Protein expression signatures: an application of proteomics

Pikeperch muscle tissues: a comparative study of structure, enzymes, genes, and proteins in wild and farmed fish

Pikeperch (Sander lucioperca) is a freshwater species and an internationally highly demanded fish in aquaculture. Despite intensive research efforts on this species, fundamental knowledge of skeletal muscle biology and structural characteristics is missing. Therefore, we conducted a comprehensive analysis of skeletal muscle parameters in adult pikeperch from two different origins, wild-caught specimens from a lake and those reared in a recirculating aquaculture system. The analyses comprised the biochemical characteristics (nucleic acid, protein content), enzyme activities (creatine kinase, lactate dehydrogenase, NADP-dependent isocitrate dehydrogenase), muscle-specific gene and protein expression (related to myofibre formation, regeneration and permanent growth, muscle structure), and muscle fibre structure. The findings reveal distinct differences between the skeletal muscle of wild and farmed pikeperch. Specifically, nucleic acid content, enzyme activity, and protein expression varied significantly. The higher enzyme activity observed in wild pikeperch suggests greater metabolically activity in their muscles. Conversely, farmed pikeperch indicated a potential for pronounced muscle growth. As the data on pikeperch skeletal muscle characteristics is sparse, the purpose of our study is to gain fundamental insights into the characteristics of adult pikeperch muscle. The presented data serve as a foundation for further research on percids' muscle biology and have the potential to contribute to advancements and adaptations in aquaculture practices.

Environmental factors influence cross-talk between a heat shock protein and an oxidative stress protein modification in the lizard Gallotia galloti

Better understanding how organisms respond to their abiotic environment, especially at the biochemical level, is critical in predicting population trajectories under climate change. In this study, we measured constitutive stress biomarkers and protein post-translational modifications associated with oxidative stress in Gallotia galloti, an insular lizard species inhabiting highly heterogeneous environments on Tenerife. Tenerife is a small volcanic island in a relatively isolated archipelago off the West coast of Africa. We found that expression of GRP94, a molecular chaperone protein, and levels of protein carbonylation, a marker of cellular stress, change across different environments, depending on solar radiation-related variables and topology. Here, we report in a wild animal population, cross-talk between the baseline levels of the heat shock protein-like GRP94 and oxidative damage (protein carbonylation), which are influenced by a range of available temperatures, quantified through modelled operative temperature. This suggests a dynamic trade-off between cellular homeostasis and oxidative damage in lizards adapted to this thermally and topologically heterogeneous environment.

Omics approach reveals metabolic disorders associated with the cytotoxicity of airborne particulate matter in human lung carcinoma cells

Exposure to airborne particulate matter (PM) _2.5 induced various adverse health effects, such as metabolic syndrome, systemic inflammation and respiratory infection. However, a global influence of PM_2.5-induced metabolic and proteomic disorders remains confusing, and the underlying mechanism is still under-explored. Herein, LC-MS/MS-based metabolomics, lipidomics and isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics were applied to analyze the toxicological characteristics of PM_2.5 from Taiyuan City in China (Taiyuan-PM_2.5) on human lung carcinoma cells (A549) after the 24-h treatment. Metabolites, lipids and proteins that have distinctive differences were screened by SIEVE, LipidSearch and Proteome Discoverer, respectively. The abundance of 56 metabolites (40 increased and 16 decreased), 22 lipids (19 increased and 3 decreased) and 81 proteins (55 up-regulated and 26 down-regulated) were significantly changed upon the PM_2.5 treatment. Among the proteomics analysis, 16 proteins were specifically related to RNA splicing, mainly including up-regulated serine/arginine-rich splicing factor 1 (SRSF1), SRSF2, small nuclear ribonucleoprotein 70 kDa (snRNP70), small nuclear ribonucleoprotein polypeptide B (SNRPB), SNRPC, SNRPE and down-regulated heterogeneous nuclear ribonucleoprotein U-like 2 (hnRNP UL2). At the metabolic level, PM_2.5 exposure significantly altered the sphingolipid metabolism, including ceramide, serine, sphingosine and sphingomyelin. It was proposed that excessive accumulation of ceramide and expression of key enzymes (ceramide synthases, phingomyelinase, sphingosine kinase types 2 and protein phosphatase-1) induced the secretion of pro-inflammatory cytokines, generation of lipotoxicity and alterations of RNA splicing in PM_2.5-treated A549  cells. In general, our results demonstrated that ceramide accumulation and altered RNA splicing could becritical contributors to PM_2.5-induced cytotoxicity at metabolic and proteomic level, which might be considered as potential markers for toxicological evaluation of PM_2.5 samples.

iTRAQ-based quantitative proteomic analysis identified Eno1 as a cadmium stress response gene in Propsilocerus akamusi (Tokunaga) hemolymph

Propsilocerus akamusi (Tokunaga) is a common species of midge in Siberia, Japan, and China and an important prey species for fish and aquatic birds. Furthermore, this species has been shown to have an extraordinary capacity to resist cadmium (Cd) toxicity. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) coupled liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to analyze relative changes in the P. akamusi hemolymph proteome following exposure to a sublethal concentration of Cd²⁺. The results showed that Cd²⁺ stress affects energy metabolism in P. akamusi. After examining the differentially expressed proteins (DEPs), only one up-regulated protein associated with metabolism, α-enolase (Eno1) was identified and further isolated and characterized. Sequence alignments showed that the deduced P. akamusi Eno1 amino acid sequence is highly conserved, with similarities of 77-95% noted when compared to other Dipteran Eno1 sequences. Furthermore, prolonged Cd²⁺ exposure impacted Eno1 transcription, protein expression and enzyme activity levels. These results suggest that Eno1 may play a role in the response to Cd²⁺ stress in P. akamusi.

