Multiparametric Profiling of Engineered Nanomaterials: Unmasking the Surface Coating Effect

A Network Toxicology Approach for Mechanistic Modelling of Nanomaterial Hazard and Adverse Outcomes

Hazard assessment is the first step in evaluating the potential adverse effects of chemicals. Traditionally, toxicological assessment has focused on the exposure, overlooking the impact of the exposed system on the observed toxicity. However, systems toxicology emphasizes how system properties significantly contribute to the observed response. Hence, systems theory states that interactions store more information than individual elements, leading to the adoption of network based models to represent complex systems in many fields of life sciences. Here, they develop a network-based approach to characterize toxicological responses in the context of a biological system, inferring biological system specific networks. They directly link molecular alterations to the adverse outcome pathway (AOP) framework, establishing direct connections between omics data and toxicologically relevant phenotypic events. They apply this framework to a dataset including 31 engineered nanomaterials with different physicochemical properties in two different in vitro and one in vivo models and demonstrate how the biological system is the driving force of the observed response. This work highlights the potential of network-based methods to significantly improve their understanding of toxicological mechanisms from a systems biology perspective and provides relevant considerations and future data-driven approaches for the hazard assessment of nanomaterials and other advanced materials.

Bioinformatics and machine learning to support nanomaterial grouping

Nanomaterials (NMs) offer plenty of novel functionalities. Moreover, their physicochemical properties can be fine-tuned to meet the needs of specific applications, leading to virtually unlimited numbers of NM variants. Hence, efficient hazard and risk assessment strategies building on New Approach Methodologies (NAMs) become indispensable. Indeed, the design, the development and implementation of NAMs has been a major topic in a substantial number of research projects. One of the promising strategies that can help to deal with the high number of NMs variants is grouping and read-across. Based on demonstrated structural and physicochemical similarity, NMs can be grouped and assessed together. Within an established NM group, read-across may be performed to fill in data gaps for data-poor variants using existing data for NMs within the group. Establishing a group requires a sound justification, usually based on a grouping hypothesis that links specific physicochemical properties to well-defined hazard endpoints. However, for NMs these interrelationships are only beginning to be understood. The aim of this review is to demonstrate the power of bioinformatics with a specific focus on Machine Learning (ML) approaches to unravel the NM Modes-of-Action (MoA) and identify the properties that are relevant to specific hazards, in support of grouping strategies. This review emphasizes the following messages: 1) ML supports identification of the most relevant properties contributing to specific hazards; 2) ML supports analysis of large omics datasets and identification of MoA patterns in support of hypothesis formulation in grouping approaches; 3) omics approaches are useful for shifting away from consideration of single endpoints towards a more mechanistic understanding across multiple endpoints gained from one experiment; and 4) approaches from other fields of Artificial Intelligence (AI) like Natural Language Processing or image analysis may support automated extraction and interlinkage of information related to NM toxicity. Here, existing ML models for predicting NM toxicity and for analyzing omics data in support of NM grouping are reviewed. Various challenges related to building robust models in the field of nanotoxicology exist and are also discussed.

The role of Eudragit® as a component of hydrogel formulations for medical devices

Over the last decade, significant progress has been made in developing hydrogels as medical devices. By physically cross-linking pharmaceutically approved polymers into three-dimensional matrices, we can ensure their biocompatibility and facilitate their seamless transition from the laboratory to clinical applications. Moreover, the reversible nature of their physical cross-links allows hydrogels to dissolve in the presence of external stimuli. Particularly, their high degree of hydration, high molecular weight, and superior flexibility of the polymer chains facilitate their interaction with complex biological barriers (e.g., mucus layer), making them ideal candidates for mucosal drug delivery. However, fine-tuning the composition of the hydrogel formulations is of great importance to optimize the performance of the medical device and its therapeutic cargo. Herein, we investigated the influence of different Eudragits® on the properties of hydrogels based on polyvinylpyrrolidone (PVP), polyvinyl alcohol (PVA), and polyethylene glycol (PEG), which were originally proposed as ocular inserts in previous reports. Our research aims to determine the effects that including different Eudragits® have on the structure and protein ocular delivery ability of various hydrogel formulations. Properties such as matrix stability, protein encapsulation, release kinetics, mucoadhesion, and biocompatibility have been analyzed in detail. Our study represents a guideline of the features that Eudragits® have to exhibit to endow hydrogels with good adhesion to the eye's conjunctiva, biocompatibility, and structural strength to cope with the ocular biointerface and allow sustained protein release. This work has important implications for the design of new hydrogel materials containing Eudragits® in their composition, particularly in mucosal drug delivery.

