of furan and lycopene on a diabetic rat's heart. Diabetes increases prevalence with a sedentary lifestyle and obesity. Furan, a carcinogen, was detected in foods that had undergone thermal treatment. Two groups were formed, such as: the control and diabetic groups. Diabetic groups fall into four allocated groups: control, lycopene, furan, and furan + lycopene. The changes in malondialdehide levels, antioxidant enzymes' activities, and histopathology of the heart were pointed out. We observed that the changes in both the MDA level and the antioxidant enzymes' activities were due to diabetes. Furan-induced increment in MDA levels, but GST, CAT, SOD, and GPx activities showed a decrease. Lycopene influenced these changes positively. In terms of the pathological studies, changes were also observed in diabetic rats. The histological damage in the diabetic furan groups was found to be very serious. Lycopene was protective against furan that caused histopathological changes. Diabetes and furan resulted into heart damages in rats and lycopene showed preventive effects. But this was not a complete protection. PRACTICAL APPLICATIONS: Furan by product of chlorinated chemical compounds production and chemical processes including combustion, are virtually ubiquitous in the environment. Because of this, furan occur potential risk for human health. Furan is known to exist at higher levels in fatty foods, such as full-fat milk and dairy products, meat and eggs. They can accumulate in the fatty tissues of animals and humans. Diabetes increase in the prevalence of a sedentary lifestyle and obesity. Diabetes with furan-induced cardiotoxicity. Foods should not be heated over and over again, especially diabetic heart patients should stay away from this situation.

Differential susceptibility of kidneys and livers to proliferative processes and transcriptional level of the genes encoding desmin, vimentin, connexin 43, and nestin in rats exposed to furan

In this study, we aimed to assess the differential toxic impact, induced by furan exposure, on the liver and kidney tissues by estimating reactive oxygen species (ROS) level, total antioxidant capacity (TAC), oxidative damage, and the tissue injury markers in a male rat model. To explain such impacts, 20 rats were assigned into two groups: a control group, where rats were administered corn oil as a vehicle, and a furan-administered group, where furan was orally administered to rats at a dose of 16 mg/kg b wt/day (five days per week over eight weeks). The transcriptional levels of intermediate filament proteins (desmin, vimentin, nestin, and connexin 43) were assessed by using quantitative real-time polymerase chain reaction (PCR), and the cell proliferation markers (proliferating cell nuclear antigen [PCNA] and proliferation-associated nuclear antigen [Ki-67]) were recognized by immunohistochemical analysis. Furthermore, the ultrastructural changes of liver and kidney were monitored using electron microscopy. Our findings showed that furan exposure could induce hepatic and renal damage to different extents. Furan can increase the ROS content, oxidative damage indices, and liver tissue injury indices but not kidney injury indices. Furthermore, it decreases the TAC in the serum of exposed rats. In addition, furan exposure was associated with changes in the mRNA expression pattern of intermediate filament proteins in both kidney and liver tissues. Moreover, furan enhances the expression of PCNA and Ki-67 in the liver tissues but not in the kidney tissues. The ultrastructure evaluation revealed the incidence of glomerular podocyte degeneration and hepatocyte injury. These results conclusively demonstrate that the deleterious effects of furan are caused by promoting fibrosis and hepatocyte proliferation in liver tissues and triggering podocyte injury in the kidney tissues.

Risks for public health related to the presence of furan and methylfurans in food

The European Commission asked EFSA for a scientific evaluation on the risk to human health of the presence of furan and methylfurans (2-methylfuran, 3-methylfuran and 2,5-dimethylfuran) in food. They are formed in foods during thermal processing and can co-occur. Furans are produced from several precursors such as ascorbic acid, amino acids, carbohydrates, unsaturated fatty acids and carotenoids, and are found in a variety of foods including coffee and canned and jarred foods. Regarding furan occurrence, 17,056 analytical results were used in the evaluation. No occurrence data were received on methylfurans. The highest exposures to furan were estimated for infants, mainly from ready-to-eat meals. Grains and grain-based products contribute most for toddlers, other children and adolescents. In adults, elderly and very elderly, coffee is the main contributor to dietary exposure. Furan is absorbed from the gastrointestinal tract and is found in highest amounts in the liver. It has a short half-life and is metabolised by cytochrome P450 2E1 (CYP2E1) to the reactive metabolite, cis-but-2-ene-1,4-dialdehyde (BDA). BDA can bind covalently to amino acids, proteins and DNA. Furan is hepatotoxic in rats and mice with cholangiofibrosis in rats and hepatocellular adenomas/carcinomas in mice being the most prominent effects. There is limited evidence of chromosomal damage in vivo and a lack of understanding of the underlying mechanism. Clear evidence for indirect mechanisms involved in carcinogenesis include oxidative stress, gene expression alterations, epigenetic changes, inflammation and increased cell proliferation. The CONTAM Panel used a margin of exposure (MOE) approach for the risk characterisation using as a reference point a benchmark dose lower confidence limit for a benchmark response of 10% of 0.064 mg/kg body weight (bw) per day for the incidence of cholangiofibrosis in the rat. The calculated MOEs indicate a health concern. This conclusion was supported by the calculated MOEs for the neoplastic effects.