Innovative methods for biomarker discovery in the evaluation and development of cancer precision therapies

The discovery of biomarkers able to detect cancer at an early stage, to evaluate its aggressiveness, and to predict the response to therapy remains a major challenge in clinical oncology and precision medicine. In this review, we summarize recent achievements in the discovery and development of cancer biomarkers. We also highlight emerging innovative methods in biomarker discovery and provide insights into the challenges faced in their evaluation and validation.

Proteomic evaluation of human umbilical cord tissue exposed to polybrominated diphenyl ethers in an e-waste recycling area

Parental exposure to polybrominated diphenyl ethers (PBDEs) is associated with adverse birth outcomes. This study aims to examine differentially-expressed protein profiles in umbilical cord tissue, derived from mothers exposed to PBDEs, and investigate candidate biomarkers to reveal the underlying molecular mechanisms. Umbilical cord samples were obtained from women residing in an electronic waste (e-waste) recycling area (Guiyu) and reference area (Haojiang) in China. The concentration of PBDEs in umbilical cord tissue was determined by gas chromatography and mass spectrometry (GC/MS). Isobaric tagging for relative and absolute quantification (iTRAQ)-based proteomic technology was conducted to analyze differentially-expressed protein profiles. The total PBDE concentration was approximately five-fold higher in umbilical cords from Guiyu than from Haojiang (median 71.92ng/g vs. 15.52ng/g lipid, P<0.01). Neonatal head circumference, body-mass index (BMI) and Apgar1 score were lower in Guiyu and negatively correlated with PBDE concentration (P<0.01). Proteomic analysis showed 697 proteins were differentially expressed in the e-waste-exposed group compared with the reference group. The differentially-expressed proteins were principally involved in antioxidant defense, apoptosis, cell structure and metabolism. Among them, catalase and glutathione S-transferase omega-1, were down-regulated, and cytochrome c was found to be up-regulated, changes which were further verified by enzyme-linked immunosorbent assays. These results suggest that an antioxidant imbalance and cell apoptosis in the umbilical cord following PBDE exposure is associated with neonatal birth outcomes.

Investigating the emerging role of comparative proteomics in the search for new biomarkers of metal contamination under varying abiotic conditions

This study aims at investigating the potential use of comparative proteomics as a multi-marker approach of metal contamination, taking into account the potential confounding effect of water temperature. The major objective was to identify combinations of proteins specifically responding to a given metal, even if included in a metal mixture. The diagnostic approach was performed via the comparative analysis of protein expression on spot mapping provided by adult males of Gammarus pulex (Amphipoda, Crustacea) respectively exposed to arsenate (As), cadmium (Cd) or a binary mixture of these metals (AsCd) at three realistic temperatures (5, 10 and 15°C). Proteomic expression analysis was performed by Differential in-Gel Electrophoresis (2D-DiGE), and completed by an adapted inferential statistical approach. Combinations of under/over-expressed protein spots discriminated the metal identity. However, none of these spots discriminated both the individual metal effect (As or Cd) and its effect in metal mixture (AsCd) whatever the tested temperature. Some limits of the two-dimensional analysis of protein spot maps in G. pulex have been highlighted: (i) the presence of contaminating peptides and/or abundant "déja-vu" proteins which can mask the responses of other proteins of interest or (ii) the presence of post-translational modifications. An optimization of the experimental design (especially during the sample preparation) has been described for future investigations. This study has also highlighted (i) the importance of precisely identifying the protein spots of interest to avoid erroneous interpretations in terms of action mechanisms of chemicals and (ii) the importance of working under controlled laboratory conditions with a temperature close to 10°C. In such conditions, we have demonstrated a higher impact of As than Cd on the energetic metabolism of Gammarus. This As impact is reduced in AsCd mixture confirming the antagonistic interaction of this binary mixture previously observed on G. pulex mortality at 10°C.

Changes in protein expression of pacific oyster Crassostrea gigas exposed in situ to urban sewage

The composition and concentration of substances in urban effluents are complex and difficult to measure. These contaminants elicit biological responses in the exposed organisms. Proteomic analysis is a powerful tool in environmental toxicology by evidencing alterations in protein expression due to exposure to contaminants and by providing a useful framework for the development of new potential biomarkers. The aim of this study was to determine changes in protein expression signatures (PES) in the digestive gland of oysters Crassostrea gigas transplanted to two farming areas (LIS and RIB) and to one area contaminated by sanitary sewage (BUC) after 14 days of exposure. This species is one of the most cultivated molluscs in the world. The identified proteins are related to the cytoskeleton (CKAP5 and ACT2), ubiquitination pathway conjugation (UBE3C), G protein-coupled receptor and signal transduction (SVEP1), and cell cycle/division (CCNB3). CKAP5 showed higher expression in oysters kept at BUC in comparison with those kept at the farming areas, while ACT2, UBE3C, SVEP1, and CCNB3 were suppressed. The results suggest that these changes might lead to DNA damage, apoptosis, and interference with the immune system in oyster C. gigas exposed to sewage and give initial information on PES of C. gigas exposed to sanitary sewage, which can subsequently be useful in the development of more sensitive tools for biomonitoring coastal areas, particularly those devoted mainly to oyster farming activities.

