Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells

References

• Aggarwala, V., and B. F. Voight. 2016. “An Expanded Sequence Context Model Broadly Explains Variability in Polymorphism Levels across the Human Genome.” Nature Genetics 48 (4): 349–355. doi:10.1038/ng.3511.
   PubMed Web of Science ®Google Scholar
• Andrews, S. 2010. “FastQC: A Quality Control Tool for High Throughput Sequence Data.” http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
   Google Scholar
• Avalos, A., A. I. Haza, D. Mateo, and P. Morales. 2014. “Cytotoxicity and ROS Production of Manufactured Silver Nanoparticles of Different Sizes in Hepatoma and Leukemia Cells.” Journal of Applied Toxicology 34 (4): 413–423. doi:10.1002/jat.2957.
   PubMed Web of Science ®Google Scholar
• Barkat, M. A., S. B. Harshita, M. J. Naim, F. H. Pottoo, S. P. Singh, and F. J. Ahmad. 2018. “Current Progress in Synthesis, Characterization and Applications of Silver Nanoparticles: Precepts and Prospects.” Recent Patents on Anti-Infective Drug Discovery 13: 53–69. doi:10.2174/1574891X12666171006102833.
   PubMedGoogle Scholar
• Bembom, O., and R. Ivanek. 2019. SeqLogo: Sequence Logos for DNA Sequence Alignments. R package version 1.52.0. https://github.com/ivanek/seqLogo.
   Google Scholar
• Blokzijl, F., R. Janssen, R. van Boxtel, and E. Cuppen. 2018. “MutationalPatterns: Comprehensive Genome-Wide Analysis of Mutational Processes.” Genome Medicine 10 (1): 33. doi:10.1186/s13073-018-0539-0.
   PubMedGoogle Scholar
• Cariello, N. F., W. W. Piegorsch, W. T. Adams, and T. R. Skopek. 1994. “Computer Program for the Analysis of Mutational Spectra: application to p53 mutations.” Carcinogenesis 15 (10): 2281–2285. doi:10.1093/carcin/15.10.2281.
   PubMed Web of Science ®Google Scholar
• Chaloupka, K., Y. Malam, and A. M. Seifalian. 2010. “Nanosilver as a New Generation of Nanoproduct in Biomedical Applications.” Trends in Biotechnology 28 (11): 580–588. doi:10.1016/j.tibtech.2010.07.006.
   PubMed Web of Science ®Google Scholar
• Cheng, K. C., D. S. Cahill, H. Kasai, S. Nishimura, and L. A. Loeb. 1992. “8-Hydroxyguanine, an Abundant Form of Oxidative DNA Damage, Causes G––T and a––C Substitutions.” The Journal of Biological Chemistry 267 (1): 166–172. doi:10.1016/S0021-9258(18)48474-8.
   PubMed Web of Science ®Google Scholar
• Chen, T., K. Harrington-Brock, and M. M. Moore. 2002. “Mutant Frequency and Mutational Spectra in the Tk and Hprt Genes of N-ethyl-N-Nitrosourea-Treated Mouse Lymphoma Cellsdagger.” Environmental and Molecular Mutagenesis 39 (4): 296–305. doi:10.1002/em.10075.
   PubMed Web of Science ®Google Scholar
• Chen, T., and M. M. Moore. 2004. “Screening for Chemical Mutagens Using the Mouse Lymphoma Assay.” In Optimization in Drug Discovery: In-Vitro Methods, edited by Z. Yan and G. W. Caldwell, 337–352. Totowa, NJ: Humana Press.
   Google Scholar
• Chen, X., and H. J. Schluesener. 2008. “Nanosilver: A Nanoproduct in Medical Application.” Toxicology Letters 176 (1): 1–12. doi:10.1016/j.toxlet.2007.10.004.
   PubMed Web of Science ®Google Scholar
• Cooke, M. S., M. D. Evans, M. Dizdaroglu, and J. Lunec. 2003. “Oxidative DNA Damage: Mechanisms, Mutation, and Disease.” FASEB Journal 17 (10): 1195–1214. doi:10.1096/fj.02-0752rev.
   PubMed Web of Science ®Google Scholar
• Downes, D. J., M. Chonofsky, K. Tan, B. T. Pfannenstiel, S. L. Reck-Peterson, and R. B. Todd. 2014. “Characterization of the Mutagenic Spectrum of 4-Nitroquinoline 1-Oxide (4-NQO) in Aspergillus nidulans by Whole Genome Sequencing.” G3 4 (12): 2483–2492. doi:10.1534/g3.114.014712.
