Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor

Health effects associated with phthalate activity on nuclear receptors

Phthalates are endocrine disruptors, widely used as plasticizers to impart flexibility in plastics, and as solvents in personal care products. Due to their nearly ubiquitous use in consumer products, most humans are exposed to phthalates daily. There has been extensive research on the reproductive health effects associated with phthalate exposure, but less attention has been paid to other actions. This review aims to summarize the known action of phthalates on different nuclear receptors. Some phthalates bind to and activate the estrogen receptor, making them weakly estrogenic. However, other phthalates antagonize androgen receptors. Some high molecular weight phthalates antagonize thyroid receptors, affecting metabolism. Several phthalates activate and interfere with the normal function of different peroxisome proliferator-activated receptors (PPARs), receptors that have critical roles in lipid metabolism and energy homeostasis. Some phthalates activate the aryl hydrocarbon receptor, which is critical for xenobiotic metabolism. Although phthalates have a short half-life in vivo, because people are continuously exposed, studies should examine the health effects of phthalates associated with long-term exposure. There is limited research on the effects of phthalates on health outcomes aside from reproductive function, particularly concerning are childhood adiposity, behavior, and learning. There is also limited information on actions of phthalates not mediated via nuclear receptors. Humans are exposed to multiple chemicals simultaneously, and how chemical mixtures act on nuclear receptor activity needs study. Although we know a great deal about phthalates, there is still much that remains uncertain. Future studies need to further examine their other potential health effects.

Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity

Background

Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying physiological regulation by the AHR remain poorly characterized. Previous studies identified several core genes that respond to xenobiotic AHR ligands across a broad range of species and tissues. However, only limited inferences have been made regarding its role in regulating constitutive gene activity, i.e. in the absence of exogenous ligands. To address this, we profiled transcriptomic variations between AHR-active and AHR-less-active animals in the absence of an exogenous agonist across five tissues, three of which came from rats (hypothalamus, white adipose and liver) and two of which came from mice (kidney and liver). Because AHR status alone has been shown sufficient to alter transcriptomic responses, we reason that by contrasting profiles amongst AHR-variant animals, we may elucidate effects of the AHR on constitutive mRNA abundances.

Results

We found significantly more overlap in constitutive mRNA abundances amongst tissues within the same species than from tissues between species and identified 13 genes (Agt, Car3, Creg1, Ctsc, E2f6, Enpp1, Gatm, Gstm4, Kcnj8, Me1, Pdk1, Slc35a3, and Sqrdl) that are affected by AHR-status in four of five tissues. One gene, Creg1, was significantly up-regulated in all AHR-less-active animals. We also find greater overlap between tissues at the pathway level than at the gene level, suggesting coherency to the AHR signalling response within these processes. Analysis of regulatory motifs suggests that the AHR mostly mediates transcriptional regulation via direct binding to response elements.

Conclusions

These findings, though preliminary, present a platform for further evaluating the role of the AHR in regulation of constitutive mRNA levels and physiologic function.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1053) contains supplementary material, which is available to authorized users.

Role of aryl hydrocarbon receptor in cancer

Aryl hydrocarbon receptor (AHR), a cytosolic ligand-activated transcription factor, belongs to the member of bHLH/PAS family of heterodimeric transcriptional regulators and is widely expressed in a variety of animal species and humans. Recent animal and human data suggested that AHR is involved in various signaling pathways critical to cell normal homeostasis, which covers multiple aspects of physiology, such as cell proliferation and differentiation, gene regulation, cell motility and migration, inflammation and others. Dysregulation of these physiological processes is known to contribute to events such as tumor initiation, promotion, and progression. Increasing epidemiological and experimental animal data provided substantial support for an association between abnormal AHR function and cancer, implicating AHR may be a novel drug-interfering target for cancers. The proposed underlying mechanisms of its actions in cancer involved multiple aspects, (a) inhibiting the functional expression of the key anti-oncogenes (such as p53 and BRCA1), (b) promoting stem cells transforming and angiogenesis, (c) altering cell survival, proliferation and differentiation by influencing the physiologic processes of cell-cycle, apoptosis, cell contact-inhibition, metabolism and remodel of extracellular matrix, and cell-matrix interaction, (d) cross-talking with the signaling pathways of estrogen receptor and inflammation. This review aims to provide a brief overview of recent investigations into the role of AHR and the underlying mechanisms of its actions in cancer, which were explored by the new technologies emerging in recent years.