Investigation on the proteome response of transplanted blue mussel (Mytilus sp.) during a long term exposure experiment at differently impacted field stations in the German Bight (North Sea)

In a pilot field study the proteome response of Mytilus sp. was analyzed in relation to the concentration of different trace metal contaminants. Over a period of eight month test organisms have been exposed at a near-shore station in the anthropogenic impacted estuary of the river Elbe and at an off-shore station in the vicinity of the Island of Helgoland in the German Bight (North Sea). The stations differ in their hydrological as well as chemical characteristics. The physiological biomarkers, such as condition index which have been continuously monitored during the experiment clearly indicate the effects of the different environmental conditions. Multiple protein abundance changes were detected utilizing the techniques of two dimensional gel electrophoresis (2dGE) and consequently proteins arising as potential candidates for ecotoxicological monitoring have been identified by MALDI-ToF and ToF/ToF mass spectrometry. Different cytoskeletal proteins, enzymes of energy metabolism, stress proteins and one protein relevant for metal detoxification have been pointed out.

Next-generation proteomics: toward customized biomarkers for environmental biomonitoring

Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.

[Sleep-apnea syndrome, mechanical ventilation and critical care in Archivos de Bronconeumología (December 2009-December 2010)]

The present study aims to review all the major articles on respiratory sleep disorders, mechanical ventilation, and respiratory critical care published in the last year in Archivos de bronconeumología. Between December 2009 and November 2010, 15 studies on these topics were published in Archivos de bronconeumología. Ten of these studies dealt with respiratory sleep disorders, consisting of six original articles, one special article, one review article, one letter to the editor and one supplement on chronic obstructive pulmonary disease and its association with sleep apneas. Five articles were published on non-invasive mechanical ventilation: one editorial, one special article, one article in a supplement and two original articles. As in previous years, there was a marked difference in the number of articles published on non-invasive mechanical ventilation and sleep-apnea syndrome, with a greater number of articles being published on the latter. Although some articles highlight the importance of the place where ventilation is commenced, no study specifically dealing with intermediate care units was published in Archivos de bronconeumología in 2010. This absence could be interpreted as a result of the low implantation of this type of unit in Spain, contrasting with the high activity undertaken in this field by pneumology services.

Proteomic Analysis of the Reproductive Organs of the Hermaphroditic Gastropod Lymnaea stagnalis Exposed to Different Endocrine Disrupting Chemicals

Many studies have reported perturbations of mollusc reproduction following exposure to low concentrations (ng/L range) of endocrine disrupting chemicals (EDCs). However, the mechanisms of action of these molecules on molluscs are still poorly understood. Investigation of the modifications of protein expression in organisms exposed to chemicals using proteomic methods can provide a broader and more comprehensive understanding of adverse impacts of pollution on organisms than conventional biochemical biomarkers (e.g., heat-shock proteins, metallothioneins, GST, EROD). In this study we have investigated the impacts of four chemicals, which exhibit different endocrine disrupting properties in vertebrates, on the proteome of the hermaphroditic freshwater pulmonate gastropod Lymnaea stagnalis after 21 days of exposure. Testosterone, tributyltin, chlordecone and cyproterone acetate were chosen as tested compounds as they can induce adverse effects on the reproduction of this snail. The 2D-DIGE method was used to identify proteins whose expression was affected by these compounds. In addition to modifying the expression of proteins involved in the structure and function of the cytoskeleton, chemicals had impacts on the expression of proteins involved in the reproduction of L. stagnalis. Exposure to 19.2 µg/L of chlordecone increased the abundance of ovipostatin, a peptide transmitted during mating through seminal fluid, which reduces oviposition in this species. The expression of yolk ferritin, the vitellogenin equivalent in L. stagnalis, was reduced after exposure to 94.2 ng Sn/L of tributyltin. The identification of yolk ferritin and the modification of its expression in snails exposed to chemicals were refined using western blot analysis. Our results showed that the tested compounds influenced the abundance of yolk ferritin in the reproductive organs. Alteration in proteins involved in reproductive pathways (e.g., ovipostatin and yolk ferritin) could constitute relevant evidence of interaction of EDCs with reproductive pathways that are under the control of the endocrine system of L. stagnalis.

Polybrominated diphenyl ethers do not affect metamorphosis but alter the proteome of the invasive slipper limpet Crepidula onyx

Man-made polybrominated diphenyl ethers (PBDEs) used as flame retardants in various consumer products may be harmful to marine organisms. Larvae of some marine invertebrates, especially invasive species, can develop resistance to PBDEs through altered protein expression patterns or proteome plasticity. This is the first report of a proteomics approach to study BDE-47 induced molecular changes in the invasive limpet Crepidula onyx. Larvae of C. onyx were cultured for 5 days (hatching to metamorphosis) in the presence of BDE-47 (1 μg L(-1)). Using a 2-DE proteomics approach with triple quadrupole and high-resolution TOF-MS, we showed that BDE-47 altered the proteome structure but not the growth or metamorphosis of C. onyx larvae. We found eight significant differentially expressed proteins in response to BDE-47, deemed the protein expression signature, consisting of cytoskeletal, stress tolerance, metabolism and energy production related proteins. Our data suggest C. onyx larvae have adequate proteome plasticity to tolerate BDE-47 toxicity.