Functional and cellular consequences of covalent target protein modification by furan in rat liver

Furan hepatotoxicity is thought to be linked to covalent binding of its reactive metabolite, cis-2-butene-1,4-dial, to hepatic proteins critical for cell homeostasis and survival. We previously identified 61 putative furan target proteins, which participate in various cellular processes including carbohydrate metabolism, fatty acid β-oxidation, adenosine triphosphate (ATP) synthesis, protein folding and maintenance of redox homeostasis. To further investigate the biological significance of target protein modification, this study was designed to determine the impact of furan on the activity of key target enzymes involved in glycolysis, β-oxidation, ATP synthesis, and redox regulation in rat liver, and to link these functional changes to alterations in cellular processes. While cis-2-butene-1,4-dial inhibited thioredoxin 1 (Txn1) in a cell-free assay, in livers of rats treated with a single high dose of furan Txn1 activity was markedly increased due to rapid up-regulation of Txn1 mRNA expression. Significant inhibition of glyceraldehyde-3-phosphate dehydrogenase and metabolic changes consistent with blocked glycolytic breakdown of glucose were observed in rat liver in response to a single high dose of furan. In contrast, furan treatment resulted in increased activity of enoyl-CoA hydratase and enhanced production of ketone bodies, indicative of increased utilization of fatty acids as energy source. Consistent with changes in TCA cycle metabolites, furan treatment resulted in a reduction of succinate dehydrogenase activity, supporting mitochondrial dysfunction as a critical event in furan toxicity. No significant changes in target protein function were observed following repeated administration of furan at lower dose (0.1 and 0.5mg/kg bw for 4 weeks) closer to estimated human exposure to furan via food. Although the relative contribution of furan mediated alterations in metabolic pathways and antioxidant defense to the overall toxic response to furan, including considerations of dose and time, remains to be established, our work contributes to mapping biological processes and toxicity pathways modulated by reactive electrophiles.

A novel bis-furan scaffold for transthyretin stabilization and amyloid inhibition

The design and synthesis of a novel bis-furan scaffold tailored for high efficiency at inhibiting transthyretin amyloid formation is reported. In vitro results show that the discovered compounds are more efficient inhibitors of amyloid formation than tafamidis, a drug currently used in the treatment of familial amyloid polyneuropathy (FAP), despite their lower molecular weight and lipophilicity. Moreover, ex vivo experiments with the strongest inhibitor in the series, conducted in human blood plasma from normal and FAP Val30Met-transthyretin carriers, disclose remarkable affinity and selectivity profiles. The promises and challenges facing further development of this compound are discussed under the light of increasing evidence implicating transthyretin stability as a key factor not only in transthyretin amyloidoses and several associated co-morbidities, but also in Alzheimer's disease.

Protective effects of apigenin against furan-induced toxicity in mice

Furan, a food contaminant formed by heating, is possibly carcinogenic to humans. In this study, we discussed the effect of administration of apigenin on furan-induced toxicity by determining the ROS content, oxidative damage, cytokine levels, DNA damage, and the liver and kidney damage in a mouse model. Our data showed that apigenin administered at 5, 10, and 20 mg kg(-1) bw per day could decrease the toxicity induced by furan to different extents. On one hand, apigenin has the ability to increase the oxidative damage indexes of glutathione (GSH) and glutathione-S-transferase (GST) as well as superoxide dismutase (SOD) activities but decrease myeloperoxidase (MPO) activities and maleic dialdehyde (MDA) content in the liver and kidney of mice treated with furan. On the other hand, it could decrease cytokine levels of tumor necrosis factor α (TNF-α), interleukin (IL)-1β, and interleukin (IL)-6 but increase interleukin (IL)-10 in the serum of furan-treated mice. At the same time, the three concentrations of apigenin elected in this paper all could decrease the ROS content, DNA damage index of 8-hydroxy-desoxyguanosine (8-OHdG), the liver and kidney damage indexes of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and lactic dehydrogenase (LDH), and blood urea nitrogen (BUN) and creatinine content in furan-treated mice to different extents. The protective effects of apigenin against furan-induced toxicity damage were mainly due to its excellent ability to scavenge free radicals and inhibit lipid oxidation. This is important when considering the use of apigenin as a dietary supplement for beneficial chemoprevention of furan toxicity.

