A SELDI-TOF approach to ecotoxicology: comparative profiling of low molecular weight proteins from a marine diatom exposed to CdSe/ZnS quantum dots

Top-Down Proteomics of Human Saliva, Analyzed with Logistic Regression and Machine Learning Methods, Reveal Molecular Signatures of Ovarian Cancer

Ovarian cancer (OC) is the most lethal of all gynecological cancers. Due to vague symptoms, OC is mostly detected at advanced stages, with a 5-year survival rate (SR) of only 30%; diagnosis at stage I increases the 5-year SR to 90%, suggesting that early diagnosis is essential to cure OC. Currently, the clinical need for an early, reliable diagnostic test for OC screening remains unmet; indeed, screening is not even recommended for healthy women with no familial history of OC for fear of post-screening adverse events. Salivary diagnostics is considered a major resource for diagnostics of the future. In this work, we searched for OC biomarkers (BMs) by comparing saliva samples of patients with various stages of OC, breast cancer (BC) patients, and healthy subjects using an unbiased, high-throughput proteomics approach. We analyzed the results using both logistic regression (LR) and machine learning (ML) for pattern analysis and variable selection to highlight molecular signatures for OC and BC diagnosis and possibly re-classification. Here, we show that saliva is an informative test fluid for an unbiased proteomic search of candidate BMs for identifying OC patients. Although we were not able to fully exploit the potential of ML methods due to the small sample size of our study, LR and ML provided patterns of candidate BMs that are now available for further validation analysis in the relevant population and for biochemical identification.

An update on the biological effects of quantum dots: From environmental fate to risk assessment based on multiple biological models

Quantum dots (QDs) are zero-dimension nanomaterials with excellent physical and chemical properties, which have been widely used in environmental science and biomedicine. Therefore, QDs are potential to cause toxicity to the environment and enter organisms through migration and bioenrichment effects. This review aims to provide a comprehensive and systematic analysis on the adverse effects of QDs in different organisms based on recently available data. Following PRISMA guidelines, this study searched PubMed database according to the pre-set keywords, and included 206 studies according to the inclusion and elimination criteria. CiteSpace software was firstly used to analyze the keywords of included literatures, search for breaking points of former studies, and summarize the classification, characterization and dosage of QDs. The environment fate of QDs in the ecosystems were then analyzed, followed with comprehensively summarized toxicity outcomes at individual, system, cell, subcellular and molecular levels. After migration and degradation in the environment, aquatic plants, bacteria, fungi as well as invertebrates and vertebrates have been found to be suffered from toxic effects caused by QDs. Aside from systemic effects, toxicity of intrinsic QDs targeting to specific organs, including respiratory system, cardiovascular system, hepatorenal system, nervous system and immune system were confirmed in multiple animal models. Moreover, QDs could be taken up by cells and disturb the organelles, which resulted in cellular inflammation and cell death, including autophagy, apoptosis, necrosis, pyroptosis and ferroptosis. Recently, several innovative technologies, like organoids have been applied in the risk assessment of QDs to promote the surgical interventions of preventing QDs' toxicity. This review not only aimed at updating the research progress on the biological effects of QDs from environmental fate to risk assessment, but also overcame the limitations of available reviews on basic toxicity of nanomaterials by interdisciplinarity and provided new insights for better applications of QDs.