A proteomic evaluation of the effects of the pharmaceuticals diclofenac and gemfibrozil on marine mussels (Mytilus spp.): evidence for chronic sublethal effects on stress-response proteins

Human pharmaceuticals (e.g. the lipid regulator gemfibrozil and the non-steroidal anti-inflammatory drug diclofenac) are an emerging environmental threat in the aquatic environment. This study aimed to evaluate sublethal effects of these two commonly found pharmaceuticals on the protein profiles of marine mussels (Mytilus spp.). Mytilus spp. was exposed to environmentally relevant and elevated concentrations (1 and 1000 µg/l respectively) of both drugs for 14 days. In addition, mussels were maintained for seven days post treatment to examine the potential of blue mussels to recover from such an exposure. Differential protein expression signatures (PES) in the digestive gland of mussels were obtained using two-dimensional gel electrophoresis after 7, 14, and 21 days of exposure. Twelve spots were significantly increased or decreased by gemfibrozil and/or diclofenac, seven of which were successfully identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. These proteins were involved in energy metabolism, oxidative stress response, protein folding, and immune responses. Changes in the PES over time suggested that mussels were still experiencing oxidative stress for up to seven days post exposure. In addition, a suite of biomarkers comprising glutathione transferase, lipid peroxidation, and DNA damage were studied. An oxidative stress response was confirmed by biomarker responses. To our knowledge, this is the first investigation using proteomics to assess the potential effects of human pharmaceuticals on a non-target species in an environmentally-relevant model. The successful application of this proteomic approach supports its potential use in pollution biomonitoring and highlights its ability to aid in the discovery of new biomarkers.

Biochemical responses in seabream (Sparus aurata) caged in-field or exposed to benzo(a)pyrene and paraquat. Characterization of glutathione S-transferases

Gilthead seabream (Sparus aurata) specimens were caged in-field at the Téboulba harbour or exposed to benzo(a)pyrene [B(a)P] or to paraquat [PQ] plus B(a)P, and several biochemical biomarker responses were investigated. Antioxidant enzymes, such as glutathione peroxidase, catalase and glutathione reductase, significantly increased in the in-field and B(a)P+PQ exposures, but were only moderately affected by B(a)P alone. Glucose-6-phosphate and 6-phosphogluconate dehydrogenases significantly diminished after in-field exposure. Different responses with biotransformation enzymes were observed: the P4501A-associated EROD activity was highly induced in response to B(a)P and B(a)P+PQ exposures, while total activity of the glutathione S-transferase (GST) was similar to control. However, after purification of the GST proteins by affinity chromatograpy and analysis by two-dimensional electrophoresis, nineteen highly reproducible isoforms were resolved. In addition, some of reproducible isoforms showed different and specific expression patterns in response to contaminants. Thus, proteomic analysis of the purified GST subunits is a reliable tool for ecotoxicological research, useful in polluted marine ecosystem as an effective biomarker of contamination.

Analysis of Pacific oyster larval proteome and its response to high-CO2

Most calcifying organisms show depressed metabolic, growth and calcification rates as symptoms to high-CO(2) due to ocean acidification (OA) process. Analysis of the global expression pattern of proteins (proteome analysis) represents a powerful tool to examine these physiological symptoms at molecular level, but its applications are inadequate. To address this knowledge gap, 2-DE coupled with mass spectrophotometer was used to compare the global protein expression pattern of oyster larvae exposed to ambient and to high-CO(2). Exposure to OA resulted in marked reduction of global protein expression with a decrease or loss of 71 proteins (18% of the expressed proteins in control), indicating a wide-spread depression of metabolic genes expression in larvae reared under OA. This is, to our knowledge, the first proteome analysis that provides insights into the link between physiological suppression and protein down-regulation under OA in oyster larvae.

Finding biomarkers is getting easier

Single biomarkers are rarely accurate. Even suites of biomarkers can give conflicting results. Ideally potent combinations of variables are isolated which accurately identify specific analytes and their level of toxicity. The search for such combinations can be done by reducing the thousands of candidate variables to the small number necessary for treatment classification. When the key variables are recognized by machine learning (ML) the results are quite surprising, given the apparent failure of other searching methods to produce good diagnostics. Proteins seem especially useful for portable field tests of a variety of adverse conditions. This review shows how ML, in particular artificial neural networks, can find potent biomarkers embedded in any type of expression data, mainly proteins in this article. A computer does multiple iterations to produce sets of proteins which systematically identify (to near 100% accuracy) the treatment classes of interest. Whether these proteins are useful in actual diagnoses is tested by presenting the computer model with unknown classes. Finding the biomarkers is getting easier but there still must be confirmation, by multivariable statistics and with field studies.

Proteomic discovery of biomarkers of metal contamination in Sydney Rock oysters (Saccostrea glomerata)

In the current study we examined the effects of metal contamination on the protein complement of Sydney Rock oysters. Saccostrea glomerata were exposed for 4 days to three environmentally relevant concentrations (100 μg/l, 50 μg/l and 5 μg/l) of cadmium, copper, lead and zinc. Protein abundances in oyster haemolymph from metal-exposed oysters were compared to those from non-exposed controls using two-dimensional electrophoresis to display differentially expressed proteins. Differentially expressed proteins were subsequently identified using tandem mass spectrometry (LC-MS/MS), to assign their putative biological functions. Unique sets of differentially expressed proteins were affected by each metal, in addition to proteins that were affected by more than one metal. The proteins identified included some that are commonly associated with environmental monitoring, such as HSP 70, and other novel proteins not previously considered as candidates for molecular biomonitoring. The most common biological functions of proteins were associated with stress response, cytoskeletal activity and protein synthesis.