CXCR4 activation maintains a stem cell population in tamoxifen-resistant breast cancer cells through AhR signalling

Background:

Tamoxifen is commonly used for breast cancer therapy. However, tamoxifen resistance is an important clinical problem. Continuous treatment with conventional therapy may contribute to cancer progression in recurring cancers through the accumulation of drug-resistant cancer progenitors.

Methods:

To investigate signalling mechanisms important for the maintenance and viability of drug-resistant cancer progenitors, we used microarray analysis, PCR array for genes involved in cancer drug resistance and metabolism, flow cytometry, soft agar colony formation assay, in vivo tumourigenicity assay and immunohistochemical analysis using tamoxifen-sensitive and tamoxifen-resistant breast cancer MCF7 cells.

Results:

Downregulation of CXCR4 signalling by small molecule antagonist AMD3100 specifically inhibits growth of progenitor cell population in MCF7(TAM-R) cells both in vitro and in vivo. Microarray analysis revealed aryl hydrocarbon receptor (AhR) signalling as one of the top networks that is differentially regulated in MCF7(TAM-R) and MCF7 xenograft tumours treated with AMD3100. Further, small molecule antagonists of AhR signalling specifically inhibit the progenitor population in MCF7(TAM-R) cells and growth of MCF7(TAM-R) xenografts in vivo.

Conclusion:

The chemokine receptor CXCR4 maintains a cancer progenitor population in tamoxifen-resistant MCF7 cells through AhR signalling and could be a putative target for the treatment of tamoxifen-resistant breast cancers.

In vitro Toxicity Testing in the Twenty-First Century

The National Research Council (NRC) article “Toxicity Testing in the 21st Century: A vision and A Strategy” (National Research Council, 2007) was written to bring attention to the application of scientific advances for use in toxicity tests so that chemicals can be tested in a more time and cost efficient manner while providing a more relevant and mechanistic insight into the toxic potential of a compound. Development of tools for in vitro toxicity testing constitutes an important activity of this vision and contributes to the provision of test systems as well as data that are essential for the development of computer modeling tools for, e.g., system biology, physiologically based modeling. This article intends to highlight some of the issues that have to be addressed in order to make in vitro toxicity testing a reality in the twenty-first century.

External influences on the immune system via activation of the aryl hydrocarbon receptor

The aryl hydrocarbon receptor (AhR), subject of intensive research over three decades by the pharmacology/toxicology field has recently made its entry into mainstream immunology research and is set to continue to intrigue with ever more complex modes of modulating immune responses. The discovery of high and selective AhR expression on Th17 cells and its role in induction of the cytokine IL-22 attributed new immunological functions to this transcription factor and stimulated further research into physiological functions of the AhR in the immune system. A number of recent reviews have highlighted potential new avenues of research. This review addresses recent new insight into physiological roles of AhR in the immune system.

Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice

The aryl hydrocarbon receptor (AHR) is a widely expressed ligand-dependent transcription factor that mediates cellular responses to dioxins and other planar aromatic hydrocarbons. Ahr-null mice are refractory to the toxic effects of dioxin exposure. Although some mechanistic aspects of AHR activity are well understood, the tissue specificity of AHR effects remains unclear, both during development and following administration of exogenous ligands. To address the latter issue, we defined and compared transcriptional responses to dioxin exposure in the liver and kidney of wild-type and Ahr-null adult C57BL/6J mice treated with either 2,3,7,8-tetrachlorodibenzo-p-dioxin or corn-oil vehicle. In both tissues, essentially all effects of dioxin on hepatic mRNA levels were mediated by the AHR. Although 297 genes were altered by dioxin exposure in the liver, only 17 were changed in the kidney, including a number of well-established AHR target genes. Ahr genotype had a large effect in both tissues, profoundly remodeling both the renal and hepatic transcriptomes. Surprisingly, a large number of genes were affected by Ahr genotype in both tissues, suggesting the presence of a basal AHR gene battery. Alterations of the renal transcriptome in Ahr-null animals were associated with perturbation of specific functional pathways and enrichment of specific DNA motifs. Our results demonstrate the importance of intertissue comparisons, highlight the basal role of the AHR in liver and kidney, and support a role in development or normal physiology.

The pleiotropy of dioxin toxicity--xenobiotic misappropriation of the aryl hydrocarbon receptor's alternative physiological roles

The aryl hydrocarbon receptor is a signal regulated transcription factor that has best been characterised as regulating the xenobiotic response to a variety of planar aromatic hydrocarbons. There is compelling evidence that it mediates most, if not all, of the toxic effects of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin). Dioxin exposure results in a wide variety of toxic outcomes including severe wasting syndrome, chloracne, thymic involution, severe immune suppression, reduced fertility, hepatotoxicity, teratogenicity, tumour promotion and death. The pleiotropy of toxic outcomes implies the disruption of a wide range of normal physiological functions. The aryl hydrocarbon receptor has developmentally restricted expression as well as developmental defects in gene-targeted mice. It has a wide range of target genes that do not fit into the classical xenobiotic metabolising gene battery and has recently been shown to interact with NF-kappa B and the estrogen receptor. There is also evidence for its activation in the absence of exogenous ligand, all of which point to various roles outside xenobiotic metabolism. Ligands so far identified display differential activation potential with respect to receptor activity. This article addresses activities of the aryl hydrocarbon receptor that are outside the xenobiotic response. Known physiological roles are discussed as well as how their disruption contributes to the pleiotropic toxicity of TCDD.

Genetic regulatory networks of nephrogenesis: deregulation of WT1 splicing by benzo(a)pyrene

Recent studies have identified AHR as a master regulator of Wilms' tumor suppressor gene (WT1) signaling in the developing kidney. Activation of AHR signaling by environmental chemical is associated with proteasome-mediated degradation of AHR protein, disruption of WT1 alternative splicing, and marked alterations in the regulation of genetic programs of developmental progression in the developing kidney. The complexity of genetic regulatory networks of nephrogenesis controlled by AHR-WT1 interactions will be discussed here with particular emphasis given to the biological and medical consequences that may result from deficits in nephrogenesis that compromise reserve capacity and renal function later in life. Understanding the impact of early-life environmental exposures to chemicals that disrupt AHR signaling can help minimize negative health consequences to pregnant women and their offspring.

Unraveling genetic regulatory networks of mammalian retroelements

Advances in the science of toxicogenomics have opened the door to major advances in our understanding of the molecular basis of environmental pathogenesis and the role of environmental factors in human disease. This report summarizes major findings in the laboratory defining the molecular basis of L1 retroelement activation in mammalian cells and the architecture of gene regulatory networks involved in phenotypic control.

