Hepatic proteome analysis of Atlantic salmon (Salmo salar) after exposure to environmental concentrations of human pharmaceuticals

Proteomic analysis in the brain and liver of sea bream (Sparus aurata) exposed to the antibiotics ciprofloxacin, sulfadiazine, and trimethoprim

Antibiotics, frequently detected in aquatic ecosystems, can negatively impact the health of resident organisms. Although the study on the possible effects of antibiotics on these organisms has been increasing, there is still little information available on the molecular effects on exposed non-target organisms. In our study we used a label free proteomic approach and sea bream, Sparus aurata, to evaluate the effects of exposure to environmentally relevant concentrations of the antibiotic compounds ciprofloxacin (CIP), sulfadiazine (SULF) and trimethoprim (TRIM) produced at the protein level. Individuals of sea bream were exposed to single compounds at 5.2 ± 2.1 μg L-1 of CIP, 3.8 ± 2.7 μg L-1 of SULF and 25.7 ± 10.8 μg L-1 of TRIM for 21 days. After exposure, the number of differentially expressed proteins in the liver was 39, 73 and 4 for CIP, SULF and TRIM respectively. In the brain, there was no alteration of proteins after CIP and TRIM treatment, while 9 proteins were impacted after SULF treatment. The differentially expressed proteins were involved in cellular biological, metabolic, developmental, growth and biological regulatory processes. Overall, our study evidences the vulnerability of Sparus aurata, after exposure to environmentally relevant concentrations of the major antibiotics CIP, SULF and TRIM and that their chronic exposure could lead to a stress situation, altering the proteomic profile of key organs such as brain and liver.

Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species

New approach methodologies (NAM), including omics and in vitro approaches, are contributing to the implementation of 3R (reduction, refinement and replacement) strategies in regulatory science and risk assessment. In this study, we present an integrative transcriptomics and proteomics analysis workflow for the validation and revision of complex fish genomes and demonstrate how proteogenomics expression matrices can be used to support multi-level omics data integration in non-model species in vivo and in vitro. Using Atlantic salmon as an example, we constructed proteogenomic databases from publicly available transcriptomic data and in-house generated RNA-Seq and LC-MS/MS data. Our analysis identified ∼80,000 peptides, providing direct evidence of translation for over 40,000 RefSeq structures. The data also highlighted 183 co-located peptide groups that supported a single transcript each, and in each case, either corrected a previous annotation, supported Ensembl annotations not present in RefSeq, or identified novel previously unannotated genes. Proteogenomics data-derived expression matrices revealed distinct profiles for the different tissue types analyzed. Focusing on proteins involved in defense against xenobiotics, we detected distinct expression patterns across different salmon tissues and observed homology in the expression of chemical defense proteins between in vivo and in vitro liver systems. Our study demonstrates the potential of proteogenomic analyses in extending our understanding of complex fish genomes and provides an advanced bioinformatic toolkit to support the further development of NAMs and their application in regulatory science and (eco)toxicological studies of non-model species.

Multi-level assessment of the origin, feeding area and organohalogen contamination on salmon from the Baltic Sea

The Atlantic salmon (Salmo salar) population in the Baltic Sea consists of wild and hatchery-reared fish that have been released into the sea to support salmon stocks. During feeding migration, salmon migrate to different parts of the Baltic Sea and are exposed to various biotic and abiotic stressors, such as organohalogen compounds (OHCs). The effects of salmon origin (wild or hatchery-reared), feeding area (Baltic Main Basin, Bothnian Sea, and Gulf of Finland), and OHC concentration on the differences in hepatic proteome of salmon were investigated. Multi-level analysis of the OHC concentration, transcriptome, proteome, and oxidative stress biomarkers measured from the same salmon individuals were performed to find the key variables (origin, feeding area, OHC concentrations, and oxidative stress) that best account for the differences in the transcriptome and proteome between the salmon groups. When comparing wild and hatchery-reared salmon, differences were found in xenobiotic and amino acid metabolism-related pathways. When comparing salmon from different feeding areas, the amino acid and carbohydrate metabolic pathways were notably different. Several proteins found in these pathways are correlated with the concentrations of polychlorinated biphenyls (PCBs). The multi-level analysis also revealed amino acid metabolic pathways in connection with PCBs and oxidative stress variables related to glutathione metabolism. Other pathways found in the multi-level analysis included genetic information processes related to ribosomes, signaling and cellular processes related to the cytoskeleton, and the immune system, which were connected mainly to the concentrations of Polychlorinated biphenyls and Dichlorodiphenyltrichloroethane and their metabolites. These results suggest that the hepatic proteome of salmon in the Baltic Sea, together with the transcriptome, is more affected by the OHC concentrations and oxidative stress of the feeding area than the origin of the salmon.

