Molecular responses to xenoestrogens: mechanistic insights from toxicogenomics

Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol

Sex differentiation in fish is a highly labile process easily reversed by the use of exogenous hormonal treatment and has led to environmental concerns since low doses of estrogenic molecules can adversely impact fish reproduction. The goal of this study was to identify pathways altered by treatment with ethynylestradiol (EE2) in developing fish and to find new target genes to be tested further for their possible role in male-to-female sex transdifferentiation. To this end, we have successfully adapted a previously developed bioinformatics workflow to a meta-analysis of two datasets studying sex reversal following exposure to EE2 in juvenile rainbow trout. The meta-analysis consisted of retrieving the intersection of the top gene lists generated for both datasets, performed at different levels of stringency. The intersecting gene lists, enriched in true positive differentially expressed genes (DEGs), were subjected to over-representation analysis (ORA) which allowed identifying several statistically significant enriched pathways altered by EE2 treatment and several new candidate pathways, such as progesterone-mediated oocyte maturation and PPAR signalling. Moreover, several relevant key genes potentially implicated in the early transdifferentiation process were selected. Altogether, the results show that EE2 has a great effect on gene expression in juvenile rainbow trout. The feminization process seems to result from the altered transcription of genes implicated in normal female gonad differentiation, resulting in expression similar to that observed in normal females (i.e. the repression of key testicular markers cyp17a1, cyp11b, tbx1), as well as from other genes (including transcription factors) that respond specifically to the EE2 treatment. The results also showed that the bioinformatics workflow can be applied to different types of microarray platforms and could be generalized to (eco)toxicogenomics studies for environmental risk assessment purposes.

Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout

Sex steroids play a key role in triggering sex differentiation in fish, the use of exogenous hormone treatment leading to partial or complete sex reversal. This phenomenon has attracted attention since the discovery that even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development) and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find out mechanisms of actions (MOA) and identify biomarkers related to the toxic action of a compound. However, high throughput data interpretation relies on statistical analysis, species genomic resources, and bioinformatics tools. The goals of this study are to improve the knowledge of feminisation in fish, by the analysis of molecular responses in the gonads of rainbow trout fry after chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L) of ethynylestradiol (EE2) and to offer target genes as potential biomarkers of ovotestis development. We successfully adapted a bioinformatics microarray analysis workflow elaborated on human data to a toxicogenomic study using rainbow trout, a fish species lacking accurate functional annotation and genomic resources. The workflow allowed to obtain lists of genes supposed to be enriched in true positive differentially expressed genes (DEGs), which were subjected to over-representation analysis methods (ORA). Several pathways and ontologies, mostly related to cell division and metabolism, sexual reproduction and steroid production, were found significantly enriched in our analyses. Moreover, two sets of potential ovotestis biomarkers were selected using several criteria. The first group displayed specific potential biomarkers belonging to pathways/ontologies highlighted in the experiment. Among them, the early ovarian differentiation gene foxl2a was overexpressed. The second group, which was highly sensitive but not specific, included the DEGs presenting the highest fold change and lowest p-value of the statistical workflow output. The methodology can be generalized to other (non-model) species and various types of microarray platforms.

Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors.

DNA microarray-based gene expression profiling of estrogenic chemicals

We summarize updated information about DNA microarray-based gene expression profiling by focusing on its application to estrogenic chemicals. First, estrogenic chemicals, including natural/industrial estrogens and phytoestrogens, and the methods for detection and evaluation of estrogenic chemicals were overviewed along with a comprehensive list of estrogenic chemicals of natural or industrial origin. Second, gene expression profiling of chemicals using a focused microarray containing estrogen-responsive genes is summarized. Third, silent estrogens, a new type of estrogenic chemicals characterized by their estrogenic gene expression profiles without growth stimulative or inhibitory effects, have been identified so far exclusively by DNA microarray assay. Lastly, the prospect of a microarray assay is discussed, including issues such as commercialization, future directions of applications and quality control methods.

Estrogenic endocrine-disrupting chemicals: molecular mechanisms of actions on putative human diseases

Endocrine-disrupting chemicals (EDC), including phthalates, bisphenol A (BPA), phytoestrogens such as genistein and daidzein, dichlorodiphenyltrichloroethane (DDT), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), are associated with a variety of adverse health effects in organisms or progeny by altering the endocrine system. Environmental estrogens, including BPA, phthalates, and phytoestrogens, are the most extensively studied and are considered to mimic the actions of endogenous estrogen, 17β-estradiol (E2). Diverse modes of action of estrogen and estrogen receptors (ERα and ERβ) have been described, but the mode of action of estrogenic EDC is postulated to be more complex and needs to be more clearly elucidated. This review examines the adverse effects of estrogenic EDC on male or female reproductive systems and molecular mechanisms underlying EDC effects that modulate ER-mediated signaling. Mechanisms of action for estrogenic EDC may involve both ER-dependent and ER-independent pathways. Recent findings from systems toxicology of examining estrogenic EDC are also discussed.