Modulation of Biological Regulatory Networks During Nephrogenesis

Mesenchymal-to-epithelial transition is an important biological event during the course of renal cell differentiation as condensing mesenchyme gives rise to tubuloepithelial structures. Wilms' tumor suppressor gene (Wt1) has been identified as a master regulator of the complex genetic events that mediate mesenchymal transdifferentiation. Evidence is summarized here showing that the tightly regulated series of genetic and biochemical events during nephrogenesis is disrupted by superactivation of aryl hydrocarbon receptor (Ahr) by benzo(a)pyrene (BaP), a ubiquitous polycyclic aromatic hydrocarbon and renal carcinogen (Falahatpisheh and Ramos, 2003). Nephron formation is inhibited by BaP, a response that involves inhibition of metanephric cell differentiation and shifts in the relative abundance of Wt1 splice variants. A systems biology paradigm that combined approaches from genomics, transcriptomics, and bioinformatics revealed that the global response of murine metanephric cultures to BaP involves downregulation of Ahr and disruption of downstream targets of Wt1. Discrete networks of genetic regulation were resolved using Boolean idealizations and included genes involved in renal cell differentiation and metabolic control. This work has established a role for Ahr in renal cell differentiation and kidney development and resolved putative molecular interactions between Ahr and Wt1.

Treatment of mice with the Ah receptor agonist and human carcinogen dioxin results in altered numbers and function of hematopoietic stem cells

The aryl hydrocarbon receptor (AhR) mediates the carcinogenicity of a family of environmental contaminants, the most potent being 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Increased incidence of lymphoma and leukemia in humans is associated with TCDD exposure. Although AhR activation by TCDD has profound effects on the immune system, precise cellular and molecular mechanisms have yet to be determined. These studies tested the hypothesis that alteration of marrow populations following treatment of mice with TCDD is due to an effect on hematopoietic stem cells (HSCs). Treatment with TCDD resulted in an increased number and proliferation of bone marrow (BM) populations enriched for HSCs. There was a time-dependent decrease in B-lineage cells with a concomitant increase in myeloid populations. The decrease in the B-cell lineage colony-forming unit-preB progenitors along with a transient increase in myeloid progenitors were consistent with a skewing of lineage development from lymphoid to myeloid populations. However, HSCs from TCDD-treated mice exhibited diminished capacity to reconstitute and home to marrow of irradiated recipients. AhR messenger RNA was expressed in progenitor subsets but is downregulated during HSC proliferation. This result was consistent with the lack of response following the exposure of 5-fluorouracil-treated mice to TCDD. The direct exposure of cultured BM cells to TCDD inhibited the growth of immature hematopoietic progenitor cells, but not more mature lineage-restricted progenitors. Overall, these data are consistent with the hypothesis that TCDD, through AhR activation, alters the ability of HSCs to respond appropriately to signals within the marrow microenvironment.

Functional pharmacogenetics/genomics of human cytochromes P450 involved in drug biotransformation

We investigated the elimination routes for the 200 drugs that are sold most often by prescription count in the United States. The majority (78%) of the hepatically cleared drugs were found to be subject to oxidative metabolism via cytochromes P450 of the families 1, 2 and 3, with major contributions from CYP3A4/5 (37% of drugs) followed by CYP2C9 (17%), CYP2D6 (15%), CYP2C19 (10%), CYP1A2 (9%), CYP2C8 (6%), and CYP2B6 (4%). Clinically well-established polymorphic CYPs (i.e., CYP2C9, CYP2C19, and CYP2D6) were involved in the metabolism of approximately half of those drugs, including (in particular) NSAIDs metabolized mainly by CYP2C9, proton-pump inhibitors metabolized by CYP2C19, and beta blockers and several antipsychotics and antidepressants metabolized by CYP2D6. In this review, we provide an up-to-date summary of the functional polymorphisms and aspects of the functional genomics of the major human drug-metabolizing cytochrome P450s, as well as their clinical significance.

Genetic networks of cooperative redox regulation of osteopontin

Osteopontin is a primary cytokine and matrix-associated protein involved in medial thickening and neointima formation. Osteopontin binds integrin receptors, activates cell migration and matrix metalloproteinases, and mediates arteriosclerotic lesion formation and vessel calcification. To understand the complex biology of osteopontin, computational methodology was employed to identify sets of genes whose transcriptional states were predictive of osteopontin gene expression based on the transcriptional states of 12,400 genes and ESTs across 235 independent Affymetrix Murine Genome Array MG_U74Av2 hybridizations. Arginase [GenBank: U51805] and Mac-2 antigen [GenBank: X16834] were identified as primary attractors within the gene-gene interaction network of osteopontin. Resolution of molecular interactions among these genes indicated that the majority of predictor genes could be linked through redox regulated transcription by nuclear factor kappa-B and transforming growth factor beta inducible early gene 1 regulatory elements. Subsequent molecular analyses established redox sensitivity of a 200 bp region within the 5' UTR of opn promoter and implicated nuclear factor kappa-B and transforming growth factor beta inducible early gene 1 cis-acting elements in the regulation of osteopontin.

