Liver tumors in wild flatfish: a histopathological, proteomic, and metabolomic study

Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Applications for Metabolomics

Metabolomics is an interdisciplinary field that aims to study all metabolites < 1500 Da that are ubiquitously found within all organisms. Metabolomics is experiencing exponential growth and commonly relies on high-resolution mass spectrometry (HRMS). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a form of HRMS that is particularly well suited for metabolomics research due to its exceptionally high resolution (105-106) and sensitivity with a mass accuracy in parts per billion (ppb). In this regard, FT-ICR-MS can provide valuable insights into the metabolomics analysis of complex biological systems due to unique capabilities such as the easy separation of isobaric and isomeric species, isotopic fine structure analysis, spatial resolution of metabolites in cells and tissues, and a high confidence (<1 ppm mass error) in metabolite identification. Alternatively, the large and complex data sets, long acquisition times, high cost, and limited access mainly through national mass spectrometry facilities may impede the routine adoption of FT-ICR-MS by metabolomics researchers. This review examines recent applications of FT-ICR-MS metabolomics in the search for clinical and non-human biomarkers; for the analysis of food, beverage, and environmental samples; and for the high-resolution imaging of tissues and other biological samples. We provide recent examples of metabolomics studies that highlight the advantages of FT-ICR-MS for the detailed and reliable characterization of the metabolome. Additionally, we offer some practical considerations for implementing FT-ICR-MS into a research program by providing a list of FT-ICR-MS facilities and by identifying different high-throughput interfaces, varieties of sample types, analysis methods (e.g., van Krevelen diagrams, Kendrick mass defect plot, etc.), and sample preparation and handling protocols used in FT-ICR-MS experiments. Overall, FT-ICR-MS holds great promise as a vital research tool for advancing metabolomics investigations.

The arachidonic acid and its metabolism pathway play important roles for Apostichopus japonicus infected by Vibrio splendens

Improving the immune ability and guiding healthy culture for sea cucumber by purposefully screening the significant differential metabolites when Apostichopus japonicus (A. japonicus) is infected by pathogens is important. In this study, 35 types of significant differential metabolites appeared when A. japonicus were infected by Vibrio splendens (VSI group) compared with the control A. japonicus group (CK group) by using liquid chromatography-mass spectrometry (LC-MS/MS)-based untargeted metabolomics. Based on that finding, the 10 types of key metabolic pathways were analyzed by MetPA. The "arachidonic acid (ARA) metabolism" pathway, which was screened by three elevated biomarkers: ARA, prostaglandin F2α and 2-arachidonoyl glycerol, had an important impact on immune stress in A. japonicus. Due to the similar changes in several metabolites in its metabolic pathway, the ARA metabolic pathway was selected for further study. The activities of ACP, AKP and lysozyme, which are important innate immune-related enzymes, the survival rates of A. japonicus infected with V. splendidus and the relative content of ARA in the body wall detected by GC-MS were all upregulated significantly by exogenous daily 0.60% and 1.09% ARA consumption over a short period of approximately 7 days. These results demonstrated that ARA and its metabolic pathway indeed played important roles in the immunity of A. japonicus infected by the pathogen. The findings also provide novel insights for the effects of metabolites in A. japonicum healthy culture.

Research-Relevant Background Lesions and Conditions in Common Avian and Aquatic Species

Non-mammalian vertebrates including birds, fish, and amphibians have a long history of contributing to ground-breaking scientific discoveries. Because these species offer several experimental advantages over higher vertebrates and share extensive anatomic and genetic homology with their mammalian counterparts, they remain popular animal models in a variety of fields such as developmental biology, physiology, toxicology, drug discovery, immunology, toxicology, and infectious disease. As with all animal models, familiarity with the anatomy, physiology, and spontaneous diseases of these species is necessary for ensuring animal welfare, as well as accurate interpretation and reporting of study findings. Working with avian and aquatic species can be especially challenging in this respect due to their rich diversity and array of unique adaptations. Here, we provide an overview of the research-relevant anatomic features, non-infectious conditions, and infectious diseases that impact research colonies of birds and aquatic animals, including fish and Xenopus species.

The use of Atlantic hagfish (Myxine glutinosa) as a bioindicator species for studies on effects of dumped chemical warfare agents in the Skagerrak. 1: Liver histopathology

Within the framework of the international project DAIMON (Decision Aid for Marine Munitions), the impact of dumped chemical munitions on fish health was investigated. The Skagerrak Straight (North Sea, at 600 m depth) contains munitions with chemical warfare agents (CWA), scuttled after the end of World War II. Studies of liver histopathology in Atlantic hagfish (Myxine glutinosa) were carried out at three sampling sites: at a wreck with CWA in the Skagerrak (n = 82), a Skagerrak reference site considered to be free of CWA (n = 14) and at a reference site in the northern North Sea outside the Skagerrak (n = 17). Liver lesions were diagnosed and categorized according to standardized ICES and BEQUALM protocols and OSPAR guidelines. Non-specific liver lesions were found in 87.6% of 113 hagfish examined. The prevalence of pre-neoplastic lesions was 7.1% and of neoplastic lesions 6.2%. There was no statistically significant difference in prevalence between hagfish samples from the wreck site and from the reference site near the wrecks. However, at the reference site in the northern North Sea, the prevalence of non-specific lesions was low and neither pre-neoplastic nor neoplastic lesions were observed.