Molecular crosstalk between a chemical and a biological stressor and consequences on disease manifestation in rainbow trout

The aim of the present study was to examine the molecular and organism reaction of rainbow trout, Oncorhynchus mykiss, to the combined impact of two environmental stressors. The two stressors were the myxozoan parasite, Tetracapsuloides bryosalmonae, which is the etiological agent of proliferative kidney disease (PKD) and a natural stressor to salmonid populations, and 17β-estradiol (E2) as prototype of estrogen-active chemical stressors in the aquatic environment. Both stressors, the parasite and estrogenic contaminants, co-exist in Swiss rivers and are discussed as factors contributing to the decline of Swiss brown trout populations over the last decades. Using a microarray approach contrasting parasite-infected and non-infected rainbow trout at low or high estrogen levels, it was observed that molecular response patterns under joint exposure differed from those to the single stressors. More specifically, three major response patterns were present: (i) expression responses of gene transcripts to one stressor are weakened by the presence of the second stressor; (ii) expression responses of gene transcripts to one stressor are enhanced by the presence of the second stressor; (iii) expression responses of gene transcripts at joint treatment are dominated by one of the two stressors. Organism-level responses to concurrent E2 and parasite treatment - assessed through measuring parasite loads in the fish host and cumulative mortalities of trout - were dominated by the pathogen, with no modulating influence of E2. The findings reveal function- and level-specific responses of rainbow trout to stressor combinations, which are only partly predictable from the response to the single stressors.

Screening estrogenic activity of environmental contaminants and water samples using a transgenic medaka embryo bioassay

Many natural or synthetic chemicals may act as exogenous estrogens and affect the reproductive health of humans and wildlife. Since these xenoestrogens are ubiquitous, it is essential to monitor their presence in the environment. Hence, we developed a bioassay using the transgenic medaka (Oryzias latipes) embryo, in which the green fluorescent protein (GFP) was placed under the control of the gnrh3 promoter, one of the three paralogous gonadotropin-releasing hormone (GnRH) genes that regulate reproductive function and behavior. As medaka embryos are transparent, the fluorescent expression of GFP can be easily observed in vivo during development. We exposed newly fertilized medaka embryos to varying solutions of bisphenol A (BPA), nonylphenol (NP), 17β-estradiol (E2), or a river water sample, and monitored their development. During embryonic development, the mRNA levels of GnRHs, GnRH receptors, and estrogen receptors (ERs) were measured with quantitative real-time reverse transcription-PCR. Our results showed that the chemicals and the river water significantly decreased the fluorescent intensity of the GnRH3 neurons, postponed the eye development, and retarded the growth of the embryos. The three xenoestrogens also lowered the heart rate, lengthened the time to hatch, suppressed the expression of the three GnRH genes, and up-regulated the ERα mRNA level. In addition, the GnRH3 mRNA level was significantly correlated with the fluorescence intensity of the GnRH neurons. We concluded that the transgenic medaka embryo is a rapid and sensitive bioassay for screening environmental water samples. We also found that xenoestrogens had significant effects on GnRH gene expression and embryonic development.

Survey of public domain software for docking simulations and virtual screening

Progress in functional genomics and structural studies on biological macromolecules are generating a growing number of potential targets for therapeutics, adding to the importance of computational approaches for small molecule docking and virtual screening of candidate compounds. In this review, recent improvements in several public domain packages that are widely used in the context of drug development, including DOCK, AutoDock, AutoDock Vina and Screening for Ligands by Induced-fit Docking Efficiently (SLIDE) are surveyed. The authors also survey methods for the analysis and visualisation of docking simulations, as an important step in the overall assessment of the results. In order to illustrate the performance and limitations of current docking programs, the authors used the National Center for Toxicological Research (NCTR) oestrogen receptor benchmark set of 232 oestrogenic compounds with experimentally measured strength of binding to oestrogen receptor alpha. The methods tested here yielded a correlation coefficient of up to 0.6 between the predicted and observed binding affinities for active compounds in this benchmark.

