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Articles

Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs

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Pages 238-256 | Received 17 Jun 2020, Accepted 10 Nov 2020, Published online: 17 Dec 2020

References

  • Almuttaqi, H., and I. A. Udalova. 2019. “Advances and Challenges in Targeting IRF5, a Key Regulator of Inflammation.” The FEBS Journal 286 (9): 1624–1637. doi:10.1111/febs.14654.
  • Argelaguet, R., B. Velten, D. Arnol, S. Dietrich, T. Zenz, J. C. Marioni, F. Buettner, W. Huber, and O. Stegle. 2018. “Multi-Omics Factor Analysis – a Framework for Unsupervised Integration of Multi-Omics Data Sets.” Molecular Systems Biology 14 (6): e8124. doi:10.15252/msb.20178124.
  • Bie, L. Y., D. Li, Y. Wei, N. Li, X. B. Chen, and S. X. Luo. 2019. “SOX13 Dependent PAX8 Expression Promotes the Proliferation of Gastric Carcinoma cells.” Artificial Cells, Nanomedicine, and Biotechnology 47 (1): 3180–3187. doi:10.1080/21691401.2019.1646751.
  • Bolstad, B. M., R. A. Irizarry, M. Astrand, and T. P. Speed. 2003. “A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Variance and Bias.” Bioinformatics (Oxford, England) 19 (2): 185–193. doi:10.1093/bioinformatics/19.2.185.
  • Caberoy, N. B., D. Maiguel, Y. Kim, and W. Li. 2010. “Identification of Tubby and Tubby-like Protein 1 as Eat-Me Signals by Phage Display.” Experimental Cell Research 316 (2): 245–257. doi:10.1016/j.yexcr.2009.10.008.
  • Chezeau, L., S. Sebillaud, R. Safar, C. Seidel, D. Dembele, M. Lorcin, C. Langlais, et al. 2018. “Short- and Long-Term Gene Expression Profiles Induced by Inhaled TiO2 Nanostructured Aerosol in Rat Lung.” Toxicology and Applied Pharmacology 356: 54–64. doi:10.1016/j.taap.2018.07.013.
  • Cox, J., M. Y. Hein, C. A. Luber, I. Paron, N. Nagaraj, and M. Mann. 2014. “Accurate Proteome-Wide Label-Free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ.” Molecular & Cellular Proteomics : MCP 13 (9): 2513–2526. doi:10.1074/mcp.M113.031591.
  • Ellinger-Ziegelbauer, H., and J. Pauluhn. 2009. “Pulmonary Toxicity of Multi-Walled Carbon Nanotubes (Baytubes) Relative to Alpha-Quartz Following a Single 6h Inhalation Exposure of Rats and a 3 Months Post-Exposure Period.” Toxicology 266 (1-3): 16–29. doi:10.1016/j.tox.2009.10.007.
  • Fujita, K., M. Fukuda, S. Endoh, J. Maru, H. Kato, A. Nakamura, N. Shinohara, K. Uchino, and K. Honda. 2015. “Size Effects of Single-Walled Carbon Nanotubes on In Vivo and In Vitro Pulmonary Toxicity.” Inhalation Toxicology 27 (4): 207–223. doi:10.3109/08958378.2015.1026620.
  • Gabay, M., Y. Li, and D. W. Felsher. 2014. MYC Activation Is a Hallmark of Cancer Initiation and Maintenance. Cold Spring Harbor Perspectives in Medicine 4: a014241.
  • Gate, L., K. B. Knudsen, C. Seidel, T. Berthing, L. Chezeau, N. R. Jacobsen, S. Valentino, et al. 2019. “Pulmonary Toxicity of Two Different Multi-Walled Carbon Nanotubes in Rat: Comparison Between Intratracheal Instillation and Inhalation Exposure.” Toxicology and Applied Pharmacology 375: 17–31. doi:10.1016/j.taap.2019.05.001.
  • Girvan, M., and M. E. Newman. 2002. “Community Structure in Social and Biological Networks.” Proceedings of the National Academy of Sciences of the United States of America 99 (12): 7821–7826. doi:10.1073/pnas.122653799.