Reactive metabolites in the biotransformation of molecules containing a furan ring

Many xenobiotics containing a furan ring are toxic and/or carcinogenic. The harmful effects of these compounds require furan ring oxidation. This reaction generates an electrophilic intermediate. Depending on the furan ring substituents, the intermediate is either an epoxide or a cis-enedione with more ring substitution favoring epoxide formation. Either intermediate reacts with cellular nucleophiles such as protein or DNA to trigger toxicities. The reactivity of the metabolite determines which cellular nucleophiles are targeted. The toxicity of a particular furan is also influenced by the presence of competing metabolic pathways or efficient detoxification routes. GSH plays an important role in modulating the harmful effects of this class of compound by reacting with the reactive metabolite. However, this may not represent a detoxification step in all cases.

Toxicity of food contaminant furan on liver and kidney of growing male rats

Furan is a chemical used in some industrial products and occurs naturally in heat-treated foods. We aimed to investigate the effects of orally administered furan on liver and kidney in growing Wistar male rats for 90 days. In this respect, biochemical, morphological, histopathological, and histomorphometrical examinations were performed. Three- to 4-week aged rats were divided into five groups of eight animals each; control, oil control; 2, 4, 8 mg/kg/day furan treatment groups. At the end of the experiment, antioxidant enzyme activities and serum AST, ALT, HDL, Urea, etc. levels were analyzed. Malondialdehyde (MDA) levels, superoxide dismutase (SOD), catalase (CAT), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) were also measured in liver homogenates. Also, liver and kidney were examined morphologically and histopathologically under light microscopy. According to the results of biochemical analysis, ALT, ALP, and LDL levels in treatment groups were significantly different compared with control groups. While LDL levels in treatment groups increased significantly, ALT and ALP levels decreased significantly. No significant changes were observed in liver MDA levels, superoxide dismutase and catalase activities in treatment groups. While IL-6 levels did not change in treatment groups, furan caused dose-dependent increases in liver TNF-α level of rats. In treatment groups, absolute and relative liver weights changed significantly, however, no significant changes were observed in kidney and relative kidney weights. Hyperemic blood vessels in the liver and congestion, edema, fibrosis, and tubular damage in the kidney of rats treated with furan were observed histopathologically. According to histomorphometric examinations, glomeruli diameters and glomerular volume decreased in the kidneys of rats in treatment groups.

Furan carcinogenicity: DNA binding and genotoxicity of furan in rats in vivo

SCOPE

Furan is a potent hepatotoxicant and liver carcinogen in rodents. However, short-term tests for genotoxicity of furan are inconclusive. The aim of this study was to assess the potential of furan to covalently bind to DNA, and to assess furan genotoxicity in rats in vivo.

MATERIALS AND METHODS

Accelerator mass spectrometry was used to determine the (14) C-content in DNA following administration of [3,4-(14) C]-furan (0.1 and 2.0 mg/kg bw) to F344 rats. DNA damage, micronuclei, chromosomal aberrations, and sister chromatid exchanges were analyzed in F344 rats treated with furan for up to 28 days.

CONCLUSION

The (14) C-content in liver DNA was significantly increased in a dose-dependent manner, with mean concentrations of 7.9 ± 3.5 amol (14) C/μg DNA and 153.3 ± 100.2 amol (14) C/μg DNA, corresponding to 16.5 ± 7.4 and 325.2 ± 212.7 adducts/10(9) nucleotides at 0.1 and 2.0 mg/kg bw, respectively. There was no evidence for genotoxicity of furan in peripheral blood and bone marrow cells. However, a dose-related increase in the incidence of chromosomal aberrations in rat splenocytes and some indication of DNA damage in liver were observed. Collectively, results from this study indicate that furan may operate-at least in part-by a genotoxic mode of action.

Furan in heat-treated foods: formation, exposure, toxicity, and aspects of risk assessment

Furan is formed in a variety of heat-treated foods through thermal degradation of natural food constituents. Relatively high levels of furan contamination are found in ground roasted coffee, instant coffee, and processed baby foods. European exposure estimates suggest that mean dietary exposure to furan may be as high as 1.23 and 1.01 μg/kg bw/day for adults and 3- to 12-month-old infants, respectively. Furan is a potent hepatotoxin and hepatocarcinogen in rodents, causing hepatocellular adenomas and carcinomas in rats and mice, and high incidences of cholangiocarcinomas in rats at doses ≥ 2 mg/kg bw. There is therefore a relatively low margin of exposure between estimated human exposure and doses that cause a high tumor incidence in rodents. Since a genotoxic mode of action cannot be excluded for furan-induced tumor formation, the present exposures may indicate a risk to human health and need for mitigation. This review summarizes the current knowledge on mechanisms of furan formation in food, human dietary exposure to furan, and furan toxicity, and highlights the need to establish the risk resulting from the genotoxic and carcinogenic properties of furan at doses lower than 2 mg/kg bw.