Metabolomics in the study of spontaneous animal diseases

Using analytical chemistry techniques such as nuclear magnetic resonance (NMR) spectroscopy and liquid or gas chromatography-mass spectrometry (LC/GC-MS), metabolomics allows detection of most endogenous and exogenous metabolites in a biological sample. Metabolomics has a wide range of applications, and has been employed in nutrition science, toxicology, environmental studies, and systems biology. Metabolomics is particularly useful in biomedical science, and has been used for diagnostic laboratory testing, identifying targets for drug development, and monitoring drug metabolism, mode of action, and toxicity. Despite its immense potential, metabolomics remains underutilized in the study of spontaneous animal diseases. Our aim was to comprehensively review the existing literature on the use of metabolomics in spontaneous veterinary diseases. Three databases were used to find journal articles that applied metabolomics in veterinary medicine. A screening process was then conducted to eliminate references that did not meet the eligibility criteria; only primary research studies investigating spontaneous animal disease were included; 38 studies met the inclusion criteria. The main techniques used were NMR and MS. All studies detected metabolite alterations in diseased animals compared with non-diseased animals. Metabolomics was mainly used to study diseases of the digestive, reproductive, and musculoskeletal systems. Inflammatory conditions made up the largest proportion of studies when articles were categorized by disease process. Following a comprehensive analysis of the literature on metabolomics in spontaneous veterinary diseases, we concluded that metabolomics, although in its early stages in veterinary research, is a promising tool regarding diagnosis, biomarker discovery, and in uncovering new insights into disease pathophysiology.

Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

BACKGROUND

T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses. Understanding of the cold-tolerance mechanisms of this species is still limited. Integrated application of multi-omics research can provide a wealth of information to help us improve our understanding of low-temperature tolerance in fish.

RESULTS

To gain a comprehensive and unbiased molecular understanding of cold-tolerance in T. fasciatus, we characterized mRNA-seq and metabolomics of T. fasciatus livers using Illumina HiSeq 2500 and UHPLC-Q-TOF MS. We identified 2544 up-regulated and 2622 down-regulated genes in the liver of T. fasciatus. A total of 40 differential metabolites were identified, including 9 down-regulated and 31 up-regulated metabolites. In combination with previous studies on proteomics, we have established an mRNA-protein-metabolite interaction network. There are 17 DEMs (differentially-expressed metabolites) and 14 DEGs-DEPs (differentially co-expressed genes and proteins) in the interaction network that are mainly involved in fatty acids metabolism, membrane transport, signal transduction, and DNA damage and defense. We then validated a number of genes in the interaction network by qRT-PCR. Additionally, a number of SNPs (single nucleotide polymorphisms) were revealed through the transcriptome data. These results provide key information for further understanding of the molecular mechanisms of T. fasciatus under cold stress.

CONCLUSION

The data generated by integrated application of multi-omics can facilitate our understanding of the molecular mechanisms of fish response to low temperature stress. We have not only identified potential genes and SNPs involved in cold tolerance, but also show that some nutrient metabolites may be added to the diet to help the overwintering of T. fasciatus.

Biomarker Discovery in Animal Health and Disease: The Application of Post-Genomic Technologies

The causes of many important diseases in animals are complex and multifactorial, which present unique challenges. Biomarkers indicate the presence or extent of a biological process, which is directly linked to the clinical manifestations and outcome of a particular disease. Identifying biomarkers or biomarker profiles will be an important step towards disease characterization and management of disease in animals. The emergence of post-genomic technologies has led to the development of strategies aimed at identifying specific and sensitive biomarkers from the thousands of molecules present in a tissue or biological fluid. This review will summarize the current developments in biomarker discovery and will focus on the role of transcriptomics, proteomics and metabolomics in biomarker discovery for animal health and disease.

Current knowledge of metabolomic approach in infectious fish disease studies

The approaches of transcriptomic and proteomic have been widely used to study host-pathogen interactions in fish diseases, and this is comparable to the recently emerging application of metabolomic in elucidating disease-resistant mechanisms in fish that gives new insight into potential therapeutic strategies to improve fish health. Metabolomic is defined as the large-scale study of all metabolites within an organism and represents the frontline in the 'omics' approaches, providing direct information on the metabolic responses and perturbations in metabolic pathways. In this review, the current research in infectious fish diseases using metabolomic approach will be summarized. The metabolomic approach in economically important fish infected with viruses, bacteria and nematodes will also be discussed. The potential of the metabolomic approach for management of these infectious diseases as well as the challenges and the limitations of metabolomic in fish disease studies will be explored. Current review highlights the impacts of metabolomic studies in infectious fish diseases, which proposed the potential of new therapeutic strategies to enhance disease resistance in fish.

