This is an RDFied version of the dataset published in Choi, JS., Ha, M.K., Trinh, T.X. et al. Towards a generalized toxicity prediction model for oxide nanomaterials using integrated data from different sources. Sci Rep 8, 6110 (2018). The original dataset publication DOI: https://doi.org/10.1038/s41598-018-24483-z. The Original publication authors: Jang-Sik Choi, My Kieu Ha, Tung Xuan Trinh, Tae Hyun Yoon & Hyung-Gi Byun

Manufactured nanomaterials with unique properties have been extensively applied in various industrial, agricultural or medical fields. However, some of the properties have been identified to be closely related to nanomaterial toxicity. The “nano-paradox” has aroused concerns over the use and development of nanotechnology, which makes it difficult for regulatory agencies to regulate nanomaterials. The key to fulfilling proper nanomaterial regulation lies in the adequate understanding of the impact of nanomaterial properties on nano-bio interactions. To this end, we start the present work with a brief introduction to nano-bio interactions at different levels. Based on that, how key toxicity-associated properties of manufactured nanomaterials (i.e., size, shape, chemical composition, surface properties, biocorona formation, agglomeration and/or aggregation state, and biodegradability) impact their toxicokinetics, cellular uptake, trafficking and responses, and toxicity mechanisms is deeply explored. Moreover, advanced analytical methods for studying nano-bio interactions are introduced. Furthermore, the current regulatory and legislative frameworks for nanomaterial-containing products in different regions and/or countries are presented. Finally, we propose several challenges facing the nanotoxicology field and their possible solutions to shed light on the safety evaluation of nanomaterials.

This study aims to implement methods for toxicological profiling of engineered nanomaterials using toxicogenomics, proteomics, and metabolomics along with computational analyses. For all three omics layers the human cell lines A549 (lung epithelial cells) and THP1 (monocytes) were separately exposed to the nanomaterials TiO2 NM104, MWNCT NM401, and Ag NM300k. Proteomics and metabolomics samples have been performed as biological triplicates and were taken after 0, 6, 12, 24, and 48 hours. To assess ecotoxic effects C. elegans worms were grown in soil treated with NM300k. Ecotox samples were taken only at 0 and 24 hours. Integrating all three omics layers will enable the identification of (novel) ENM specific modes of action (MoA).

This dataset houses a research poster, its poster abstract, and its award certificate. The set of documents was first presented at The Virtual 10th International Conference on Nanotoxicology (NanoTox2021) poster presentation, 20th - 22nd April 2021. Poster Title: "New descriptors in toxicology prediction of nanomaterials: Using quasi-ab initio MD simulations for the estimation of aqueous ZnO and TiO2 surface structure parameters.” Our research focuses on understanding the toxicity of nanomaterials, highlighting the need for in-silico methods due to their diverse structures and compositions. We investigate the interactions and surface parameters of ZnO and TiO2 nanoparticles with water using Molecular Dynamics simulations at Density Functional – Tight Binding level methods. By incorporating new structural parameters, we aim to contribute toxicology prediction models and improve safety assessments of nanomaterials. The poster selected and awarded with attendees’ bursary, which is given to 49 attendees over 384 registered attendees, and one of the "Best Student Poster - Highly Commended" prize among 117 poster presentations.

The model identified, among the factors determining the cytotoxic properties of metal oxide nanoparticles against HaCaT cell lines, a number of variables related to the processes occurring on the surface of nanoparticles in a biological medium, including the ability to form protein corona. The selected descriptors describe both the electronic structure of the metal oxides that are the components of the nanoparticles, i.e. the ionization potential (IP_ActivM_SM_#1, IP_ActivM_SM_#2) and the initial nanoforms, i.e. the particle size (Primary size) and the percentage content of the metal oxide which is the main component of the nanoparticle (Purity_#1) ; characterize nanoparticles in the medium, i.e. the isoelectric point (PZZP_#2), stability (Stability), potential for dissolution (Dissolution), generation of reactive oxygen species (ROS production) and protein adsorption (Protein adsorption). The listed descriptors reflect the features that are discussed in the literature as potentially related to the toxic effect of nanoparticles.