A Comprehensive Assessment of the Biocompatibility and Safety of Diamond Nanoparticles on Reconstructed Human Epidermis

Diamond nanoparticles, also known as nanodiamonds (NDs), exhibit remarkable, awe-inspiring properties that make them suitable for various applications in the field of skin care products. However, a comprehensive assessment of their compatibility with human skin, according to the irritation criteria established by the Organization for Economic Cooperation and Development (OECD), has not yet been conducted. The purpose of this study was to evaluate if diamond nanoparticles at a concentration of 25 μg/mL, incubated with reconstituted human epidermis (EpiDermTM) for 18 h, conform to the OECD TG439 standard used to classify chemical irritants. For this purpose, a cell viability test (MTT assay), histological assessment, and analysis of pro-inflammatory cytokine expression were performed. The results indicated that NDs had no toxic effect at the tested concentration. They also did not adversely affect tissue structure and did not lead to a simultaneous increase in protein and mRNA expression of the analyzed cytokines. These results confirm the safety and biocompatibility of NDs for application in skincare products, thereby creating a wide range of possibilities to exert an impact on the advancement of contemporary cosmetology in the future.

Toxicity evaluation of silica nanoparticles for delivery applications

Silica nanoparticles (SiNPs) are being explored as nanocarriers for therapeutics delivery, which can address a number of intrinsic drawbacks of therapeutics. To translate laboratory innovation into clinical application, their potential toxicity has been of great concern. This review attempts to comprehensively summarize the existing literature on the toxicity assessment of SiNPs. The current data suggest that the composition of SiNPs, their physicochemical properties, their administration route, their frequency and duration of administration, and the sex of animal models are related to their tissue and blood toxicity, immunotoxicity, and genotoxicity. However, the correlation between in vitro and in vivo toxicity has not been well established, mainly because both the in vitro and the in vivo-dosed quantities are unrealistic. This article also discusses important factors to consider in the toxicology of SiNPs and current approaches to reducing their toxicity. The aim is to give readers a better understanding of the toxicology of silica nanoparticles and to help identify key gaps in knowledge and techniques.

PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping

Toxicological evaluation of substances in regulation still often relies on animal experiments. Understanding the substances' mode-of-action is crucial to develop alternative test strategies. Omics methods are promising tools to achieve this goal. Until now, most attention was focused on transcriptomics, while proteomics is not yet routinely applied in toxicology despite the large number of datasets available in public repositories. Exploiting the full potential of these datasets is hampered by differences in measurement procedures and follow-up data processing. Here we present the tool PROTEOMAS, which allows meta-analysis of proteomic data from public origin. The workflow was designed for analyzing proteomic studies in a harmonized way and to ensure transparency in the analysis of proteomic data for regulatory purposes. It agrees with the Omics Reporting Framework guidelines of the OECD with the intention to integrate proteomics to other omic methods in regulatory toxicology. The overarching aim is to contribute to the development of AOPs and to understand the mode of action of substances. To demonstrate the robustness and reliability of our workflow we compared our results to those of the original studies. As a case study, we performed a meta-analysis of 25 proteomic datasets to investigate the toxicological effects of nanomaterials at the lung level. PROTEOMAS is an important contribution to the development of alternative test strategies enabling robust meta-analysis of proteomic data. This workflow commits to the FAIR principles (Findable, Accessible, Interoperable and Reusable) of computational protocols.

