Toxicoproteomics: New paradigms in toxicology research

Non-targeted proteomics reveals altered immune response in geographically distinct populations of green sea turtles (Chelonia mydas)

All seven species of sea turtle are facing increasing pressures from human activities that are impacting their health. Changes in circulating blood proteins of an individual, or all members of a population, can provide an early indicator of adverse health outcomes. Non-targeted measurement of all detectable proteins in a blood sample can indicate physiological changes. In the context of wildlife toxicology, this technique can provide a powerful tool for discovering biomarkers of chemical exposure and effect. This study presents a non-targeted examination of the protein abundance in sea turtle plasma obtained from three geographically distinct foraging populations of green turtles (Chelonia mydas) on the Queensland coast. Relative changes in protein expression between sites were compared, and potential markers of contaminant exposure were investigated. Blood plasma protein profiles were distinct between populations, with 85 out of the 116 identified proteins differentially expressed (p < 0.001). The most strongly dysregulated proteins were predominantly acute phase proteins, suggestive of differing immune status between the populations. The highest upregulation of known markers of immunotoxicity, such as pentraxin fusion and complement factor h, was observed in the Moreton Bay turtles. Forty-five different organohalogens were also measured in green turtle plasma samples as exposure to some organohalogens (e.g., polychlorinated biphenyls) has previously been identified as a cause for immune dysregulation in marine animals. The few detected organohalogens were at very low (pg/mL) concentrations in turtles from all sites, and are unlikely to be the cause of the proteome differences observed. However, the changes in protein expression may be indicative of exposure to other chemicals or environmental stressors. The results of this study provide important information about differences in protein expression between different populations of turtles, and guide future toxicological and health studies on east-Australian green sea turtles.

A proteomic view of cellular responses of macrophages to copper when added as ion or as copper-polyacrylate complex

Copper is an essential metal for life, but is toxic at high concentrations. In mammalian cells, two copper transporters are known, CTR1 and CTR2. In order to gain insights on the possible influence of the import pathway on cellular responses to copper, two copper challenges were compared: one with copper ion, which is likely to use preferentially CTR1, and one with a copper-polyacrylate complex, which will be internalized via the endosomal pathway and is likely to use preferentially CTR2. A model system consisting in the J774A1 mouse macrophage system, with a strong endosomal/lysosomal pathway, was used. In order to gain wide insights into the cellular responses to copper, a proteomic approach was used. The proteomic results were validated by targeted experiments, and showed differential effects of the import mode on cellular physiology parameters. While the mitochondrial transmembrane potential was kept constant, a depletion in the free glutahione content was observed with copper (ion and polylacrylate complex). Both copper-polyacrylate and polyacrylate induced perturbations in the cytoskeleton and in phagocytosis. Inflammatory responses were also differently altered by copper ion and copper-polyacrylate. Copper-polyacrylate also perturbed several metabolic enzymes. Lastly, enzymes were used as a test set to assess the predictive value of proteomics. SIGNIFICANCE: Proteomic profiling provides an in depth analysis of the alterations induced on cells by copper under two different exposure modes to this metal, namely as the free ion or as a complex with polyacrylate. The cellular responses were substantially different between the two exposure modes, although some cellular effects are shared, such as the depletion in free glutathione. Targeted experiments were used to confirm the proteomic results. Some metabolic enzymes showed altered activities after exposure to the copper-polyacrylate complex. The basal inflammatory responses were different for copper ion and for the copper-polyacrylate complex, while the two forms of copper inhibited lipopolysaccharide-induced inflammatory responses.

Changes in global protein expression in sea turtle cells exposed to common contaminants indicates new biomarkers of chemical exposure

Non-targeted protein expression at the cellular level can provide insights into mechanistic effects of contaminants in wildlife, and hence new and potentially more accurate biomarkers of exposure and effect. However, this technique has been relatively unexplored in the realm of in vitro biomarker discovery in threatened wildlife, despite the vulnerability of this group of animals to adverse sublethal effects of contaminant exposure. Here we examined the usefulness of non-targeted protein expression for biomarker discovery in green sea turtles (Chelonia mydas) by investigating differences in the response of primary cells from five different tissue types that were exposed to three contaminants known to accumulate in this species. Cells derived from C. mydas skin, liver, kidney, ovary and small intestine were exposed to 100 μg/L of either polychlorinated biphenyl 153 (PCB153), perfluorononanoic acid (PFNA) or phenanthrene for 24 h. The global protein expression was then quantitatively evaluated using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Comparison of the global protein profiles revealed that, while a majority of proteins were mutually expressed in controls of all tissue types (~90%), the response to exposure in terms of protein expression strength was significantly different between tissue types. Furthermore, a comparison to known markers of chemical exposure in sea turtles from the literature indicated that in vitro response can reflect known in vivo responses. In particular, markers such as heat shock protein (HSP) 60, glutathione S-transferases (GSTs) and superoxide dismutases (SODs), cytochrome P450 and catalase were dysregulated in response to exposure. Furthermore, potential new markers of exposure were discovered such as annexin, an important protein in cell signalling processes. While this methodology proved promising further studies are required to confirm the accuracy of in vitro protein expression as a tool for biomarker discovery in wildlife.