Alterations of protein profile in zebrafish liver cells exposed to methyl parathion: a membrane proteomics approach

Methyl parathion (MP) is an extensively used organophosphorus pesticide, which has been associated with a wide spectrum of toxic effects on environmental organisms. The aim of this study is to investigate the alterations of membrane protein profiles in zebrafish liver (ZFL) cell line exposed to MP for 24 h using proteomic approaches. Two-dimensional gel electrophoresis revealed a total of 13 protein spots, whose expression levels were significantly altered by MP. These differential proteins were subjected to matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry analysis, and nine proteins were identified to be membrane proteins, among which seven were up-regulated, while two were down-regulated. In addition, the mRNA levels corresponding to these differential membrane proteins were further analyzed by quantitative real-time PCR. And the differential expression of arginase-2 was specially validated via Western blotting. Regarding the physiological functions, these proteins are involved in molecular chaperon, cytoskeleton system, cell metabolism, signal transduction, transport and hormone receptor respectively, suggesting the complexity of MP-mediated toxicity to ZFL cell. These data could provide useful insights for better understanding the hepatotoxic mechanisms of MP and develop novel protein biomarkers for effectively monitoring MP contamination level in aquatic environment.

Response of larval barnacle proteome to CO(2)-driven seawater acidification

The majority of benthic marine invertebrates have a complex life cycle, during which the pelagic larvae select a suitable substrate, attach to it, and then metamorphose into benthic adults. Anthropogenic ocean acidification (OA) is postulated to affect larval metamorphic success through an altered protein expression pattern (proteome structure) and post-translational modifications. To test this hypothesis, larvae of an economically and ecologically important barnacle species Balanus amphitrite, were cultured from nauplius to the cyprid stage in the present (control) and in the projected elevated concentrations of CO(2) for the year 2100 (the OA treatment). Cyprid response to OA was analyzed at the total proteome level as well as two protein post-translational modification (phosphorylation and glycosylation) levels using a 2-DE based proteomic approach. The cyprid proteome showed OA-driven changes. Proteins that were differentially up or down regulated by OA come from three major groups, namely those related to energy-metabolism, respiration, and molecular chaperones, illustrating a potential strategy that the barnacle larvae may employ to tolerate OA stress. The differentially expressed proteins were tentatively identified as OA-responsive, effectively creating unique protein expression signatures for OA scenario of 2100. This study showed the promise of using a sentinel and non-model species to examine the impact of OA at the proteome level.

A proteomic analysis of the effects of metal contamination on Sydney Rock Oyster (Saccostrea glomerata) haemolymph

The current study uses proteomics to assess the effects of metal contamination on Sydney Rock oyster haemolymph. Saccostrea glomerata were exposed in aquaria for four days to three environmentally relevant metals (copper, lead or zinc). Oyster haemolymph proteins from metal-exposed oysters were then compared to haemolymph from non-exposed controls using 2-dimensional electrophoresis to identify proteins that differed significantly in intensity. These proteins were then subjected to tandem mass spectrometry so that putative protein identities could be assigned. The data suggest that there are unique protein expression profiles for each metal. Exposure to 100 μg/l of copper, lead or zinc yielded a total of 25 differentially expressed proteins. However, only one of these protein spots exhibited altered intensities in response to all three metals. Eighteen of the 25 spots were significantly affected by just one of the three metals. Differentially expressed proteins were assigned to five different categories of biological function. Proteins affecting shell properties were the most common functional group accounting for 34% of the identified proteins. Cytoskeletal activities and metabolism/stress responses each accounted for a further 25% of the proteins.

Biomarker discovery and proteomic evaluation of cadmium toxicity on a collembolan species, Paronychiurus kimi (Lee)

The goal of this study was to identify promising new biomarkers of cadmium by identifying differentially expressed proteins in Paronychiurus kimi after exposure to cadmium. Through proteomic analysis of P. kimi using 1-D PAGE and nano-LC-MS/MS, 36 downregulated proteins and 40 upregulated proteins were found. Some of the downregulated and upregulated proteins were verified by LC-MS/MS analysis after 2-D PAGE. Downregulated proteins in response to cadmium exposure were involved in glycolysis and energy metabolism, chaperones, transcription, reproduction, and neuron growth. In contrast, proteins involved in glycolysis and energy production, neurogenesis, defense systems response to bacteria, and protein biosynthesis were upregulated in cadmium-treated collembolans. Cubulin may be a potential biomarker for the detection of cadmium in P. kimi since this biomarker was able to low levels (3.5 mg/kg) of cadmium. The 14-3-3 ζ was also found to be a potential biomarker for the detection of medium levels (14 mg/kg) of cadmium. Collembolans may be an alternative tool to humans because many collembolans proteins show a high homology to human proteins.

Review of recent proteomic applications in aquatic toxicology

Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates.

Proteomic analysis of a model fish species exposed to individual pesticides and a binary mixture

Pesticides are nearly ubiquitous in surface waters of the United States, where they often are found as mixtures. The molecular mechanisms underlying the toxic effects of sub-lethal exposure to pesticides as both individual and mixtures are unclear. The current work aims to identify and compare differentially expressed proteins in brains of male fathead minnows (Pimephales promelas) exposed for 72 h to permethrin (7.5 μg/L), terbufos (57.5 μg/L) and a binary mixture of both. Twenty-four proteins were found to be differentially expressed among all three treatments relative to the control using an ANOVA followed by a Dunnett's post hoc test (p ≤0.05). One protein was found to be differentially expressed among all treatment groups and one protein was in common between the terbufos and the mixture group. Fifteen spots were successfully sequenced using LC-MS/MS sequencing. Proteins associated with the ubiquitin-proteasome system, glycolysis, the cytoskeleton and hypoxia were enriched. As a second objective, we attempted to establish protein expression signatures (PES) for individual permethrin and terbufos exposures. We were unable to generate a useable PES for terbufos; however, the permethrin PES was able to distinguish between control and permethrin-exposed individuals in an independent experiment with an accuracy of 87.5%. This PES also accurately classified permethrin exposed individuals when the exposure occurred as part of a mixture. The identification of proteins differentially expressed as a result of pesticide exposure represent a step forward in the understanding of mechanisms of toxicity of permethrin and terbufos. They also allow a comparison of molecular responses of the binary mixture to single exposures. The permethrin PES is the first step in establishing a method to determine exposures in real-world scenarios.