Die hard: cell death mechanisms and their implications in nanotoxicology

Cell death is a fundamental biological process, and its fine-tuned regulation is required for life. However, the complexity of regulated cell death is often reduced to a matter of live-dead discrimination. Here, we provide a perspective on programmed or regulated cell death, focusing on apoptosis, pyroptosis, necroptosis, and ferroptosis (the latter three cell death modalities are examples of regulated necrosis). We also touch on other, recently described manifestations of (pathological) cell death including cuproptosis. Furthermore, we address how engineered nanomaterials impact on regulated cell death. We posit that an improved understanding of nanomaterial-induced perturbations of cell death may allow for a better prediction of the consequences of human exposure and could also yield novel approaches by which to mitigate these effects. Finally, we provide examples of the harnessing of nanomaterials to achieve cancer cell killing through the induction of regulated cell death.

Influence of different functionalized CdTe quantum dots on the accumulation of metals, developmental toxicity and respiration in different development stages of the zebrafish (Danio rerio)

Introduction: The bioaccumulation and differential effects of cadmium tellurium quantum dot (CdTe QDs) nanomaterials with different functional groups are poorly understood in aquatic organisms. This study aimed to investigate the metal uptake, developmental effects, and respiratory effects of CdTe QDs with different functional groups (COOH, NH3, and PEG) on zebrafish embryos. Methods: Zebrafish embryos were exposed to carboxylate (COOH), ammonia (NH3), and polyethylene glycol (PEG) functionalized CdTe QDs at nominal concentrations of 0.5, 2, 4, 6, and 20 mg QDs/L. The materials were characterized in E3 exposure media and the metal uptake, developmental effects, and respiratory effects of zebrafish embryos were recorded. Results: The total Cd or Te concentrations in the larvae could not be explained by the metal concentrations or dissolution of the materials in the exposure media. The metal uptake in the larvae was not dose-dependent, except for the QD-PEG treatment. The QD-NH3 treatment caused respiration inhibition at the highest exposure concentration and hatching delays and severe malformations at low concentrations. The toxicities observed at low concentrations were attributed to particles crossing the pores in the chorion, and toxicities at higher concentrations were linked to the aggregation of particle agglomerates to the surface of the chorion impairing respiration. Developmental defects were recorded following exposure to all three functional groups, but the QD-NH3 group had the most severe response. The LC50 values for embryo development of QD-COOH and QD-PEG groups were higher than 20 mg/L, and the LC50 of the QD-NH3 group was 20 mg/L. Discussion: The results of this study suggest that CdTe QDs with different functional groups have differential effects on zebrafish embryos. The QD-NH3 treatment caused the most severe effects, including respiration inhibition and developmental defects. These findings provide valuable information for understanding the effects of CdTe QDs on aquatic organisms and highlight the need for further investigation.

Biomarkers of nanomaterials hazard from multi-layer data

There is an urgent need to apply effective, data-driven approaches to reliably predict engineered nanomaterial (ENM) toxicity. Here we introduce a predictive computational framework based on the molecular and phenotypic effects of a large panel of ENMs across multiple in vitro and in vivo models. Our methodology allows for the grouping of ENMs based on multi-omics approaches combined with robust toxicity tests. Importantly, we identify mRNA-based toxicity markers and extensively replicate them in multiple independent datasets. We find that models based on combinations of omics-derived features and material intrinsic properties display significantly improved predictive accuracy as compared to physicochemical properties alone.

Copper oxide nanoparticles trigger macrophage cell death with misfolding of Cu/Zn superoxide dismutase 1 (SOD1)

Background

Copper oxide (CuO) nanoparticles (NPs) are known to trigger cytotoxicity in a variety of cell models, but the mechanism of cell death remains unknown. Here we addressed the mechanism of cytotoxicity in macrophages exposed to CuO NPs versus copper chloride (CuCl₂).

Methods

The mouse macrophage cell line RAW264.7 was used as an in vitro model. Particle uptake and the cellular dose of Cu were investigated by transmission electron microscopy (TEM) and inductively coupled plasma mass spectrometry (ICP-MS), respectively. The deposition of Cu in lysosomes isolated from macrophages was also determined by ICP-MS. Cell viability (metabolic activity) was assessed using the Alamar Blue assay, and oxidative stress was monitored by a variety of methods including a luminescence-based assay for cellular glutathione (GSH), and flow cytometry-based detection of mitochondrial superoxide and mitochondrial membrane potential. Protein aggregation was determined by confocal microscopy using an aggresome-specific dye and protein misfolding was determined by circular dichroism (CD) spectroscopy. Lastly, proteasome activity was investigated using a fluorometric assay.