This dataset comprises particle-specific mortality estimates from acute toxicity tests with silver and zinc oxide nanoparticles in zebrafish larvae under germ-free and microbially-colonized conditions.Details of this experiment have been published in Nanotoxicology: Brinkmann BW, Koch BEV, Spaink HP, Peijnenburg WJGM, and Vijver MG, 2020. Colonizing microbiota protect zebrafish larvae against silver nanoparticle toxicity. Nanotoxicology, 14(6): 725-739. Doi: 10.1080/17435390.2020.1755469The six parameters of the dataset are:- Compound. One of the two nanoparticles that were tested in the acute toxicity test, including: nAg, silver nanoparticles; and nZnO, zinc oxide nanoparticles.- Concentration. The nominal silver and zinc oxide nanoparticle concentrations, expressed in mg Ag/L and mg ZnO/L respectively.- TWA_total. The actual time-weighted average concentrations of the total of nanoparticles and their shed ions in exposure media, expressed in mg Ag/L and mg ZnO/L, respectively.- TWA_particle. The actual time-weighted average exposure concentration of nanoparticles, expressed in mg Ag/L and mg ZnO/L, respectively.- Condition. The germ-free or microbially-colonized condition of zebrafish larvae.- Mortality. The estimated percentage of larvae that have died in the toxicity test due to the presence of particles in the exposure medium.This dataset has been saved in a tab-delimited text file format.

Large amounts of nanotoxicity data from alternative non-animal (in vitro) test methods have been generated, but there is a lack of harmonized quality evaluation approaches for these types of data. Tools for scientifically sound and structured evaluation of the reliability and relevance of in vitro toxicity data to effectively inform regulatory hazard assessment of nanomaterials (NMs), are needed. Here, we present the development of a pragmatic approach to facilitate such evaluation. The tool was developed based on the Science in Risk Assessment and Policy (SciRAP) tool currently applicable to quality evaluation of chemical toxicity studies. The approach taken to develop the tool, referred to as SciRAPnano, included refinement of the original SciRAP in vitro tool through implementation of identified NM-relevant criteria, and further refined based on a set of case studies involving evaluation of 11 studies investigating in vitro toxicity of nano-sized titanium dioxide. Parameters considered cover key physicochemical properties as well as assay-specific aspects that impact NM toxicity, including NM interference with test methods and NM transformation. The final SciRAPnano tool contains 38 criteria for reporting quality, 19 criteria for methodological quality, and 4 guidance items to evaluate relevance. The approach covers essential parameters for pragmatic and harmonized evaluation of NM in vitro toxicity studies and allows for structured use of in vitro data in regulatory hazard assessment of NMs, including transparency on data quality.

Impact of passage number on cell toxicity.

Over the past decade, the development of nanomaterials (NMs) has surged, highlighting their potential benefits across multiple industries. However, concerns regarding human and environmental exposure remain significant. Traditional in vivo models for safety assessments are increasingly viewed as unfeasible and unethical due to the diverse forms and biological effects of NMs. This has prompted the design of Novel Approach Methods (NAMs) to streamline risk assessment and predict human hazards without relying on animal testing. A critical aspect of advancing NAMs is the urgent need to replace animal-derived products in assay protocols. Incorporating human or synthetic alternatives can significantly reduce the ethical burden of animal use while enhancing the relevance of toxicity testing. This study evaluates the impact of removing animal-derived products from standard acellular and in vitro assays recommended in a published Integrated Approaches to Testing and Assessment (IATA) for inhaled NMs. We specifically assessed the effects of replacing fetal bovine serum with human platelet lysate in acellular reactivity tests and in vitro toxicity testing using a panel of well-characterized NMs. Significant differences in acellular NM reactivity and dramatic changes in A549 cell growth rates and responses to NMs were observed under different media conditions. Our findings demonstrate that variations in experimental setup can fundamentally impact NM hazard assessment, influencing the interpretation of results within specific assays and across tiered testing strategies. Further investigation is needed to support a shift toward more ethical toxicity testing that does not rely on animal-derived materials.

