Mass spectrometry assay as an alternative to the enzyme-linked immunosorbent assay test for biomarker quantitation in ecotoxicology: Application to vitellogenin in Crustacea (Gammarus fossarum)

Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum

Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.

Novel perspectives of environmental proteomics

The connection among genome expression, proteome alteration, metabolism regulation and phenotype change under environmental stresses is very vague. It is a tough task for the traditional research approaches to reveal the related scientific mechanisms of the above connection at molecular and systematic levels. Proteomics approach is an insightful tool for revealing the biological functions, metabolic networks and functional protein interaction networks of cells and organisms under stresses at the systematic level. The purpose of this review is to provide an insightful guideline on how to set up a proteomic investigation for revealing biomolecule mechanisms, protein biomarkers and metabolism networks related to stress response, pollutant recognition, transport and biodegradation, and providing an insightful high-throughput approach for screening functional enzymes and effective microbes based on bioinformatics and functional verification method. Furthermore, the toxicity evaluation of pollutants and byproducts by proteomics approaches provides a scientific insight for early diagnosis of ecological risk and determination of the effectiveness of pollutant treatment techniques.

De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species.

Measurement(s)	transcription profiling assay
Technology Type(s)	RNA sequencing
Factor Type(s)	sex • species
Sample Characteristic - Organism	Gammarus • Echinogammarus
Sample Characteristic - Environment	habitat

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9777905

Wastewater alters feeding rate but not vitellogenin level of Gammarus fossarum (Amphipoda)

Wastewater treatment plant (WWTP) effluents release complex mixtures of organic and inorganic micropollutants, including endocrine disrupting compounds, into receiving water bodies. These substances may cause adverse effects in aquatic communities as well as in ecosystem functions they provide. The aim of this study was to determine the potential impact of secondary treated wastewater released into a small Swiss stream on leaf litter decomposition based on feeding rates of the amphipod shredder Gammarus fossarum measured in situ. Additionally, endocrine disrupting effects downstream of the WWTP were investigated by measuring vitellogenin (vg) induction in male gammarids exposed in situ, as well as estrogen receptor activation using the Yeast Estrogen Screen (YES) involving passive sampler and grab water sample extracts. Extracts were also analysed for 424 organic micropollutants and selected transformation products. Gammarid feeding rate was significantly reduced 100, 200 and 400 m downstream of the WWTP effluent relative to the upstream site. While YES results showed significantly elevated estrogenicity at downstream sites, vg production in male gammarids was not induced. A laboratory experiment, in which gammarids were exposed to WWTP effluent, supported this observation. These results, hence, suggest that treated wastewater released into aquatic ecosystems impairs the ecosystem function of leaf litter decomposition. Vg levels in male gammarids measured by UPLC-MS/MS did, however, not alter.

Mass spectrometry based detection of common vitellogenin peptides across fish species for assessing exposure to estrogenic compounds in aquatic environments

The identification of myriad of chemicals in the environment that mimic hormones and affect the endocrine functions of exposed organism is a daunting analytical challenge for environmental scientists and engineers. Many of these endocrine disrupting chemicals (EDCs) are present at very low concentrations in the aquatic systems, but yet affect the metabolic, developmental, and reproductive functions in exposed fish and wildlife. Vitellogenin (VTG) protein is a widely used biomarker in fish for assessing exposure to EDCs, and is commonly measured using species-specific immunochemical techniques. In this study, we developed a liquid chromatography tandem mass spectrometry (LC-MS/MS) method that can measure common peptides from digested VTG in multiple fish species. In the initial experiments using high resolution mass spectrometry, two peptides (ALHPELR and FIELIQLLR) were identified as common fragments in the digested VTG protein isolated from three different fish species (Pimephales promelas, Micropterus salmoides, and Fundulus heteroclitus). Then, a quantitative analysis using LC-MS/MS under selected reaction monitoring mode was developed for the detection of these two peptides in trypsin-digested plasma from female fish (positive control), estrogen-exposed male fish (test sample), and unexposed male fish (negative control) using two of the same species used for identifying the common peptides (P. promelas, and M. salmoides) and one new species (Ameiurus nebulosus) that was not included during the selection of peptides. Results from this study demonstrate the potential of LC-MS/MS as an effective cross-species method to detect VTG in fish, which can be an alternative analytical technique for assessing endocrine disruption in multiple fish species.