Mechanistic profiling of the cAMP-dependent steroidogenic pathway in the H295R endocrine disrupter screening system: new endpoints for toxicity testing

The need for implementation of effects on steroid synthesis and hormone processing in screening batteries of endocrine disruptive compounds is widely acknowledged. In this perspective, hormone profiling in the H295R adrenocortical cell system is extensively examined and recently OECD validated (TG 456) as a replacement of the minced testis assay. To further elucidate the complete mechanisms and endocrine responsiveness of this cell system, microarray-based gene expression profiling of the cAMP response pathway, one of the major pathways in steroidogenesis regulation, was examined in H295R cells. Next to the steroid synthesis pathway, a broader lipid metabolic pathway, including cholesterol uptake/biosynthesis, hormone metabolization and many hormone and nuclear receptors, are sensitive towards cAMP stimulation in this cell system. Moreover, these pathways were clearly dose and time responsive, indicating early regulation (10 h) of cholesterol uptake and mobilization genes and later expression (24-48 h) of cholesterol biosynthesis and steroid synthesis. Transcription network analysis suggested several important transcription factors that could be involved in regulation of the steroid hormone pathway, of which HNF4α, a broader lipid metabolism related transcription factor, might indicate some new transcription regulation patterns in this cell line. Overall we can conclude that the time dependent gene expression patterns of the strongly coordinated cholesterol supply and steroidogenesis pathways in the H295R cell system seem to reflect well the in vivo ACTH/cAMP signalling cascade in adrenal cells. Moreover, the completeness of the steroidogenic related pathways in terms of gene expression sensitivity, indicates the H295R cell line as a promising cell line in omics-based endocrine disruption screening.

Progress and promises in toxicogenomics in aquatic toxicology: is technical innovation driving scientific innovation?

In the last decade, new technologies have been invented to analyze large amounts of information such as gene transcripts (transcriptomics), proteins (proteomics) and small cellular molecules (metabolomics). Many studies have been performed in the last few years applying these technologies to aquatic toxicology, mainly in fish. In this article, we summarize the current state of knowledge and question whether the application of modern technology for descriptive purposes truly represents scientific advancement in aquatic toxicology. We critically discuss the advantages and disadvantages of these technologies and emphasize the importance of these critical aspects. To date, these techniques have been used mainly as a proof of principle, demonstrating effects of model compounds. The potential to use these techniques to better analyze the mode-of-action of a toxicant or the effects of a compound within organisms has rarely been met. This is partly due to a lack of baseline data and the fact that the expression of mRNA and protein profiles is rarely linked to physiology or toxicologically meaningful outcomes. It seems premature to analyze mixtures or environmental samples until more is known about the expression profiles of individual toxicants. Gene transcription, protein, or metabolic data give only a partial view of these effects. Thus, we emphasize that data obtained by these technologies must be linked to physiological changes to fully understand their significance. The use of these techniques in aquatic toxicology is still in its infancy, data cannot yet be applied to environmental risk assessment or regulation until more emphasis is placed on interpreting the data within their physiological and toxicological contexts.

Estrogenic activity of bisphenol A and 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE) demonstrated in mouse uterine gene profiles

BACKGROUND

Interest and concern regarding potentially estrogenic substances have resulted in development of model systems to evaluate mechanisms of such chemicals. Microarray studies have indicated that estradiol (E2)-stimulated uterine responses can be divided into early and late phases. Comparison of E2 uterine transcript profiles and those of other estrogenic chemicals of interest in vivo indicates mechanisms and activities of test compounds.

OBJECTIVES

We compared transcript responses and mechanisms of response using mouse reproductive tracts after treatment with E2, estriol (E3), bisphenol A (BPA), and 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE).

METHODS

Uterine RNA from ovariectomized wild-type mice, estrogen receptor α (ERα) knockout (αERKO) mice, and mice expressing a DNA-binding-deficient ERα (KIKO) treated with E2, E3, BPA, or HPTE for 2 or 24 hr was analyzed by microarray. Resulting regulated transcripts were compared by hierarchical clustering and correlation analysis, and response patterns were verified by reverse-transcription real-time polymerase chain reaction (RT-PCR).

RESULTS

Both xenoestrogens, BPA and HPTE, showed profiles highly correlated to that of E2 in the early response phase (2 hr), but the correlation diminished in the later response phase (24 hr), similar to the known weak estrogen E3. Both xenoestrogens also mimicked E2 in samples from KIKO mice, indicating that they are able to utilize the indirect tethering mode of ERα signaling. No response was detected in ERα-null uteri, indicating that ERα mediates the responses.

CONCLUSION

Our study forms a basis on which patterns of response and molecular mechanisms of potentially estrogenic chemicals can be assessed.