Results

We observed rapid cellular uptake of CuO NPs in macrophages with deposition in lysosomes. CuO NP-elicited cell death was characterized by mitochondrial swelling with signs of oxidative stress including the production of mitochondrial superoxide and cellular depletion of GSH. We also observed a dose-dependent accumulation of polyubiquitinated proteins and loss of proteasomal function in CuO NP-exposed cells, and we could demonstrate misfolding and mitochondrial translocation of superoxide dismutase 1 (SOD1), a Cu/Zn-dependent enzyme that plays a pivotal role in the defense against oxidative stress. The chelation of copper ions using tetrathiomolybdate (TTM) prevented cell death whereas inhibition of the cellular SOD1 chaperone aggravated toxicity. Moreover, CuO NP-triggered cell death was insensitive to the pan-caspase inhibitor, zVAD-fmk, and to wortmannin, an inhibitor of autophagy, implying that this was a non-apoptotic cell death. ZnO NPs, on the other hand, triggered autophagic cell death.

Conclusions

CuO NPs undergo dissolution in lysosomes leading to copper-dependent macrophage cell death characterized by protein misfolding and proteasomal insufficiency. Specifically, we present novel evidence for Cu-induced SOD1 misfolding which accords with the pronounced oxidative stress observed in CuO NP-exposed macrophages. These results are relevant for our understanding of the consequences of inadvertent human exposure to CuO NPs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12989-022-00467-w.

Immunotherapeutic nanoparticles: From autoimmune disease control to the development of vaccines

The development of nanoparticles (NPs) with potential therapeutic uses represents an area of vast interest in the scientific community during the last years. Recently, the pandemic caused by COVID-19 motivated a race for vaccines creation to overcome the crisis generated. This is a good demonstration that nanotechnology will most likely be the basis of future immunotherapy. Moreover, the number of publications based on nanosystems has significantly increased in recent years and it is expected that most of these developments can go on to experimentation in clinical stages soon. The therapeutic use of NPs to combat different diseases such as cancer, allergies or autoimmune diseases will depend on their characteristics, their targets, and the transported molecules. This review presents an in-depth analysis of recent advances that have been developed in order to obtain novel nanoparticulate based tools for the treatment of allergies, autoimmune diseases and for their use in vaccines. Moreover, it is highlighted that by providing targeted delivery an increase in the potential of vaccines to induce an immune response is expected in the future. Definitively, the here gathered analysis is a good demonstration that nanotechnology will be the basis of future immunotherapy.

Nextcast: A software suite to analyse and model toxicogenomics data

The recent advancements in toxicogenomics have led to the availability of large omics data sets, representing the starting point for studying the exposure mechanism of action and identifying candidate biomarkers for toxicity prediction. The current lack of standard methods in data generation and analysis hampers the full exploitation of toxicogenomics-based evidence in regulatory risk assessment. Moreover, the pipelines for the preprocessing and downstream analyses of toxicogenomic data sets can be quite challenging to implement. During the years, we have developed a number of software packages to address specific questions related to multiple steps of toxicogenomics data analysis and modelling. In this review we present the Nextcast software collection and discuss how its individual tools can be combined into efficient pipelines to answer specific biological questions. Nextcast components are of great support to the scientific community for analysing and interpreting large data sets for the toxicity evaluation of compounds in an unbiased, straightforward, and reliable manner. The Nextcast software suite is available at: ( https://github.com/fhaive/nextcast).

Understanding the immunological interactions of engineered nanomaterials: Role of the bio-corona

Engineered nanomaterials are a broad class of materials with the potential for breakthrough applications in many sectors of society not least in medicine. Consequently, safety assessment of nanomaterials and nano-enabled products with respect to human health and the environment is of key importance. To this end, the biological interactions of nanoscale materials must be understood. Here, the dual "identities" of nanomaterials, namely, the material-intrinsic properties or synthetic identity and the acquired, context-dependent properties or biological identity, are discussed in relation to nanomaterial interactions with the immune system, our main defense against foreign intrusion. Specifically, we address whether macrophages and other innate immune cells respond to the synthetic identity or the biological identity of nanomaterials, that is, the surface adsorbed proteins and/or other biomolecules known as the bio-corona, or both? This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.