Sources of variance in baseline gene expression in the rodent liver

The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variation due to individual, environmental, and technical factors. Analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies has yielded useful information on baseline fluctuations in liver gene expression in the rodent. Here, studies which highlight contributions of different factors to gene expression variability in the rodent liver are discussed including a large meta-analysis of rat liver, which identified genes that vary in control animals in the absence of chemical treatment. Genes and their pathways that are the most and least variable were identified in a number of these studies. Life stage, fasting, sex, diet, circadian rhythm and liver lobe source can profoundly influence gene expression in the liver. Recognition of biological and technical factors that contribute to variability of background gene expression can help the investigator in the design of an experiment that maximizes sensitivity and reduces the influence of confounders that may lead to misinterpretation of genomic changes. The factors that contribute to variability in liver gene expression in rodents are likely analogous to those contributing to human interindividual variability in drug response and chemical toxicity. Identification of batteries of genes that are altered in a variety of background conditions could be used to predict responses to drugs and chemicals in appropriate models of the human liver.

Multiwalled carbon nanotube-induced gene signatures in the mouse lung: potential predictive value for human lung cancer risk and prognosis

Concerns over the potential for multiwalled carbon nanotubes (MWCNT) to induce lung carcinogenesis have emerged. This study sought to (1) identify gene expression signatures in the mouse lungs following pharyngeal aspiration of well-dispersed MWCNT and (2) determine if these genes were associated with human lung cancer risk and progression. Genome-wide mRNA expression profiles were analyzed in mouse lungs (n = 160) exposed to 0, 10, 20, 40, or 80 μg of MWCNT by pharyngeal aspiration at 1, 7, 28, and 56 d postexposure. By using pairwise statistical analysis of microarray (SAM) and linear modeling, 24 genes were selected, which have significant changes in at least two time points, have a more than 1.5-fold change at all doses, and are significant in the linear model for the dose or the interaction of time and dose. Additionally, a 38-gene set was identified as related to cancer from 330 genes differentially expressed at d 56 postexposure in functional pathway analysis. Using the expression profiles of the cancer-related gene set in 8 mice at d 56 postexposure to 10 μg of MWCNT, a nearest centroid classification accurately predicts human lung cancer survival with a significant hazard ratio in training set (n = 256) and test set (n = 186). Furthermore, both gene signatures were associated with human lung cancer risk (n = 164) with significant odds ratios. These results may lead to development of a surveillance approach for early detection of lung cancer and prognosis associated with MWCNT in the workplace.

New perspectives for in vitro risk assessment of multiwalled carbon nanotubes: application of coculture and bioinformatics

Nanotechnology is a rapidly expanding field with wide application for industrial and medical use; therefore, understanding the toxicity of engineered nanomaterials is critical for their commercialization. While short-term in vivo studies have been performed to understand the toxicity profile of various nanomaterials, there is a current effort to shift toxicological testing from in vivo observational models to predictive and high-throughput in vitro models. However, conventional monoculture results of nanoparticle exposure are often disparate and not predictive of in vivo toxic effects. A coculture system of multiple cell types allows for cross-talk between cells and better mimics the in vivo environment. This review proposes that advanced coculture models, combined with integrated analysis of genome-wide in vivo and in vitro toxicogenomic data, may lead to development of predictive multigene expression-based models to better determine toxicity profiles of nanomaterials and consequent potential human health risk due to exposure to these compounds.

Texture analysis of liver fibrosis microscopic images: a study on the effect of biomarkers

Chronic hepatic injury results in liver fibrosis with eventual progression to irreversible cirrhosis. Liver fibrogenesis involves the activation of the quiescent hepatic stellate cell into an activated myofibroblast that is characterized by α-smooth muscle actin (α-SMA) expression and the production of collagens (types I and III). In the present study, rats were randomly divided into three groups: (i) control group, where rats were only treated with a vehicle; (ii) fibrosis group, where rats were treated with carbon tetrachloride (CCl(4)) to induce liver fibrosis; and (iii) silymarin group, where rats were protected with silymarin during CCl(4) treatment. Rats were sacrificed and sections of liver tissue were counterstained with hematoxylin and eosin and Masson's trichrome. Other sections were immunostained using collagens and α-SMA primary antibodies. Fibrosis was confirmed using serum marker measurements. Microscopic images of the stained sections were acquired and digitized. The Biomarker Index of Fibrosis (BIF) was calculated from the images by quantifying the percentage of stained fibers. Statistical methods of texture analysis (TA), namely co-occurrence and run-length matrices, were applied on the digital images followed by classification using agglomerative hierarchical clustering and linear discriminant analysis with cross validation. TA applied on different biomarkers was successful in discriminating between the groups, showing 100% sensitivity and specificity for classification between the control and fibrosis groups using any biomarker. Some classification attempts showed dependence on the biomarker used, especially for classification between the silymarin and fibrosis groups, which showed optimal results using Masson's trichrome. TA results were consistent with both BIF and serum marker measurements.

