Hepatic gene expression profiling using Genechips in zebrafish exposed to 17alpha-ethynylestradiol

Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver

How a living organism maintains its healthy equilibrium in response to endless exposure of potentially harmful chemicals is an important question in current biology. By transcriptomic analysis of zebrafish livers treated by various chemicals, we defined hubs as molecular pathways that are frequently perturbed by chemicals and have high degree of functional connectivity to other pathways. Our network analysis revealed that these hubs were organized into two groups showing inverted functionality with each other. Intriguingly, the inverted activity profiles in these two groups of hubs were observed to associate only with toxicopathological states but not with physiological changes. Furthermore, these inverted profiles were also present in rat, mouse, and human under certain toxicopathological conditions. Thus, toxicopathological-associated anti-correlated profiles in hubs not only indicate their potential use in diagnosis but also development of systems-based therapeutics to modulate gene expression by chemical approach in order to rewire the deregulated activities of hubs back to normal physiology.

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.

Global gene expression profile induced by the UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) in zebrafish (Danio rerio)

Residues of the UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) are ubiquitously found in aquatic biota but potential adverse effects in fish are fairly unknown. To identify molecular effects and modes of action of EHMC we applied a gene expression profiling in zebrafish using whole genome microarrays. Transcriptome analysis and validation of targeted genes were performed after 14 days of exposure of male zebrafish. Concentrations of 2.2 μg/L and 890 μg/L EHMC lead to alteration of 1096 and 1137 transcripts, respectively, belonging to many pathways. Genes involved in lipid metabolism and estrogenic pathway (vtg1), lipid biosynthesis (ptgds), vitamin A metabolic process (rbp2a), DNA damage and apoptosis (gadd45b), and regulation of cell growth (igfbp1a) were investigated by qRT-PCR analysis in whole body, liver, brain and testis. The analysis showed tissue-specific gene profiles and revealed that EHMC slightly affects the transcription of genes involved in hormonal pathways including vtg1, esr1, esr2b, ar, cyp19b and hsd17β3.

A computational model of the hypothalamic: pituitary: gonadal axis in female fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol and 17β-trenbolone

Background

Endocrine disrupting chemicals (e.g., estrogens, androgens and their mimics) are known to affect reproduction in fish. 17α-ethynylestradiol is a synthetic estrogen used in birth control pills. 17β-trenbolone is a relatively stable metabolite of trenbolone acetate, a synthetic androgen used as a growth promoter in livestock. Both 17α-ethynylestradiol and 17β-trenbolone have been found in the aquatic environment and affect fish reproduction. In this study, we developed a physiologically-based computational model for female fathead minnows (FHM, Pimephales promelas), a small fish species used in ecotoxicology, to simulate how estrogens (i.e., 17α-ethynylestradiol) or androgens (i.e., 17β-trenbolone) affect reproductive endpoints such as plasma concentrations of steroid hormones (e.g., 17β-estradiol and testosterone) and vitellogenin (a precursor to egg yolk proteins).

Results

Using Markov Chain Monte Carlo simulations, the model was calibrated with data from unexposed, 17α-ethynylestradiol-exposed, and 17β-trenbolone-exposed FHMs. Four Markov chains were simulated, and the chains for each calibrated model parameter (26 in total) converged within 20,000 iterations. With the converged parameter values, we evaluated the model's predictive ability by simulating a variety of independent experimental data. The model predictions agreed with the experimental data well.

Conclusions

The physiologically-based computational model represents the hypothalamic-pituitary-gonadal axis in adult female FHM robustly. The model is useful to estimate how estrogens (e.g., 17α-ethynylestradiol) or androgens (e.g., 17β-trenbolone) affect plasma concentrations of 17β-estradiol, testosterone and vitellogenin, which are important determinants of fecundity in fish.

Effects of the UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) on expression of genes involved in hormonal pathways in fathead minnows (Pimephales promelas) and link to vitellogenin induction and histology