Cytocompatibility of carboxylated multi-wall carbon nanotubes in stem cells from human exfoliated deciduous teeth

Carboxylated multi-wall carbon nanotube (MWCNT-COOH) presents unique properties due to nanoscale dimensions and permits a broad range of applications in different fields, such as bone tissue engineering and regenerative medicine. However, the cytocompatibility of MWCNT-COOH with human stem cells is poorly understood. Thus, studies elucidating how MWCNT-COOH affects human stem cell viability are essential to a safer application of nanotechnologies. Using stem cells from the human exfoliated deciduous teeth model, we have evaluated the effects of MWCNT-COOH on cell viability, oxidative cell stress, and DNA integrity. Results demonstrated that despite the decreased metabolism of mitochondria, MWCNT-COOH had no toxicity against stem cells. Cells maintained viability after MWCNT-COOH exposure. MWCNT-COOH did not alter the superoxide dismutase activity and did not cause genotoxic effects. The present findings are relevant to the potential application of MWCNT-COOH in the tissue engineering and regenerative medicine fields.

Integrated in silico analysis for the identification of key genes and signaling pathways in copper oxide nanoparticles toxicity

Copper oxide nanoparticles (CuO-NPs) are used in various industrial and commercial products due to their enhanced physicochemical properties. The vast consumption increases their exposure in the environment, thereby affecting the ecosystem. Even with the rise in research towards understanding their toxicity, the major signaling cascades and key genes involved in CuO-NPs remain elusive due to the various attributes involved (size, shape, charge, coating in terms of nanoparticles, and dose, duration, and species used in the experiment). The focus of the study is to identify the key signaling cascades and genes involved in CuO-NPs toxicity irrespective of these attributes. CuO-NPs related microarray expression profiles were screened from GEO database and were subjected to toxicogenomic analysis to elucidate the toxicity mechanism. In silico tools were used to obtain the DEGs, followed by GO and KEGG functional enrichment analysis. The identified DEGs were then analyzed to determine major signaling pathways and key genes. Module and centrality parameter analysis was performed to identify the key genes. Further, the miRNAs and transcription factors involved in regulating the genes were predicted, and their interactive pathways were constructed. A total of 44 DEGs were commonly present in all the analysed datasets and all of them were downregulated. GO analysis reveals that most of the genes were enriched in functions related to cell division and chemotaxis. Cell-cycle, chemokine, cytokine-cytokine receptor interaction, and p53 signaling pathways were the key pathways with Cdk1 as the major biomarker altered irrespective of the variables (dosage, duration, species used, and surface coating). Overall, our integrated toxicogenomic analysis reveal that Cdk1 regulated cell cycle and cytokine-cytokine signaling cascades might be responsible for CuO-NPs toxicity. These findings will help us in understanding the mechanisms involved in NPs toxicity.

Profiling Non-Coding RNA Changes Associated with 16 Different Engineered Nanomaterials in a Mouse Airway Exposure Model

Perturbations in cellular molecular events and their associated biological processes provide opportunities for hazard assessment based on toxicogenomic profiling. Long non-coding RNAs (lncRNAs) are transcribed from DNA but are typically not translated into full-length proteins. Via epigenetic regulation, they play important roles in organismal response to environmental stress. The effects of nanoparticles on this important part of the epigenome are understudied. In this study, we investigated changes in lncRNA associated with hazardous inhalatory exposure of mice to 16 engineered nanomaterials (ENM)–4 ENM (copper oxide, multi-walled carbon nanotubes, spherical titanium dioxide, and rod-like titanium dioxide particles) with 4 different surface chemistries (pristine, COOH, NH₂, and PEG). Mice were exposed to 10 µg of ENM by oropharyngeal aspiration for 4 consecutive days, followed by cytological analyses and transcriptomic characterization of whole lung tissues. The number of significantly altered non-coding RNA transcripts, suggestive of their degrees of toxicity, was different for each ENM type. Particle surface chemistry and shape also had varying effects on lncRNA expression. NH₂ and PEG caused the strongest and weakest responses, respectively. Via correlational analyses to mRNA expression from the same samples, we could deduce that significantly altered lncRNAs are potential regulators of genes involved in mitotic cell division and DNA damage response. This study sheds more light on epigenetic mechanisms of ENM toxicity and also emphasizes the importance of the lncRNA superfamily as toxicogenomic markers of adverse ENM exposure.