The evolution of bioinformatics in toxicology: advancing toxicogenomics

As one reflects back through the past 50 years of scientific research, a significant accomplishment was the advance into the genomic era. Basic research scientists have uncovered the genetic code and the foundation of the most fundamental building blocks for the molecular activity that supports biological structure and function. Accompanying these structural and functional discoveries is the advance of techniques and technologies to probe molecular events, in time, across environmental and chemical exposures, within individuals, and across species. The field of toxicology has kept pace with advances in molecular study, and the past 50 years recognizes significant growth and explosive understanding of the impact of the compounds and environment to basic cellular and molecular machinery. The advancement of molecular techniques applied in a whole-genomic capacity to the study of toxicant effects, toxicogenomics, is no doubt a significant milestone for toxicological research. Toxicogenomics has also provided an avenue for advancing a joining of multidisciplinary sciences including engineering and informatics in traditional toxicological research. This review will cover the evolution of the field of toxicogenomics in the context of informatics integration its current promise, and limitations.

Low doses of the carcinogen furan alter cell cycle and apoptosis gene expression in rat liver independent of DNA methylation

BACKGROUND

Evidence of potent rodent carcinogenicity via an unclear mechanism suggests that furan in various foods [leading to an intake of up to 3.5 microg/kg body weight (bw)/day] may present a potential risk to human health.

OBJECTIVES

We tested the hypothesis that altered expression of genes related to cell cycle control, apoptosis, and DNA damage may contribute to the carcinogenicity of furan in rodents. In addition, we investigated the reversibility of such changes and the potential role of epigenetic mechanisms in response to furan doses that approach the maximum estimated dietary intake in humans.

METHODS

The mRNA expression profiles of genes related to cell cycle, apoptosis, and DNA damage in rat liver treated with furan concentrations of 0.1 and 2 mg/kg bw were measured by quantitative polymerase chain reaction (PCR) arrays. We assessed epigenetic changes by analysis of global and gene-specific DNA methylation [methylation-specific PCR, combined bisulfite restriction analysis (COBRA), and methylated DNA immunoprecipitation chip] and microRNA (miRNA) analyses.

RESULTS

The expression profiles of apoptosis-related and cell-cycle-related genes were unchanged after 5 days of treatment, although we observed a statistically significant change in the expression of genes related to cell cycle control and apoptosis, but not DNA damage, after 4 weeks of treatment. These changes were reversed after an off-dose period of 2 weeks. None of the gene expression changes was associated with a change in DNA methylation, although we detected minor changes in the miRNA expression profile (5 miRNA alterations out of 349 measured) that may have contributed to modification of gene expression in some cases.

CONCLUSION

Nongenotoxic changes in gene expression may contribute to the carcinogenicity of furan in rodents. These findings highlight the need for a more comprehensive risk assessment of furan exposure in humans.

Evidence of Oxidative Stress and Associated DNA Damage, Increased Proliferative Drive, and Altered Gene Expression in Rat Liver Produced by the Cholangiocarcinogenic Agent Furan

Furan is a potent cholangiocarcinogen in rat by an as yet undefined mechanism. The risk to man remains unclear. Using a time-course stop study design, we have investigated the potential of furan to induce oxidative stress and DNA damage associated with inflammatory and regenerative responses in rat liver. Furan was administered via oral gavage (30 mg/kg b.w. 5 daily doses per week), and livers were analyzed at time points between eight hr and three months. A one-month recovery group previously treated for three months was also included. There was a marked association between CYP2E1 expression and DNA oxidation (8-oxo-dG) in areas of centrilobular hepatocyte necrosis seen after a single dose. After one-month recovery from three-month treatment, 8-oxo-dG was still observed in areas of furan-induced cholangiofibrosis. Furan-induced changes in the expression of various genes associated with oxidative stress, DNA damage, and cell cycle control were identified during treatment and recovery. We propose that furan-induced cholangiocarcinomas emerge from areas of cholangiofibrosis as a result of a combination of chronic, persistent indirect damage to DNA through oxygen radicals coupled with persistent proliferative signals, including loss of connexin 32, that act to convert this DNA damage to fixed mutations.

Toxicogenomic biomarkers for liver toxicity

Toxicogenomics (TGx) is a widely used technique in the preclinical stage of drug development to investigate the molecular mechanisms of toxicity. A number of candidate TGx biomarkers have now been identified and are utilized for both assessing and predicting toxicities. Further accumulation of novel TGx biomarkers will lead to more efficient, appropriate and cost effective drug risk assessment, reinforcing the paradigm of the conventional toxicology system with a more profound understanding of the molecular mechanisms of drug-induced toxicity. In this paper, we overview some practical strategies as well as obstacles for identifying and utilizing TGx biomarkers based on microarray analysis. Since clinical hepatotoxicity is one of the major causes of drug development attrition, the liver has been the best documented target organ for TGx studies to date, and we therefore focused on information from liver TGx studies. In this review, we summarize the current resources in the literature in regard to TGx studies of the liver, from which toxicologists could extract potential TGx biomarker gene sets for better hepatotoxicity risk assessment.