Hepatocellular adenoma in a European flatfish (Limanda limanda): Genetic alterations in laser-capture micro-dissected tissue and global transcriptomic approach

Liver tumours in flatfish have been diagnosed using histopathology for decades to monitor the impacts of marine pollution. Here we describe the application of specific gene (retinoblastoma, Rb) profiling in laser capture micro-dissected samples, and a suppression subtractive hybridization (SSH) approach to isolate differentially expressed genes in hepatocellular adenoma (HCA) samples from dab, Limanda limanda. The Rb profiles from apparently normal and HCA micro-dissected samples of fish from the North Sea showed no significant difference, and genotypic heterogeneity within defined histological phenotypes was observed. In the SSH, sequences associated with cell signalling, cell cycle, gene expression regulation, protein transport and protein degradation were isolated. These included up-regulation of arrestin domain containing 3 (arrdc3), Rac-1 and tribbles, and down-regulation of ankyrin repeat/sterile alpha-motif domain-containing protein 1B-like (ANKS1B-like), c-fos, CDKN1B and RhoA-like sequences, previously implicated in mammalian HCA. This study offers new candidates involved in fish liver tumour development.

A glyphosate-based herbicide induces histomorphological and protein expression changes in the liver of the female guppy Poecilia reticulata

Glyphosate-based herbicides (GBH) are among the most common herbicides found in aquatic systems, but limited data are available about their mode of action and hepatotoxicity in fish. This study investigated the hepatotoxicity induced by GBH in the guppy Poecilia reticulata using a histopathological assessment associated with a proteomic approach. Guppies were exposed to GBH for 24 h at 1.8 mg of glyphosate L-1, corresponding to 50% of the LC50, 96 h. The results indicate that the GBH at 1.8 mg of glyphosate L-1 induce the development of hepatic damage in P. reticulata, which is exposure-time dependent. The histopathological indexes demonstrate that GBH cause inflammatory, regressive, vascular and progressive disorders in the liver of guppies. Using 2D gel electrophoresis associated with mass spectrometry, 18 proteins that changed by GBH were identified and were related to the cellular structure, motility and transport, energy metabolism and apoptosis. The results show that the acute exposure to GBH causes hepatic histopathological damage related to protein expression profile changes in P. reticulata, indicating that a histopathological assessment associated with a proteomic analysis provides a valuable approach to assess the toxic effects of GBH in sentinel fish species.

Effects of hypoxia in the gills of the Manila clam Ruditapes philippinarum using NMR-based metabolomics

Coastal hypoxia affects the survival, behavior, and reproduction of individual local marine organisms, and the abundance, biomass, and biodiversity of coastal ecosystems. In this study, we investigated the chronic effects of hypoxia on the metabolomics in the gills of Ruditapes (R.) philippinarum. The results indicated significant alterations in the metabolite profiles in the gills of the hypoxia-treated clams, in comparison with those maintained under normoxia. The levels of betaine, taurine, glycine, isoleucine, and alanine were significantly reduced, suggesting a disturbance of osmotic balance associated with hypoxia. Meanwhile, metabolites involved in energy metabolism, such as alanine and succinate, were also affected. Dramatic histopathological changes were observed in the gills and hepatopancreases of R. philippinarum grown in hypoxic waters, demonstrating tissue damages apparently caused by long-term exposure to hypoxia. Our findings suggest that hypoxia significantly affects the physiology of R. philippinarum, even at a sub-lethal level, and impedes health of the clams.

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.

Metabolomics-based approach for assessing the toxicity mechanisms of dibutyl phthalate to abalone (Haliotis diversicolor supertexta)

Dibutyl phthalate (DBP) is a ubiquitous contaminant in the marine environment, and relatively little is known about the toxicological mechanisms of this compound at the metabolite level. In this study, marine gastropods (abalone) were exposed to DBP at environmentally relevant concentrations (2, 10, and 50 μg/L) for 30 days. The plasma metabolite profiles were determined at the 5th, 15th, and 30th. The major metabolite changes corresponding to DBP exposure were related to osmotic regulation, energy metabolism, and environmental stress, and the effects displayed a dose-dependent pattern. The most obvious change was the increase in the levels of intracellular metabolites (betaine, dimethylglycine, homarine, glutamine, and lactate) and tricarboxylic acid cycle intermediates. The results revealed that DBP may lead to abalone oxidative stress, lipid metabolism dysfunction, energy metabolism disturbance, and osmoregulation imbalance. These results would be helpful in better understanding the mechanisms of abalone response to DBP stress at the system level.