Identification, expression, and endocrine-disruption of three ecdysone-responsive genes in the sentinel species Gammarus fossarum

Taking advantage of a large transcriptomic dataset recently obtained in the sentinel crustacean amphipod Gammarus fossarum, we developed an approach based on sequence similarity and phylogenetic reconstruction to identify key players involved in the endocrine regulation of G. fossarum. Our work identified three genes of interest: the nuclear receptors RXR and E75, and the regulator broad-complex (BR). Their involvement in the regulation of molting and reproduction, along with their sensitivity to chemical contamination were experimentally assessed by studying gene expression during the female reproductive cycle, and after laboratory exposure to model endocrine disrupting compounds (EDCs): pyriproxyfen, tebufenozide and piperonyl butoxide. RXR expression suggested a role of this gene in ecdysis and post-molting processes. E75 presented two expression peaks that suggested a role in vitellogenesis, and molting. BR expression showed no variation during molting/reproductive cycle. After exposure to the three EDCs, a strong inhibition of the inter-molt E75 peak was observed with tebufenozide, and an induction of RXR after exposure to pyriproxyfen and piperonyl butoxide. These results confirm the implication of RXR and E75 in hormonal regulation of female reproductive cycles in G. fossarum and their sensitivity towards EDCs opens the possibility of using them as specific endocrine disruption biomarkers.

Controversial use of vitellogenin as a biomarker of endocrine disruption in crustaceans: New adverse pieces of evidence in the copepod Eurytemora affinis

In recent years, the interest in the use of vitellogenin (VTG) as a biomarker of endocrine disruption in fish has led to VTG being considered as a potential tool in invertebrates. Among aquatic invertebrate models in ecotoxicology, the copepods are considered as reference species in marine, estuarine and freshwater ecosystems. In this context, we identified a VTG cDNA in Eurytemora affinis. The Ea-VTG2 cDNA is 5416bp in length with an open reading frame (ORF) of 5310bp that encodes a putative protein of 1769 amino acids residues. Phylogenetic analysis confirmed the hypothesis of a VTG duplication event before the emergence of the copepod species. The analysis of the Ea-VTG2 expression by qPCR in males and females according to their reproductive stages allowed transcript basal levels to be determined. The expression pattern revealed a gradual increase of transcript levels during maturation in females. Important inter-sex differences were observed with a VTG level in males ranging from about 1900- to 6800-fold lower than in females depending on their stage. Moreover, the protein was only detected in ovigerous females. The inducibility of Ea-VTG2 by chemicals was studied in males exposed to either a model of endocrine disruptor in vertebrates i.e. 4-nonylphenol (4-NP) or a crustacean hormone i.e. Methyl Farnesoate (MF), and in males sampled from a multi-contaminated estuary. No induction was highlighted. The VTG should not be considered as an appropriate biomarker in E. affinis as previously suggested for other crustaceans.

Assessing the relevance of a multiplexed methodology for proteomic biomarker measurement in the invertebrate species Gammarus fossarum: A physiological and ecotoxicological study

Recently, a protein sequence database was built specifically for the sentinel non-model species Gammarus fossarum using a proteogenomics approach. A quantitative multiplexed targeted proteomics assay (using Selected Reaction Monitoring mass spectrometry) was then developed for a fast and simultaneous quantification of dozens of biomarker peptides specific of this freshwater sentinel crustacean species. In order to assess the relevance of this breakthrough methodology in ecotoxicology, the response patterns of a panel of 26 peptides reporting for 20 proteins from the Gammarus fossarum proteome with putative key functional roles (homeostasis, osmoregulation, nutrition, reproduction, molting,…) were recorded through male and female reproductive cycles and after exposure to environmental concentrations of cadmium and lead in laboratory-controlled conditions. Based on these results, we validated the implication of annotated vtg-like peptides in the oogenesis process, and the implication of Na⁺/K⁺ ATPase proteins in the molt cycle of organisms. Upon metal (cadmium and lead) contamination, peptides belonging to proteins annotated as involved in antioxidant and detoxification functions, immunity and molting were significantly down-regulated. Overall, this multiplex assay allowed gaining relevant insights upon disruption of different main functions in the sentinel species Gammarus fossarum. This breakthrough methodology in ecotoxicology offers a valid and high throughput alternative to currently used protocols, paving the way for future practical applications of proteogenomics-derived protein biomarkers in chemical risk assessment and environmental monitoring.

