Unveiling the potential of proteomics in addressing food and feed safety challenges

The food and feed sector in Europe is rapidly evolving to address contemporary challenges, striving for fairer, safer, greener and more sustainable food systems. This includes the exploration of new protein sources for human consumption and animal feed such as protein derived from insects, algae or novel plant-derived proteins, and the re-evaluation of existing sources like processed animal protein (PAP). To generate reliable data on the diverse array of emerging protein sources for future food and feed safety assessments, a growing demand for the development and implementation of advanced analytical techniques exists. New approach methodologies (NAMs) including, mass spectrometry (MS)-based proteomics methods have been emerging as valuable techniques which potentially can be implemented in regulatory laboratory settings to complement conventional approaches in this realm. These MS-driven strategies have already proven their utility in diverse applications, including the detection of prohibited substances in feed, identification of allergens, differentiation of fish species in complex mixtures for fraud detection and the verification of novel foods and alternative protein sources. This EU-FORA programme was focused on three core objectives namely: (i) the training of the fellow in utilising MS-based proteomics for food and feed safety analyses, (ii) the involvement of the fellow in the development of standardised operating procedures (SOP) for targeted and non-targeted proteomic MS-based workflows for species and tissues specific PAP identification in a national reference laboratory (NRL) and (iii) the transfer and implementation of MS-based approaches and standardised protocols for PAP analysis at the fellow's home institution. Altogether, this programme facilitates the broadening and diversification of use of MS-based proteomic methodologies for reinforcing their significance within the domains of food and feed safety research and regulatory science applications.

Identification of candidate biomarkers of the exposure to PCBs in contaminated cattle: A gene expression- and proteomic-based approach

Dioxins and polychlorinated biphenyls (PCBs) are widespread and persistent contaminants. Through a combined gene expression/proteomic-based approach, candidate biomarkers of the exposure to such environmental pollutants in cattle subjected to a real eco-contamination event were identified. Animals were removed from the polluted area and fed a standard ration for 6 months. The decontamination was monitored by evaluating dioxin and PCB levels in pericaudal fat two weeks after the removal from the contaminated area (day 0) and then bimonthly for six months (days 59, 125 and 188). Gene expression measurements demonstrated that CYP1B1 expression was significantly higher in blood lymphocytes collected in contaminated animals (day 0), and decreased over time during decontamination. mRNA levels of interleukin 2 showed an opposite quantitative trend. MALDI-TOF-MS polypeptide profiling of serum samples ascertained a progressive decrease (from day 0 to 188) of serum levels of fibrinogen β-chain and serpin A3-7-like fragments, apolipoprotein (APO) C-II and serum amyloid A-4 protein, along with an augmented representation of transthyretin isoforms, as well as APOC-III and APOA-II proteins during decontamination. When differentially represented species were combined with serum antioxidant, acute phase and proinflammatory protein levels already ascertained in the same animals (Cigliano et al., 2016), bioinformatics unveiled an interaction network linking together almost all components. This suggests the occurrence of a complex PCB-responsive mechanism associated with animal contamination/decontamination, including a cohort of protein/polypeptide species involved in blood redox homeostasis, inflammation and lipid transport. All together, these results suggest the use in combination of such biomarkers for identifying PCB-contaminated animals, and for monitoring the restoring of their healthy condition following a decontamination process.

Current trends in mass spectrometry of peptides and proteins: Application to veterinary and sports-doping control

Detection of misuse of peptides and proteins as growth promoters is a major issue for sport and food regulatory agencies. The limitations of current analytical detection strategies for this class of compounds, in combination with their efficacy in growth-promoting effects, make peptide and protein drugs highly susceptible to abuse by either athletes or farmers who seek for products to illicitly enhance muscle growth. Mass spectrometry (MS) for qualitative analysis of peptides and proteins is well-established, particularly due to tremendous efforts in the proteomics community. Similarly, due to advancements in targeted proteomic strategies and the rapid growth of protein-based biopharmaceuticals, MS for quantitative analysis of peptides and proteins is becoming more widely accepted. These continuous advances in MS instrumentation and MS-based methodologies offer enormous opportunities for detection and confirmation of peptides and proteins. Therefore, MS seems to be the method of choice to improve the qualitative and quantitative analysis of peptide and proteins with growth-promoting properties. This review aims to address the opportunities of MS for peptide and protein analysis in veterinary control and sports-doping control with a particular focus on detection of illicit growth promotion. An overview of potential peptide and protein targets, including their amino acid sequence characteristics and current MS-based detection strategies is, therefore, provided. Furthermore, improvements of current and new detection strategies with state-of-the-art MS instrumentation are discussed for qualitative and quantitative approaches.

Farm animal serum proteomics and impact on human health

Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum proteomics in order to identify novel biomarkers for animal welfare, early diagnosis, prognosis and monitoring of infectious disease treatment, and develop new vaccines, aiming at determining the reciprocal benefits for humans and animals.