   Web of Science ®Google Scholar
• Du, H., B. Pan, and T. Chen. 2017. “Evaluation of Chemical Mutagenicity Using Next Generation Sequencing: A Review.” Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews 35 (3): 140–158. doi:10.1080/10590501.2017.1328831.
   PubMed Web of Science ®Google Scholar
• Elespuru, R., S. Pfuhler, M. J. Aardema, T. Chen, S. H. Doak, A. Doherty, C. S. Farabaugh, et al. 2018. “Genotoxicity Assessment of Nanomaterials: Recommendations on Best Practices, Assays, and Methods.” Toxicological Sciences 164 (2): 391–416. doi:10.1093/toxsci/kfy100.
   PubMed Web of Science ®Google Scholar
• Fang, Y., and P. Zou. 2020. “Genome-Wide Mapping of Oxidative DNA Damage via Engineering of 8-Oxoguanine DNA Glycosylase.” Biochemistry 59 (1): 85–89. doi:10.1021/acs.biochem.9b00782.
   PubMed Web of Science ®Google Scholar
• FDA. 2020. “Guidance for industry and review staff recommended approaches to integration of genetic toxicology study results.” https://www.fda.gov/media/72266/download.
   Google Scholar
• Gu, Z., L. Gu, R. Eils, M. Schlesner, and B. Brors. 2014. “Circlize Implements and Enhances Circular Visualization in R.” Bioinformatics 30 (19): 2811–2812. doi:10.1093/bioinformatics/btu393.
   PubMed Web of Science ®Google Scholar
• Gundry, M., W. Li, S. B. Maqbool, and J. Vijg. 2012. “Direct, Genome-Wide Assessment of DNA Mutations in Single Cells.” Nucleic Acids Research 40 (5): 2032–2040. doi:10.1093/nar/gkr949.
   PubMed Web of Science ®Google Scholar
• Guo, X., Y. Li, J. Yan, T. Ingle, M. Y. Jones, N. Mei, M. D. Boudreau, et al. 2016. “Size- and Coating-Dependent Cytotoxicity and Genotoxicity of Silver Nanoparticles Evaluated Using in Vitro Standard Assays.” Nanotoxicology 10 (9): 1373–1384. doi:10.1080/17435390.2016.1214764.
   PubMed Web of Science ®Google Scholar
• Guo, X., B. Pan, J. E. Seo, Y. Chen, J. Yan, N. Mei, and T. Chen. 2018. “Whole Genome Sequencing Analysis of Small and Large Colony Mutants from the Mouse Lymphoma Assay.” Archives of Toxicology 92 (12): 3585–3595. doi:10.1007/s00204-018-2318-5.
   PubMed Web of Science ®Google Scholar
• Huang, Q. M., Y. M. Zeng, H. P. Zhang, L. C. Lv, D. Y. Yang, and H. H. Lin. 2016. “4-Nitroquinoline-1-Oxide Effects Human Lung Adenocarcinoma A549 Cells by Regulating the Expression of POLD4.” Biomedical Reports 4 (3): 345–348. doi:10.3892/br.2016.583.
   PubMed Web of Science ®Google Scholar
• Huk, A., E. Izak-Nau, N. El Yamani, H. Uggerud, M. Vadset, B. Zasonska, A. Duschl, and M. Dusinska. 2015. “Impact of Nanosilver on Various DNA Lesions and HPRT Gene Mutations - Effects of Charge and Surface Coating.” Particle and Fibre Toxicology 12: 25. doi:10.1186/s12989-015-0100-x.
   PubMed Web of Science ®Google Scholar
• Inga, A., R. Iannone, P. Degan, P. Campomenosi, G. Fronza, A. Abbondandolo, and P. Menichini. 1994. “Analysis of 4-Nitroquinoline-1-Oxide Induced Mutations at the Hprt Locus in Mammalian Cells: possible Involvement of Preferential DNA Repair.” Mutagenesis 9 (1): 67–72. doi:10.1093/mutage/9.1.67.
   PubMed Web of Science ®Google Scholar
• Joshi, N., and J. Fass. 2011. “Sickle: A Sliding-Window, Adaptive, Quality-Based Trimming Tool for FastQ Files (Version 1.33) [Software].” Accessed 30 July 2018. https://github.com/najoshi/sickle
   Google Scholar
• Katarzyńska-Banasik, D., M. Grzesiak, and A. Sechman. 2017. “Selection of Reference Genes for Quantitative Real-Time PCR Analysis in Chicken Ovary following Silver Nanoparticle Treatment.” Environmental Toxicology and Pharmacology 56: 186–190. doi:10.1016/j.etap.2017.09.011.
