A multi-omics approach reveals mechanisms of nanomaterial toxicity and structure–activity relationships in alveolar macrophages

References

• Arts, J. H. E., M. Hadi, M-A. Irfan, A.M. Keene, R. Kreiling, D. Lyon, M. Maier, et al. 2015. “A Decision-Making Framework for the Grouping and Testing of Nanomaterials (DF4nanoGrouping).” Regulatory Toxicology and Pharmacology 71 (2): S1–S27. doi:10.1016/j.yrtph.2015.03.007.
   PubMed Web of Science ®Google Scholar
• Arts, J. H., M. A. Irfan, A. M. Keene, R. Kreiling, D. Lyon, M. Maier, K. Michel, et al. 2016. “Case Studies Putting the Decision-Making Framework for the Grouping and Testing of Nanomaterials (DF4nanoGrouping) into Practice.” Regulatory Toxicology and Pharmacology 76: 234–261. doi:10.1016/j.yrtph.2015.11.020.
   PubMed Web of Science ®Google Scholar
• Delaval, M., W. Wohlleben, R. Landsiedel, A. Baeza-Squiban, and S. Boland. 2017. “Assessment of the Oxidative Potential of Nanoparticles by the Cytochrome c Assay: Assay Improvement and Development of a High-Throughput Method to Predict the Toxicity of Nanoparticles.” Archives of Toxicology 91 (1): 163–177. doi:10.1007/s00204-016-1701-3.
   PubMed Web of Science ®Google Scholar
• Dierck, K., K. Machida, B. J. Mayer, and P. Nollau. 2009. Profiling the Tyrosine Phosphorylation State Using SH2 Domains. Phospho-Proteomics, 131–155. New York: Springer.
   Google Scholar
• Donaldson, K., R. Aitken, L. Tran, V. Stone, R. Duffin, G. Forrest, and A. Alexander. 2006. “Carbon Nanotubes: A Review of Their Properties in Relation to Pulmonary Toxicology and Workplace Safety.” Toxicological Sciences 92 (1): 5–22. doi:10.1093/toxsci/kfj130.
   PubMed Web of Science ®Google Scholar
• Dong, J., and Q. Ma. 2015. “Advances in Mechanisms and Signaling Pathways of Carbon Nanotube Toxicity.” Nanotoxicology 9 (5): 658–676. doi:10.3109/17435390.2015.1009187.
   PubMed Web of Science ®Google Scholar
• Driessen, M. D., S. Mues, A. Vennemann, B. Hellack, A. Bannuscher, V. Vimalakanthan, C. Riebeling, et al. 2015. “Proteomic Analysis of Protein Carbonylation: A Useful Tool to Unravel Nanoparticle Toxicity Mechanisms.” Particle and Fibre Toxicology 12 (1): 36. doi:10.1186/s12989-015-0108-2.
   PubMedGoogle Scholar
• Feliu, N., B. Pelaz, Q. Zhang, P. Del Pino, A. Nystrom, and W. J. Parak. 2016. “Nanoparticle Dosage-a Nontrivial Task of Utmost Importance for Quantitative Nanosafety Research.” Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 8 (3): 479–492. doi:10.1002/wnan.1378.
   PubMed Web of Science ®Google Scholar
• Gallud, A., K. Klöditz, J. Ytterberg, N. Östberg, S. Katayama, T. Skoog, V. Gogvadze, et al. 2019. “Cationic Gold Nanoparticles Elicit Mitochondrial Dysfunction: A Multi-Omics Study.” Scientific Reports 9 (1): 4366. doi:10.1038/s41598-019-40579-6.
   PubMedGoogle Scholar
• Gerloff, K., B. Landesmann, A. Worth, S. Munn, T. Palosaari, and M. Whelan. 2017. “The Adverse Outcome Pathway Approach in Nanotoxicology.” Computational Toxicology 1: 3–11. doi:10.1016/j.comtox.2016.07.001.
   Google Scholar
• Hsieh, S. F., D. Bello, D. F. Schmidt, A. K. Pal, A. Stella, J. A. Isaacs, and E. J. Rogers. 2013. “Mapping the Biological Oxidative Damage of Engineered Nanomaterials.” Small 9 (9–10): 1853–1865. doi:10.1002/smll.201201995.