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.

Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods

Because of their ecological importance, amphipod crustacea are employed worldwide as test species in environmental risk assessment. Although proteomics allows new insights into the molecular mechanisms related to the stress response, such investigations are rare for these organisms because of the lack of comprehensive protein sequence databases. Here, we propose a proteogenomic approach for identifying specific proteins of the freshwater amphipod Gammarus fossarum, a keystone species in European freshwater ecosystems. After deep RNA sequencing, we created a comprehensive ORF database. We identified and annotated the most relevant proteins detected through a shotgun tandem mass spectrometry analysis carried out on the proteomes from three major tissues involved in the organism's reproductive function: the male and female reproductive systems, and the cephalon, where different neuroendocrine glands are present. The 1,873 mass-spectrometry-certified proteins represent the largest crustacean proteomic resource to date, with 218 proteins being lineage specific. Comparative proteomics between the male and female reproductive systems indicated key proteins with strong sexual dimorphism. Protein expression profiles during spermatogenesis at seven different stages highlighted the major gammarid proteins involved in the different facets of reproduction.

Vitellogenin is not an appropriate biomarker of feminisation in a crustacean

The expression of the yolk protein vitellogenin (Vtg) has been used as a biomarker of feminisation in multiple fish species throughout the world. Since the late 1990s, researchers have attempted to develop similar biomarkers to address whether reproductive endocrine disruption also occurs in the males of invertebrate groups such as the Crustacea. To date, the vast majority of studies investigating Vtg induction in male Crustacea have resulted in negative or inconclusive results, leading researchers to question the utility of Vtg expression as a biomarker in this taxon. This study measured the expression of Vtg genes in two intersex phenotypes (termed internal and external) found in the male amphipod, Echinogammarus marinus, and compared them with those of normal males and females. Males presenting the external intersex phenotype are infected with known feminising parasites and display a variety of feminised traits including oviduct structures on their testes and external female brood plates (oostegites). The internal intersex male phenotype, that displays a pronounced oviduct structure on the testes without the external intersex characteristics, is not parasite infected and it is thought to be a result of environmental contamination. Given their morphology, these phenotypes might be considered highly 'feminised' or 'de-masculinised' and can be utilised to test the suitability of feminisation biomarkers. The E. marinus transcriptome was searched for genes resembling Vtg and two sequences were revealed, that we subsequently refer to as Vtg1 and Vtg2. Results from a high-throughput transcriptomic sequencing screen of gonadal cDNA libraries suggested that very low expression (in this manuscript gene transcription is taken to represent gene expression, although it is acknowledged that in addition to transcription, translation, transcript processing, mRNA stability and protein stability can regulate gene expression) of Vtg1 and Vtg2 in normal males (ESTs=1 and 0 for Vtg1 and Vtg2, respectively), internal intersex males (ESTs=0 for both Vtg sequences) and external intersex males (ESTs=5 and 0 for Vtg1 and Vtg2, respectively). In contrast, the sequencing suggested notable levels of expression of both Vtg genes in females (ESTs=1133 and 84 for Vtg1 and Vtg2, respectively). Subsequent qPCR analysis validates these expression levels, with the signal for Vtg1 and Vtg2 transcripts in all male phenotypes being indistinguishable from that caused by contamination of trace levels of genomic DNA or the low-level amplification non-target sequences. These findings suggest that Vtg expression is not notably induced in highly feminised amphipods and is therefore not an appropriate biomarker of feminisation/de-masculination in crustaceans. We discuss our findings in the context of previous attempts to measure Vtg in male crustaceans and suggest a requirement for more appropriate taxon-specific biomarkers to monitor feminisation in these groups.