UV-filters are increasingly used in cosmetics and in the protection of materials against UV-irradiation, and ultimately they reach aquatic systems. The lipophilic UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) belongs to one of the most frequently used UV-filters and accumulates in aquatic animals. Despite its ubiquitous presence in water and biota, very little is known about its potential hormonal effects on aquatic organisms. In our study, we evaluated the effects of measured water concentration of 5.4, 37.5, 244.5 and 394 μg/L EHMC on the expression of genes involved in hormonal pathways in the liver, testis and brain of male and female fathead minnows (Pimephales promelas). We compare the transcription profile with the plasma vitellogenin (VTG) content, secondary sex characteristics, and gonad histology. Transcripts of the androgen receptor (ar) were significantly down-regulated in the liver of females at 37.5, 244.5 μg/L and 394 μg/L EHMC. Additionally, the 3β-hydroxysteroid dehydrogenase (3β-HSD) transcript was significantly decreased in the liver of males at 37.5, 244.5 and 394 μg/L EHMC, and at 244.5 and 394 μg/L EHMC in females. The expressional changes were tissue-specific in most cases, being most significant in the liver. Vitellogenin plasma concentration was significantly increased at 244.5 μg/L EHMC in males. EHMC induced significant histological changes in testes and ovaries at 394 μg/L. Testes displayed a decrease in spermatocytes, and ovaries a decrease in previtellogenic oocytes. The induction of VTG plasma concentration and the histological changes in gonads suggest an estrogenic and/or antiandrogenic activity of EHMC. On the other hand, the gene expression profile shows an antiestrogenic (e.g.: down-regulation of esr1) activity of EHMC. In conclusion, our data demonstrate that EHMC displays low but multiple hormonal activities in fish.

Relationships between the transcriptome and physiological indicators of reproduction in female rainbow trout over an annual cycle

Normal transcriptomic patterns along the brain-pituitary-gonad-liver (BPGL) axis should be better characterized if endocrine-disrupting compound-induced changes in gene expression are to be understood. Female rainbow trout were studied over a complete year-long reproductive cycle. Tissue samples from pituitary, ovary, and liver were collected for microarray analysis using the 16K Genomic Research on Atlantic Salmon Project (GRASP) microarray and for quantitative polymerase chain reaction measures of estrogen receptor (ER) isoform messenger RNA (mRNA) levels. Plasma was collected to determine levels of circulating estradiol-17β (E2), follicle-stimulating hormone (FSH), and luteinizing hormone (LH). As an a priori hypothesis, changes in gene expression were correlated to either circulating levels of E2, FSH, and LH, or ER mRNAs quantified by quantitative polymerase chain reaction. In the liver, most transcriptomic patterns correlated to levels of either E2, LH, or ERs. Fewer ovarian transcripts could be correlated to levels of E2, ERα, or FSH. No significant associations were obvious in the pituitary. As a post hoc hypothesis, changes in transcript abundance were compared with microarray features with known roles in gonadal maturation. Many altered transcripts in the ovary correlated to transcript levels of estradiol 17-beta-dehydrogenase 8 or 17 B HSD12, or to glycoprotein alpha chain 1 or 2. In the pituitary, genes involved with the growth axis (e.g., growth hormone, insulin-related growth factor binding protein) correlated with the most transcripts. These results suggest that transcriptional networks along the BPGL axis may be regulated by factors other than circulating steroid hormones.

Differential response of multiple zebrafish hepatic F-box protein genes to 17alpha-ethinylestradiol treatment

Estrogens are accumulating in environment and their effects on a variety of reproductive processes and tumorigenesis were reported by previous study, but the mechanism of estrogen promoting neoplasia was still not clear. F-box protein (FBP) is the component of E3 ubiquitin ligase which takes part in a variety of key biological processes. In this study, using mature male zebrafish, which are more sensitive to estrogen treatment, we examined influence of 17alpha-ethinylestradiol (EE2) exposure on the expression of a series of hepatic FBP genes, which take part in a variety of biological processes, including tumorigenesis. The influence of EE2 on the expression of hepatic mRNA concentrations of FBP genes were quantified based on the expression of the optimal internal control gene in male zebrafish after 7-day exposure to EE2, from a low-dose concentration (1 ng/L) to environmentally relevant concentrations (10, 100 ng/L). Our results showed that EE2 exposure reduced the expression of fbxl14a, fbxl14b, fbxo25 and beta-TRCP2b, but enchanced the expression of skp2. While the alterations in fbxl2, fbxw7, fbxo9, beta-TRCP2a, fbxl18 and fbxo45 mRNA levels were not observed after EE2 exposure. Thus, our results showed that the expression of hepatic FBP genes exhibited differentially in male zebrafish exposed EE2. The changes of the expression level of FBP genes induced by EE2 may be an important clue to elucidate the correlations of estrogen and hepatic tumors.