Assessing research activity is an important step for planning future initiatives oriented toward filling the remaining gaps in a field. Therefore, the objective of the current study was to review recently published research on pulmonary toxicity caused by nanomaterials. However, here, instead of reviewing possible toxic effects and discussing their mode of action, the goal was to establish trends considering for example examined so far nanomaterials or used testing strategies. A total of 2316 related articles retrieved from the three most cited databases (PubMed Scopus, Web of Science), selected based on the title and abstract requirements, were used as the source of the review. Based on the bibliometric analysis, the nano-meter metal oxides, and carbon-based nanotubes were identified as the most frequently studied nanomaterials, while quantum dots, which might induce possible harmful effects, were not considered so far. The majority of testing of pulmonary safety is based on in vitro studies with observed growth of the contribution of novel testing strategies, such as 3D lung model, air-liquid interface system, or omic analysis.

Results obtained from developed model indicated that the cytotoxicity of hybrid TiO2-based nanomaterials is related to additive electronegativity (χmix) of studied nanomaterials that are indirectly related to the electron generation and ROS formation. ROS production is the most common toxicity cause as discussed in the literature in the case of nanoparticles. The high efficiency of surface modified TiO2-based semiconductors can be attributed to the involvement of TiO2 band gap (Eg) excitation and absence of noble metals at the TiO2 surface. It can be expected that noble metals (i.e. Pd/Pt) may trap holes (h+), at the same time photo-generated electrons can be then transferred from the valence band to the conduction band of TiO2 and to its surface where redox processes were initiated. Thus, observed reduction of the electron–hole pair recombination influences the reactive oxygen species (ROS) formation and the photocatalytic redox process initiation. Since the electronegativity was positively correlated with the cytotoxicity it can be expected that some ions are released from the TiO2 surface easier than others.

Spectral fits and linear combination data for ZnO and CuO nanoparticles exposure during toxicity testing.

This dataset is associated with the following publication: Ivask, A., K. Scheckel, P. Kapruwan, V. Stone, H. Yin, N. Voelcker, and E. Lombi. Complete transformation of ZnO and CuO nanoparticles in culture medium and lymphocyte cells during toxicity testing. Prof. Hakan Wallin, and Dr. Alison Elder Nanotoxicology. Informa Healthcare, London, UK, 11(2): 150-156, (2017).

Nanomaterials represent a new class of materials with numerous industrial applications. Considering the projected increase in the production and use of nanomaterials, a corresponding increase in occupational exposure to nanomaterials and their resulting adverse health effects may be anticipated among workers. There is substantial evidence in the literature, based on cell culture and animal studies, supporting the potential toxicity and detrimental health effects associated with exposure to nanomaterials. Intervention and/or prevention of adverse health effects associated with occupational exposure to toxic nanomaterials is a concern for health providers and regulatory and non-regulatory government agencies as the use of nanomaterials expand. A key element in the intervention and/or prevention of the adverse health effects associated with occupational exposure to toxic nanomaterials is a clear understanding of the molecular mechanisms underlying the pulmonary toxicity induced by nanomaterials.

Due to its physicochemical and mechanical properties, multi-walled carbon nanotubes (MWCNT) have found many industrial applications. There is potential for human exposure to MWCNT or products that contain MWCNT both during the production and use of the materials that contain MWCNT. The objectives of the current study were to investigate MWCNT-induced lung toxicity and the molecular mechanisms underlying that toxicity. A rat inhalation exposure model was employed to determine the lung toxicity induced by MWCNT. Global gene expression profiles in the lung and blood were conducted to determine the molecular mechanisms underlying MWCNT-induced lung toxicity.

The documentation will include: for the in vitro and in vivo studies all the data acquired after the exposure of cells or zebrafish to the nano-sized CaCO3 particles.

Supprto data to: Toxicological profile of calcium carbonate nanoparticles for industrial applications article.

*Significantly different compared to control.