Proteomic evaluation of nanotoxicity in aquatic organisms: A review

The alteration of organisms protein functions by engineered nanoparticles (ENPs) is dependent on the complex interplay between their inherent physicochemical properties (e.g., size, surface coating, shape) and environmental conditions (e.g., pH, organic matter). To date, there is increasing interest on the use of 'omics' approaches, such as proteomics, genomics, and others, to study ENPs-biomolecules interactions in aquatic organisms. However, although proteomics has recently been applied to investigate effects of ENPs and associated mechanisms in aquatic organisms, its use remain limited. Herein, proteomics techniques widely applied to investigate ENPs-protein interactions in aquatic organisms are reviewed. Data demonstrates that 2DE and mass spectrometry and/or their combination, thereof, are the most suitable techniques to elucidate ENPs-protein interactions. Furthermore, current status on ENPs and protein interactions, and possible mechanisms of nanotoxicity with emphasis on those that exert influence at protein expression levels, and key influencing factors on ENPs-proteins interactions are outlined. Most reported studies were done using synthetic media and essay protocols and had wide variability (not standardized); this may consequently limit data application in actual environmental systems. Therefore, there is a need for studies using realistic environmental concentrations of ENPs, and actual environmental matrixes (e.g., surface water) to aid better model development of ENPs-proteins interactions in aquatic systems.

Assessing the Environmental Effects Related to Quantum Dot Structure, Function, Synthesis and Exposure

Quantum dots (QDs) are engineered semiconductor nanocrystals with unique fluorescent, quantum confinement, and quantum yield properties, making them valuable in a range of commercial and consumer imaging, display, and lighting technologies. Production and usage of QDs are increasing, which increases the probability of these nanoparticles entering the environment at various phases of their life cycle. This review discusses the major types and applications of QDs, their potential environmental exposures, fates, and adverse effects on organisms. For most applications, release to the environment is mainly expected to occur during QD synthesis and end-product manufacturing since encapsulation of QDs in these devices prevents release during normal use or landfilling. In natural waters, the fate of QDs is controlled by water chemistry, light intensity, and the physicochemical properties of QDs. Research on the adverse effects of QDs primarily focuses on sublethal endpoints rather than acute toxicity, and the differences in toxicity between pristine and weathered nanoparticles are highlighted. A proposed oxidative stress adverse outcome pathway framework demonstrates the similarities among metallic and carbon-based QDs that induce reactive oxygen species formation leading to DNA damage, reduced growth, and impaired reproduction in several organisms. To accurately evaluate environmental risk, this review identifies critical data gaps in QD exposure and ecological effects, and provides recommendations for future research. Future QD regulation should emphasize exposure and sublethal effects of metal ions released as the nanoparticles weather under environmental conditions. To date, human exposure to QDs from the environment and resulting adverse effects has not been reported.

High-throughput proteomics and metabolomic studies guide re-engineering of metabolic pathways in eukaryotic microalgae: A review

Eukaryotic microalgae are a rich source of commercially important metabolites including lipids, pigments, sugars, amino acids and enzymes. However, their inherent genetic potential is usually not enough to support high level production of metabolites of interest. In order to move on from the traditional approach of improving product yields by modification of the cultivation conditions, understanding the metabolic pathways leading to the synthesis of the bioproducts of interest is crucial. Identification of new targets for strain engineering has been greatly facilitated by the rapid development of high-throughput sequencing and spectroscopic techniques discussed in this review. Despite the availability of high throughput analytical tools, examples of gathering and application of proteomic and metabolomic data for metabolic engineering of microalgae are few and mainly limited to lipid production. The present review highlights the application of contemporary proteomic and metabolomic techniques in eukaryotic microalgae for redesigning pathways for enhanced production of algal metabolites.

Advances of proteomics technologies for multidrug-resistant mechanisms

Multidrug resistance (MDR) is a vital issue in cancer treatment. Drug resistance can be developed through a variety of mechanisms, including increased drug efflux, activation of detoxifying systems and DNA repair mechanisms, and escape of drug-induced apoptosis. Identifying the exact mechanism related in a particular case is a difficult task. Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. In recent years, comparative proteomic methods have been performed to analyze MDR mechanisms in drug-selected model cancer cell lines. In this paper, we review the recent developments and progresses by comparative proteomic approaches to identify potential MDR mechanisms in drug-selected model cancer cell lines, which may help understand and design chemical sensitizers.

Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outcome of such studies regarding common responses and toxicity pathways is currently lacking. We developed an R-scripted computational pipeline to perform reanalysis and functional analysis of relevant transcriptomic data sets using a common approach, independent from the ENM type, and across different organisms, including Arabidopsis thaliana, Caenorhabditis elegans, and Danio rerio. Using the pipeline that can semiautomatically process data from different microarray technologies, we were able to determine the most common molecular mechanisms of nanotoxicity across extremely variable data sets. As expected, we found known mechanisms, such as interference with energy generation, oxidative stress, disruption of DNA synthesis, and activation of DNA-repair but also discovered that some less-described molecular responses to ENMs, such as DNA/RNA methylation, protein folding, and interference with neurological functions, are present across the different studies. Results were visualized in radar charts to assess toxicological response patterns allowing the comparison of different organisms and ENM types. This can be helpful to retrieve ENM-related hazard information and thus fill knowledge gaps in a comprehensive way in regard to the molecular underpinnings and mechanistic understanding of nanotoxicity.

Current Status and Future Prospects of Semiconductor Quantum Dots in Botany

The development of botanical applications of nanomaterials has produced a new generation of technologies that can profoundly impact botanical research. Semiconductor quantum dots (QDs) are an archetype nanomaterial and have received significant interest from diverse research communities, owing to their unique and optimizable optical properties. In this review, we describe the most recent progress on QD-based botanical research and discuss the uptake, translocation, and effects of QDs on plants and the potential applications of QDs in botany. A critical evaluation of the current limitations of QD technologies is discussed, along with the future prospects in QD-based botanical research.

Effect of the exposure to Mn-doped ZnS nanoparticles on biomarkers in the freshwater western mosquitofish Gambusia affinis

Synthesized Mn-doped ZnS nanoparticles, with 10% of Mn dopant, were used to investigate their environmental toxicity. Mn-doped ZnS quantum dots (QDs) stabilized by 3-mercaptopropionic acid (MPA) were synthesized in a basic aqueous solution using the nucleation doping. The optical properties and structure of the obtained Mn (10%):ZnS QDs have been characterized by X-ray diffraction, UV-vis, photoluminescence spectroscopies and transmission electron microscopy. The brain, gills and liver stained sections from Gambusia affinis were dissected. Antioxidant enzyme activities (acetylcholinesterase and catalase), as well as malondialdehyde and H₂O₂ levels, were determined after exposure (94 h) to 14 and 28 mg/L of nanoparticles. The obtained nearly monodisperse Mn(10%):ZnS@MPA QDs have an average diameter of ca. 2.8 nm and a zinc-blende crystal structure. Mn-doped ZnS acts differently on the activities of the biomarkers in a dose-dependent manner. The recorded alterations varied between organs. Such findings provide information on the biological target of nanoparticles and their behaviour within the environment.

Toxicological effects of CdSe nanocrystals on the marine diatom Phaeodactylum tricornutum: The first mass spectrometry-based proteomic approach

In the marine environment, benthic diatoms from estuarine and coastal sediments are among the first targets of nanoparticle pollution whose potential toxicity on marine organisms is still largely unknown. It is therefore relevant to improve our knowledge of interactions between these new pollutants and microalgae, the key players in the control of marine resources. In this study, the response of P. tricornutum to CdSe nanocrystals (CdSe NPs) of 5 nm (NP5) and 12 nm (NP12) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches. NP5 and NP12 affected cell growth but oxygen production was only slightly decreased by NP5 after 1-d incubation time. In our experimental conditions, a high CdSe NP dissolution was observed during the first day of culture, leading to Cd bioaccumulation and oxidative stress, particularly with NP12. However, after a 7-day incubation time, proteomic analysis highlighted that P. tricornutum responded to CdSe NP toxicity by regulating numerous proteins involved in protection against oxidative stress, cellular redox homeostasis, Ca²⁺ regulation and signalling, S-nitrosylation and S-glutathionylation processes and cell damage repair. These proteome changes allowed algae cells to regulate their intracellular ROS level in contaminated cultures. P. tricornutum was also capable to control its intracellular Cd concentration at a sufficiently low level to preserve its growth. To our knowledge, this is the first work allowing the identification of proteins differentially expressed by P. tricornutum subjected to NPs and thus the understanding of some molecular pathways involved in its cellular response to nanoparticles.