A synthesis on the sub-lethal toxicity of atenolol, a beta-blocker, in teleost fish

Blood pressure medications like atenolol are detected in aquatic ecosystems. The objectives here were to (1) map the global presence of atenolol in surface water and sewage; (2) present current knowledge regarding removal efficiency and degradation of atenolol; (3) identify biological endpoints sensitive to exposure; (4) reveal molecular biomarkers that may be useful for exposure studies in fish; (5) determine whether toxicology studies are within environmental relevance. In fish, atenolol exposure affects endocrine and immune systems, metabolism, and epigenetics. Fewer than half of all studies measuring biological responses use environmentally-relevant concentrations. Heart rate appeared most sensitive to atenolol exposure relative to other endpoints. Data are lacking for behavioral responses to atenolol. Molecular biomarkers for atenolol may include those associated with acute kidney injury, cholestasis, and hypertriglyceridemia. Head kidney and liver may therefore be useful for detecting atenolol-induced effects. This review synthesizes knowledge regarding atenolol-induced toxicity in fish.

Variant expression signatures of microRNAs and protein related to growth in a crossbreed between two strains of Nile tilapia (Oreochromis niloticus)

Nile tilapia (Oreochromis niloticus) is a species of worldwide importance for aquaculture. A crossbred lineage was developed through introgressive backcross breeding techniques and combines the high growth performance of the Chitralada (CHIT) lwith attractive reddish color of the Red Stirling (REDS) strains. Since the crossbreed has an unknown genetically improved background, the objective of this work was to characterize expression signatures that portray the advantageous phenotype of the crossbreeds. We characterized the microRNA transcriptome by high throughput sequencing (RNA-seq) and the proteome through mass spectrometry (ESI-Q-TOF-MS) and applied bioinformatics for the comparative analysis of such molecular data on the three strains. Crossbreed expressed a distinct set of miRNAs and proteins compared to the parents. They comprised several microRNAs regulate traits of economic interest. Proteomic profiles revealed differences between parental and crossbreed in expression of proteins associated with glycolisis. Distinctive miRNA and protein signatures contribute to the phenotype of crossbreed.

Proteomic changes in the solitary ascidian Herdmania momus following exposure to the anticonvulsant medication carbamazepine

The increasing use of pharmaceuticals in human and veterinary medicine, along with their poor removal rates at wastewater treatment facilities is resulting in the chronic release of pharmaceutically-active compounds (PhACs) into the marine environment, where they pose a threat to non-target organisms. A useful approach, as applied in the current study for assessing the effects of PhACs on non-target organisms, is the proteomic approach: the large-scale study of an organism's proteins. Using 'shotgun' proteomics, we identified differentially-expressed proteins based on peptide fragments in the solitary ascidian, Herdmania momus, following a 14-day laboratory experimental exposure to the PhAC carbamazepine (CBZ), an anticonvulsant and antidepressant medication, frequently detected in the aquatic environment. Individuals were exposed to environmentally relevant concentrations: 5 or 10 µg/L of CBZ, in addition to a control treatment. Out of 199 identified proteins, 24 were differentially expressed (12%) between the treatment groups, and thus can potentially be developed as biomarkers for CBZ contamination. Ascidians' phylogenetic position within the closest sister group to vertebrates presents an advantage in examining the pathological effects of PhACs on vertebrate-related organs and systems. Together with the world-wide distribution of some model ascidian species, and their ability to flourish in pristine and polluted sites, they provide a promising tool through which to study the extent and effects of PhAC contamination on marine organisms.