   PubMed Web of Science ®Google Scholar
• Kennedy, S. R., M. W. Schmitt, E. J. Fox, B. F. Kohrn, J. J. Salk, E. H. Ahn, M. J. Prindle, et al. 2014. “Detecting Ultralow-Frequency Mutations by Duplex Sequencing.” Nature Protocols 9 (11): 2586–2606. doi:10.1038/nprot.2014.170.
   PubMed Web of Science ®Google Scholar
• Kim, S., and D. Y. Ryu. 2013. “Silver Nanoparticle-Induced Oxidative Stress, Genotoxicity and Apoptosis in Cultured Cells and Animal Tissues.” Journal of Applied Toxicology 33 (2): 78–89. doi:10.1002/jat.2792.
   PubMed Web of Science ®Google Scholar
• Kucab, J. E., X. Zou, S. Morganella, M. Joel, A. S. Nanda, E. Nagy, C. Gomez, et al. 2019. “A Compendium of Mutational Signatures of Environmental Agents.” Cell 177 (4): 821–836. doi:10.1016/j.cell.2019.03.001.
   PubMed Web of Science ®Google Scholar
• Lee, S. H., and B. H. Jun. 2019. “Silver Nanoparticles: Synthesis and Application for Nanomedicine.” International Journal of Molecular Sciences 20
   Web of Science ®Google Scholar
• Li, Y., J. A. Bhalli, W. Ding, J. Yan, M. G. Pearce, R. Sadiq, C. K. Cunningham, et al. 2014. “Cytotoxicity and Genotoxicity Assessment of Silver Nanoparticles in Mouse.” Nanotoxicology 8 (1): 36–45. doi:10.3109/17435390.2013.855827.
   PubMedGoogle Scholar
• Li, Y., and T. Chen. 2014. “Genotoxicity of Silver Nanoparticles.” In Handbook of Nanotoxology, Nanomedicne and Stem Cells, 87–98. Hoboken, NJ: Wiley.
   Google Scholar
• Li, Y., D. H. Chen, J. Yan, Y. Chen, R. A. Mittelstaedt, Y. Zhang, A. S. Biris, R. H. Heflich, and T. Chen. 2012. “Genotoxicity of Silver Nanoparticles Evaluated Using the Ames Test and in Vitro Micronucleus Assay.” Mutation Research 745 (1–2): 4–10. doi:10.1016/j.mrgentox.2011.11.010.
   PubMed Web of Science ®Google Scholar
• Li, H., and R. Durbin. 2009. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics 25 (14): 1754–1760. doi:10.1093/bioinformatics/btp324.
   PubMed Web of Science ®Google Scholar
• Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and S. Genome. 2009. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352.
   PubMed Web of Science ®Google Scholar
• Li, Y., T. Qin, T. Ingle, J. Yan, W. He, J. J. Yin, and T. Chen. 2017. “Differential Genotoxicity Mechanisms of Silver Nanoparticles and Silver Ions.” Archives of Toxicology 91 (1): 509–519. doi:10.1007/s00204-016-1730-y.
   PubMed Web of Science ®Google Scholar
• Liu, W., Y. Wu, C. Wang, H. C. Li, T. Wang, C. Y. Liao, L. Cui, Q. F. Zhou, B. Yan, and G. B. Jiang. 2010. “Impact of Silver Nanoparticles on Human Cells: effect of Particle Size.” Nanotoxicology 4 (3): 319–330. doi:10.3109/17435390.2010.483745.
   PubMed Web of Science ®Google Scholar
• Matsuda, T., M. Takamune, Y. Matsuda, and M. Yamada. 2013. “A Pilot Study for the Mutation Assay Using a High-Throughput DNA Sequencer.” Genes and Environment 35 (2): 53–56. doi:10.3123/jemsge.35.53.
   Google Scholar
• McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, et al. 2010. “The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data.” Genome Research 20 (9): 1297–1303. doi:10.1101/gr.107524.110.
   PubMed Web of Science ®Google Scholar
• Mei, N., Y. Zhang, Y. Chen, X. Guo, W. Ding, S. F. Ali, A. S. Biris, P. Rice, M. M. Moore, and T. Chen. 2012. “Silver Nanoparticle-Induced Mutations and Oxidative Stress in Mouse Lymphoma Cells.” Environmental and Molecular Mutagenesis 53 (6): 409–419. doi:10.1002/em.21698.