Genetic alterations and cancer formation in a European flatfish at sites of different contaminant burdens

Fish diseases are an indicator for marine ecosystem health since they provide a biological end-point of historical exposure to stressors. Liver cancer has been used to monitor the effects of exposure to anthropogenic pollution in flatfish for many years. The prevalence of liver cancer can exceed 20%. Despite the high prevalence and the opportunity of using flatfish to study environmentally induced cancer, the genetic and environmental factors driving tumor prevalence across sites are poorly understood. This study aims to define the link between genetic deterioration, liver disease progression, and anthropogenic contaminant exposures in the flatfish dab (Limanda limanda). We assessed genetic changes in a conserved cancer gene, Retinoblastoma (Rb), in association with histological diagnosis of normal, pretumor, and tumor pathologies in the livers of 165 fish from six sites in the North Sea and English Channel. The highest concentrations of metals (especially cadmium) and organic chemicals correlated with the presence of tumor pathology and with defined genetic profiles of the Rb gene, from these sites. Different Rb genetic profiles were found in liver tissue near each tumor phenotype, giving insight into the mechanistic molecular-level cause of the liver pathologies. Different Rb profiles were also found at sampling sites of differing contaminant burdens. Additionally, profiles indicated that histological "normal" fish from Dogger sampling locations possessed Rb profiles associated with pretumor disease. This study highlights an association between Rb and specific contaminants (especially cadmium) in the molecular etiology of dab liver tumorigenesis.

Extraction for metabolomics: access to the metabolome

INTRODUCTION

The value of information obtained from a metabolomic study depends on how much of the metabolome is present in analysed samples. Thus, only a comprehensive and reproducible extraction method will provide reliable data because the metabolites that will be measured are those that were extracted and all conclusions will be built around this information.

OBJECTIVE

To discuss the efficiency and reliability of available sample pre-treatment methods and their application in different fields of metabolomics.

METHODS

The review has three sections: the first deals with pre-extraction techniques, the second discusses the choice of extraction solvents and their main features and the third includes a brief description of the most used extraction techniques: microwave-assisted extraction, solid-phase extraction, supercritical fluid extraction, Soxhlet and a new method developed in our laboratory--the comprehensive extraction method.

RESULTS

Examination of over 200 studies showed that sample collection, homogenisation, grinding and storage could affect the yield and reproducibility of results. They also revealed that apart from the solvent used for extraction, the extraction techniques have a decisive role on the metabolites available for analysis.

CONCLUSION

It is essential to evaluate efficacy and reproducibility of sample pre-treatment as a first step to ensure the reliability of a metabolomic study. Among the reviewed methods, the comprehensive extraction method appears to provide a promising approach for extracting diverse types of metabolites.

The metabolomic window into hepatobiliary disease

The emergent discipline of metabolomics has attracted considerable research effort in hepatology. Here we review the metabolomic data for non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), cirrhosis, hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), alcoholic liver disease (ALD), hepatitis B and C, cholecystitis, cholestasis, liver transplantation, and acute hepatotoxicity in animal models. A metabolomic window has permitted a view into the changing biochemistry occurring in the transitional phases between a healthy liver and hepatocellular carcinoma or cholangiocarcinoma. Whether provoked by obesity and diabetes, alcohol use or oncogenic viruses, the liver develops a core metabolomic phenotype (CMP) that involves dysregulation of bile acid and phospholipid homeostasis. The CMP commences at the transition between the healthy liver (Phase 0) and NAFLD/NASH, ALD or viral hepatitis (Phase 1). This CMP is maintained in the presence or absence of cirrhosis (Phase 2) and whether or not either HCC or CCA (Phase 3) develops. Inflammatory signalling in the liver triggers the appearance of the CMP. Many other metabolomic markers distinguish between Phases 0, 1, 2 and 3. A metabolic remodelling in HCC has been described but metabolomic data from all four Phases demonstrate that the Warburg shift from mitochondrial respiration to cytosolic glycolysis foreshadows HCC and may occur as early as Phase 1. The metabolic remodelling also involves an upregulation of fatty acid β-oxidation, also beginning in Phase 1. The storage of triglycerides in fatty liver provides high energy-yielding substrates for Phases 2 and 3 of liver pathology. The metabolomic window into hepatobiliary disease sheds new light on the systems pathology of the liver.

Advanced diagnostics applied to fish liver tumours: relating pathology to underlying molecular aetiology

Liver tumours in flatfish have been diagnosed using histopathology for decades in order to monitor the impacts of marine pollution in coastal and estuarine environments. This traditional method has been coupled with molecular analyses of tumours in the liver of the dab, Limanda limanda, in order to elucidate underpinning molecular level aetiology of such disease. A laser capture microdissection technique for molecular investigation of cancer has been applied in fish. The present study provides optimized steps for environmental sample utilisation: a procedure for field sample collection and handling; a method allowing reliable identification of lesions on frozen tissue sections; and, downstream molecular analyses of tumourigenesis markers (retinoblastoma gene) in laser microdissected samples. This approach facilitates the use of wild flatfish as a model of environmentally-induced tumourigenesis, and has wide applicability to any disease pathology for which the underpinning molecular aetiology is required.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