Environmentally relevant exposure to 17alpha-ethinylestradiol affects the telencephalic proteome of male fathead minnows

Estrogens are key mediators of neuronal processes in vertebrates. As such, xenoestrogens present in the environment have the potential to alter normal central nervous system (CNS) function. The objectives of the present study were (1) to identify proteins with altered abundance in the male fathead minnow telencephalon as a result of low-level exposure to 17alpha-ethinylestradiol (EE(2)), and (2) to better understand the underlying mechanisms of 17beta-estradiol (E(2)) feedback in this important neuroendocrine tissue. Male fathead minnows exposed to a measured concentration of 5.4 ng EE(2)/L for 48 h showed decreased plasma E(2) levels of approximately 2-fold. Of 77 proteins that were quantified statistically, 14 proteins were down-regulated after EE(2) exposure, including four histone proteins, ATP synthase, H+ transporting subunits, and metabolic proteins (lactate dehydrogenase B4, malate dehydrogenase 1b). Twelve proteins were significantly induced by EE(2) including microtubule-associated protein tau (Mapt), astrocytic phosphoprotein, ependymin precursor, and calmodulin. Mapt showed an increase in protein abundance but a decrease in mRNA expression after EE(2) exposure(,) suggesting there may be a negative feedback response in the telencephalon to decreased mRNA transcription with increasing Mapt protein abundance. These results demonstrate that a low, environmentally relevant exposure to EE(2) can rapidly alter the abundance of proteins involved in cell differentiation and proliferation, neuron network morphology, and long-term synaptic potentiation. Together, these findings provide a better understanding of the molecular responses underlying E(2) feedback in the brain and demonstrate that quantitative proteomics can be successfully used in ecotoxicology to characterize affected cellular pathways and endocrine physiology.

An integrated transcriptomic and proteomic approach characterizing estrogenic and metabolic effects of 17 alpha-ethinylestradiol in zebrafish (Danio rerio)

Nowadays there is much concern about the presence of endocrine disrupting compounds (EDCs) in the environment due to their ability to interfere with the endocrine system. In the presented study, adult zebrafish (Danio rerio) were exposed to 30 ng L(-1) 17alpha-ethinylestradiol (EE2) for 4 and 28 days. The underlying molecular mechanisms of EE2 were studied in the zebrafish liver by applying a combined transcriptomics and proteomics approach. In addition, we assessed the added value of such an integrated-omics approach. Oligo microarrays, spotted with 3479 zebrafish-specific oligos, were employed to generate differential gene expression levels. The proteomic responses were evaluated by means of differential in-gel electrophoresis (DiGE), combined with MALDI-tandem mass spectrometry. Assessment of the major biological functions of the differentially expressed transcripts and proteins illustrated that both individual platforms could profile a clear estrogenic interference, next to numerous metabolism-related effects and stress responses. Cross-comparison of both transcriptomics and proteomics datasets displayed limited concordance, though, thorough revision of the results illustrated that transcriptional effects were projected on protein level as downstream effects of affected signalling pathways. Overall, this study demonstrated that a proteomics approach can lift the biological interpretation of microarrays to a higher level, and moreover, opens a window for identification of possible new biomarkers.

Disruption of the steroid metabolome in fish caused by exposure to the environmental estrogen 17alpha-ethinylestradiol

Exposure to environmental estrogens such as 17alpha-ethinylestradiol (EE2) has been associated with feminization and a decline in fertility of male fish. To investigate the effect of estrogen exposure on steroid homeostasis, we exposed roach (Rutilus rutilus) to EE2 (1-29 ng/L) for 18 days and analyzed steroid profiles in bile and plasma using targeted analyses and in liver and gonadal tissues using mass spectrometry metabolite profiling techniques (metabolomics). Exposure to EE2 resulted in a concentration dependent reduction of estrogens and androgens in bile and plasma of both male and female fish. At 10 ngEE2/L, significant reductions in concentrations of hydroxyprogesterone, androstenedione, 11-hydroxyandrostenedione, and 11-ketotestosterone were detected in the testes metabolome, indicating disruption of steroid biosynthesis upstream of androgen metabolism. Estrogen exposure also resulted in increased biosynthesis of cortisol and cortisone in testes and ovaries, respectively, but did not alter glucocorticoid concentrations in the liver or plasma. This first report on the effect of EE2 exposure on the steroid metabolome in fish tissues suggests that both sex steroid and glucocorticoid pathways are one of the primary targets of estrogen exposure in fish gonads and provides further insights into the mode of action of this endocrine disrupting chemical.