Quality control of microarray assays for toxicogenomic and in vitro diagnostic applications

The generation of high-quality microarray data for toxicogenomics can be affected by the study design and methods used for sample acquisition, preparation, and processing. Bias can be introduced during animal treatment, tissue handling, and sample preparation. Metrics and controls used in assessing RNA integrity and the quality of microarray sample generation are reviewed in this chapter. Regulations and guidelines involved in the application of microarrays as a commercial in vitro diagnostic device are also described.

Anatomy of data integration

Producing reliable information is the ultimate goal of data processing. The ocean of data created with the advances of science and technologies calls for integration of data coming from heterogeneous sources that are diverse in their purposes, business rules, underlying models and enabling technologies. Reference models, Semantic Web, standards, ontology, and other technologies enable fast and efficient merging of heterogeneous data, while the reliability of produced information is largely defined by how well the data represent the reality. In this paper, we initiate a framework for assessing the informational value of data that includes data dimensions; aligning data quality with business practices; identifying authoritative sources and integration keys; merging models; uniting updates of varying frequency and overlapping or gapped data sets.

Identification of genes implicated in methapyrilene-induced hepatotoxicity by comparing differential gene expression in target and nontarget tissue

BACKGROUND

Toxicogenomics experiments often reveal thousands of transcript alterations that are related to multiple processes, making it difficult to identify key gene changes that are related to the toxicity of interest.

OBJECTIVES

The objective of this study was to compare gene expression changes in a nontarget tissue to the target tissue for toxicity to help identify toxicity-related genes.

METHODS

Male rats were given the hepatotoxicant methapyrilene at two dose levels, with livers and kidneys removed 24 hr after one, three, and seven doses for gene expression analysis. To identify gene changes likely to be related to toxicity, we analyzed genes on the basis of their temporal pattern of change using a program developed at the National Institute of Environmental Health Sciences, termed "EPIG" (extracting gene expression patterns and identifying co-expressed genes).

RESULTS

High-dose methapyrilene elicited hepatic damage that increased in severity with the number of doses, whereas no treatment-related lesions were observed in the kidney. High-dose methapyrilene elicited thousands of gene changes in the liver at each time point, whereas many fewer gene changes were observed in the kidney. EPIG analysis identified patterns of gene expression correlated to the observed toxicity, including genes associated with endoplasmic reticulum stress and the unfolded protein response.

CONCLUSIONS

By factoring in dose level, number of doses, and tissue into the analysis of gene expression elicited by methapyrilene, we were able to identify genes likely to not be implicated in toxicity, thereby allowing us to focus on a subset of genes to identify toxicity-related processes.

Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretation

Gene expression profiling, metabolomic screens, and other high-dimensional methods have become an integral part of many biological investigations. To facilitate interpretation of these data, it is important to have detailed phenotypic data--including histopathology--to which these data can be associated, or anchored. However, as the amount of phenotypic data increases, associations within and across these data can be difficult to visualize and interpret. We have developed an approach for categorizing and clustering biologically related histopathological diagnoses to facilitate their visualization, thereby increasing the possibility of identifying associations and facilitating the comparison with other data streams. In this study, we utilize histopathological data generated as part of a standardized toxicogenomics compendium study to generate composite histopathological scores and to develop visualizations that facilitate biological insight. The validity of this approach is illustrated by the identification of transcripts that correlate with the pathology diagnoses that comprise the categories of "response to hepatocellular injury" and "repair." This approach is broadly applicable to studies in which histopathology is used to phenotypically anchor other data, and results in visualizations that facilitate biological interpretation and the identification of associations and relationships within the data.

PPARalpha siRNA-treated expression profiles uncover the causal sufficiency network for compound-induced liver hypertrophy

Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response. Genome-wide RNA interference (RNAi) phenotypic screening has emerged as an effective tool in unveiling the genes essential for specific cellular functions and biological activities. However, eliciting the relative contribution of and sufficiency relationships among the genes identified remains challenging. In the rodent, the most widely used animal model in preclinical studies, it is unrealistic to exhaustively examine all potential interactions by RNAi screening. Application of existing computational approaches to infer regulatory networks with biological outcomes in the rodent is limited by the requirements for a large number of targeted permutations. Therefore, we developed a two-step relay method that requires only one targeted perturbation for genome-wide de novo pathway discovery. Using expression profiles in response to small interfering RNAs (siRNAs) against the gene for peroxisome proliferator-activated receptor alpha (Ppara), our method unveiled the potential causal sufficiency order network for liver hypertrophy in the rodent. The validity of the inferred 16 causal transcripts or 15 known genes for PPARalpha-induced liver hypertrophy is supported by their ability to predict non-PPARalpha-induced liver hypertrophy with 84% sensitivity and 76% specificity. Simulation shows that the probability of achieving such predictive accuracy without the inferred causal relationship is exceedingly small (p < 0.005). Five of the most sufficient causal genes have been previously disrupted in mouse models; the resulting phenotypic changes in the liver support the inferred causal roles in liver hypertrophy. Our results demonstrate the feasibility of defining pathways mediating drug-induced toxicity from siRNA-treated expression profiles. When combined with phenotypic evaluation, our approach should help to unleash the full potential of siRNAs in systematically unveiling the molecular mechanism of biological events.

PAGE: phase-shifted analysis of gene expression

Grouping of gene expression patterns across biological experiments, treatments and time-series data is performed in q-intervals of measurements using phase-shifted analysis of gene expression (PAGE); a Java-based tool to find clusters of genes that share trends of expression profiles within the dataset. The patterns and genes within q-Clusters are visualized in trend plots and compared to determine biological relevance from the gene annotations.

Dynamic gene expression changes precede dioxin-induced liver pathogenesis in medaka fish

A major challenge for environmental genomics is linking gene expression to cellular toxicity and morphological alteration. Herein, we address complexities related to hepatic gene expression responses after a single injection of the aryl hydrocarbon receptor (AHR) agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) and illustrate an initial stress response followed by cytologic and adaptive changes in the teleost fish medaka. Using a custom 175-gene array, we find that overall hepatic gene expression and histological changes are strongly dependent on dose and time. The most pronounced dioxin-induced gene expression changes occurred early and preceded morphologic alteration in the liver. Following a systematic search for putative Ah response elements (AHREs) (5'-CACGCA-3') within 2000 bp upstream of the predicted transcriptional start site, the majority (87%) of genes screened in this study did not contain an AHRE, suggesting that gene expression was not solely dependent on AHRE-mediated transcription. Moreover, in the highest dosage, we observed gene expression changes associated with adaptation that persisted for almost two weeks, including induction of a gene putatively identified as ependymin that may function in hepatic injury repair. These data suggest that the cellular response to dioxin involves both AHRE- and non-AHRE-mediated transcription, and that coupling gene expression profiling with analysis of morphologic pathogenesis is essential for establishing temporal relationships between transcriptional changes, toxicity, and adaptation to hepatic injury.

Gene expression profiling of mouse host response to Listeria monocytogenes infection

The purpose of this study was to evaluate gene expression profiles in the liver and blood for prediction of infection severity from Listeria monocytogenes (LM). Mice were injected with medium broth (control) or a nonlethal or lethal dose of LM and sacrificed 6 h later. Gene expression changes were determined using Affymetrix MGU74Av2 GeneChips and confirmed by real-time polymerase chain reaction analysis. We identified discernable genes whose gene expression profiles can be used in pattern recognition to predict and classify samples in differently treated groups, with >or=90% accuracy in liver samples and 80% accuracy in blood at prediction; however, different genes were predictive in each tissue. Our results suggest that gene expression profiling in response to LM in mice may be able to distinguish samples in groups with varying severity of infection and provide information in finding molecular mechanisms and early biomarkers for subsequent conventional clinical endpoints.

Toxicogenomics in the pharmaceutical industry: hollow promises or real benefit?

Almost 10 years ago, microarray technology was established as a new powerful tool for large-scale analysis of gene expression. Soon thereafter the new technology was discovered by toxicologists for the purpose of deciphering the molecular events underlying toxicity, and the term "Toxicogenomics" appeared in scientific literature. Ever since, the toxicology community was fascinated by the multiplicity of sophisticated possibilities toxicogenomics seems to offer: genome-wide analysis of toxicant-induced expression profiles may provide a means for prediction of toxicity prior to classical toxicological endpoints such as histopathology or clinical chemistry. Some researchers even speculated of the classical methods being superfluous before long. It was assumed that by using toxicogenomics it would be possible to classify compounds early in drug development and consequently save animals, time, and money in pre-clinical toxicity studies. Moreover, it seemed within reach to unravel the molecular mechanisms underlying toxicity. The feasibility of bridging data derived from in vitro and in vivo systems, identifying new biomarkers, and comparing toxicological responses "across-species" was also excessively praised. After several years of intensive application of microarray technology in the field of toxicology, not only by the pharmaceutical industry, it is now time to survey its achievements and to question how many of these wishes and promises have really come true.