Key developments in endocrine disrupter research and human health

Environmental etiologies involving exposures to chemicals that mimic endogenous hormones are proposed for a number of adverse human health effects, including infertility, abnormal prenatal and childhood development, and reproductive cancers (National Research Council, 1999; World Health Organization, 2002). Endocrine disrupters represent a significant area of environmental research with important implications for human health. This article provides an overview of some of the key developments in this field that may enhance our ability to assess the human health risks posed by exposure to endocrine disrupters. Advances in methodologies of hazard identification (toxicogenomics, transcriptomics, proteomics, metabolomics, bioinformatics) are discussed, as well as epigenetics and emerging biological endpoints.

Environmental contaminants as risk factors for developing diabetes

The contribution of exposure to persistent organic pollutants (POPs) to the incidence of diabetes has received little attention until recently. A number of reports have emerged, however, concerning elevated diabetes in persons occupationally exposed to dioxin. United States (US) Air Force personnel in Vietnam who sprayed Agent Orange containing dioxin as a contaminant had elevated rates of diabetes, leading to US government compensation for diabetes in these veterans. Recent studies in populations exposed to polychlorinated biphenyls (PCBs) and chlorinated pesticides found a dose-dependent elevated risk of diabetes. An elevation in risk of diabetes in relation to levels of several POPs has been demonstrated by two different groups using the National Health and Nutrition Examination Survey (NHANES), a random sampling of US citizens. The strong associations seen in quite different studies suggest the possibility that exposure to POPs could cause diabetes. One striking observation is that obese persons that do not have elevated POPs are not at elevated risk of diabetes, suggesting that the POPs rather than the obesity per se is responsible for the association. Although a specific mechanism is not known, most POPs induce a great number and variety of genes, including several that alter insulin action. Because diabetes is a dangerous disease that is increasing in frequency throughout the world, further study of the possibility that exposure to POPs contributes to the etiology of diabetes is critical.

Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon

Computational approaches were used to define structural and functional determinants of a putative genetic regulatory network of murine LINE-1 (long interspersed nuclear element-1), an active mammalian retrotransposon that uses RNA intermediates to populate new sites throughout the genome. Polymerase (RNA) II polypeptide E AI845735 and mouse DNA homologous to Drosophila per fragment M12039 were identified as primary attractors. siRNA knockdown of the aryl hydrocarbon receptor NM_013464 modulated gene expression within the network, including LINE-1, Sgpl1, Sdcbp, and Mgst1. Genes within the network did not exhibit physical proximity and instead were dispersed throughout the genome. The potential impact of individual members of the network on the global dynamical behavior of LINE-1 was examined from a theoretical and empirical framework.

A statistical model for assessing genetic susceptibility as a risk factor in multifactorial diseases: lessons from occupational asthma

BACKGROUND

Incorporating the influence of genetic variation in the risk assessment process is often considered, but no generalized approach exists. Many common human diseases such as asthma, cancer, and cardiovascular disease are complex in nature, as they are influenced variably by environmental, physiologic, and genetic factors. The genetic components most responsible for differences in individual disease risk are thought to be DNA variants (polymorphisms) that influence the expression or function of mediators involved in the pathological processes.

OBJECTIVE

The purpose of this study was to estimate the combinatorial contribution of multiple genetic variants to disease risk.