Improving in vitro Sertoli cell/gonocyte co-culture model for assessing male reproductive toxicity: Lessons learned from comparisons of cytotoxicity versus genomic responses to phthalates

Gonocytes exist in the neonatal testis and represent a transient population of male germ-line stem cells. It has been shown that stem cell self-renewal and progeny production is probably controlled by the neighboring differentiated cells and extracellular matrix (ECM) in vivo known as niches. Recently, we developed an in vitro three-dimensional (3D) Sertoli cell/gonocyte co-culture (SGC) model with ECM overlay, which creates an in vivo-like niche and supports germ-line stem cell functioning within a 3D environment. In this study, we applied morphological and cytotoxicity evaluations, as well as microarray-based gene expression to examine the effects of different phthalate esters (PE) on this model. Known in vivo male developmentally toxic PEs (DTPE) and developmentally non-toxic PEs (DNTPE) were evaluated. We observed that DTPE induced significantly greater dose-dependent morphological changes, a decrease in cell viability and an increase in cytotoxicity compared to those treated with DNTPE. Moreover, the gene expression was more greatly altered by DTPE than by DNTPE and non-supervised cluster analysis allowed the discrimination of DTPE from the DNTPE. Our systems-based GO-Quant analysis showed significant alterations in the gene pathways involved in cell cycle, phosphate transport and apoptosis regulation with DTPE but not with DNTPE treatment. Disruptions of steroidogenesis related-gene expression such as Star, Cyp19a1, Hsd17b8, and Nr4a3 were observed in the DTPE group, but not in the DNTPE group. In summary, our observation on cell viability, cytotoxicity, and microarray-based gene expression analysis induced by PEs demonstrate that our in vitro 3D-SGC system mimicked in vivo responses for PEs and suggests that the 3D-SGC system might be useful in identifying developmental reproductive toxicants.

Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)

The First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007) was held at the North Carolina State University McKimmon Center in Raleigh, North Carolina on October 25th and 26th, 2007. Based on the presentations at the conference and the commitment or interest of the presenters to contribute a manuscript of their research, we compiled this collection of articles as proceedings of the conference and an in-depth topical review of the utility of bioinformatics in the fields of toxicogenomics and environmental genomics.

Sexual reprogramming and estrogenic sensitization in wild fish exposed to ethinylestradiol

Globally, feminization responses in wild male freshwater fish are caused by exposure to estrogenic chemicals, including natural and synthetic estrogens, contained in effluentsfromwastewater treatment works. In U.K. rivers, feminization responses, including intersex, are widespread in wild roach (Rutilus rutilus) populations, and severely affected fish have a reduced reproductive success. We exposed roach to environmentally relevant concentrations of the contraceptive estrogen 17alpha-ethinylestradiol (EE2) for up to 2 years, including intermittent and repeated exposures,to determine effects on sexual development and subsequent responsiveness to estrogen. Exposure of roach to EE2 (at 4 ng/L) for 2 years resulted in sex reversal in males, leading to an all-female population with two cohorts in terms of their stages of ovarian development one paralleling the control females and one at a significantly less advanced stage, which we propose were sex-reversed males. Differing developmental and maturing rates of the putative sex-reversed males compared with control females would question their functional capability as females in the wild. Early-life exposure to environmentally relevant concentrations of EE2 sensitized females to estrogen, as determined by the measurement of the responses of estrogen-sensitive genes in a further EE2 challenge 398 days after the original exposure. In the wild, exposure to environmentally relevant concentrations of EE2 during early life has significantly wider implications for the sexual physiology in fish than has thus far been determined.

Prospective study of metal fume-induced responses of global gene expression profiling in whole blood

Metal particulate inhalation causes pulmonary and cardiovascular diseases. Our previous results showed that systemic responses to short-term occupational welding-fume exposure could be assessed by microarray analyses in whole-blood total RNA sampled before and after exposure. To expand our understanding of the duration of particulate-induced gene expression changes, we conducted a study using a similar population 1 yr after the original study and extended our observations in the postexposure period. We recruited 15 individuals with welding fume exposure and 7 nonexposed individuals. Thirteen of the 22 individuals (9 in exposed group and 4 in nonexposed group) had been monitored in the previous study. Whole-blood total RNA was analyzed at 3 time points, including baseline, immediately following exposure (approximately 5 h after baseline), and 24 h after baseline, using cDNA microarray technology. We replicated the patterns of Gene Ontology (GO) terms associated with response to stimulus, cell death, phosphorus metabolism, localization, and regulation of biological processes significantly enriched with altered genes in the nonsmoking exposed group. Most of the identified genes had opposite expression changes between the exposure and postexposure periods in nonsmoking welders. In addition, we found dose-dependent patterns that were affected by smoking status. In conclusion, short-term occupational exposure to metal particulates causes systemic responses in the peripheral blood. Furthermore, the acute particulate-induced effects on gene expression profiling were transient in nonsmoking welders, with most effects diminishing within 19 h following exposure.

