Risk assessments in nanotoxicology: bioinformatics and computational approaches

Abstract A massive-scale production of engineered nanoparticles (ENPs) becomes one of the most important environmental issues. The mechanisms of ENPs' (eco)toxic action are not fully understood, and the estimation of those mechanisms is a complicated task because even slight changes in particle characteristics could dramatically change their toxicity. As a result of continuous manufacturing of ENPs with specific functionality and different physicochemical properties, conventional methods of in vivo and in vitro testing would not be able to fill the existing knowledge gap in nanotoxicology. The objectives of this review are to overlook the current achievements based on the new approaches of ENPs' risk assessment, such as bioinformatics approaches and machine learning tools. These methods confirmed their ability to reliable prediction and evaluation of ENPs' behavior and their toxic endpoints. Databases and projects based on these methods and approaches would be highly useful in addressing the problem of ENPs’ regulation.

[1]  Pravin Ambure,et al.  QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models , 2019, J. Chem. Inf. Model..

[2]  M. Natália D. S. Cordeiro,et al.  MitoTarget Modeling Using ANN-Classification Models Based on Fractal SEM Nano-Descriptors: Carbon Nanotubes as Mitochondrial F0F1-ATPase Inhibitors. , 2018, Journal of chemical information and modeling.

[3]  D. Cowan,et al.  Genotoxicity of metal based engineered nanoparticles in aquatic organisms: A review. , 2017, Mutation research.

[4]  Peter Kearns,et al.  Physico-chemical properties of manufactured nanomaterials - Characterisation and relevant methods. An outlook based on the OECD Testing Programme , 2018, Regulatory toxicology and pharmacology : RTP.

[5]  David M. Brown,et al.  Transcriptional profiling reveals gene expression changes associated with inflammation and cell proliferation following short‐term inhalation exposure to copper oxide nanoparticles , 2018, Journal of applied toxicology : JAT.

[6]  Andrea Haase,et al.  EU US Roadmap Nanoinformatics 2030 , 2018 .

[7]  Metin Sitti,et al.  Review of emerging concepts in nanotoxicology: opportunities and challenges for safer nanomaterial design , 2019, Toxicology mechanisms and methods.

[8]  Antonios D. Niros,et al.  Optimized Classification Predictions with a New Index Combining Machine Learning Algorithms , 2018, Int. J. Artif. Intell. Tools.

[9]  A Worth,et al.  Grouping of nanomaterials to read-across hazard endpoints: a review , 2018, Nanotoxicology.

[10]  Ulf Norinder,et al.  Development and validation of computational models for predicting oxidative stress responses using comprehensive series of drug-like compounds , 2018 .

[11]  Qixing Zhou,et al.  Screening Priority Factors Determining and Predicting the Reproductive Toxicity of Various Nanoparticles. , 2018, Environmental science & technology.

[12]  Bengt Fadeel,et al.  Close encounters of the small kind: adverse effects of man-made materials interfacing with the nano-cosmos of biological systems. , 2010, Annual review of pharmacology and toxicology.

[13]  Ashok K. Singh Engineered Nanoparticles: Structure, Properties and Mechanisms of Toxicity , 2015 .

[14]  G. Oberdörster,et al.  Nanotoxicology: An Emerging Discipline Evolving from Studies of Ultrafine Particles , 2005, Environmental health perspectives.

[15]  A. Tsatsakis,et al.  Effect of surfactant in mitigating cadmium oxide nanoparticle toxicity: Implications for mitigating cadmium toxicity in environment , 2017, Environmental research.

[16]  Egon L. Willighagen,et al.  eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment , 2015, Journal of Biomedical Semantics.

[17]  Maryam Mobed-Miremadi,et al.  Machine learning provides predictive analysis into silver nanoparticle protein corona formation from physicochemical properties. , 2018, Environmental science. Nano.

[18]  Irini Furxhi,et al.  Machine learning prediction of nanoparticle in vitro toxicity: A comparative study of classifiers and ensemble-classifiers using the Copeland Index. , 2019, Toxicology letters.

[19]  Joel G. Burken,et al.  Using artificial neural network to investigate physiological changes and cerium oxide nanoparticles and cadmium uptake by Brassica napus plants. , 2019, Environmental pollution.

[20]  Nicklas Raun Jacobsen,et al.  Transcriptional profiling identifies physicochemical properties of nanomaterials that are determinants of the in vivo pulmonary response , 2015, Environmental and molecular mutagenesis.

[21]  Anders Baun,et al.  A critical analysis of the environmental dossiers from the OECD sponsorship programme for the testing of manufactured nanomaterials , 2017 .

[22]  Bengt Fadeel,et al.  Advanced tools for the safety assessment of nanomaterials , 2018, Nature Nanotechnology.

[23]  Michael K Danquah,et al.  Review on nanoparticles and nanostructured materials: history, sources, toxicity and regulations , 2018, Beilstein journal of nanotechnology.

[24]  V. Kuznetsov,et al.  Effects of carbon and silicon nanotubes and carbon nanofibers on marine microalgae Heterosigma akashiwo , 2018, Environmental research.