Next generation of food allergen quantification using mass spectrometric systems

Food allergies are increasing worldwide and becoming a public health concern. Food legislation requires detailed declarations of potential allergens in food products and therefore an increased capability to analyze for the presence of food allergens. Currently, antibody-based methods are mainly utilized to quantify allergens; however, these methods have several disadvantages. Recently, mass spectrometry (MS) techniques have been developed and applied to food allergen analysis. At present, 46 allergens from 11 different food sources have been characterized using different MS approaches and some specific signature peptides have been published. However, quantification of allergens using MS is not routinely employed. This review compares the different aspects of food allergen quantification using advanced MS techniques including multiple reaction monitoring. The latter provides low limits of quantification for multiple allergens in simple or complex food matrices, while being robust and reproducible. This review provides an overview of current approaches to analyze food allergens, with specific focus on MS systems and applications.

Hydrophilic interaction liquid chromatography as second dimension in multidimensional chromatography with an anionic trapping strategy: application to prostate-specific antigen quantification

Liquid chromatography (LC) coupled with tandem mass spectrometry (MS-MS) in selected reaction monitoring mode (SRM) has become a widely used technique for the quantification of protein biomarkers in plasma and has already proven to give similar results compared to the conventional immunoassays. To improve the lack of insufficient sensitivity for quantification of low abundance protein, we propose a new two dimensional liquid chromatography (2D-LC-SRM) method for the quantitation of prostate specific antigen (PSA) in human plasma. The method centers on anion exchange cartridge between reversed-phase chromatography and hydrophilic interaction liquid chromatography (HILIC) in an on-line arrangement. The use of the anionic cartridge allows an easier online transfer of the analytes between both dimensions. Moreover, it provides an additional selectivity since the more basic peptides are not retained on this support. This setup has been applied to the quantification of prostate specific antigen (PSA) protein in plasma on a previous generation of mass spectrometer, which enabled a limit of quantification (LOQ) of 1ng/mL without any upfront immuno-depletion or intense off-line fractionation before the SRM analysis. The obtained LOQ is compatible with the required sensitivity for the clinically relevant plasma-based PSA tests.

Vitellogenin-like protein measurement in caged Gammarus fossarum males as a biomarker of endocrine disruptor exposure: inconclusive experience

A vitellogenin (Vg) mass spectrometry-based assay was recently developed to actively biomonitor and assess the exposure of the amphipod Gammarus fossarum to endocrine-disrupting chemicals in freshwater hydrosystems. This paper focuses on the appropriate use of this biomarker, which requires good knowledge of its basal level in males and its natural variability related to intrinsic biotic and environmental abiotic factors. To obtain the lowest biomarker variability, we first studied some of these confounding factors. We observed that the spermatogenesis stage did not have an impact on the Vg level, allowing flexibility in the choice of transplanted gammarids. In the second part of the study, males were transplanted in two clean stations for 21 days, with results indicating a spatial and temporal variability of Vg levels. These Vg changes could not be correlated to environmental factors (e.g., temperature, pH and hardness of waters). Vg induction was then assessed in 21 stations having various levels of contamination. Inductions were observed for only two of the impacted stations studied. Under reference and contaminated conditions, a high interindividual variability of Vg levels was observed in caged organisms, severely limiting the sensitivity of the biomarker and its ability to detect a significant endocrine-disruptor effect. This may be explained by unidentified environmental factors that should later be determined to improved the use of Vg as a biomarker in male G. fossarum. Moreover, as discussed in this paper, recent advancements regarding the pleiotropic functions of the Vg gene in some species may complicate the application of this biomarker in males of invertebrate species.

Vitellogenin-like proteins among invertebrate species diversity: potential of proteomic mass spectrometry for biomarker development