METHODS

We used a logistic regression model to help estimate the joint contribution that multiple genetic variants would have on disease risk. This model was developed using data collected from molecular epidemiology studies of allergic asthma that examined variants in 16 susceptibility genes.

RESULTS

Based on the product of single gene variant odds ratios, the risk of developing asthma was assigned to genotype profiles, and the frequency of each profile was estimated for the general population. Our model predicts that multiple disease variants broaden the risk distribution, facilitating the identification of susceptible populations. This model also allows for incorporation of exposure information as an independent variable, which will be important for risk variants associated with specific exposures.

CONCLUSION

The present model provided an opportunity to estimate the relative change in risk associated with multiple genetic variants. This will facilitate identification of susceptible populations and help provide a framework to model the genetic contribution in probabilistic risk assessment.

Application of data mining approaches to drug delivery

Computational approaches play a key role in all areas of the pharmaceutical industry from data mining, experimental and clinical data capture to pharmacoeconomics and adverse events monitoring. They will likely continue to be indispensable assets along with a growing library of software applications. This is primarily due to the increasingly massive amount of biology, chemistry and clinical data, which is now entering the public domain mainly as a result of NIH and commercially funded projects. We are therefore in need of new methods for mining this mountain of data in order to enable new hypothesis generation. The computational approaches include, but are not limited to, database compilation, quantitative structure activity relationships (QSAR), pharmacophores, network visualization models, decision trees, machine learning algorithms and multidimensional data visualization software that could be used to improve drug delivery after mining public and/or proprietary data. We will discuss some areas of unmet needs in the area of data mining for drug delivery that can be addressed with new software tools or databases of relevance to future pharmaceutical projects.

Transcriptional profiling and functional genomics reveal a role for AHR transcription factor in nephrogenesis

Transcriptional profiling and functional genomics experiments using E11.5 metanephros organ cultures from Ahr(-/-) and Ahr(+/+) have shown that aryl hydrocarbon receptor (AHR) transcription factor is involved in the regulation of mesenchymal-to-epithelial transition (MET) during nephrogenesis. This response is mediated by alterations in the post-transcriptional control of Wilms' tumor suppressor (Wt1) gene and Wt1 splicing. In this article, biologically relevant gene predictor sets of the nephrogenic response were calculated for target genes of interest. The predictability of the gene set for each target was quantified by the coefficient of determination which provided a good criterion for identification of predictor sets that define the complex gene-gene interactions co-regulated by Ahr and Wt1. A subset of the signature genes was found to be co-regulated by Ahr and Wt1 and was responsible for shifts in renal cell transdifferentiation.

Role of the aryl hydrocarbon receptor in drug metabolism

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that regulates the transcription of certain key enzymes involved in the metabolism of xenobiotic substances including some drugs. The AhR can be activated by a wide range of classes of compounds (e.g. polycyclic aromatic hydrocarbons, benzimidazoles and flavonoids), and interacts with a number of other proteins, including nuclear hormone receptors such as the oestrogen and androgen receptors. Activation of the AhR antagonises the oestrogen receptor and can lead to modulation of its transcriptional activity; thus, activating the AhR may serve as a target for breast cancer therapy. Disruption of normal signalling by drug interactions with the AhR or downstream components of this pathway could result in adverse effects, such as the bioactivation of procarcinogens or the disruption of normal homeostasis. The cytochrome P450s CYP1A1, -1B1, -1A2 and -2S1 are regulated by the AhR, and they are all involved in the metabolism of endogenous substrates as well as xenobiotics. Polymorphisms in the AhR, or polymorphisms in enzymes regulated by the AhR, may cause variations in response to certain drugs in different individuals; this needs to be taken into consideration when administering drugs that interact with this pathway.