Fish metalloproteins as biomarkers of environmental contamination

Fish are well-recognized bioindicators of environmental contamination. Several recent proteomic studies have demonstrated the validity and value of using fish in the search and discovery of new biomarkers. Certain analytical tools, such as comparative protein expression analyses, both in field and lab exposure studies, have been used to improve the understanding of the potential for chemical pollutants to cause harmful effects. The metallomic approach is in its early stages of development, but has already shown great potential for use in ecological and environmental monitoring contexts. Besides discovering new metalloproteins that may be used as biomarkers for environmental contamination, metallomics can be used to more comprehensively elucidate existing biomarkers, which may enhance their effectiveness. Unfortunately, metallomic profiling for fish has not been explored, because only a few fish metalloproteins have thus far been discovered and studied. Of those that have, some have shown ecological importance, and are now successfully used as biomarkers of environmental contamination. These biomarkers have been shown to respond to several types of environmental contamination, such as cyanotoxins, metals, and sewage effluents, although many do not yet possess any known function. Examples of successes include MMPs, superoxide dismutases, selenoproteins, and iron-bound proteins. Unfortunately, none of these have, as yet, been extensively studied. As data are developed for them, valuable new information on their roles in fish physiology and in inducing environmental effects should become available.

Benzo(a)pyrene-induced metabolic responses in Manila clam Ruditapes philippinarum by proton nuclear magnetic resonance ((1)H NMR) based metabolomics

Benzo(a)pyrene is an important polycyclic aromatic hydrocarbon (PAH) which causes carcinogenic, teratogenic and mutagenic effects in various species and the level of contamination of this toxic agent in the marine environment is of great concern. In this study, metabolic responses induced by two doses (0.02 and 0.2μM) of BaP were characterized in the gill tissues of Manila clam Ruditapes philippinarum after exposure for 24, 48 and 96h. The high dose (0.2μM) of BaP induced the disturbances in energy metabolism and osmotic regulation based on the metabolic biomarkers such as succinate, alanine, glucose, glycogen, branched chain amino acids, betaine, taurine, homarine, and dimethylamine in clam gills after 24h of exposure. In addition, hormesis induced by BaP was found in clams exposed to both doses of BaP. Overall, our results demonstrated the applicability of metabolomics for the elucidation of toxicological effects of marine environmental contaminants in a selected bioindicator species such as the Manila clam.

Metabolic responses in gills of Manila clam Ruditapes philippinarum exposed to copper using NMR-based metabolomics

Copper is an important heavy metal contaminant with high ecological risk in the Bohai Sea. In this study, the metabolic responses in the bioindicator, Manila clam (Ruditapes philippinarum), to the environmentally relevant copper exposures were characterized using NMR-based metabolomics. The significant metabolic changes corresponding to copper exposures were related to osmolytes, intermediates of the Krebs cycle and amino acids, such as the increase in homarine, branched chain amino acids and decrease in succinate, alanine and dimethylamine in the copper-exposed clam gills during 96 h exposure period. Overall, Cu may lead to the disturbances in osmotic regulation and energy metabolism in clams during 96 h experimental period. These results demonstrate that NMR-based metabolomics is applicable for the discovery of metabolic biomarkers which could be used to elucidate the toxicological mechanisms of marine heavy metal contaminants.

Tissue-specific toxicological effects of cadmium in green mussels (Perna viridis): nuclear magnetic resonance-based metabolomics study

Toxicity tests for metals have traditionally focused on selected biomarkers to characterize the biological stress induced by metals in marine organisms. Here nuclear magnetic resonance (NMR)-based metabolomics, a system biology tool, was applied to the marine green mussel, Perna viridis, to investigate the toxicological effects of Cd in both digestive gland and adductor muscle tissues. After Cd exposure for either two or four weeks, there was no significant metabolic change in the mussels exposed to Cd at 2 µg/L. At 20 µg/L, there were major metabolite changes related to amino acids, osmolytes, and energy metabolites. Digestive gland tissue was more sensitive to Cd than adductor muscle tissue. The adductor muscle tissue showed elevated levels of glutamine, glutamate, and lactate, and reduced levels of branched chain amino acids, aspartate, phenylalanine, and tyrosine. Overall, four weeks of Cd exposure produced neurotoxicity and metabolic disturbances and disturbed osmoregulation. These results suggest that the adductor muscle tissue of mussels may be a suitable supplemental biomarker for exposure to toxicants. In addition, the results demonstrate that (1) H-NMR-based metabolomic analysis can provide a systematic view of the toxicological effects of metals on mussels, suggesting that it might be employed to investigate the toxicological effects of other marine pollutants.