Measuring multiple hormones from a single water sample using enzyme immunoassays

Many aquatic species, such as teleosts, release into the water and detect multiple bioactive substances to assist in schooling, migration, alarm reactions, and to stimulate behavioral and physiological responses during reproduction and in parent-offspring interactions. Understanding the complex relationship between hormones, behavior and their function in communication requires the simultaneous examination of multiple circulating hormones. However, repeated blood sampling within a short time period is not possible in smaller animals without impacting the very behaviors under investigation. The non-invasive technique of collecting and measuring hormone values in holding water using either radioimmunoassay (RIA) or enzyme immunoassay (EIA) is becoming widely used in teleost research. Commercial assay kits in particular enable rapid and reliable data generation, yet their assay buffers are often specific and potentially incompatible with each other, which can hinder measuring multiple hormones from the same sample. We present here the validation and application of a "nested" elution technique we developed that allows for repeated sampling of multiple reproductive hormones - testosterone (T), 17beta-estradiol (E2), progesterone (P), prostaglandin F(2 alpha) (PGF) and 11-ketotestosterone (11KT) - from individual samples of animal holding water by using commercial EIA systems. Our results show that when using appropriate controls to account for possible technical and biological confounds, this technique provides a powerful new tool for research in aquatic endocrinology and physiology.

The methods of identification, analysis, and removal of endocrine disrupting compounds (EDCs) in water

The information regarding endocrine disrupting compounds (EDCs) was reviewed, including the definition and characteristics, the recent research trends concerning identification and analytical methods, and the applicable removal processes. EDCs include various types of natural and synthetic chemical compounds presenting the mimicking or inhibition of the reproductive action of the endocrine system in animals and humans. The ubiquitous presence with trace level concentrations and the wide diversity are the reported characteristics of EDCs. Biologically based assays seem to be a promising method for the identification of EDCs. On the other hand, mass-based analytical methods show excellent sensitivity and precision for their quantification. Several extraction techniques for the instrumental analysis have been developed since they are crucial in determining overall analytical performances. Conventional treatment techniques, including coagulation, precipitation, and activated sludge processes, may not be highly effective in removing EDCs, while the advanced treatment options, such as granular activated carbon (GAC), membrane, and advanced oxidation processes (AOPs), have shown satisfactory results. The oxidative degradation of some EDCs was associated with aromatic moieties in their structure. Further studies on EDCs need to be conducted, such as source reduction, limiting exposure to vulnerable populations, treatment or remediation of contaminated sites, and the detailed understanding of transport mechanisms in the environment.

Towards functional genomics in fish using quantitative proteomics

Microarray and gene expression analysis have been key in our understanding of molecular pathways underlying physiological responses. Arguably, a large number of microarray based studies in fish have examined steroid nuclear receptor signaling (e.g., estrogens, androgens) in the context of both physiology and toxicology. Following close behind the advances in gene expression analysis, novel proteomic tools are available that have been under utilized in fish endocrinology studies. Quantitative proteomic approaches include both gel based (e.g., 2D gel electrophoresis, 2-D Fluorescence Difference Gel Electrophoresis; DIGE) and non-gel based methods that can be separated further into labeling approaches such as stable isotope labeling (SILAC), isotope coded affinity tags (ICAT), and isobaric tagging (iTRAQ) and label-free approaches (e.g., spectral counting and absolute quantitation). This review summarizes quantitative proteomic approaches and describes a successful application of iTRAQ) to study changes in the liver proteome in fathead minnows in response to the androgen, 17beta-trenbolone. The challenge remains to integrate molecular datasets in such a manner as to be able to consider temporal effects and complex regulation at the level of the genome and proteome.

Stimulation of growth and changes in the hepatic transcriptome by 17β-estradiol in the yellow perch (Perca flavescens)

The effects of dietary 17β-estradiol (E2) on growth and liver transcriptomics were investigated in the yellow perch ( Perca flavescens). After a 3-mo treatment, E2 significantly stimulated an increase in length and weight of juvenile male and female perch relative to control animals. The increase was significantly greater in females compared with males. Separate, unnormalized cDNA libraries were constructed from equal quantities of RNA from 6 male and 6 female livers of E2-treated and control perch, and 3,546 and 3,719 expressed sequence tags (ESTs) were obtained, respectively. To characterize E2-regulated transcripts, EST frequencies between libraries were calculated within contiguous sequences that were assembled from the combined ESTs of both libraries. Frequencies were also determined in EST transcript groupings produced by aligning all of the ESTs from both libraries at the nucleotide level. From these analyses, there were 28 annotated transcripts that were regulated by 75% between libraries and for which there were at least 5 ESTs of the same transcript between libraries. Regulation of a subset ( 14 ) of these transcripts was confirmed by quantitative reverse transcription-polymerase chain reaction (QPCR). Transcripts that were upregulated by E2 included reproduction-related proteins, binding proteins, and proteases and protease inhibitors. While not part of the transcript frequency analysis, QPCR showed significant upregulation of estrogen receptor esr1 and of insulin-like growth factor I (IGF-I) in E2 livers. E2-downregulated transcripts represented a variety of functional categories including components of the respiratory chain, lipid transport and metabolism, glycolysis, amino acid and nitrogen metabolism, binding proteins, a hydrolytic enzyme, and a transcriptional regulator. In perch it appears that exogenous estrogen drastically shifts liver metabolism toward the production of lipoproteins and carbohydrate binding proteins, and that the growth-promoting action may involve an increase in hepatic IGF-I production.