Systems-ADME/Tox: resources and network approaches

The increasing cost of drug development is partially due to our failure to identify undesirable compounds at an early enough stage of development. The application of higher throughput screening methods have resulted in the generation of very large datasets from cells in vitro or from in vivo experiments following the treatment with drugs or known toxins. In recent years the development of systems biology, databases and pathway software has enabled the analysis of the high-throughput data in the context of the whole cell. One of the latest technology paradigms to be applied alongside the existing in vitro and computational models for absorption, distribution, metabolism, excretion and toxicology (ADME/Tox) involves the integration of complex multidimensional datasets, termed toxicogenomics. The goal is to provide a more complete understanding of the effects a molecule might have on the entire biological system. However, due to the sheer complexity of this data it may be necessary to apply one or more different types of computational approaches that have as yet not been fully utilized in this field. The present review describes the data generated currently and introduces computational approaches as a component of ADME/Tox. These methods include network algorithms and manually curated databases of interactions that have been separately classified under systems biology methods. The integration of these disparate tools will result in systems-ADME/Tox and it is important to understand exactly what data resources and technologies are available and applicable. Examples of networks derived with important drug transporters and drug metabolizing enzymes are provided to demonstrate the network technologies.

Do we need genomic research for the prevention of common diseases with environmental causes?

Concerns have been raised about the value of genomic research for prevention and public health, especially for complex diseases with risk factors that are amenable to environmental modification. Given that gene-environment interactions underlie almost all human diseases, the public health significance of genomic research on common diseases with modifiable environmental risks is based not necessarily on finding new genetic "causes" but on improving existing approaches to identifying and modifying environmental risk factors to better prevent and treat disease. Such applied genomic research for environmentally caused diseases is important, because 1) it could help stratify disease risks and differentiate interventions for achieving population health benefits; 2) it could help identify new environmental risk factors for disease or help confirm suspected environmental risk factors; and 3) it could aid our understanding of disease occurrence in terms of transmission, natural history, severity, etiologic heterogeneity, and targets for intervention at the population level. While genomics is still in its infancy, opportunities exist for developing, testing, and applying the tools of genomics to clinical and public health research, especially for conditions with known or suspected environmental causes. This research is likely to lead to population-wide health promotion and disease prevention efforts, not only to interventions targeted according to genetic susceptibility.

Elucidating mechanisms of drug-induced toxicity

The early and high-throughput application of assays for non-genetic toxicity is of great interest to the pharmaceutical industry, although few systems have been validated as being of good predictive value. New technologies could enable toxicity to be studied in the context of systems biology. An important factor to be considered is the metabolism of drugs to reactive intermediates. Chemical reactions of these with cell and tissue nucleophiles are relatively well understood, but predicting how biological modifications will affect signalling and regulatory networks remains a challenge. Some of these pathways could be useful as sentinels for toxicity. This article will cover some examples of drug toxicity and the prospects for future technology development.

Toxicogenomics and systems toxicology: aims and prospects

Toxicogenomics combines transcript, protein and metabolite profiling with conventional toxicology to investigate the interaction between genes and environmental stress in disease causation. The patterns of altered molecular expression that are caused by specific exposures or disease outcomes have revealed how several toxicants act and cause disease. Despite these success stories, the field faces noteworthy challenges in discriminating the molecular basis of toxicity. We argue that toxicology is gradually evolving into a systems toxicology that will eventually allow us to describe all the toxicological interactions that occur within a living system under stress and use our knowledge of toxicogenomic responses in one species to predict the modes-of-action of similar agents in other species.

Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth

A major challenge in the emerging field of toxicogenomics is to define the relationships between chemically induced changes in gene expression and alterations in conventional toxicologic parameters such as clinical chemistry and histopathology. We have explored these relationships in detail using the rodent uterotrophic assay as a model system. Gene expression levels, uterine weights, and histologic parameters were analyzed 1, 2, 4, 8, 24, 48, and 72 hr after exposure to the reference physiologic estrogen 17 beta-estradiol (E2). A multistep analysis method, involving unsupervised hierarchical clustering followed by supervised gene ontology-driven clustering, was used to define the transcriptional program associated with E2-induced uterine growth and to identify groups of genes that may drive specific histologic changes in the uterus. This revealed that uterine growth and maturation are preceded and accompanied by a complex, multistage molecular program. The program begins with the induction of genes involved in transcriptional regulation and signal transduction and is followed, sequentially, by the regulation of genes involved in protein biosynthesis, cell proliferation, and epithelial cell differentiation. Furthermore, we have identified genes with common molecular functions that may drive fluid uptake, coordinated cell division, and remodeling of luminal epithelial cells. These data define the mechanism by which an estrogen induces organ growth and tissue maturation, and demonstrate that comparison of temporal changes in gene expression and conventional toxicology end points can facilitate the phenotypic anchoring of toxicogenomic data.