Toxicogenomic Profiling of 28 Nanomaterials in Mouse Airways

Toxicogenomics opens novel opportunities for hazard assessment by utilizing computational methods to map molecular events and biological processes. In this study, the transcriptomic and immunopathological changes associated with airway exposure to a total of 28 engineered nanomaterials (ENM) are investigated. The ENM are selected to have different core (Ag, Au, TiO2, CuO, nanodiamond, and multiwalled carbon nanotubes) and surface chemistries (COOH, NH2, or polyethylene glycosylation (PEG)). Additionally, ENM with variations in either size (Au) or shape (TiO2) are included. Mice are exposed to 10 µg of ENM by oropharyngeal aspiration for 4 consecutive days, followed by extensive histological/cytological analyses and transcriptomic characterization of lung tissue. The results demonstrate that transcriptomic alterations are correlated with the inflammatory cell infiltrate in the lungs. Surface modification has varying effects on the airways with amination rendering the strongest inflammatory response, while PEGylation suppresses toxicity. However, toxicological responses are also dependent on ENM core chemistry. In addition to ENM-specific transcriptional changes, a subset of 50 shared differentially expressed genes is also highlighted that cluster these ENM according to their toxicity. This study provides the largest in vivo data set currently available and as such provides valuable information to be utilized in developing predictive models for ENM toxicity.

Surface chemistry modification of silica nanoparticles alters the activation of monocytes

Aim: Nanoparticles (NPs) interaction with immune system is a growing topic of study. Materials & methods: Bare and amine grafted silica NPs effects on monocytes/macrophages cells were analyzed by flow cytometry, MTT test and LIVE/DEAD^® viability/cytotoxicity assay. Results: Bare silica NPs inhibited proliferation and induced monocyte/macrophages activation (increasing CD40/CD80 expression besides pro-inflammatory cytokines and nitrite secretion). Furthermore, silica NPs increased cell membrane damage and reduced the number of living cells. In contrast, amine grafted silica NPs did not alter these parameters. Conclusion: Cell activation properties of bare silica NPs could be hindered after grafting with amine moieties. This strategy is useful to tune the immune system stimulation by NPs or to design NPs suitable to transport therapeutic molecules.

3D Printed Masks for Powders and Viruses Safety Protection Using Food Grade Polymers: Empirical Tests

The production of 3D printed safety protection devices (SPD) requires particular attention to the material selection and to the evaluation of mechanical resistance, biological safety and surface roughness related to the accumulation of bacteria and viruses. We explored the possibility to adopt additive manufacturing technologies for the production of respirator masks, responding to the sudden demand of SPDs caused by the emergency scenario of the pandemic spread of SARS-COV-2. In this study, we developed different prototypes of masks, exclusively applying basic additive manufacturing technologies like fused deposition modeling (FDM) and droplet-based precision extrusion deposition (db-PED) to common food packaging materials. We analyzed the resulting mechanical characteristics, biological safety (cell adhesion and viability), surface roughness and resistance to dissolution, before and after the cleaning and disinfection phases. We showed that masks 3D printed with home-grade printing equipment have similar performances compared to the industrial-grade ones, and furthermore we obtained a perfect face fit by customizing their shape. Finally, we developed novel approaches to the additive manufacturing post-processing phases essential to assure human safety in the production of 3D printed custom medical devices.

Brave new world revisited: Focus on nanomedicine

Nanomedicine is at a crossroads: with relatively few success stories in terms of clinical translation despite more and more research on increasingly sophisticated nanomaterials, it is important to consider whether we are on the right track. Indeed, it is crucial that we address the fact that while considerable efforts are being made to overcome barriers to translation from the bench to the clinic, scientists are still struggling to decipher fundamental aspects of nanomaterial interactions with biological systems. We believe that a key to the successful adoption of nanomedicines in oncology and beyond lies in a deeper understanding of underlying biological processes and in decoding interactions between engineered nanomaterials and biological systems. Here we provide an overview of progress in nanomedicine during the past 5 years.