Changes in the relative expression pattern of multiple vitellogenin genes in adult male and larval zebrafish exposed to exogenous estrogens

Production of the lipoprotein vitellogenin (Vg) is induced in fish upon exposure to estrogens and is a biomarker of endocrine disruption in fish. In some fish, three types of Vg (VgA, VgB, and VgC) are recognized and transcribed from at least three distinct Vg genes (vtg). We investigated expression of vtg coding for Vg1A/B, Vg2A/B, and VgC in adult male and larval zebrafish exposed to various estrogenic substances. Quantitative PCR was conducted for transcripts of each vtg and a control gene (beta-actin). Male fish were exposed to 17beta-estradiol (E2) and 17alpha-ethinylestradiol, total RNA was extracted from excised liver, and histopathology of liver, trunk kidney, and gonads was conducted. Larval fish were exposed to 10 different estrogenic substances and total RNA was extracted from groups of whole larvae. In adult male fish, the relative fold change varied, but pattern of expression change (i.e., Vg1A/B > Vg2A/B > VgC) was consistent. Larger males exposed to E2 had significantly higher induction of each vtg. In larval zebrafish, the relative fold change in vtg expression varied according to specific estrogenic substance tested, but the pattern of change (i.e., Vg2A/B > Vg1A/B > VgC) was consistent for each substance that induced vtg.

Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling

Background

In oviparous vertebrates, including fish, vitellogenesis consists of highly regulated pathways involving 17β-estradiol (E2). Previous studies focused on a relatively small number of hepatic expressed genes during vitellogenesis. This study aims to identify hepatic genes involved in vitellogenesis and regulated by E2, by using zebrafish microarray gene expression profiling, and to provide information on functional distinctive genes expressed in the liver of a vitellogenic female, using zebrafish as a model fish.

Results

Genes associated with vitellogenesis were revealed by the following paired t-tests (SAM) comparisons: a) two-month old vitellogenic (Vit2) females were compared with non-vitellogenic (NV) females, showing 825 differentially expressed transcripts during early stages of vitellogenesis, b) four-month old vitellogenic (Vit4) females were compared with NV females, showing 1,046 differentially expressed transcripts during vitellogenesis and c) E2-treated males were compared with control males, showing 1,828 differentially expressed transcripts regulated by E2. A Venn diagram revealed 822 common transcripts in the three groups, indicating that these transcripts were involved in vitellogenesis and putatively regulated by E2. In addition, 431 transcripts were differentially expressed in Vit2 and Vit4 females but not in E2-treated males, indicating that they were putatively not up-regulated by E2. Correspondence analysis showed high similarity in expression profiles of Vit2 with Vit4 and of NV females with control males. The E2-treated males differed from the other groups. The repertoire of genes putatively regulated by E2 in vitellogenic females included genes associated with protein synthesis and reproduction. Genes associated with the immune system processes and biological adhesion, were among the genes that were putatively not regulated by E2. E2-treated males expressed a large array of transcripts that were not associated with vitellogenesis.

The study revealed several genes that were not reported before as being regulated by E2. Also, the hepatic expression of several genes was reported here for the first time.

Conclusion

Gene expression profiling of liver samples revealed 1,046 differentially expressed transcripts during vitellogenesis of which at least ~64% were regulated by E2. The results raise the question on the regulation pattern and temporal pleiotropic expression of hepatic genes in vitellogenic females.

Zebrafish (Danio rerio) as a model organism for investigating endocrine disruption

Endocrine-disrupting compounds (EDCs) are widespread in the aquatic environment and can cause alterations in development, physiological homeostasis and health of vertebrates. Zebrafish, Danio rerio, has been suggested as a model species to identify targets as well as modes of EDC action. In fact, zebrafish has been found useful in EDC screening, in EDC effects assessment and in studying targets and mechanisms of EDC action. Since many of the environmental EDCs interfere with the sex steroid system of vertebrates, most EDC studies with zebrafish addressed disruption of sexual differentiation and reproduction. However, other targets of EDCs action must not be overlooked. For using a species as a toxicological model, a good knowledge of the biological traits of this species is a pre-requisite for the rational design of test protocols and endpoints as well as for the interpretation and extrapolation of the toxicological findings. Due to the genomic resources available for zebrafish and the long experience with zebrafish in toxicity testing, it is easily possible to establish molecular endpoints for EDC effects assessment. Additionally, the zebrafish model offers a number of technical advantages including ease and cost of maintenance, rapid development, high fecundity, optical transparency of embryos supporting phenotypic screening, existence of many mutant strains, or amenability for both forward and reverse genetics. To date, the zebrafish has been mainly used to identify molecular targets of EDC action and to determine effect thresholds, while the potential of this model species to study immediate and delayed physiological consequences of molecular interactions has been instrumentalized only partly. One factor that may limit the exploitation of this potential is the still rather fragmentary knowledge of basic biological and endocrine traits of zebrafish. Information on species-specific features in endocrine processes and biological properties, however, need to be considered in establishing EDC test protocols using zebrafish, in extrapolating findings from zebrafish to other vertebrate species, and in understanding how EDC-induced gene expression changes translate into disease.