Ligand-induced activation of ERK1/2 signaling by constitutively active Gs-coupled 5-HT receptors

5-HT₄R, 5-HT₆R, and 5-HT_7AR are three constitutively active G_s-coupled 5-HT receptors that have key roles in brain development, learning, memory, cognition, and other physiological processes in the central nervous system. In addition to G_s signaling cascade mediated by these three 5-HT receptors, the ERK1/2 signaling which is dependent on cyclic adenosine monophosphate (cAMP) production and protein kinase A (PKA) activation downstream of G_s signaling has also been widely studied. In this study, we investigated these two signaling pathways originating from the three G_s-coupled 5-HT receptors in AD293 cells. We found that the phosphorylation and activation of ERK1/2 are ligand-induced, in contrast to the constitutively active G_s signaling. This indicates that G_s signaling alone is not sufficient for ERK1/2 activation in these three 5-HT receptors. In addition to G_s, we found that β-arrestin and Fyn are essential for the activation of ERK1/2. Together, these results put forth a novel mechanism for ERK1/2 activation involving the cooperative action of G_s, β-arrestin, and Fyn.

Application of Bayesian networks in determining nanoparticle-induced cellular outcomes using transcriptomics

Inroads have been made in our understanding of the risks posed to human health and the environment by nanoparticles (NPs) but this area requires continuous research and monitoring. Machine learning techniques have been applied to nanotoxicology with very encouraging results. This study deals with bridging physicochemical properties of NPs, experimental exposure conditions and in vitro characteristics with biological effects of NPs on a molecular cellular level from transcriptomics studies. The bridging is done by developing and implementing Bayesian Networks (BNs) with or without data preprocessing. The BN structures are derived either automatically or methodologically and compared. Early stage nanotoxicity measurements represent a challenge, not least when attempting to predict adverse outcomes and modeling is critical to understanding the biological effects of exposure to NPs. The preprocessed data-driven BN showed improved performance over automatically structured BN and the BN with unprocessed datasets. The prestructured BN captures inter relationships between NP properties, exposure condition and in vitro characteristics and links those with cellular effects based on statistic correlation findings. Information gain analysis showed that exposure dose, NP and cell line variables were the most influential attributes in predicting the biological effects. The BN methodology proposed in this study successfully predicts a number of toxicologically relevant cellular disrupted biological processes such as cell cycle and proliferation pathways, cell adhesion and extracellular matrix responses, DNA damage and repair mechanisms etc., with a success rate >80%. The model validation from independent data shows a robust and promising methodology for incorporating transcriptomics outcomes in a hazard and, by extension, risk assessment modeling framework by predicting affected cellular functions from experimental conditions.

Proteomic Analysis of Zebrafish (Danio rerio) After Chemical Exposure

Traditional toxicological screens based on the zebrafish model use observable phenotypic endpoints during their development to determine the toxicity of teratogens. Yet toxicity does not always translate to obvious phenotypic changes and the criteria used to score the toxicity of a teratogen are frequently subjected to human perception. The advancement in omics-based technologies has allowed us to quantitatively and objectively determine the toxicity of a teratogen based on biomolecular changes. The field of proteomics has been gaining popularity as a valuable tool in toxicology. Hence, in this chapter, we described a protocol for both label-free and label-based proteomic methods to analyse proteomic changes in both embryos and adult livers of zebrafish exposed to the teratogen TCDD (tetrachlorodibenzo-p-dioxin) as an example.