   PubMed Web of Science ®Google Scholar
• Hughes, C. S., S. Foehr, D. A. Garfield, E. E. Furlong, L. M. Steinmetz, and J. Krijgsveld. 2014. “Ultrasensitive Proteome Analysis Using Paramagnetic Bead Technology.” Molecular Systems Biology 10 (10): 757. doi:10.15252/msb.20145625.
   PubMed Web of Science ®Google Scholar
• Hughes, C. S., S. Moggridge, T. Muller, P. H. Sorensen, G. B. Morin, and J. Krijgsveld. 2018. “Single-Pot, Solid-Phase-Enhanced Sample Preparation for Proteomics Experiments.” *Nature Protocols. doi:10.1038/s41596-018-0082-x.
   Google Scholar
• Kroll, A., C. Dierker, C. Rommel, D. Hahn, W. Wohlleben, C. Schulze-Isfort, C. Göbbert, et al. 2011. Cytotoxicity screening of 23 engineered nanomaterials using a test matrix of ten cell lines and three different assays. Particle and Fibre Toxicology. 8, 9. doi:10.1186/1743-8977-8-9.
   PubMed Web of Science ®Google Scholar
• Krug, H. F. 2014. “Nanosafety Research—Are We on the Right Track?” Angewandte Chemie International Edition 53: 12304–12319. doi:10.1002/anie.201403367.
   PubMed Web of Science ®Google Scholar
• Landsiedel, R., E. Fabian, L. Ma-Hock, B. Van Ravenzwaay, W. Wohlleben, K. Wiench, and F. Oesch. 2012. “Toxico-/Biokinetics of Nanomaterials.” Archives of Toxicology 86 (7): 1021–1060. doi:10.1007/s00204-012-0858-7.
   PubMed Web of Science ®Google Scholar
• Landsiedel, R., L. Ma-Hock, T. Hofmann, M. Wiemann, V. Strauss, S. Treumann, W. Wohlleben, S. Groters, K. Wiench, and B. Van Ravenzwaay. 2014. “Application of Short-Term Inhalation Studies to Assess the Inhalation Toxicity of Nanomaterials.” Particle and Fibre Toxicology 11 (1): 16. doi:10.1186/1743-8977-11-16.
   PubMedGoogle Scholar
• Langfelder, P., and S. Horvath. 2008. “WGCNA: An R Package for Weighted Correlation Network Analysis.” BMC Bioinformatics 9 (1): 559. doi:10.1186/1471-2105-9-559.
   PubMed Web of Science ®Google Scholar
• Li, N., T. Xia, and A. E. Nel. 2008. “The Role of Oxidative Stress in Ambient Particulate Matter-Induced Lung Diseases and Its Implications in the Toxicity of Engineered Nanoparticles.” Free Radical Biology and Medicine 44 (9): 1689–1699. doi:10.1016/j.freeradbiomed.2008.01.028.
   PubMed Web of Science ®Google Scholar
• Lin, Z., L. Ma, Z. G. X, H. Zhang, and B. Lin. 2013. “A Comparative Study of Lung Toxicity in Rats Induced by Three Types of Nanomaterials.” Nanoscale Research Letters 8 (1): 521. doi:10.1186/1556-276X-8-521.
   PubMed Web of Science ®Google Scholar
• Louro, H. 2018. “Relevance of Physicochemical Characterization of Nanomaterials for Understanding Nano-Cellular Interactions.” Advances in Experimental Medicine and Biology 1048: 123–142.
   Google Scholar
• Love, M. I., W. Huber, and S. Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2.” Genome Biology 15 (12): 550. doi:10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar
• Lujan, H., and C. M. Sayes. 2017. “Cytotoxicological Pathways Induced after Nanoparticle Exposure: Studies of Oxidative Stress at the 'Nano-Bio' Interface.” Toxicology Research 6 (5): 580–594. doi:10.1039/C7TX00119C.
   Web of Science ®Google Scholar
• Mcshan, D., P. C. Ray, and H. Yu. 2014. “Molecular Toxicity Mechanism of Nanosilver.” Journal of Food and Drug Analysis 22 (1): 116–127. doi:10.1016/j.jfda.2014.01.010.