Effects of mercury on Dictyostelium discoideum: proteomics reveals the molecular mechanisms of physiological adaptation and toxicity

Dictyostelium discoideum amoebae were exposed to Hg 2 microM corresponding to a sublethal concentration and Hg 10 microM with the first effects on mortality and replication rate. A total of 900 spots were visualized by 2-DE electrophoresis. Two-hundred fifty single proteins were identified by mass spectrometry. Low Hg concentration (2 microM) treatment induced up-regulation of 13 spots, mainly involved in oxidative stress response/detoxification, oxidoreductase activity, and metabolic processes. High Hg concentration (10 microM) treatment showed a different PES with 12 proteins downregulated and only two up-regulated, mainly involved in cellular metabolic processes, metal ion binding, and transferase activity. The analyses for the carbonylation show no changes after 2 microM Hg(2+) treatment and 13 differentially carbonylated proteins after 10 microM Hg(2+) involved in a broad range of cellular processes. Our findings provide insight into the mechanisms of physiological adaptation and toxicity to a low and an high mercury concentration, respectively, of Dictyostelium amoebae.

Proteins in ecotoxicology - how, why and why not?

The growing interest in the application of proteomic technologies to solve toxicology issues and its relevance in ecotoxicology research has resulted in the emergence of "ecotoxicoproteomics". There is a general consensus that ecotoxicoproteomics is a powerful tool to spot early molecular events involved in toxicant responses, which are responsible for the adverse effects observed at higher levels of biological organization, thus contributing to elucidate the mode of action of stressors and to identify specific biomarkers. Ultimately, early-warning indicators can then be developed and deployed in "in situ" bioassays and in environmental risk assessment. The number of field experiments or laboratory trials using ecologically relevant test-species and involving proteomics has been, until recently, insufficient to allow a critical analysis of the real benefits of the application of this approach to ecotoxicology. This article intends to present an overview on the applications of proteomics in the context of ecotoxicology, focusing mainly on the prospective research to be done in invertebrates. Although these represent around 95% of all animal species and in spite of the key structural and functional roles they play in ecosystems, proteomic research in invertebrates is still in an incipient stage. We will review applications of ecotoxicoproteomics by evaluating the technical methods employed, the organisms and the contexts studied, the advances achieved until now and lastly the limitations yet to overcome will be discussed.

In vivo assessment and potential diagnosis of xenobiotics that perturb the thyroid pathway: Proteomic analysis of Xenopus laevis brain tissue following exposure to model T4 inhibitors

As part of a multi-endpoint systems approach to develop comprehensive methods for assessing endocrine stressors in vertebrates, differential protein profiling was used to investigate expression patterns in the brain of the amphibian model (Xenopus laevis) following in vivo exposure to a suite of T4 synthesis inhibitors. We specifically address the application of Two Dimensional Polyacrylamide Gel Electrophoresis (2D PAGE), Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) and LC-MS/MS to assess changes in relative protein expression levels. 2D PAGE and iTRAQ proved to be effective complementary techniques for distinguishing protein changes in the developing amphibian brain in response to T4 synthesis inhibition. This information served to evaluate the use of distinctive protein profiles as a potential mechanism to screen chemicals for endocrine activity in anurans. Regulatory pathways associated with proteins expressed as a result of chemical effect are reported. To our knowledge, this is also the first account of the anuran larvae brain proteome characterization using proteomic technologies. Correlation of protein changes to other cellular and organism-level responses will aid in the development of a more rapid and cost-effective, non-mammalian screening assay for thyroid axis-disrupting chemicals.

[Variation in protein expression depending on the severity of sleep apnoea-hypopnoea syndrome]

OBJECTIVE

A prospective study with a consecutive sample and a control group to determine whether protein expression in patients with sleep apnoea-hypopnoea syndrome (SAHS) is different from that of the control group (IAH < or =5).

PATIENTS AND METHODS

A total of 32 patients aged between 35 and 60 years who had a polysomnograph performed were included. Patients with an acute or chronic were excluded. The first dimension of the proteomic study was carried out on IPG strips (18cm, pH 4-7) and the second on SDS-PAGE gels in triplicate for each group. The gels were stained with SYPRO-Ruby (Bio-Rad((R))), the images obtained with an FX-Imager laser scanner and the spots were analysed using ProteomWeaver v. 4.0 (Bio-Rad((R))) software. Significant changes between the gels were analysed by replicates and separately, being considered a significant change if the relative intensity of the spots was three times higher or lower than that of the control and if it was observed in 2 of the 3 replicates of each group, with a coefficient of variation of <20%.

RESULTS

The patients were divided into 8 subjects per group (control, mild, moderate and severe). The comparison of the gels showed significant differences between the control group and the 3 clinical groups, with significant over-expression being observed in 3 spots, and under-expression in 7 spots in the control group.

CONCLUSION

There are significant changes in protein expression between a control group and patients in different stages of disease. The proteomic study can identify biomarkers associated with the diagnosis and severity of the SAHS.