Screening Strategies and Methods for Better Off-Target Liability Prediction and Identification of Small-Molecule Pharmaceuticals

Pharmaceutical discovery and development is a long and expensive process that, unfortunately, still results in a low success rate, with drug safety continuing to be a major impedance. Improved safety screening strategies and methods are needed to more effectively fill this critical gap. Recent advances in informatics are now making it possible to manage bigger data sets and integrate multiple sources of screening data in a manner that can potentially improve the selection of higher-quality drug candidates. Integrated screening paradigms have become the norm in Pharma, both in discovery screening and in the identification of off-target toxicity mechanisms during later-stage development. Furthermore, advances in computational methods are making in silico screens more relevant and suggest that they may represent a feasible option for augmenting the current screening paradigm. This paper outlines several fundamental methods of the current drug screening processes across Pharma and emerging techniques/technologies that promise to improve molecule selection. In addition, the authors discuss integrated screening strategies and provide examples of advanced screening paradigms.

Nanomaterial and toxicity: what can proteomics tell us about the nanotoxicology?

1. In the last few years, a substantial scientific work is focused to identify the potential toxicity of nanomaterials by studying the cellular pathways under in vitro and in vivo conditions. Owing to high surface area to volume ratio nanoparticles (NPs) can pass through cell membranes which might be responsible for creating adverse interactions in biological systems. Simultaneously, researchers are also interested to assess the fate of NP inside the living system, which may lead to altered protein expression as well as protein corona formation. 2. According to published reports, NP-mediated toxicity involves altered cellular system including cell morphology, cell differentiation, cell metabolism, cell mobility, cellular immunity, which is derived from the side effects of nanoformulation and leading to apoptosis and necrosis. These results indicate the existence of potential toxic effect of these particles to human health. 3. The advent of proteomics with sophisticated technical improvement coupled with advanced bioinformatics has led to identify altered proteins due to nanomaterial exposure that could provide a new avenue to biomarker discovery. 4. This review aims to provide the current status of safe production and use of nanomaterials.

Translational biomarkers of acetaminophen-induced acute liver injury

Acetaminophen (APAP) is a commonly used analgesic drug that can cause liver injury, liver necrosis and liver failure. APAP-induced liver injury is associated with glutathione depletion, the formation of APAP protein adducts, the generation of reactive oxygen and nitrogen species and mitochondrial injury. The systems biology omics technologies (transcriptomics, proteomics and metabolomics) have been used to discover potential translational biomarkers of liver injury. The following review provides a summary of the systems biology discovery process, analytical validation of biomarkers and translation of omics biomarkers from the nonclinical to clinical setting in APAP-induced liver injury.

Development of novel tools for the in vitro investigation of drug-induced liver injury

INTRODUCTION

Due to its complex mechanisms and unpredictable occurrence, drug-induced liver injury (DILI) complicates drug identification and classification. Since species-specific differences in metabolism and pharmacokinetics exist, data obtained from animal studies may not be sufficient to predict DILI in humans.

AREAS COVERED

Over the last few decades, numerous in vitro models have been developed to replace animal testing. The advantages and disadvantages of commonly used liver-derived in vitro models (e.g., cell lines, hepatocyte models, liver slices, three-dimensional (3D) hepatospheres, etc.) are discussed. Toxicogenomics-based methodologies (genomics, epigenomics, transcriptomics, proteomics and metabolomics) and next-generation sequencing have also been used to enhance the reliability of DILI prediction. This review presents an overview of the currently used alternative toxicological models and of the most advanced approaches in the field of DILI research.

EXPERT OPINION

It seems unlikely that a single in vitro system will be able to mimic the complex interactions in the human liver. Three-dimensional multicellular systems may bridge the gap between conventional 2D models and in vivo clinical studies in humans and provide a reliable basis for hepatic toxicity assay development. Next-generation sequencing technologies, in comparison to microarray-based technologies, may overcome the current limitations and are promising for the development of predictive models in the near future.

Proteomics in pharmaceutical research and development

In the 20 years since its inception, the evolution of proteomics in pharmaceutical industry has mirrored the developments within academia and indeed other industries. From initial enthusiasm and subsequent disappointment in global protein expression profiling, pharma research saw the biggest impact when relating to more focused approaches, such as those exploring the interaction between proteins and drugs. Nowadays, proteomics technologies have been integrated in many areas of pharmaceutical R&D, ranging from the analysis of therapeutic proteins to the monitoring of clinical trials. Here, we review the development of proteomics in the drug discovery process, placing it in a historical context as well as reviewing the current status in light of the contributions to this special issue, which reflect some of the diverse demands of the drug and biomarker pipelines.