Toxicogenomics: transcription profiling for toxicology assessment

Toxicogenomics, the application of transcription profiling to toxicology, has been widely used for elucidating the molecular and cellular actions of chemicals and other environmental stressors on biological systems, predicting toxicity before any functional damages, and classification of known or new toxicants based on signatures of gene expression. The success of a toxicogenomics study depends upon close collaboration among experts in different fields, including a toxicologist or biologist, a bioinformatician, statistician, physician and, sometimes, mathematician. This review is focused on toxicogenomics studies, including transcription profiling technology, experimental design, significant gene extraction, toxicological results interpretation, potential pathway identification, database input and the applications of toxicogenomics in various fields of toxicological study.

10th Anniversary Perspective: Reflections on endocrine disruption in the aquatic environment: from known knowns to unknown unknowns (and many things in between)

Endocrine disruption in the aquatic environment has been a much-researched topic worldwide for the last fifteen years. We have not attempted to write a traditional review of the topic with this paper. Instead, based on unpublished reports and our own personal memories, we provide a history of the development of endocrine disruption research in the last 30 years, since the initial, accidental discovery of intersex fish in an English river in 1978. We focus on how the key questions were tackled, and the often surprising answers to some of these questions. We cover what we now know, and what we still do not know. Based on our current understanding, we emphasize the crucial role played by interdisciplinary research in moving the issue forward. The paper concludes with a selection of general messages about chemicals in the environment which have emerged from endocrine disruption research, and how these have changed our understanding of chemicals in the environment. If lessons have been learnt, and are acted upon when the next chemical 'scare' emerges (as it inevitably will), then it should be possible to act more efficiently and effectively to better protect the environment than was achieved during the "oestrogens in the environment" era.

Derivation of a bisphenol A oral reference dose (RfD) and drinking-water equivalent concentration

Human exposure to bisphenol A (BPA) is due to that found in the diet, and BPA and its metabolites were detected at parts per billion (or less) concentrations in human urine, milk, saliva, serum, plasma, ovarian follicular fluid, and amniotic fluid. Adverse health effects in mice and rats may be induced after parenteral injection or after massive oral doses. Controlled ingestion trials in healthy adult volunteers with 5 mg d16-BPA were unable to detect parent BPA in plasma despite exquisitely sensitive (limit of detection = 6 nM) methods, but by 96 h 100% of the administered dose was recovered in urine as the glucuronide. The extensive BPA glucuronidation following ingestion is not seen after parenteral injection; only the parent BPA binds plasma proteins and estrogen receptors (ER). The hypothesis that BPA dose-response may be described by a J- or U-shape curve was not supported by toxicogenomic data collected in fetal rat testes and epididymes (after repeated parenteral exposure at 2-400,000 microg/kg-d), where a clear monotonic dose-response both in the numbers of genes and magnitude of individual gene expression was evident. There is no clear indication from available data that the BPA doses normally consumed by humans pose an increased risk for immunologic or neurologic disease. There is no evidence that BPA poses a genotoxic or carcinogenic risk and clinical evaluations of 205 men and women with high-performance liquid chromatography (HPLC)-verified serum or urinary BPA conjugates showed (1) no objective signs, (2) no changes in reproductive hormones or clinical chemistry parameters, and (3) no alterations in the number of children or sons:daughters ratio. Results of benchmark dose (BMD10 and BMDL10) calculations and no-observed-adverse-effect level (NOAEL) inspections of all available and reproducible rodent studies with oral BPA found BMD and NOAEL values all greater than the 5 mg/kg-d NOAELs from mouse and rat multigeneration reproduction toxicity studies. While allometric and physiologically based pharmacokinetic (PBPK) models were constructed for interspecies scaling of BPA and its interaction with ER, multigeneration feeding studies with BPA at doses spanning 5 orders of magnitude failed to identify signs of developmental toxicity or adverse changes in reproductive tract tissues; the 5-mg/kg-d NOAELs identified for systemic toxicity in rats and mice were less than the oral NOAELs for reproductive toxicity. Thus, it is the generalized systemic toxicity of ingested BPA rather than reproductive, immunologic, neurobehavioral, or genotoxic hazard that represents the point of departure. Using U.S. Environmental Protection Agency (EPA) uncertainty factor guidance and application of a threefold database uncertainty factor (to account for the fact that the carcinogenic potential of transplacental BPA exposure has yet to be fully defined and comprehensive neurobehavioral and immunotoxicologic evaluations of BPA by relevant routes and at relevant doses have yet to be completed) to the administered dose NOAEL results in an oral RfD of 0.016 mg/kg-d. Assuming the 70-kg adult consumes 2 L of water each day and adopting the default 20% U.S. EPA drinking water relative source contribution yields a 100 microg/L BPA total allowable concentration (TAC).