Protein expression profiling

Protein expression profiling is defined in general as identifying the proteins expressed in a particular tissue, under a specified set of conditions and at a particular time, usually compared to expression in reference samples. This information is useful in drug discovery and diagnosis as well as in understanding response mechanisms at the protein level. We may identify all the proteins responding to a particular stimulus and select those whose expression changes most. Or we may isolate significant protein variables and then identify them. These definitive sets of proteins (protein expression signatures; PES) are specific to diseases, toxicants, physical stresses, and to degrees of stress severity. Here we describe a method, based on machine learning, for isolating the sets of proteins, before identifying them by name, which classify accurately the treatment classes in a study. The principle in this chapter is that if proteins associated with known classes of interest can be used to identify unknown classes then the proteins are definitive for diagnosis.The proteins in each class, including controls, are converted to digital data and serve as input to artificial neural network (ANN) models. Multiple two-dimensional electrophoresis (2DE) gel patterns are included in each treatment class. A training subset of digitized individual, not composite, gel images is used to construct an ANN model which is then applied to a test set of images. Successful classification of the unknown (test) data confirms that the variables included in the model are indeed significant in discrimination among the classes. In the study described here the misclassifications were 5% or less using the ANN models. The ANN method seems to be a useful complement to image analysis, described in Chapter "Troubleshooting Image Analysis in 2DE". The reduction in protein variables permits multivariable statistics such as cluster and discriminant analyses.

Assessment of Doñana National Park contamination in Procambarus clarkii: integration of conventional biomarkers and proteomic approaches

Aquatic ecosystems of Doñana National Park (DNP) were monitored using Procambarus clarkii as bioindicator in four campaigns carried out between 2003 and 2004 to assess environmental quality possibly threatened by agrochemicals used in nearby areas. An integrated approach was carried out, by combining the responses of well-established biomarkers and the massive analysis of biological effects at the proteomic level. In sites potentially polluted, lower catalase, glucose-6-P dehydrogenase, and esterase activities, and higher malondialdehyde, metallothionein and glutathione levels were found. Two-dimensional gel electrophoresis resolved >2500 gill spots, and image analysis detected that 35 showed significant intensity differences between the reference site and the other seven sites studied. The superiority of proteomic approaches was clearly recognized in our study since four different protein expression patterns were established based in the fold-number of up-/down-regulation of the 35 differentially expressed proteins. Sites located within Doñana Biological Reserve were essentially free of contaminants and those near the DNP limits were only slightly polluted. The higher proteomic responses found at the upper "Rocina" and "Partido" courses indicate that non-persistent agrochemicals are mainly used in Doñana surroundings. The highest responses corresponded to rice growing areas placed between the Guadiamar stream and the Guadalquivir River, according to the extended and intensive use of agrochemicals in such areas.

Analysis of environmental stress response on the proteome level

Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers.

Peroxisomal proteomic approach for protein profiling in blue mussels (Mytilus edulis) exposed to crude oil

Peroxisomal proteomic protein profiles of exposure to marine pollution have been recently introduced in biomonitoring experiments. However, laboratory experiments to study the independent effect of common pollutants are needed to define a minimal protein expression signature (PES) of exposure to a specific pollutant. The aim of this study was to obtain PESs in blue mussels (Mytilus edulis) exposed to two different crude oil mixtures for future application in biomonitoring areas affected by oil spills. In the study, peroxisome-enriched fractions from digestive gland of M. edulis (L., 1758) were analysed by two-dimensional fluorescence difference electrophoresis (DIGE) and mass spectrometry (MS) after 3 weeks of exposure to crude oil mixtures: crude oil or crude oil spiked with alkylated phenols (AP) and extra polycyclic aromatic hydrocarbons (PAH) in a laboratory flow-through system. A minimal PES composed by 13 protein spots and unique PESs of exposure to the two different mixtures were identified. A total of 22 spots from the two-dimensional maps that had shown a significant increase or decrease in abundance in each of the exposed groups exposed were analysed. The hierarchical clustering analysis succeeded in discriminating the exposed groups from the control groups based on the unique PES. The PESs obtained were consistent with protein patterns obtained in previous field experiments. The results suggest that the protein profiles obtained by peroxisomal proteomics could be used to assess oil exposure in marine pollution assessments.

Environmental proteomics and metallomics

Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.

Proteomics-based method for risk assessment of peroxisome proliferating pollutants in the marine environment

Pollution in aquatic environment is of increasing concern for its impact on both human and natural populations. Applying proteomics to monitor marine pollution is a new approach to evaluate the effects of environmental pollutants on the biota. Aquatic organisms living in coastal and estuarine areas are particularly prone to exposures to a variety of pollutants, some of which can act as peroxisome proliferators. However, peroxisomal responses in particular and biomarker responses in general can be influenced by several biotic and abiotic factors. Utilizing proteomics-based techniques that permit the evaluation of hundreds to thousands of proteins in a single experiment can circumvent those drawbacks. Applying this method, the peroxisomal proteome from digestive glands of mussels Mytilus sp. can be analyzed by two-dimensional electrophoresis (2-DE) and the 2-DE maps from control samples and samples obtained in a polluted area can be compared. The up- and down-regulated proteins compose the protein expression signature (PES) associated with exposure to peroxisome proliferating pollutants. This method generates highly reproducible patterns that can be applied to laboratory or field experiments.