Pathway and time-resolved benzo[a]pyrene toxicity on Hepa1c1c7 cells at toxic and subtoxic exposure

Benzo[a]pyrene (B[a]P) is an environmental contaminant mainly studied for its toxic/carcinogenic effects. For a comprehensive and pathway orientated mechanistic understanding of the effects directly triggered by a toxic (5 μM) or a subtoxic (50 nM) concentration of B[a]P or indirectly by its metabolites, we conducted time series experiments for up to 24 h to study the effects in murine hepatocytes. These cells rapidly take up and actively metabolize B[a]P, which was followed by quantitative analysis of the concentration of intracellular B[a]P and seven representative degradation products. Exposure with 5 μM B[a]P led to a maximal intracellular concentration of 1604 pmol/5 × 10(4) cells, leveling at 55 pmol/5 × 10(4) cells by the end of the time course. Changes in the global proteome (>1000 protein profiles) and metabolome (163 metabolites) were assessed in combination with B[a]P degradation. Abundance profiles of 236 (both concentrations), 190 (only 5 μM), and 150 (only 50 nM) proteins were found to be regulated in response to B[a]P in a time-dependent manner. At the endogenous metabolite level amino acids, acylcarnitines and glycerophospholipids were particularly affected by B[a]P. The comprehensive chemical, proteome and metabolomic data enabled the identification of effects on the pathway level in a time-resolved manner. So in addition to known alterations, also protein synthesis, lipid metabolism, and membrane dysfunction were identified as B[a]P specific effects.

A proteomic approach to investigate AuNPs effects in Balb/3T3 cells

Although gold nanoparticles (AuNPs) are currently used in several industrial products and biomedical applications, information about their biological effects is very limited. Thus, it is becoming crucial to assess their safety and adequately investigate the complexity of cell-nanoparticles interactions. In this work, the Balb/3T3 mouse fibroblast cell line was selected as an in vitro model to study the effects of AuNPs. Alteration of cellular processes and biochemical pathways caused by AuNPs exposure was investigated by analysing the differentially expressed proteome. Of interest was the difference observed in the protein pattern expression of cells exposed to AuNPs. It was found that 88 and 83 proteins were de-regulated after exposure to 5 and 15nm AuNPs, respectively. Analysis of the proteome revealed that AuNPs triggers several pathways related to cellular growth and proliferation, cell morphology, cell cycle regulation, cellular function and maintenance, oxidative stress, and inflammatory response. Moreover, SPR analysis showed an increase of ECM proteins biosynthesis in cells exposed to AuNPs. We observed by TEM analysis that NPs are internalized and confined mainly in autophagosomes. Endoplasmic reticulum stressed and modification at mitochondrial level occurred. This study aims to improve existing knowledge necessary for a correct assessment of the balance between AuNPs potential adverse and beneficial effects and might have important implications for biomedical applications (e.g. nanomedicine). To conclude proteomics link to system biology analysis is a valuable tool to understand and predict nanoparticles' toxicity, furthermore it has the potential to reveal pathways that may not be immediately evident with classical toxicological assays.

Post-translational modification of proteins in toxicological research: focus on lysine acylation

Toxicoproteomics integrates the proteomic knowledge into toxicology by enabling protein quantification in biofluids and tissues, thus taking toxicological research to the next level. Post-translational modification (PTM) alters the three-dimensional (3D) structure of proteins by covalently binding small molecules to them and therefore represents a major protein function diversification mechanism. Because of the crucial roles PTM plays in biological systems, the identification of novel PTMs and study of the role of PTMs are gaining much attention in proteomics research. Of the 300 known PTMs, protein acylation, including lysine formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, and crotonylation, regulates the crucial functions of many eukaryotic proteins involved in cellular metabolism, cell cycle, aging, growth, angiogenesis, and cancer. Here, I reviewed recent studies regarding novel types of lysine acylation, their biological functions, and their applicationsin toxicoproteomics research.

Proteomics and systems biology: application in drug discovery and development

Studies of complex biological systems aimed at understanding their functions at a global level are the goals of systems biology. Proteomics, generally regarded as the comprehensive study of the expression of all the proteins at a particular time in different organs, tissues, and cell types is a key enabling technology for the systems biology approach. Rapid advances in this regard have been made following the success of the human genome project as well as those of various animals and microorganisms. Possibly, one of the most promising outcomes from studies on the human genome and proteome is the identification of potential new drugs for the treatment of different diseases and tailoring the drugs for individualized patient therapy. Following the identification of a new drug candidate, knowledge on organ and system-level responses helps prioritize the drug targets and design clinical trials based on their efficacy and safety. Toxicoproteomics is playing an important role in that respect. In essence, over the past decade, proteomics has played a major role in drug discovery and development. In this review article, we explain systems biology, discuss the current proteomic technologies, and highlight some important applications of proteomics and systems biology approaches in drug discovery and development.