MALDI MS imaging analysis of apolipoprotein E and lysyl oxidase-like 1 in human lens capsules affected by pseudoexfoliation syndrome

Pseudoexfoliation (PEX) syndrome is an age-related systemic disease of the extracellular matrix, characterized by the presence of amyloid-like fibrillar deposits on the anterior lens capsule. The pathological deposits (PEX material) can obstruct aqueous outflow leading to increased intraocular pressure that in turn can result in glaucoma. PEX syndrome is the most common risk factor for glaucoma. In our previous work, we reported a protocol for the analysis of human lens capsules by MALDI MS imaging. Here, we extend our previous work applying the developed protocol to the analysis of human lens capsules affected by PEX syndrome. We focus our investigation on known components of the PEX material, namely lysyl oxidase-like 1 (LOXL1) and apolipoprotein E (APOE). Our results show that LOXL1 is more abundant in the deposits in the iris region and, alternatively APOE is concentrated in the PEX material accumulated in the pupillary area of the anterior lens capsule. Furthermore, we identify potentially relevant post-translational modifications which may have an important role in promoting the cross-linking processes in PEX syndrome and stabilize aggregate structures within the proteinaceous PEX material.

BIOLOGICAL SIGNIFICANCE

This paper is about the identification and localization of apolipoprotein E and lysyl oxidase-like 1 in human lens capsules affected by PEX syndrome by MALDI MS imaging. With this study we expand the clinical application of MALDI MSI toward the use of non-sectioned tissue samples analyzed after in situ enzymatic digestion and advance the knowledge regarding a common pathology like PEX syndrome.

Effect-based proteomic detection of growth promoter abuse

Unregulated growth promoter use in food-producing animals is an issue of concern both from food safety and animal welfare perspectives. However, the monitoring of such practices is analytically challenging due to the concerted actions of users to evade detection. Techniques based on the monitoring of biological responses to exogenous administrations have been proposed as more sensitive methods to identify treated animals. This study has, for the first time, profiled plasma proteome responses in bovine animals to treatment with nortestosterone decanoate and 17β-oestradiol benzoate, followed by dexamethasone administration. Two-dimensional fluorescence differential in-gel electrophoresis analysis revealed a series of hepatic and acute-phase proteins within plasma whose levels were up- or down-regulated within phases of the treatment regime. Surface plasmon resonance (SPR) immuno-assays were developed to quantify responses of identified protein markers during the experimental treatment study with a view to developing methods which can be used as screening tools for growth promoter abuse detection. SPR analysis demonstrated the potential for plasma proteins to be used as indicative measures of growth promoter administrations and concludes that the sensitivity and robustness of any detection approach based on plasma proteome analysis would benefit from examination of a range of proteins representative of diverse biological processes rather being reliant on specific individual markers.

Protein expression changes in skeletal muscle in response to growth promoter abuse in beef cattle

The fraudulent treatment of cattle with growth promoting agents (GPAs) is a matter of great concern for the European Union (EU) authorities and consumers. It has been estimated that 10% of animals are being illegally treated in the EU. In contrast, only a much lower percentage of animals (<0.5%) are actually found as being noncompliant by conventional analytical methods. Thus, it has been proposed that methods should be developed that can detect the use of the substances via the biological effects of these substances on target organs, such as the alteration of protein expression profiles. Here we present a study aimed at evaluating if a correlation exists between the treatment with GPAs and alterations in the two-dimensional electrophoresis (2DE) protein pattern obtained from the biceps brachii skeletal muscle from mixed-bred cattle. After image analysis and statistical evaluation, protein spots that differentiate between treated and control groups were selected for analysis by mass spectrometry. A set of proteins could be defined that accurately detect the use of glucocorticoids and β(2)-agonists as growth promoters through the changes caused in muscle differentiation. As a further validation, we repeated the analysis using an independent set of samples from a strain of pure-bred cattle and verified these proteins by Western blot analysis.

Disturbance in sex-steroid serum profiles of cattle in response to exogenous estradiol: a screening approach to detect forbidden treatments

Estradiol benzoate (EB) has been one of the most widely used estrogenic agents in animal husbandry, as a way of exogenously introducing the natural hormone estradiol-17β into the animal organism. Estradiol was previously employed to induce anabolic effects or reproductive improvements in cattle. However, the employment of EB in European countries has been permanently forbidden by Directive 2008/97/EC to guarantee consumers' health. Despite this prohibition, the control of estradiol-17β and its esters continues to be a difficult task for residue-monitoring plans in European Communities because official analyses of natural thresholds for hormones in cattle have not yet been established, leading to a lack of confirmation for any exogenous administration of natural hormones. Several researchers have worked on excretion profiles of metabolites, variation in specific hormonal ratios and metabolomic fingerprints after hormonal treatments. This research focuses on the possible existence of disturbances in the serum profile of animals treated with EB in terms of steroid sex hormones (androgens, oestrogens and progestogens), by investigating the serum levels of several of these hormones. The serum samples were collected from three groups of cows: one treated with an intramuscular injection of EB, one treated with a combination of intravaginal EB and progesterone and a control (non-treated) group. The samples have been analysed by a validated high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method, and 17 natural hormones were identified and quantified. Subsequently, data from the serum profiles were submitted for statistic and multivariate analysis, and it was possible to observe a manifest variation between animal groups. The obtained results can help in the development of a viable screening tool for monitoring purposes in cattle.