The mode of action of organic carcinogens on cellular structures

Most genotoxic organic carcinogens require metabolic activation to exert their detrimental effects. The present review summarizes the mechanisms of how organic carcinogens are bioactivated into DNA-reactive descendants. Beginning with the history of discovery of some important human organic carcinogens, the text guides through the development of the knowledge on their molecular mode of action that has grown over the past decades. Some of the most important molecular mechanisms in chemical carcinogenesis, the role of the enzymes involved in bioactivation, the target gene structures of some ultimate carcinogenic metabolites, and implications for human cancer risk assessment are discussed.

Expression profiling of estrogen-responsive genes in breast cancer cells treated with alkylphenols, chlorinated phenols, parabens, or bis- and benzoylphenols for evaluation of estrogenic activity

We examined expression profiles of estrogen-responsive genes after treatment with alkylphenols (p-cresol (pC), 4-n-ethylphenol (4EP), 4-n-heptylphenol (4HP), 4-t-octylphenol (4OP) and nonylphenol (NP)), chlorinated phenols (4-chlorophenol (4CP), 4-chloro-3,5-dimethylphenol (CDP), 2,4-dichlorophenol (DCP) and pentachlorophenol (PCP)), parabens (methylparaben (MPB), ethylparaben (EPB) propylparaben (PPB) and butylparaben (BuPB)), or bis- and benzoylphenols (bisphenols A and B and p-hydroxybenzophenone (pHBP)) by means of a DNA microarray assay first to evaluate the estrogenic activity of these chemicals and then to understand the structural basis for the activity. By selecting a set of 120 genes showing greater statistical reliability for estrogen, a more reliable assay for each of the chemicals was achieved and, for the chemicals for which data were available, the results were consistent with those of previously reported estrogen receptor-binding and yeast two-hybrid assays except for chlorinated and few other phenols. Evaluation of the chemicals based on gene function indicated that the genes related to proliferation, transcription and transport were mostly up-regulated while significant numbers of genes related to enzymes and signaling were down-regulated. The genes related to transcription showed the highest degree of variation among the six functional categories (enzymes, signaling, proliferation, transcription, transport and others) for the chemicals with relatively high levels of estrogenic activity. These results indicate that the variations in chemicals and their biological effects can be monitored by the appropriate grouping of estrogen-responsive genes.

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.

Toxicogenomics in Risk Assessment: Applications and Needs

Since its inception, there have been high expectations for the science of toxicogenomics to decrease the uncertainties associated with the risk assessment process by providing valuable insights into toxic mechanisms of action. However, the application of these data into risk assessment practices is still in the early stages of development, and proof of principle experiments have yet to emerge. The following discusses some potential applications as well as impediments that warrant a concerted investigation from all stakeholders in order to facilitate the acceptance and subsequent incorporation of toxicogenomics into regulatory decision making.

Immunolocalization of CYP1B1 in normal, human, fetal and adult eyes

CYP1B1 is a cytochrome P450 enzyme implicated in autosomal recessive primary congenital glaucoma (PCG). The mechanism and function of CYP1B1 in the development of the PCG phenotype is unknown. Previously, investigators have reported detection of Cyp1b1 mRNA in the ciliary body and epithelium and neuroepithelium in the developing mouse eye, employing in situ hybridization techniques. Similarly, additional investigators have detected CYP1B1 mRNA in the iris, ciliary body, non-pigmented ciliary epithelial line, cornea, retinal-pigment epithelium, and retina in the human adult eye, using Northern blotting. This study was designed to immunolocalize CYP1B1 protein in the various ocular structures of normal, human fetal and adult eyes. Normal fetal and adult eyes were immunolabeled with a polyclonal antibody against human CYP1B1 using indirect immunofluorescence, and then compared with appropriate controls. The intensity of immunolabeling of the various ocular structures was assessed by qualitative and semi-quantitative techniques. In the anterior segment anti-CYP1B1 immunoreactivity (IR) was detected early in fetal development in the primitive ciliary epithelium. As well, the most intense CYP1B1 IR was in the non-pigmented ciliary epithelium. In addition, CYP1B1 IR was also present in the corneal epithelium and keratocytes, both layers of the iris pigmented epithelium, and retina. However, CYP1B1 IR was absent in the trabecular meshwork in all of the samples. In general, CYP1B1 immunolabeling in the human fetal eyes was more intense when compared to adult eyes. CYP1B1 IR was primarily immunolocalized to the non-pigmented ciliary epithelium and early in fetal development. In addition, CYP1B1 IR was not detected in the trabecular meshwork. These findings suggest that the abnormalities in the development of the trabecular meshwork in PCG may result from diminished or absent metabolism of important endogenous substrates in the ciliary epithelium due to non-functional CYP1B1 enzyme.