Proteomic applications in ecotoxicology

Within the growing body of proteomics studies, issues addressing problems of ecotoxicology are on the rise. Generally speaking, ecotoxicology uses quantitative expression changes of distinct proteins known to be involved in toxicological responses as biomarkers. Unlike these directed approaches, proteomics examines how multiple expression changes are associated with a contamination that is suspected to be detrimental. Consequently, proteins involved in toxicological responses that have not been described previously may be revealed. Following identification of key proteins indicating exposure or effect, proteomics can potentially be employed in environmental risk assessment. To this end, bioinformatics may unveil protein patterns specific to an environmental stress that would constitute a classifier able to distinguish an exposure from a control state. The combined use of sets of marker proteins associated with a given pollution impact may prove to be more reliable, as they are based not only on a few unique markers which are measured independently, but reflect the complexity of a toxicological response. Such a proteomic pattern might also integrate some of the already established biomarkers of environmental toxicity. Proteomics applications in ecotoxicology may also comprise functional examination of known classes of proteins, such as glutathione transferases or metallothioneins, to elucidate their toxicological responses.

Proteomics for the analysis of environmental stress responses in organisms

Thousands of man-made chemicals are constantly released into the environment by agricultural and industrial production processes, traffic, and countless other human activities. Hence, very complex mixtures of anthropogenic chemicals and the transformation products of non-persistent compounds can be found in the aquatic environment. They reflect regional input but are also influenced by long-range transport. Thus, predicting effects on organisms and assessing the quality of a specific ecosystem based on chemical analysis is a challenge. This is not only because of the wide variety of chemicals, with far ranging physicochemical properties, but also because of the sometimes very low effect levels and concerted effects caused by concentration additivity or even synergism. The situation is further complicated by the temporal variability of the exposure concentrations caused, for example, by rain events or regular daily fluctuations as seen in wastewater treatment plant effluents. The analysis of an organism's proteome allows the detection of subtle changes in the level of individual proteins in response to environmental stressors. This potentially leads to the discovery of biomarkers of exposure and helps to gain insights into underlying mechanisms of toxicity. Today, studies using environmental proteomics have investigated many organisms, ranging from microorganisms and plants to invertebrates and vertebrates. Nevertheless, proteomics is a field of environmental research still in its infancy, due to a number of caveats, such as the limited number of organisms fully covered in the sequence databases, the high genetic variability, and the dependence on environmental factors. However, it is gradually becoming an established technology. This review article highlights recent advances in the field of proteomics, mainly focusing on experimental techniques that have the potential to help us understand toxic modes of action and identify novel ecotoxicological biomarkers.

A proteome analysis of Corynebacterium glutamicum after exposure to the herbicide 2,4-dichlorophenoxy acetic acid (2,4-D)

The herbicide 2,4-dichlorophenoxy acetic acid (2,4-D) induces a wide spectrum of toxic responses in living organisms. In this study, we analyzed the stress-induced responses of Corynebacterium glutamicum cells on protein level upon treatment with 2,4-D. For this, growing C. glutamicum cells were exposed to sublethal concentrations of 2,4-D, and changes of the gene expression profiles in comparison to non-exposed organisms were analyzed by two-dimensional gel electrophoresis and mass spectrometry. 2,4-D induced the over-expression of at least six C. glutamicum proteins, four of which could be identified by MALDI-TOF-MS. One protein (Cg2521; long-chain acyl-CoA synthetase) was related to the energy metabolism, and two proteins were involved in cell envelope synthesis (Cg2410; glutamine-dependent amidotransferase, and Cg1672; glycosyltransferase). The last induced protein was the ABC type transport system (Cg2695, ATPase component). The newly observed proteins, except for the ABC transport system, were not in general stress-related proteins, but were specifically expressed upon 2,4-D exposure and, therefore, can be used as respective biomarkers. Moreover, since these proteins seem to play a pivotal role in the adaptation of the cell to 2,4-D, they may help to gain deeper insight into the damage mechanisms of 2,4-D induced in the living cell.

Proteomics-Based Method for the Assessment of Marine Pollution Using Liquid Chromatography Coupled with Two-Dimensional Electrophoresis

Using a proteomic approach, we have developed a new method for the assessment of marine pollution that generates highly reproducible protein expression patterns and it is simple and scalable. The protocol is based on applying liquid chromatography (LC) coupled with two-dimensional electrophoresis (2-DE) to analyze changes in the protein expression pattern after exposure to marine pollution. The digestive gland of the sentinel "blue mussel" (Mytilus edulis) was batch-processed through a simple cell fractionation followed by ion-exchange chromatography and 2-DE. The selection of ligands, elution method, and small volume design was carefully considered to define a protocol that could be mainly robotized. A pilot study with samples collected from different Gothenburg harbor areas indicated that the clean area could be distinguished from the polluted ones based on a protein expression pattern (PES) composed of 13 proteins. Principal component analysis (PCA) and hierarchical clustering confirmed that the PES was sufficient to discriminate polluted and unpolluted areas and to provide a spatial gradient from the polluted source. Several proteins from the PES were identified by electrospray ionization tandem mass spectrometry (ESI-MS/MS), and they are involved in beta-oxidation, amino acid metabolism, detoxification, protein degradation, organelle biogenesis, and protein folding. In the near future, this methodology could show potential advantages to assess marine pollution and could become a stable platform to elucidate ecotoxicological questions.

Proteomics as a route to identification of toxicity targets in environmental toxicology

Ecotoxicology describes a three-way relationship between ecosystems, chemical pollutants and living organisms. It is predicated on the fact that chemical pollution can exert toxic effects on organisms at the individual and population levels. These toxic effects may provide important information to supplement chemical analysis of environmental samples and aid in assessing the environmental quality of specific ecosystems. Traditionally, effects have been detected by means of biomarkers which, of necessity, were often molecules or processes known to be affected by pollutants. Proteomics provides a means of achieving high-throughput analysis of effects on protein populations and sub-populations with the potential to identify novel biomarkers. This review summarises the main approaches currently used in this area and assesses the potential of proteomics for identification of novel toxicity targets.