   PubMed Web of Science ®Google Scholar
• Nath Roy, D., R. Goswami, and A. Pal. 2017. “Nanomaterial and Toxicity: What Can Proteomics Tell us about the Nanotoxicology?” Xenobiotica 47 (7): 632–643. doi:10.1080/00498254.2016.1205762.
   PubMed Web of Science ®Google Scholar
• Nel, A., T. Xia, L. Mädler, and N. Li. 2006. “Toxic Potential of Materials at the Nanolevel.” Science 311 (5761): 622–627. doi:10.1126/science.1114397.
   PubMed Web of Science ®Google Scholar
• Oberdörster, G., E. Oberdörster, and J. Oberdörster. 2005. “Nanotoxicology: An Emerging Discipline Evolving from Studies of Ultrafine Particles.” Environmental Health Perspectives 113 (7): 823–839. doi:10.1289/ehp.7339.
   PubMed Web of Science ®Google Scholar
• OECD. 2012., Proposal for a template and guidance on developing and assessing the completeness of adverse outcome pathways.
   Google Scholar
• OECD. 2018. Report on considerations from case studies on integrated approaches for testing and assessment (IATA), ENV/JM/MONO(2018)25, Series on Testing and Assessment No. 289.
   Google Scholar
• Olson, H., G. Betton, D. Robinson, K. Thomas, A. Monro, G. Kolaja, P. Lilly, et al. 2000. “Concordance of the Toxicity of Pharmaceuticals in Humans and in Animals.” Regulatory Toxicology and Pharmacology 32 (1): 56–67. doi:10.1006/rtph.2000.1399.
   PubMed Web of Science ®Google Scholar
• Pei, G., L. Chen, and W. Zhang. 2017. “WGCNA Application to Proteomic and Metabolomic Data Analysis.” Methods in Enzymology 585: 135–158. doi:10.1016/bs.mie.2016.09.016.
   PubMed Web of Science ®Google Scholar
• Potratz, S., P. Tarnow, H. Jungnickel, S. Baumann, M. Von Bergen, T. Tralau, and A. Luch. 2017. “Combination of Metabolomics with Cellular Assays Reveals New Biomarkers and Mechanistic Insights on Xenoestrogenic Exposures in MCF-7 Cells.” Chemical Research in Toxicology 30 (4), 883–892. doi:10.1021/acs.chemrestox.6b00106.
   PubMed Web of Science ®Google Scholar
• Rahi, A., N. Sattarahmady, and H. Heli. 2014. “Toxicity of Nanomaterials-Physicochemical Effects.” Austin Journal of Nanomedicine & Nanotechnology 2: 1034–1042.
   Google Scholar
• Riebeling, C., H. Jungnickel, A. Luch, and A. Haase. 2017. “Systems Biology to Support Nanomaterial Grouping.” Advances in Experimental Medicine and Biology 947: 143–171.
   PubMedGoogle Scholar
• Sandberg, A., R. M. M. Branca, J. Lehtiö, and J. Forshed. 2014. “Quantitative Accuracy in Mass Spectrometry Based Proteomics of Complex Samples: The Impact of Labeling and Precursor Interference.” Journal of Proteomics 96: 133–144. doi:10.1016/j.jprot.2013.10.035.
   PubMed Web of Science ®Google Scholar
• Scala, G., P. Kinaret, V. Marwah, J. Sund, V. Fortino, and D. Greco. 2018. “Multi-Omics Analysis of Ten Carbon Nanomaterials Effects Highlights Cell Type Specific Patterns of Molecular Regulation and Adaptation.” NanoImpact 11: 99–108. doi:10.1016/j.impact.2018.05.003.
   PubMed Web of Science ®Google Scholar
• Shanks, N., R. Greek, and J. Greek. 2009. “Are Animal Models Predictive for Humans?” Philosophy, Ethics, and Humanities in Medicine 4 (1): 2–2. doi:10.1186/1747-5341-4-2.
   PubMedGoogle Scholar
• Shatkin, J. A., and K. J. Ong. 2016. “Alternative Testing Strategies for Nanomaterials: State of the Science and Considerations for Risk Analysis.” Risk Analysis. 36: 1564–1580. doi:10.1111/risa.12642.