Optimization and evaluation of metabolite extraction protocols for untargeted metabolic profiling of liver samples by UPLC-MS

A series of six protocols were evaluated for UPLC-MS based untargeted metabolic profiling of liver extracts in terms of reproducibility and number of metabolite features obtained. These protocols, designed to extract both polar and nonpolar metabolites, were based on (i) a two stage extraction approach or (ii) a simultaneous extraction in a biphasic mixture, employing different volumes and combinations of extraction and resuspension solvents. A multivariate statistical strategy was developed to allow comparison of the multidimensional variation between the methods. The optimal protocol for profiling both polar and nonpolar metabolites was found to be an aqueous extraction with methanol/water followed by an organic extraction with dichloromethane/methanol, with resuspension of the dried extracts in methanol/water before UPLC-MS analysis. This protocol resulted in a median CV of feature intensities among experimental replicates of <20% for aqueous extracts and <30% for organic extracts. These data demonstrate the robustness of the proposed protocol for extracting metabolites from liver samples and make it well suited for untargeted liver profiling in studies exploring xenobiotic hepatotoxicity and clinical investigations of liver disease. The generic nature of this protocol facilitates its application to other tissues, for example, brain or lung, enhancing its utility in clinical and toxicological studies.

Systems toxicology approaches for understanding the joint effects of environmental chemical mixtures

Environmental mixtures of chemicals constitute a prevalent issue in ecotoxicology and the development of new methods to reduce the uncertainties associated with their ecological risk assessment is a critical research need. Historically, a number of models have been explored to predict the potential combined effects of chemicals on species. These models, especially concentration addition and the independent action, have been applied to a number of mixtures. While often providing a good prediction of joint effect, there are cases where these models can have limitations: notably in cases where there are interactions for which they fail to adequately predict joint effects. To support the better mechanistic understanding of interactions in mixture toxicology a framework to support experimental studies to investigate the basis of observed interactions is proposed. The conceptual framework is derived from the extension of a three stage scheme which has previously been applied to understand chemical bioavailability. The framework considers that interactions in mixtures result from processes related to 1) the speciation, binding and transport of chemicals in the exposure medium (external exposure); 2) the adsorption, distribution, metabolism and excretion of chemicals within the organisms (toxicokinetics); 3) associations governing the binding and toxicity of the chemical(s) at the target site (toxicodynamics). The current state of the art in (eco)toxicology in relation to investigation of the mechanisms of interactions between chemicals is discussed with particular emphasis towards the multi-disciplinary tools and techniques within environmental chemistry; toxicology; biochemistry and systems biology that can be used to address such effects.

A signal filtering method for improved quantification and noise discrimination in fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data

Direct-infusion electrospray-ionization Fourier transform ion cyclotron resonance mass spectrometry (DI ESI FT-ICR MS) is increasingly being utilized in metabolomics, including the high sensitivity selected ion monitoring (SIM)-stitching approach. Accurate signal quantification and the discrimination of real signals from noise remain major challenges for this approach, with both adversely affected by factors including ion suppression during electrospray, ion-ion interactions in the detector cell, and thermally-induced white noise. This is particularly problematic for complex mixture analysis where hundreds of metabolites are present near the noise level. Here we address relative signal quantification and noise discrimination issues in SIM-stitched DI ESI FT-ICR MS-based metabolomics. Using liver tissue, we first optimized the number of scans (n) acquired per SIM window to address the balance between quantification accuracy versus acquisition time (and thus sample throughput); a minimum of n = 5 is recommended. Secondly, we characterized and computationally-corrected an effect whereby an ion's intensity is dependent upon its location within a SIM window, exhibiting a 3-fold higher intensity at the high m/z end. This resulted in significantly improved quantification accuracy. Finally, we thoroughly characterized a three-stage filter to discriminate noise from real signals, which comprised a signal-to-noise-ratio (SNR) hard threshold, then a "replicate" filter (retaining only peaks in r-out-of-3 replicate analyses), and then a "sample" filter (retaining only peaks in >s% of biological samples). We document the benefits of three-stage filtering versus one- and two-stage filters, and show the importance of selecting filter parameters that balance the confidence that a signal is real versus the total number of peaks detected.

Finfish and aquatic invertebrate pathology resources for now and the future

Utilization of finfish and aquatic invertebrates in biomedical research and as environmental sentinels has grown dramatically in recent decades. Likewise the aquaculture of finfish and invertebrates has expanded rapidly worldwide as populations of some aquatic food species and threatened or endangered aquatic species have plummeted due to overharvesting or habitat degradation. This increasing intensive culture and use of aquatic species has heightened the importance of maintaining a sophisticated understanding of pathology of various organ systems of these diverse species. Yet, except for selected species long cultivated in aquaculture, pathology databases and the workforce of highly trained pathologists lag behind those available for most laboratory animals and domestic mammalian and avian species. Several factors must change to maximize the use, understanding, and protection of important aquatic species: 1) improvements in databases of abnormalities across species; 2) standardization of diagnostic criteria for proliferative and nonproliferative lesions; and 3) more uniform and rigorous training in aquatic morphologic pathology.