Molecular characterization and expression of angiopoietin-like protein 3 in the chicken, Gallus gallus

Angiopoietin-like protein 3 (ANGPTL3) is a 70 kDa secretory glycoprotein, which has been identified as a plasma triacylglycerol (TG)-increasing factor in KK/San mice. In this study, we have characterized the expression profile and activity of ANGPTL3 in the chicken, Gallus gallus. This is the first report of this protein in a pre-mammalian species and reveals novel details about the molecular structure of, and specific features of the expression of, important molecules in lipid metabolism. Recombinant chicken ANGPTL3 inhibited chicken lipoprotein lipase activity in vitro and increased plasma TG concentrations in vivo. Chicken ANGPTL3 mRNA expression was detected only in the liver. ANGPTL3 mRNA expression was significantly higher in mature (i.e. egg producing) chickens than in immature chickens. However, this increase was not associated with estradiol, although estradiol does enhance triacylglycerol and very low density lipoprotein secretion by the chicken liver. Changes in chicken ANGPTL3 mRNA expression with nutritional state were examined. ANGPLT3 expression was affected by certain nutritional treatments, i.e. fasting and re-feeding, and ANGPTL3 gene expression in the livers of chickens fed a cholesterol-supplemented diet was lower than that in the livers of chickens fed a control diet. The present study is the first to molecularly characterize and analyze the gene expression of ANGPTL3, and suggests that in avian species ANGPTL3 plays a key role in lipid delivery to the yolk.

Variation of the genetic expression pattern after exposure to estradiol-17beta and 4-nonylphenol in male zebrafish (Danio rerio)

There is much concern about the increasing presence in the environment of synthetic chemicals that are able to disrupt the endocrine system. Among these compounds, 4-nonylphenol (4-NP) is one of the most studied xenoestrogens, due to its widespread accumulation in water sediment and consequent presence in fatty acid of aquatic organisms. Here, we have used a zebrafish microarray representing 16,399 genes to study the effects of 4-NP and estradiol-17beta (E2) in adult male zebrafish in order to elucidate the mechanism of action of 4-NP compared with that of E2. The microarray results showed that both 4-NP and E2 induced a strong expression of vitellogenin (VTG), the sex related precursor of the yolk proteins in oviparous vertebrates. Both treatments induced elevated protein turnover upregulating genes involved in proteolysis and those that are constituents of the ribosome. Many genes regulated by 4-NP and E2 are involved in energy metabolism, oxidative stress defense mechanisms, xenobiotic metabolism, and lipid metabolism. A different pattern of expression in the two treatments was found for genes involved in oxidative stress, since E2 seems to induce the mechanism of detoxification, while 4-NP seems to inhibit this protective mechanism of the cell. Overall, these findings demonstrate that the microarray approach can contribute significantly to the understanding of expression patterns induced by E2 and 4-NP in male zebrafish. The results also demonstrate that 4-NP is able to act through an alternative pattern to that of estradiol-17beta, modulating the expression of the same genes in a different manner.

Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology

A novel custom microarray for largemouth bass (Micropterus salmoides) was designed with sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. This approach yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17beta-oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology.

Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio)

In this study, we tested for the presence of sexual dimorphism in the hepatic transcriptome of the adult zebrafish and examined the effect of long term manipulation of dietary carbohydrate on gene expression in both sexes. Zebrafish were fed diets comprised of 0%, 15%, 25%, or 35% carbohydrate from the larval stage through sexual maturity, then sampled for hepatic tissue, growth, proximate body composition, and retention efficiencies. Using Affymetrix microarrays and qRT-PCR, we observed substantial sexual dimorphism in the hepatic transcriptome. Males up-regulated genes associated with oxidative metabolism, carbohydrate metabolism, energy production, and amelioration of oxidative stress, while females had higher expression levels of genes associated with translation. Restriction of dietary carbohydrate (0% diet) significantly affected hepatic gene expression, growth performance, retention efficiencies of protein and energy, and percentages of moisture, lipid, and ash. The response of some genes to dietary manipulation varied by sex; with increased dietary carbohydrate, males up-regulated genes associated with oxidative metabolism (e.g. hadhbeta) while females up-regulated genes associated with glucose phosphorylation (e.g. glucokinase). Our data support the use of the zebrafish model for the study of fish nutritional genomics, but highlight the importance of accounting for sexual dimorphism in these studies.