Effects of p,p'-DDE exposure on gonadal development and gene expression in Japanese medaka (Oryzias latipes)

Although 1,1-dichloro-2,2-bis(p-chlorophenyl)-ethylene (p,p'-DDE), the major and most persistent metabolite of dichlorodiphenyltrichloroethane (DDT), was continually detected in wild fishes that showed abnormal gonad development such as intersex, little is known about the impact of p,p'-DDE exposure on gonad development in fishes. To survey the effects of p,p'-DDE on gonadal development and gene expressions, male juvenile (20-d post hatch) Japanese medaka (Oryzias latipes) was exposed to 1, 5, 20, and 100 microg/L p,p'-DDE for two months. Increased hepatosomatic index (HSI) and decreased gonadosomatic index (GSI) were found in the p,p'-DDE-treated groups. Intersex was found in 100 microg/L p,p'-DDE exposure group, as well as 100 ng/L 17alpha-ethynylestradiol (EE2) group. By quantitative real-time RT-PCR, it was found that gene expressions of vitellogenins (VTG-1, VTG-2), choriogenins (CHG-H, CHG-L), and estrogen receptor alpha (ER-alpha) in the liver of the fish were significantly up-regulated byp,p'-DDE exposure. VTG-1 and VTG-2 were recommended as the preferred biomarker for assessing anti-androgenic p,p'-DDE because they were the highest up-regulated among the genes and showed good dose-response relationship. The up-regulated ER-alpha suggested that a potential synergetic effect would occur when p,p'-DDE coexists with other ER-alpha-binding endocrine-disrupting chemicals (EDCs).

Genomic profiling in nuclear receptor-mediated toxicity

Nuclear receptors (NRs) are attractive drug targets due to their role in regulation of a wide range of physiologic responses. In addition to providing therapeutic value, many pharmaceutical agents along with environmental chemicals are ligands for NRs and can cause adverse health effects that are directly related to activation of NRs. Identifying the molecular events that produce a toxic response may be confounded by the fact that there is a significant overlap in the biological processes that NRs regulate. Microarrays and other methods for gene expression profiling have served as useful, sensitive tools for discerning the mechanisms by which therapeutics and environmental chemicals invoke toxic effects. The capability to probe thousands of genes simultaneously has made genomics a prime technology for identifying drug targets, biomarkers of exposure/toxicity and key players in the mechanisms of disease. The complex intertwining networks regulated by NRs are hard to probe comprehensively without global approaches and genomics has become a key technology that facilitates our understanding of NR-dependent and -independent events. The future of drug discovery, design and optimization, and risk assessment of chemical toxicants that activate NRs will inevitably involve genomic profiling. This review will focus on genomics studies related to PPAR, CAR, PXR, RXR, LXR, FXR, and AHR.

Effect of bisphenol A on human chorionic gonadotrophin-stimulated gene expression of cultured mouse Leydig tumour cells

Endocrine disrupting chemicals (EDCs) have been reported to affect the reproductive system of various animal species. However, their specific effects and modes of action on gonadal function remain largely unclear. We studied the effects of a model EDC, bisphenol A (BPA), on human chorionic gonadotrophin (hCG)-stimulated global gene expression of cultured mouse Leydig tumour cells (mLTC-1). The time and dose of BPA exposure were set after semiquantitative (sq) RT-PCR analysis of response of candidate genes (StAR, Cyp 17 a1 and AR) to 3h at 10 microg/l hCG +/- 10(-5)M BPA. Affymetrix microarray analysis demonstrated > or =1.5-fold up-regulation of 8- and < or =1.5-fold down-regulated of 16 genes by BPA. Several of these genes were related to steroid/cholesterol metabolism/transport and cell cycle regulation. sqRT-PCR demonstrated induction of StAR expression by hCG stimulation and no effect of BPA. In conclusion, our results indicate that BPA has only subtle modulating effects on gene expression of gonadotrophin-stimulated mLTC-1 cells.