Environmental metabolomics using 1H-NMR spectroscopy

Environmental metabolomics is a subdiscipline of metabolomics and focuses on the study of metabolic changes in organisms in response to environmental challenges. This approach is ideal for studying multiple species within an ecosystem because it is not dependent on knowledge of an organism's genome. Unbiased measurements of an organism's metabolic composition can in principle be used to identify novel biomarker profiles and modes of action of stressors. This chapter presents protocols for the extraction of metabolites from biological samples, the measurement of metabolites using 1H nuclear magnetic resonance (NMR) spectroscopy, and finally the analysis of the metabolic data using multivariate statistical methods. First, the preparation of biofluids (e.g., blood and urine) for NMR analysis is described together with a methanol-chloroform protocol for extracting metabolites from tissue samples. Next the NMR methods are presented, comprising a standard one-dimensional (1-D) 1H-NMR method and a two-dimensional (2-D) 1H-1H J-resolved NMR experiment. The advantages and limitations of each method are discussed. Finally, two methods for analyzing the multivariate metabolic NMR data are presented. These include a traditional fingerprinting approach that comprises of a spectral preprocessing step followed by multivariate statistical analysis. Although reliable and proven, this method often produces results in terms of unidentified metabolites that are of limited value to the biologist. The second and newer method is based on metabolic profiling in which NMR spectra are deconvoluted into a list of metabolites and their concentrations. Although more biologically insightful, this latter approach can prove labor intensive.

Comparison of histological, genetic, metabolomics, and lipid-based methods for sex determination in marine mussels

Omics technologies are increasingly being used to monitor organismal responses to environmental stressors. Previous studies have shown that species identification, an appreciation of life history traits, and organism phenotype (e.g., gender) are essential for the accurate interpretation of omics data from field samples. As marine mussels are increasingly being used in ecotoxicogenomics and monitoring, a technique to determine mussel gender throughout their annual reproductive cycle is urgently needed. This study examines four methods for sex determination in the two mussel species found in the United Kingdom, Mytilus edulis and Mytilus galloprovincialis, and their hybrid. Each of these methods-histology, a lipid-based assay, a new reverse transcriptase polymerase chain reaction (RT-PCR) assay, and nuclear magnetic resonance (NMR)-based metabolomics-initially was evaluated using sexually mature ("ripe") mussels whose gender was clearly distinguishable using histology. The methods subsequently were tested on spawned ("spent") mussels. For ripe animals, all techniques yielded high classification accuracies: histology, 100%; RT-PCR, 94.6%; lipid analysis, 90.6%; and metabolomics, 89.5%. The gender of spent animals, however, could not be determined by histology (0%) or lipid analysis (55.6%), but RT-PCR (100%) and metabolomics (88.9%) both proved to be successful. In addition, the RT-PCR, metabolomics, and lipid-based methods identified animals of mixed sex. Our findings highlight the application of a novel RT-PCR method as a robust technique for gender determination of ripe and spent mussels.

Proteomic analyses indicate induction of hepatic carbonyl reductase/20beta-hydroxysteroid dehydrogenase B in rainbow trout exposed to sewage effluent

Proteomic analyses were performed to identify regulated liver proteins in rainbow trout (Oncorhynchus mykiss) caged upstream and downstream from a sewage treatment works (STW). Two-dimensional gel electrophoresis, image analysis and FT-ICR mass-spectrometry revealed four regulated protein spots. The three down-regulated spots contained betaine aldehyde dehydrogenase, lactate dehydrogenase and an unidentified protein respectively. The only up-regulated spot consisted of both mitochondrial ATP synthase alpha-subunit and carbonyl reductase/20beta-hydroxysteroid dehydrogenase (CR/20beta-HSD). Further studies using quantitative PCR revealed a 13.5-fold induction of CR/20beta-HSD B mRNA following STW effluent exposure. The CR/20beta-HSD B gene was not regulated by 17alpha-ethinylestradiol, suggesting that its induction downstream from the STW is due to other factors than exposure to estrogens. Image analysis was initially performed on four gels from each group. These analyses suggested 15 regulated spots. However, validation of the 15 spots by increasing the number of replicates confirmed only four regulated spots. Hence, the present study also demonstrates the need for sufficient biological/technical replication in the interpretation of proteomic data.

Metabolic profile biomarkers of metal contamination in a sentinel terrestrial species are applicable across multiple sites

In this study, we addressed the question of whether an omic approach could genuinely be useful for biomarker profile analysis across different field sites with different physicochemical characteristics. We collected earthworms (Lumbricus rubellus) from seven sites with very different levels of metal contamination and prevailing soil type and analyzed tissue extracts by 1H nuclear magnetic resonance spectroscopy. Pattern recognition analysis of the data showed that both site- and contaminant-specific effects on the metabolic profiles could be discerned. Zinc was identified as the probable major contaminant causing a metabolic change in the earthworms. Individual sites could be resolved on the basis of NMR spectral profiles by principal component analysis; these site differences may also have been caused by additional abiotic factors such as soil pH. Despite an inevitable degree of confounding between site and contaminant concentrations, it was possible to identify metabolites which were correlated with zinc across all different sites. This study therefore acts as a proof of principle for the use of NMR-based metabolic profiling as a diagnostic tool for ecotoxicological research in polluted field soils.

Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method

Direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry (DI nESI FT-ICR MS) offers high mass accuracy and resolution for analyzing complex metabolite mixtures. High dynamic range across a wide mass range, however, can only be achieved at the expense of mass accuracy, since the large numbers of ions entering the ICR detector induce adverse space-charge effects. Here we report an optimized strategy for wide-scan DI nESI FT-ICR MS that increases dynamic range but maintains high mass accuracy. It comprises the collection of multiple adjacent selected ion monitoring (SIM) windows that are stitched together using novel algorithms. The final SIM-stitching method, derived from several optimization experiments, comprises 21 adjoining SIM windows each of width m/z 30 (from m/z 70 to 500; adjacent windows overlap by m/z 10) with an automated gain control (AGC) target of 1 x 10(5) charges. SIM-stitching and wide-scan range (WSR; Thermo Electron) were compared using a defined standard to assess mass accuracy and a liver extract to assess peak count and dynamic range. SIM-stitching decreased the maximum mass error by 1.3- and 4.3-fold, and increased the peak count by 5.3- and 1.8-fold, versus WSR (AGC targets of 1 x 10(5) and 5 x 10(5), respectively). SIM-stitching achieved an rms mass error of 0.18 ppm and detected over 3000 peaks in liver extract. This novel approach increases metabolome coverage, has very high mass accuracy, and at 5.5 min/sample is conducive for high-throughput metabolomics.

Environmental Metabolomics: A SWOT Analysis (Strengths, Weaknesses, Opportunities, and Threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.

Plasma proteome analysis reveals the geographical origin and liver tumor status of Dab (Limanda limanda) from UK marine waters

The flatfish species dab (Limanda limanda) is the sentinel for offshore marine monitoring in the United Kingdom National Marine Monitoring Programme (NMMP). At certain sites in the North and Irish Seas, the prevalence of macroscopic liver tumors can exceed 10%. The plasma proteome of these fish potentially contains reporter proteins or "biomarkers" that may enable development of diagnostic tests for liver cancer and further our understanding of the disease. Following selection of sample groups by quality-assured histopathology ("phenotype anchoring"), we used surface-enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry to produce proteomic profiles of plasma from 213 dab collected during the 2004 UK NMMP. The resulting protein profiles were compared between fish from the North and Irish Seas and between fish with liver neoplasia or nondiseased liver. Significant differences were found between the plasma proteomes of dab from the North Sea and Irish Sea, which in conjunction with artificial neural networks can correctly determine from which sea dab were captured in 85% of the cases. In addition, the presence of liver tumors is associated with significant changes in the plasma proteome. We conclude that SELDI-based plasma profiling is potentially of use in nonlethal marine monitoring using wild sentinels such as dab. Furthermore, accurate selection of sample groups is critical for avoiding effects of confounding factors such as age, gender, and geographic origin of samples.

Metabolic effects of dinoseb, diazinon and esfenvalerate in eyed eggs and alevins of Chinook salmon (Oncorhynchus tshawytscha) determined by 1H NMR metabolomics

Pesticide pulses in the Sacramento River, California, originate from storm-water discharges and non-point source aquatic pollution that can last from a few days to weeks. The Sacramento River and its tributaries have historically supported the majority of California's Chinook salmon (Oncorhynchus tshawytscha) spawning grounds. Three pesticides currently used in the Sacramento Valley-- dinoseb, diazinon, and esfenvalerate-- were chosen to model the exposure of salmon embryos to storm-water discharges. Static-renewal (96 h) exposures to eyed eggs and alevins resulted in both toxicity and significant changes in metabolism assessed in whole-embryo extracts by (1)H nuclear magnetic resonance (NMR) spectroscopy based metabolomics and HPLC with UV detection (HPLC-UV). The 96-h LC(50) values of eyed eggs and alevins exposed to dinoseb were 335 and 70.6 ppb, respectively, and the corresponding values for diazinon were 545 and 29.5 ppm for eyed eggs and alevins, respectively. The 96-h LC(50) of eyed eggs exposed to esfenvalerate could not be determined due to lack of mortality at the highest exposure concentration, but in alevins was 16.7 ppb. All esfenvalerate exposed alevins developed some degree of lordosis or myoskeletal abnormality and did not respond to stimulus or exhibit normal swimming behavior. ATP concentrations measured by HPLC-UV decreased significantly in eyed eggs due to 250 ppb dinoseb and 10 and 100 ppb esfenvalerate (p < 0.05). Phosphocreatine, as measured by HPLC-UV, decreased significantly in eyed eggs due to 250 ppb dinoseb, 10 and 100 ppb esfenvalerate, and 100 ppm diazinon (p < 0.05). Principal components analyses of (1)H NMR metabolite fingerprints of eyed egg and alevin extracts revealed both dose-dependent and mechanism of action-specific metabolic effects induced by the pesticides. Furthermore, NMR based metabolomics proved to be more sensitive than HPLC-UV in identifying significant changes in sublethal metabolism of pesticide exposed alevins. In conclusion, we have demonstrated several benefits of a metabolomics approach for chemical risk assessment, when used in conjunction with a fish embryo assay, and have identified significant metabolic perturbations to the early life stages of Chinook salmon by currently used pesticides.