BMDExpress: a software tool for the benchmark dose analyses of genomic data

BACKGROUND

Dose-dependent processes are common within biological systems and include phenotypic changes following exposures to both endogenous and xenobiotic molecules. The use of microarray technology to explore the molecular signals that underlie these dose-dependent processes has become increasingly common; however, the number of software tools for quantitatively analyzing and interpreting dose-response microarray data has been limited.

RESULTS

We have developed BMDExpress, a Java application that combines traditional benchmark dose methods with gene ontology classification in the analysis of dose-response data from microarray experiments. The software application is designed to perform a stepwise analysis beginning with a one-way analysis of variance to identify the subset of genes that demonstrate significant dose-response behavior. The second step of the analysis involves fitting the gene expression data to a selection of standard statistical models (linear, 2 degrees polynomial, 3 degrees polynomial, and power models) and selecting the model that best describes the data with the least amount of complexity. The model is then used to estimate the benchmark dose at which the expression of the gene significantly deviates from that observed in control animals. Finally, the software application summarizes the statistical modeling results by matching each gene to its corresponding gene ontology categories and calculating summary values that characterize the dose-dependent behavior for each biological process and molecular function. As a result, the summary values represent the dose levels at which genes in the corresponding cellular process show transcriptional changes.

CONCLUSION

The application of microarray technology together with the BMDExpress software tool represents a useful combination in characterizing dose-dependent transcriptional changes in biological systems. The software allows users to efficiently analyze large dose-response microarray studies and identify reference doses at which particular cellular processes are altered. The software is freely available at http://sourceforge.net/projects/bmdexpress/ and is distributed under the MIT Public License.

Microarray analysis in the zebrafish (Danio rerio) liver and telencephalon after exposure to low concentration of 17alpha-ethinylestradiol

17alpha-ethinylestradiol (EE2) is detected in sewage effluent at concentrations that can disrupt normal reproductive function in fish. The objectives of this study were to identify novel genomic responses to EE2 exposure using microarray and real-time RT-PCR analysis in the liver and telencephalon of male zebrafish. Zebrafish were exposed to an environmentally relevant nominal concentration of 10ng/L EE2 for a 21-day period. In the liver, common biomarkers for estrogenic exposure such as vitellogenin 1 and 3 (vtg1; vtg3), estrogen receptor alpha (esr1), and apolipoprotein A1 (apoA1) mRNA were identified by microarray analysis as being differentially regulated. Real-time RT-PCR confirmed that vtg1 was induced approximately 700-fold, vtg3 was induced approximately 100-fold and esr1 was induced approximately 20-fold. As determined by microarray analysis, ATPase Na+/K+ alpha 1a.4 (atp1a1a.4) and ATPase Na+/K+ beta 1a (atp1b1a) mRNA were down-regulated in the liver. Gene ontology (GO) analysis revealed that there were common biological processes and molecular functions regulated by EE2 in both tissues (e.g. electron transport and cell communication) but there were tissue specific changes in gene categories. For example, genes involved in protein metabolism, carbohydrate metabolism were down-regulated in the liver but were induced in the telencephalon. This study demonstrates that (1) tissues exhibit different gene responses to low EE2 exposure; (2) there are pronounced genomic effects in the liver and (3) multi-tissue gene profiling is needed to improve understanding of the effects of human pharmaceuticals on aquatic organisms.

Sensitive and robust gene expression changes in fish exposed to estrogen--a microarray approach

Background

Vitellogenin is a well established biomarker for estrogenic exposure in fish. However, effects on gonadal differentiation at concentrations of estrogen not sufficient to give rise to a measurable vitellogenin response suggest that more sensitive biomarkers would be useful. Induction of zona pellucida genes may be more sensitive but their specificities are not as clear. The objective of this study was to find additional sensitive and robust candidate biomarkers of estrogenic exposure.