   PubMed Web of Science ®Google Scholar
• Moussa, S. H., A. A. Tayel, A. S. Alsohim, and R. R. Abdallah. 2013. “Botryticidal Activity of Nanosized Silver-Chitosan Composite and Its Application for the Control of Gray Mold in Strawberry.” Journal of Food Science 78 (10): M1589–M1594. doi:10.1111/1750-3841.12247.
   PubMed Web of Science ®Google Scholar
• Najm, J., M. Rath, W. Schroder, and U. Felbor. 2018. “Diagnostic Single Gene Analyses beyond Sanger.” Hamostaseologie 38 (3): 158–165. doi:10.5482/HAMO-17-01-0008.
   PubMedGoogle Scholar
• OECD. 2018. “Evaluation of in vitro methods for human hazard assessment applied in the OECD testing program for the safety of manufactured nanomaterials.” Accessed on 20 March 2020. http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=ENV/JM/MONO(2018)4&doclanguage=en.
   Google Scholar
• Paladini, F., and M. Pollini. 2019. “Antimicrobial Silver Nanoparticles for Wound Healing Application: Progress and Future Trends.” Materials 12 (16): 2540. doi:10.3390/ma12162540.
   PubMed Web of Science ®Google Scholar
• Pulit-Prociak, J., M. Banach. 2016. “Silver Nanoparticles – A Material of the Future…?” Open Chemistry 14 (1): 76–91. doi:10.1515/chem-2016-0005.
   Web of Science ®Google Scholar
• Revollo, J. R., A. Dad, L. P. McDaniel, M. G. Pearce, and V. N. Dobrovolsky. 2018. “Genome-Wide Mutation Detection by Interclonal Genetic Variation.” Mutation Research. Genetic Toxicology and Environmental Mutagenesis 829–830: 61–69. doi:10.1016/j.mrgentox.2018.03.011.
   PubMed Web of Science ®Google Scholar
• Ryu, J., J. Youn, Y. Kim, O. Kwon, Y. Song, H. Kim, K. Cho, and I. Chang. 1999. “Mutation Spectrum of 4-Nitroquinoline N-Oxide in the lacI Transgenic Big Blue Rat2 Cell Line.” Mutation Research 445 (1): 127–135. doi:10.1016/S1383-5718(99)00136-9.
   PubMed Web of Science ®Google Scholar
• Sawyer, J. R., R. L. Binz, J. Wang, and M. M. Moore. 2006. “Multicolor Spectral Karyotyping of the L5178Y Tk+/− −3.7.2C Mouse Lymphoma Cell Line.” Environmental and Molecular Mutagenesis 47 (2): 127–131. doi:10.1002/em.20175.
   PubMed Web of Science ®Google Scholar
• Storer, R. D., A. R. Kraynak, T. W. McKelvey, M. C. Elia, T. L. Goodrow, and J. G. DeLuca. 1997. “The Mouse Lymphoma L5178Y Tk+/− Cell Line is Heterozygous for a Codon 170 Mutation in the p53 Tumor Suppressor Gene.” Mutation Research 373 (2): 157–165. doi:10.1016/S0027-5107(96)00227-8.
   PubMed Web of Science ®Google Scholar
• Szikriszt, B., A. Poti, O. Pipek, M. Krzystanek, N. Kanu, J. Molnar, D. Ribli, et al. 2016. “A Comprehensive Survey of the Mutagenic Impact of Common Cancer Cytotoxics.” Genome Biology 17: 99. doi:10.1186/s13059-016-0963-7.
   PubMed Web of Science ®Google Scholar
• Thorvaldsdottir, H., J. T. Robinson, and J. P. Mesirov. 2013. “Integrative Genomics Viewer (IGV): High-Performance Genomics Data Visualization and Exploration.” Briefings in Bioinformatics 14 (2): 178–192. doi:10.1093/bib/bbs017.
   PubMed Web of Science ®Google Scholar
• Van der Auwera, G. A., M. O. Carneiro, C. Hartl, R. Poplin, G. Del Angel, A. Levy-Moonshine, T. Jordan, et al. 2013. “From FastQ Data to High Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline.” Current Protocols in Bioinformatics 43: 1–33.
   PubMedGoogle Scholar
• Wong, W. H., R. S. Tong, A. L. Young, and T. E. Druley. 2018. “Rare Event Detection Using Error-Corrected DNA and RNA Sequencing.” Journal of Visualized Experiments 138: 57509.
   Google Scholar