   PubMed Web of Science ®Google Scholar
• Stark, W. J., P. R. Stoessel, W. Wohlleben, and A. J. C. S. R. Hafner. 2015. “Industrial Applications of Nanoparticles.” Chemical Society Reviews. 44: 5793–5805. doi:10.1039/C4CS00362D.
   PubMed Web of Science ®Google Scholar
• Taurozzi, J. S., V. A. Hackley, and M. R. Wiesner. 2011. “Ultrasonic Dispersion of Nanoparticles for Environmental, Health and Safety Assessment–Issues and Recommendations.” Nanotoxicology 5 (4): 711–729. doi:10.3109/17435390.2010.528846.
   PubMed Web of Science ®Google Scholar
• Tee, J. K., C. N. Ong, B. H. Bay, H. K. Ho, and D. T. Leong. 2016. “Oxidative stress by inorganic nanoparticles.” Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 8, 414–438. doi:10.1002/wnan.1374.
   PubMed Web of Science ®Google Scholar
• Thompson, A., J. Schafer, K. Kuhn, S. Kienle, J. Schwarz, G. Schmidt, T. Neumann, R. Johnstone, A. K. Mohammed, and C. Hamon. 2003. “Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS.” Analytical Chemistry 75 (8): 1895–1904. doi:10.1021/ac0262560.
   PubMed Web of Science ®Google Scholar
• Wall, R. J., and M. Shani. 2008. “Are Animal Models as Good as we Think?” Theriogenology 69 (1): 2–9. doi:10.1016/j.theriogenology.2007.09.030.
   PubMed Web of Science ®Google Scholar
• Wewering, F., F. Jouy, D. K. Wissenbach, S. Gebauer, M. Blüher, R. Gebhardt, R. Pirow, M. Von Bergen, S. Kalkhof, and A. Luch. 2016. “Characterization of Chemical-Induced Sterile Inflammation in Vitro: Application of the Model Compound Ketoconazole in a Human Hepatic co-Culture System.” Archives of Toxicology 91: 1–12. doi:10.1007/s00204-016-1686-y.
   PubMed Web of Science ®Google Scholar
• Wiemann, M., A. Vennemann, U. G. Sauer, K. Wiench, L. Ma-Hock, and R. Landsiedel. 2016. “An in Vitro Alveolar Macrophage Assay for Predicting the Short-Term Inhalation Toxicity of Nanomaterials.” Journal of Nanobiotechnology 14 (1): 16. doi:10.1186/s12951-016-0164-2.
   PubMedGoogle Scholar
• Wiemann, M., A. Vennemann, M. Stintz, R. R. Retamal Marin, F. Babick, G. G. Lindner, T. B. Schuster, U. Brinkmann, and N. Krueger. 2018. “Effects of Ultrasonic Dispersion Energy on the Preparation of Amorphous SiO(2) Nanomaterials for in Vitro Toxicity Testing.” Nanomaterials 9 (1): 11. doi:10.3390/nano9010011.
   Web of Science ®Google Scholar
• Xia, T., R. F. Hamilton, J. C. Bonner, E. D. Crandall, A. Elder, F. Fazlollahi, T. A. Girtsman, et al. 2013. “Interlaboratory Evaluation of in Vitro Cytotoxicity and Inflammatory Responses to Engineered Nanomaterials: The NIEHS Nano GO Consortium.” Environmental Health Perspectives 121 (6): 683–690. doi:10.1289/ehp.1306561.
   PubMed Web of Science ®Google Scholar
• Zhang, B., and S. Horvath. 2005. “A General Framework for Weighted Gene co-Expression Network Analysis.” Statistical Applications in Genetics and Molecular Biology 4 (1): Article17.
   PubMed Web of Science ®Google Scholar
• Zhang, H., Z. Ji, T. Xia, H. Meng, C. Low-Kam, R. Liu, S. Pokhrel, et al. 2012. “Use of Metal Oxide Nanoparticle Band Gap to Develop a Predictive Paradigm for Oxidative Stress and Acute Pulmonary Inflammation.” ACS Nano 6 (5): 4349–4368. doi:10.1021/nn3010087.
   PubMed Web of Science ®Google Scholar