Results

Hepatic mRNA expression profiles were characterized in juvenile rainbow trout exposed to a measured concentration of 0.87 and 10 ng ethinylestradiol/L using a salmonid cDNA microarray. The higher concentration was used to guide the subsequent identification of generally more subtle responses at the low concentration not sufficient to induce vitellogenin. A meta-analysis was performed with data from the present study and three similar microarray studies using different fish species and platforms. Within the generated list of presumably robust responses, several well-known estrogen-regulated genes were identified. Two genes, confirmed by quantitative RT-PCR (qPCR), fulfilled both the criteria of high sensitivity and robustness; the induction of the genes encoding zona pellucida protein 3 and a nucleoside diphosphate kinase (nm23).

Conclusion

The cross-species, cross-platform meta-analysis correctly identified several robust responses. This adds confidence to our approach used for identifying candidate biomarkers. Specifically, we propose that analyses of an nm23 gene together with zona pellucida genes may increase the possibilities to detect an exposure to low levels of estrogenic compounds in fish.

Effects of 17alpha-ethynylestradiol on EROD activity, spiggin and vitellogenin in three-spined stickleback (Gasterosteus aculeatus)

The three-spined stickleback (Gasterosteus aculeatus) has quantifiable biomarkers of exposure to estrogens (vitellogenin), androgens (spiggin) and aryl hydrocarbon receptor (AhR) agonists (EROD activity) and is therefore a promising test species for biomonitoring of reprotoxic chemicals in aquatic environments. In this study we evaluated the effects of 17alpha-ethynylestradiol (EE(2)) on EROD activity, induction of vitellogenin and spiggin, hepatosomatic index (HSI), ovarian somatic index (OSI) and nephrosomatic index (NSI). Adult male and female three-spined sticklebacks were exposed to concentrations of 0-170 ng EE(2)/l (measured concentrations) in a flow-through system for 21 days. Exposure to 170 ng EE(2)/l resulted in a significant 8- and 9-fold induction of gill EROD activity in males and females, respectively. In livers, EROD activity expressed in relation to microsomal protein content was suppressed due to a significant increase in microsomal protein content. Hepatic EROD activity per se expressed as picomol/min was not affected by exposure to EE(2). The lowest observed effect concentration for induction of vitellogenin in males was 53.7 ng EE(2)/l. In females, vitellogenin levels were significantly higher in those exposed to 170 ng EE(2)/l compared to controls. Spiggin production was significantly inhibited and NSI lower in males exposed to 170 ng EE(2)/l. In both females and males LSI was significantly higher in fish exposed to 170 ng EE(2)/l than in controls. In females exposed to 170 ng EE(2)/l, OSI was significantly lower and NSI higher than controls. The observed results from this study show that a synthetic estrogen can affect the well-known biomarker of exposure for dioxin-like compounds, EROD activity, and further that this response can differ between tissues. These findings are important for interpretation of biomonitoring data.

Appropriate 'housekeeping' genes for use in expression profiling the effects of environmental estrogens in fish

Background

Attempts to develop a mechanistic understanding of the effects of environmental estrogens on fish are increasingly conducted at the level of gene expression. Appropriate application of real-time PCR in such studies requires the use of a stably expressed 'housekeeping' gene as an internal control to normalize for differences in the amount of starting template between samples.

Results

We sought to identify appropriate genes for use as internal controls in experimental treatments with estrogen by analyzing the expression of eight functionally distinct 'housekeeping' genes (18S ribosomal RNA [18S rRNA], ribosomal protein l8 [rpl8], elongation factor 1 alpha [ef1a], glucose-6-phosphate dehydrogenase [g6pd], beta actin [bactin], glyceraldehyde-3-phosphate dehydrogenase [gapdh], hypoxanthine phosphoribosyltransferase 1 [hprt1], and tata box binding protein [tbp]) following exposure to the environmental estrogen, 17α-ethinylestradiol (EE₂), in the fathead minnow (Pimephales promelas). Exposure to 10 ng/L EE₂ for 21 days down-regulated the expression of ef1a, g6pd, bactin and gapdh in the liver, and bactin and gapdh in the gonad. Some of these effects were gender-specific, with bactin in the liver and gapdh in the gonad down-regulated by EE₂ in males only. Furthermore, when ef1a, g6pd, bactin or gapdh were used for normalization, the hepatic expression of two genes of interest, vitellogenin (vtg) and cytochrome P450 1A (cyp1a) following exposure to EE₂ was overestimated.

Conclusion

Based on the data presented, we recommend 18S rRNA, rpl8, hprt1 and/or tbp, but not ef1a, g6pd, bactin and/or gapdh, as likely appropriate internal controls in real-time PCR studies of estrogens effects in fish. Our studies show that pre-validation of control genes considering the scope and nature of the experiments to be performed, including both gender and tissue type, is critical for accurate assessments of the effects of environmental estrogens on gene expression in fish.