Protein Signatures to Trace Seafood Contamination and Processing

This review presents some applications of proteomics and selected spectroscopic methods to validate certain aspects of seafood traceability. After a general introduction to traceability and the initial applications of proteomics to authenticate traceability information, it addresses the application of proteomics to trace seafood exposure to some increasingly abundant emergent health hazards with the potential to indicate the geographic/environmental origin, such as microplastics, triclosan and human medicinal and recreational drugs. Thereafter, it shows the application of vibrational spectroscopy (Fourier-Transform Infrared Spectroscopy (FTIR) and Fourier-Transform Raman Spectroscopy (FT Raman)) and Low Field Nuclear Magnetic Resonance (LF-NMR) relaxometry to discriminate frozen fish from thawed fish and to estimate the time and temperature history of frozen fillets by monitoring protein modifications induced by processing and storage. The review concludes indicating near future trends in the application of these techniques to ensure seafood safety and traceability.

Environmentally relevant concentrations of carbamazepine induce liver histopathological changes and a gender-specific response in hepatic proteome of Chinese rare minnows (Gobiocypris rarus)

To assess hepatotoxicity and to determine the underlying mechanisms of carbamazepine (CBZ) toxicity in fish, histopathology and the liver proteome were examined after Chinese rare minnow (Gobiocypris rarus) were exposed to 1, 10, and 100 μg/L CBZ for 28 days. Histopathological changes included disruption of spatial structure, pyknotic nuclei, cellular vacuolization and deformation of cell nuclei, in addition to marked swelling of hepatocytes in all treatment groups. Protein analysis revealed that there were gender-specific responses in rare minnow following exposure, and there were 47 proteins in females and 22 proteins in males identified as differentially abundant following CBZ treatments. Pathway analysis revealed that cellular processes affected by CBZ included apoptosis, cell differentiation, cell proliferation, and the respiratory chain, indicating impaired energy homeostasis. Noteworthy was that 15 proteins identified as different in abundance were associated with carcinogenicity. Relative mRNA levels for select transcripts were consistent with the changes of proteins N-myc downstream regulated gene (NDRG), Tropomyosin 2-Beta (TPM2) and annexin A4 (ANXA4). Protein pyruvate kinase, liver and RBC (PKLR) were increased at 1 and 100 μg/L CBZ without significant difference in transcript levels. These findings characterize molecular responses and histological changes in the liver that generate new insights into CBZ hepatotoxicity in Chinese rare minnow.

Top-Down Proteomics and Farm Animal and Aquatic Sciences

Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

Proteomic changes in Corbicula fluminea exposed to wastewater from a psychiatric hospital

The increase use of pharmaceutical compounds in veterinary practice and human population results in the ubiquitous presence of these compounds in aquatic ecosystems. Because pharmaceuticals are highly bioactive, there is concern about their toxicological effects in aquatic organisms. Therefore, the aim of this study was to assess the effects of an effluent from a psychiatric hospital (containing a complex mixture of 25 pharmaceutical compounds from eleven therapeutic classes) on the freshwater clam Corbicula fluminea using a proteomic approach. The exposure of C. fluminea to this complex effluent containing anxiolytics, analgesics, lipid regulators, beta blockers, antidepressants, antiepileptics, antihistamines, antihypertensives, antiplatelets and antiarrhythmics induced protein changes after 1 day of exposure in clam gills and digestive gland more evident in the digestive gland. These changes included increase in the abundance of proteins associated with structural (actin and tubulin), cellular functions (calreticulin, proliferating cell nuclear antigen (PCNA), T complex protein 1 (TCP1)) and metabolism (aldehyde dehydrogenase (ALDH), alcohol dehydrogenase, 6 phosphogluconate dehydrogenase). Results from this study indicate that calreticulin, PCNA, ALDH and alcohol dehydrogenase in the digestive gland and T complex protein 1 (TCP1)) and 6 phosphogluconate dehydrogenase in the gills represent useful biomarkers for the ecotoxicological characterization of psychiatric hospital effluents in this species.

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.