Uterine Temporal Response to Acute Exposure to 17α-Ethinyl Estradiol in the Immature Rat

The rat uterus responds to acute estrogen treatment with a series of well-characterized physiological responses; however, the gene expression changes required to elicit these responses have not been fully characterized. In order to understand early events induced by estrogen exposure in vivo, we evaluated the temporal gene expression in the uterus of the immature rat after a single dose of 17 alpha-ethinyl estradiol (EE) by microarray analysis, evaluating the expression of 15,923 genes. Immature 20-day-old rats were exposed to a single dose of EE (10 microg/kg), and the effects on uterine histology, weight, and gene expression were determined after 1, 2, 8, 24, 48, 72, and 96 h. EE induced changes in the expression of 3867 genes, at least at one time point (p < or = 0.0001), and at least 1.5-fold (up- or downregulated). Specifically, the expression of 8, 116, 3030, 2076, 381, 445, and 125 genes was modified at 1, 2, 8, 24, 48, 72, or 96 h after exposure to EE, respectively (p < or = 0.0001, t-test). At the tissue and organ level, a clear uterotrophic response was elicited by EE after only 8 h, reaching a maximum after 24 h and remaining detectable even after 96 h of exposure. The uterine phenotypic changes were induced by sequential changes in the transcriptional status of a large number of genes, in a program that involves multiple molecular pathways. Using the Gene Ontology to better understand the temporal response to estrogen exposure, we determined that the earliest changes were in the expression of genes whose products are involved in transcriptional regulation and signal transduction, followed by genes implicated in protein synthesis, energy utilization, solute transport, cell proliferation and differentiation, tissue remodeling, and immunological responses among other pathways. The compendium of genes here presented represents a comprehensive compilation of estrogen-responsive genes involved in the uterotrophic response.

Analysis of gene expression profiles in the offspring of rats following maternal exposure to xenoestrogens

Many environmental chemicals are known endocrine disruptors (EDs). These have the potential to alter endocrine systems via various mechanisms that include binding to hormone receptors, thereby either mimicking or blocking the hormone actions and causing abnormal gene expression. Here, to elucidate the molecular mechanism(s) underlying the detrimental effects associated with the estrogenicity of these chemicals, we determined whether gene profiles were altered in rats exposed to 4-tert-octyphenol (OP) and diethylstilbestrol (DES) in utero. Pregnant rats were treated with a high dose of OP (600 mg/kg BW per day) or DES (500 microg/kg BW per day) at gestational days (GD) 17, 18 and 19. Both dams and neonates were euthanized at lactation day (LD) 5. The transcript profiles of uterine tissue were compared in treated versus control in both maternal and neonatal sites using cDNA microarray to determine the expression levels of approximately 13,000 genes and expressed sequence tags (ESTs). The expression levels of some known estrogen-responsive genes, i.e., complement component 3, epidermal growth factor receptor or c-fos oncogene and calbindin 3, as well as some other randomly selected genes, including general transcription factor IIa, transcription factor 4 and lymphocyte specific 1, were increased by OP and/or DES treatment in the uteri of both maternal and neonate groups. However, the magnitude of these alterations in gene expression differed markedly between dams and neonates, most likely reflecting the temporal susceptibility of the reproductive tract to estrogenic chemicals. Importantly, the altered gene patterns identified by microarray analysis were confirmed by RT-PCR and real-time RT-PCR. Fifteen primers were designed to amplify specific altered genes. These genes were selected for validation because of their markedly increased expression levels and they were classified on the basis of gene ontology. Overall, a high correlation was observed between microarray and real-time PCR data. Taken together, these results indicate that placental exposure to OP or DES may cause temporal changes in gene expression in the uteri of dams and neonates. Moreover, these findings may provide useful indicators of the adverse effects of EDs and prove particularly important in elucidating the effects of xenoestrogens on estrogen-responsive tissues, such as the developing reproductive tract.

Application of a yeast estrogen screen in non-biomarker species Varicorhinus barbatulus fish with two estrogen receptor subtypes to assess xenoestrogens