A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism

The increasing generation of biological data represents a challenge to understanding the complexity of systems, resulting in scientists increasingly focused on a relatively narrow area of study, thereby limiting insight that can be gained from a broader perspective. In the field of drug metabolism and toxicology we are witnessing the characterization of many proteins. Most of the key enzymes and transporters are recognized as transcriptionally regulated by the nuclear hormone receptors such as pregnane X receptor, constitutive androstane receptor, vitamin D receptor, glucocorticoid receptor, and others. There is apparent cross talk in regulation, since multiple receptors may modulate expression of a single enzyme or transporter, representing one of many areas of active research interest. We have used published data on nuclear hormone receptors, enzymes, ligands, and other biological information to manually annotate an Oracle database, forming the basis of a platform for querying (MetaDrug). Using algorithms, we have demonstrated how nuclear hormone receptors alone can form a network of direct interactions, and when expanded, this network increases in complexity to describe the interactions with target genes as well as small molecules known to bind a receptor, enzyme, or transporter. We have also described how the database can be used for visualizing high-throughput microarray data derived from a published study of MCF-7 cells treated with 4-hydroxytamoxifen, to highlight potential downstream effects of molecule treatment. The database represents a novel knowledge mining and analytical tool that, to be relevant, requires continual updating to evolve alongside other key storage systems and sources of biological knowledge.

The TAO-Gen algorithm for identifying gene interaction networks with application to SOS repair in E. coli

One major unresolved issue in the analysis of gene expression data is the identification and quantification of gene regulatory networks. Several methods have been proposed for identifying gene regulatory networks, but these methods predominantly focus on the use of multiple pairwise comparisons to identify the network structure. In this article, we describe a method for analyzing gene expression data to determine a regulatory structure consistent with an observed set of expression profiles. Unlike other methods this method goes beyond pairwise evaluations by using likelihood-based statistical methods to obtain the network that is most consistent with the complete data set. The proposed algorithm performs accurately for moderate-sized networks with most errors being minor additions of linkages. However, the analysis also indicates that sample sizes may need to be increased to uniquely identify even moderate-sized networks. The method is used to evaluate interactions between genes in the SOS signaling pathway in Escherichia coli using gene expression data where each gene in the network is over-expressed using plasmids inserts.

Gene interaction network suggests dioxin induces a significant linkage between aryl hydrocarbon receptor and retinoic acid receptor beta

Gene expression arrays (gene chips) have enabled researchers to roughly quantify the level of mRNA expression for a large number of genes in a single sample. Several methods have been developed for the analysis of gene array data including clustering, outlier detection, and correlation studies. Most of these analyses are aimed at a qualitative identification of what is different between two samples and/or the relationship between two genes. We propose a quantitative, statistically sound methodology for the analysis of gene regulatory networks using gene expression data sets. The method is based on Bayesian networks for direct quantification of gene expression networks. Using the gene expression changes in HPL1A lung airway epithelial cells after exposure to 2,3,7,8-tetrachlorodibenzo-(Italic)p(/Italic)-dioxin at levels of 0.1, 1.0, and 10.0 nM for 24 hr, a gene expression network was hypothesized and analyzed. The method clearly demonstrates support for the assumed network and the hypothesis linking the usual dioxin expression changes to the retinoic acid receptor system. Simulation studies demonstrated the method works well, even for small samples.