Cost-effective methodologies along with cross-species applicability constitute key points for biomarker development in ecotoxicology. With the advent of cheaper affordable genomic techniques and high throughput sequencing, omics tools could facilitate the assessment of effects of environmental contaminants for all taxa biodiversity. We assessed the potential of absolute quantification of proteins using mass spectrometry to develop vitellogenin (Vg)-like protein assays for invertebrates. We used available sequences in public databases to rapidly identify Vg-proteotypic peptides in seven species from different main taxa of protostome invertebrates (mollusk bivalves, crustacean amphipods, branchiopods, copepods and isopods, and insect diptera). Functional validation was performed by comparing proteomic signals from reproductive female tissue samples and negative controls (male or juvenile tissues). In a second part, we demonstrate in gammarids, daphnids, drosophilids, and gastropods that the assay validated in Vg-sequenced species can be applied to Vg-unsequenced species thanks to the evolutionary conservation of Vg-proteotypic peptide motifs. Finally, we discuss the relevance of mass spectrometry for biomarker development (specific measurement, rapid development, transferability across species). Our study supplies an illustration of the promising strategy to address the challenge of biodiversity in ecotoxicology, which consists in employing omics tools from comparative and evolutionary perspectives.

Vitellogenin-like proteins in the freshwater amphipod Gammarus fossarum (Koch, 1835): functional characterization throughout reproductive process, potential for use as an indicator of oocyte quality and endocrine disruption biomarker in males

This work focused on the validation of biological specificity of the quantitative LC-MS/MS assay by checking the natural variability of Vg levels during the reproductive cycle in Gammarus fossarum (i.e., including oogenesis and embryogenesis). Laboratory tests were performed for 21 days under controlled conditions to assess Vg changes in male and female gammarids after exposure to chemical stress. Females were exposed to two crustacean hormones, 20-hydroxyecdysone (0.01, 1 and 100 μg L⁻¹) and methyl-farnesoate (0.01, 1 and 100 μg L⁻¹). No effect was recorded for 20-hydroxyecdysone, whereas in females exposed to methyl-farnesoate a deleterious impact on Vg production was observed. Males were exposed to crustacean hormones 20-hydroxyecdysone (0.01, 1 and 100 μg L⁻¹) and methyl-farnesoate (0.01, 1 and 100 μg L⁻¹), the insecticide methoxyfenozide (0.001, 0.1 and 10 μg L⁻¹), the fungicide propiconazole (0.001, 0.1, 10 and 1000 μg L⁻¹), and the pharmaceutical products benzophenone, carbamazepine, cyproterone, and R-propranolol (0.001, 0.1, 10 and 1000 μg L⁻¹). Induction of Vg synthesis was recorded in males exposed to cyproterone, methoxyfenozide, methyl-farnesoate, and propiconazole. Finally, we validated the function of the ILIPGVGK peptide used to track vitellogenin in G. fossarum across reproductive processes (vitellogenesis and embryogenesis), and results confirmed the energy reserve role of Vg during embryo development. We show that oocyte surface measurement is directly related to Vg levels in the oocyte, constituting a reliable indicator of egg quality in G. fossarum. Consequently, it could be used as a reliable tool for biomonitoring programs. We recorded induction of Vg in male G. fossarum; however, the possible use of this tool as a specific biomarker of exposure to endocrine disruption should be confirmed in further studies.

Review of the reproductive biology of amphipods and their endocrine regulation: identification of mechanistic pathways for reproductive toxicants

The reproductive biology of amphipods is reviewed to update the knowledge of the male and female reproductive processes of oogenesis and spermatogenesis as well as the endocrine systems of amphipods with the aim of advancing studies of reproductive toxicology. The ovarian and reproduction cycles of female gammaridean amphipods are closely correlated with the molt cycle, which is under direct control by the steroid hormone 20-hydroxyecdysone. The ability of males to copulate and subsequently for females to ovulate is restricted to the early postmolt period of the females. New developments in our understanding of the molt cycle and the endocrine regulatory pathways for reproduction using genomics techniques on other crustacean species are also discussed. The arthropod sterol ponasterone A or xenobiotics such as the fungicide fenarimol have been shown to elicit endocrine disruption in some crustaceans by acting as an agonist for 20-hydroxyecdysone at the ecdysone receptor or by inhibiting the synthesis of 20-hydroxyecdysone, respectively, resulting in disruption of molting and reproduction. Recent studies suggest that cadmium can inhibit secondary vitellogenesis in amphipods. Experimental approaches for examining the metabolic pathways associated with ecdysteroid hormonal signaling or metabolism, exoskeleton maintenance and molting, and the regulation of vitellogenin in amphipods are discussed. This information should aid in the identification of useful biomarkers for reproductive toxicity.