Xenoestrogens can interfere with normal estrogen signaling by competitively binding to the estrogen receptor (ER) and activating transcription of target genes. In this study, we cloned the estrogen receptor alpha (vbERalpha) and beta 2 (vbERbeta2) genes from liver of the indigenous Taiwanese cyprinid fish Varicorhinus barbatulus and tested the direct impact of several xenoestrogens on these ERs. Transcriptional activity of xenoestrogens was measured by the enzymatic activity of estrogen responsive element (ERE)-containing beta-galactosidase in a yeast reporter system. The xenoestrogens tested were phenol derivatives, DDT-related substances, phthalic acid esters, and polychlorinated biphenyls, with 17beta-estradiol (E2) as a subjective standard. The phenol derivatives [4-nonylphenol (4-NP), 4-t-octylphenol (4-t-OP) and bisphenol A (BPA)] exhibited significant dose-dependent responses in both ligand potency and ligand efficiency. Consistent with yeast assays using human or rainbow trout ERs, we observed a general subtype preference in that vbERalpha displayed higher relative potencies and efficiencies than vbERbeta2, although our assays induced a stronger response for xenoestrogens than did human or trout ERs. Whereas 4-NP and 4-t-OP have similar EC50 values relative to E2 for both ER subtypes, the strong estrogenic response of BPA markedly differentiates vbERalpha from vbERbeta2, suggesting possible species-specific BPA sensitivity. We report that the ameliorative yeast tool is readily applicable for indigenous wildlife studies of the bio-toxic influence of xenoestrogens with wildlife-specific estrogen receptors.

Development and validation of endogenous reference genes for expression profiling of medaka (Oryzias latipes) exposed to endocrine disrupting chemicals by quantitative real-time RT-PCR

The quantitative real-time reverse transcription polymerase chain reaction (Q-RT-PCR) technique has been increasingly used in endocrine disrupting chemicals (EDCs) research. Usually, an appropriate endogenous control gene is critical for Q-RT-PCR to normalize the errors and sample-to-sample variations that occur in the course of tissue collection, RNA isolation, and RT-PCR. In this study, we cloned ribosomal protein L7 (RPL-7) from medaka (Oryzias latipes), and then used Q-RT-PCR to study its transcription characteristics and those of glyceraldehyde-3-phosphate dehydrogenase, beta-actin, mitochondrial 16S ribosomal RNA (16S rRNA), and 18S rRNA. Of the five genes, RPL-7 and 18S rRNA were expressed with the less variance among the same tissue samples, in different tissues, and stages of development and were unaffected by EDCs exposure. The expression levels of RPL-7 among different tissues were between 9.76 x 10(6) +/- 9.49 x 10(5) and 1.39 x 10(7) +/- 1.69 x 10(6) copies/microg RNA but those of 18S rRNA were as high as 4.48 x 10(11) +/- 5.95 x 10(10) to 5.90 x 10(11) +/- 1.21 x 10(10) copies/microg RNA, which is above the usual detection scope of Q-RT-PCR if no complementary DNA reaction dilution is performed. As a result, RPL-7 is the single suitable endogenous control gene for expression profiling in future studies, especially in studies on the EDCs issue using medaka.

Genome-wide approaches for identification of nuclear receptor target genes

Large-scale genomics analyses have grown by leaps and bounds with the rapid advances in high throughput DNA sequencing and synthesis techniques. Nuclear receptor signaling is ideally suited to genomics studies because receptors function as ligand-regulated gene switches. This review will survey the strengths and limitations of three major classes of high throughput techniques widely used in the nuclear receptor field to characterize ligand-dependent gene regulation: expression profiling studies (microarrays, SAGE and related techniques), chromatin immunoprecipitation followed by microarray (ChIP-on-chip), and genome-wide in silico hormone response element screens. We will discuss each technique, and how each has contributed to our understanding of nuclear receptor signaling.

A System-Based Approach to Interpret Dose- and Time-Dependent Microarray Data: Quantitative Integration of Gene Ontology Analysis for Risk Assessment

Although microarray technology has emerged as a powerful tool to explore expression levels of thousands of genes or even complete genomes after exposure to toxicants, the functional interpretation of microarray data sets still represents a time-consuming and challenging task. Gene ontology (GO) and pathway mapping have both been shown to be powerful approaches to generate a global view of biological processes and cellular components impacted by toxicants. However, current methods only allow for comparisons across two experimental settings at one particular time point. In addition, the resulting annotations are presented in extensive gene lists with minimal or limited quantitative information, data that are crucial in the application of toxicogenomic data for risk assessment. To facilitate quantitative interpretation of dose- or time-dependent genomic data, we propose to use combined average raw gene expression values (e.g., intensity or ratio) of genes associated with specific functional categories derived from the GO database. We developed an extended program (GO-Quant) to extract quantitative gene expression values and to calculate the average intensity or ratio for those significantly altered by functional gene category based on MAPPFinder results. To demonstrate its application, we applied this approach to a previously published dose- and time-dependent toxicogenomic data set (J. F. Dillman et al., 2005, Chem. Res. Toxicol. 18, 28-34). Our results indicate that the above systems approach can describe quantitatively the degree to which functional gene systems change across dose or time. Additionally, this approach provides a robust measurement to illustrate results compared to single-gene assessments and enables the user to calculate the corresponding ED(50) for each specific functional GO term, important for risk assessment.