Adverse Outcome Pathways (AOPs) have been proposed to facilitate mechanistic understanding of interactions of chemicals/materials with biological systems. Each AOP starts with a molecular initiating event (MIE) and possibly ends with adverse outcome(s) (AOs) via a series of key events (KEs). So far, the interaction of engineered nanomaterials (ENMs) with biomolecules, biomembranes, cells, and biological structures, in general, is not yet fully elucidated. There is also a huge lack of information on which AOPs are ENMs-relevant or -specific, despite numerous published data on toxicological endpoints they trigger, such as oxidative stress and inflammation. We propose to integrate related data and knowledge recently collected. Our approach combines the annotation of nanomaterials and their MIEs with ontology annotation to demonstrate how we can then query AOPs and biological pathway information for these materials. We conclude that a FAIR (Findable, Accessible, Interoperable, Reusable) representation of the ENM-MIE knowledge simplifies integration with other knowledge.

High througput imaging DB of toxicological effect of Manufactured nanomaterials on HepaRGs.

In this model the property of a nanomaterial is predicted not on the basis of descriptors characterizing the chemical composition of nanoparticles or physical properties of the initial nanoforms, but on the basis of descriptors describing the dispersion medium (pH, IP, D3_HeteroNonMetals) and the property of nanoparticles dependent on it (Potential ζ). The observed small size of the hydrodynamic diameter of TiO2 in solvents of strong acids and bases compared to other solvents may indicate stronger repulsive interactions between nanoparticles than in the case of other systems. Moreover, in the case of salt solutions, the observed large size of the hydrodynamic diameter of TiO2 may be the result of a thicker electrical layer surrounding the particles in the dispersion system.

Nanomaterials represent a new class of materials with numerous industrial applications. Considering the projected increase in the production and use of nanomaterials, a corresponding increase in occupational exposure to nanomaterials and their resulting adverse health effects should be anticipated among workers. There is substantial evidence in the literature, based on cell culture and animal studies, supporting the potential toxicity and detrimental health effects associated with exposure to nanomaterials. Intervention and/or prevention of adverse health effects associated with occupational exposure to toxic nanomaterials will be a major concern for health providers and regulatory and non-regulatory government agencies as the use of nanomaterials expand. A key element in the intervention and/or prevention of the adverse health effects associated with occupational exposure to toxic nanomaterials is a clear understanding of the molecular mechanisms underlying the pulmonary toxicity induced by nanomaterials.

Due to its physicochemical and mechanical properties, nanocellulose has found many applications in manufactured goods in the paper and food industry, cosmetics, biomedicine, and pharmaceuticals. There is potential for human exposure to nanocellulose or products that contain nanocellulose both during the production and use of the materials that contain nanocellulose. The objectives of the current study were to determine lung toxicity potential of crystalline nanocellulose (CNC) and the molecular mechanisms underlying the toxicity. A rat inhalation exposure model was employed to determine the lung toxicity potential of CNC. Global gene expression profile in the lung and bioinformatic analysis of the gene expression data were conducted to determine the molecular mechanisms underlying the CNC-induced lung toxicity.

This study aimed to assess the radioprotective efficacy of zinc oxide nanoparticles (nano-ZnO) against γ-radiation-induced DNA lesions in Vicia faba employing flow cytometry (FCM), comet assay, and RAPD-PCR bioassays. Each dose of γ-irradiated seeds was post-treated with three nano-ZnO concentrations. Exposure time pre- and post-ZnO treatments were 24 h. Dose-dependent nano-ZnO and γ-ray treatments showed specific interference with DNA. Three bioassays could successfully detect positive action of two nano-ZnO concentrations (500 and 2000 mg L-1) on DNA compared to control while high concentration nano-ZnO showed a negative interference with DNA. On the contrary, three doses of γ-ray induced major lesions in V. faba DNA. Data obtained illustrated that combination of 2000 mgL-1 nano-ZnO concentration with each γ-ray the dose had a good ability to protect DNA against their damaging when compared to the equivalent γ-ray doses prior to nano-ZnO treatment. This was evident through the significant amelioration of DNA parameters which manifested in increasing nuclear DNA content and genome size, reduction the DNA damage (tail length, Tailed DNA% and tail moment), and scoring new amplified DNA bands and increasing their number. This study concluded that nano-ZnO can be used as potent mutant and an efficient nano-radioprotector for the protection of crop plant DNA.