SIGNIFICANCE

The microalgae play a key role in the control of marine resources. Moreover, they produce 50% of the atmospheric oxygen. CdSe NPs are extensively used in the industry of renewable energies and it is regrettably expected that these pollutants will sometime soon appear in the marine environment through surface runoff, urban effluents and rivers. Since estuarine and coastal sediments concentrate pollutants, benthic microalgae which live in superficial sediments will be among the first targets of nanoparticle pollution. Thus, it is relevant to improve our knowledge of interactions between diatoms and nanoparticles. Proteomics is a powerful tool for understanding the molecular mechanisms triggered by nanoparticle exposure, and our study is the first one to use this tool to identify proteins differentially expressed by P. tricornutum subjected to CdSe nanocrystals. This work is fundamental to improve our knowledge about the defence mechanisms developed by algae cells to counteract damage caused by CdSe NPs.

Omics tools: New challenges in aquatic nanotoxicology?

In recent years, the implication of genomics into ecotoxicological studies has been studied closely to allow a better understanding of organism's responses to environmental contaminants including engineering nanomaterials (ENMs). ENMs are increasingly produced for various applications including cosmetics, electronics, sports equipment, biomedicine and agriculture. Because of their small size, ENMs possess chemical or physical characteristics improved compared to the corresponding macro-sized material. As their application expend, the release of manufactured ENMs into the environment is likely to increase and concern over impacts for the aquatic ecosystem is growing. Several studies reported deleterious effect of ENMs to aquatic organisms, but there is little information about the molecular mechanisms of toxicity. The development of ecotoxicogenomic approaches will improve the characterization of cellular and molecular modes of action of ENMs to aquatic organisms and allow a better prediction of contaminants toxicity. This paper presents an overview of transciptomic/proteomic studies in freshwater and marine organisms exposed to ENMs. Overall, induction of gene expression in relations to defense mechanisms, immune responses, growth and reproduction were measured after ENMs exposures of organisms, but with different patterns depending on exposure duration and concentrations used. In addition, some studies reported a positive correlation between gene expression and cellular modifications, but not at the individual level.

Environmental behaviour and ecotoxicity of quantum dots at various trophic levels: A review

Despite the wide application of quantum dots (QDs) in electronics, pharmacy and nanomedicine, limited data is available on their environmental health risk. To advance our current understanding of the environmental impact of these engineered nanomaterials, the aim of this review is to give a detailed insight on the existing information concerning the behaviour, transformation and fate of QDs in the aquatic environment, as well as on its mode of action (MoA), ecotoxicity, trophic transfer and biomagnification at various trophic levels (micro-organisms, aquatic invertebrates and vertebrates). Data show that several types of Cd-based QDs, even at low concentrations (<mgCdL^-1), induce different toxic effects compared to their dissolved counterpart, indicating nano-specific ecotoxicity. QD ecotoxicity at different trophic levels is highly dependent on its physico-chemical properties, environmental conditions, concentration and exposure time, as well as, species, while UV irradiation increases its toxicity. The state of the art regarding the MoA of QDs according to taxonomic groups is summarised and illustrated. Accumulation and trophic transfer of QDs was observed in freshwater and seawater species, while limited biomagnification and detoxification processes were detected. Finally, current knowledge gaps are discussed and recommendations for future research identified. Overall, the knowledge available indicates that in order to develop sustainable nanotechnologies there is an urgent need to develop Cd-free QDs and new "core-shell-conjugate" QD structures.