[25]  Anthony Seaton,et al.  Nanoscience, nanotoxicology, and the need to think small , 2005, The Lancet.

[26]  Kevin Robbie,et al.  Nanomaterials and nanoparticles: Sources and toxicity , 2007, Biointerphases.

[27]  Jaeseong Jeong,et al.  Developing adverse outcome pathways on silver nanoparticle-induced reproductive toxicity via oxidative stress in the nematode Caenorhabditis elegans using a Bayesian network model , 2018, Nanotoxicology.

[28]  B. Giese,et al.  Risks, Release and Concentrations of Engineered Nanomaterial in the Environment , 2018, Scientific Reports.

[29]  Igor V Tetko,et al.  Modelling the toxicity of a large set of metal and metal oxide nanoparticles using the OCHEM platform. , 2017, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[30]  Weihua Li,et al.  In silico prediction of pesticide aquatic toxicity with chemical category approaches. , 2017, Toxicology research.

[31]  Hyung-Gi Byun,et al.  Towards a generalized toxicity prediction model for oxide nanomaterials using integrated data from different sources , 2018, Scientific Reports.

[32]  Irini Furxhi,et al.  Application of Bayesian networks in determining nanoparticle-induced cellular outcomes using transcriptomics , 2019, Nanotoxicology.

[33]  Juan José Villaverde,et al.  Considerations of nano-QSAR/QSPR models for nanopesticide risk assessment within the European legislative framework. , 2018, The Science of the total environment.

[34]  E. Flahaut,et al.  Investigating a transcriptomic approach on marine mussel hemocytes exposed to carbon nanofibers: An in vitro/in vivo comparison. , 2019, Aquatic toxicology.

[35]  Katarzyna Odziomek,et al.  Decision tree models to classify nanomaterials according to the DF4nanoGrouping scheme , 2018, Nanotoxicology.

[36]  Marco Guida,et al.  Toxicity Effects of Functionalized Quantum Dots, Gold and Polystyrene Nanoparticles on Target Aquatic Biological Models: A Review , 2017, Molecules.

[37]  M. Junaid,et al.  Transcriptomic response and perturbation of toxicity pathways in zebrafish larvae after exposure to graphene quantum dots (GQDs). , 2018, Journal of hazardous materials.

[38]  Xue Z. Wang,et al.  (Q)SAR Modelling of Nanomaterial Toxicity - A Critical Review , 2015 .

[39]  Dana Loomis,et al.  Work in Brief , 2006 .

[40]  Phil Sayre,et al.  Review of achievements of the OECD Working Party on Manufactured Nanomaterials' Testing and Assessment Programme. From exploratory testing to test guidelines. , 2016, Regulatory toxicology and pharmacology : RTP.

[41]  Ghanima Al-Sharrah,et al.  Ranking Using the Copeland Score: A Comparison with the Hasse Diagram , 2010, J. Chem. Inf. Model..

[42]  Andrew Williams,et al.  Ranking of nanomaterial potency to induce pathway perturbations associated with lung responses , 2019, NanoImpact.

[43]  Jian Zhao,et al.  CarcinoPred-EL: Novel models for predicting the carcinogenicity of chemicals using molecular fingerprints and ensemble learning methods , 2017, Scientific Reports.

[44]  Qixing Zhou,et al.  Integrating multi-omics and regular analyses identifies the molecular responses of zebrafish brains to graphene oxide: Perspectives in environmental criteria. , 2019, Ecotoxicology and environmental safety.

[45]  B. Rihn,et al.  Cytotoxicity and global transcriptional responses induced by zinc oxide nanoparticles NM 110 in PMA-differentiated THP-1 cells. , 2019, Toxicology letters.

[46]  Jie Gu,et al.  Silver nanoparticle toxicity in silkworms: Omics technologies for a mechanistic understanding. , 2019, Ecotoxicology and environmental safety.

[47]  R. W. Lewis,et al.  Nanotoxicity of engineered nanomaterials (ENMs) to environmentally relevant beneficial soil bacteria – a critical review , 2019, Nanotoxicology.

[48]  A. Datta,et al.  Gauging the Nanotoxicity of h2D-C2N toward Single-Stranded DNA: An in Silico Molecular Simulation Approach. , 2018, ACS applied materials & interfaces.

[49]  Zhiguo Yuan,et al.  Physiological and transcriptomic analyses reveal CuO nanoparticle inhibition of anabolic and catabolic activities of sulfate-reducing bacterium. , 2019, Environment international.

[50]  Jingwen Chen,et al.  Modeling adsorption of organic pollutants onto single-walled carbon nanotubes with theoretical molecular descriptors using MLR and SVM algorithms. , 2019, Chemosphere.

[51]  Short-Time Effect of Multi-Walled Carbon Nanotubes on Some Histological and Biochemical Parameters in Marine Bivalves Crenomytilus grayanus (Dunker, 1853) and Swiftopecten swifti (Bernardi, 1858) , 2017 .