  • Guseva Canu, I., K. Batsungnoen, A. Maynard, and N. B. Hopf. 2020. “State of Knowledge on the Occupational Exposure to Carbon Nanotubes.” International Journal of Hygiene and Environmental Health 225: 113472. doi:10.1016/j.ijheh.2020.113472.
  • Hu, H., Y. R. Miao, L. H. Jia, Q. Y. Yu, Q. Zhang, and A. Y. Guo. 2019. “AnimalTFDB 3.0: A Comprehensive Resource for Annotation and Prediction of Animal Transcription Factors.” Nucleic Acids Research 47 (D1): D33–D38. doi:10.1093/nar/gky822.
  • Huynh-Thu, V. A., A. Irrthum, L. Wehenkel, and P. Geurts. 2010. “Inferring Regulatory Networks from Expression Data Using Tree-Based Methods.” PLoS One 5 (9): e12776. doi:10.1371/journal.pone.0012776.
  • IARC. 2017. “Some Nanomaterials and Some Fibres.” IARC Monographs on the Evaluation of Carcinogenic Risks to Humans 111: 35–214.
  • Joshi, N., S. Watanabe, R. Verma, R. P. Jablonski, C. I. Chen, P. Cheresh, N. S. Markov, et al. 2020. “A Spatially Restricted Fibrotic Niche in Pulmonary Fibrosis is Sustained by M-CSF/M-CSFR Signalling in Monocyte-Derived Alveolar Macrophages.” European Respiratory Journal 55 (1): 1900646. doi:10.1183/13993003.00646-2019.
  • JRC. 2014. Multi-Walled Carbon Nanotubes, NM-400, NM-401, NM-402, NM-403: Characterisation and Physico-Chemical Properties. JRC Repository: NM-Series of Representative Manufactured Nanomaterials. Luxembourg: Publications Office of the European Union.
  • Kanehisa, M., M. Furumichi, M. Tanabe, Y. Sato, and K. Morishima. 2017. “KEGG: New Perspectives on Genomes, Pathways, Diseases and Drugs.” Nucleic Acids Research 45 (D1): D353–D361. doi:10.1093/nar/gkw1092.
  • Kasai, T., Y. Umeda, M. Ohnishi, H. Kondo, T. Takeuchi, S. Aiso, T. Nishizawa, M. Matsumoto, and S. Fukushima. 2015. “Thirteen-Week Study of Toxicity of Fiber-like Multi-Walled Carbon Nanotubes with Whole-Body Inhalation Exposure in Rats.” Nanotoxicology 9 (4): 413–422. doi:10.3109/17435390.2014.933903.
  • Kasai, T., Y. Umeda, M. Ohnishi, T. Mine, H. Kondo, T. Takeuchi, M. Matsumoto, and S. Fukushima. 2016. “Lung Carcinogenicity of Inhaled Multi-Walled Carbon Nanotube in Rats.” Particle and Fibre Toxicology 13 (1): 53. doi:10.1186/s12989-016-0164-2.
  • Kim, H. 2017. “The Transcription Factor MafB Promotes Anti-Inflammatory M2 Polarization and Cholesterol Efflux in Macrophages.” Scientific Reports 7 (1): 7591. doi:10.1038/s41598-017-07381-8.
  • Liao, G. B., X. Z. Li, S. Zeng, C. Liu, S. M. Yang, L. Yang, C. J. Hu, and J. Y. Bai. 2018. “Regulation of the Master Regulator FOXM1 in Cancer.” Cell Communication and Signaling 16 (1): 57. doi:10.1186/s12964-018-0266-6.
  • Liu, J., Y. Wang, M. J. Birnbaum, and D. A. Stoffers. 2010. “Three-Amino-Acid-Loop-Extension Homeodomain Factor Meis3 Regulates Cell Survival via PDK1.” Proceedings of the National Academy of Sciences of the United States of America 107 (47): 20494–20499. doi:10.1073/pnas.1007001107.
  • Luk, I. Y., C. M. Reehorst, and J. M. Mariadason. 2018. “ELF3, ELF5, EHF and SPDEF Transcription Factors in Tissue Homeostasis and Cancer.” Molecules 23 (9): 2191. doi:10.3390/molecules23092191.
  • Muller, J., M. Delos, N. Panin, V. Rabolli, F. Huaux, and D. Lison. 2009. “Absence of Carcinogenic Response to Multiwall Carbon Nanotubes in a 2-Year Bioassay in the Peritoneal Cavity of the Rat.” Toxicological Sciences 110 (2): 442–448. doi:10.1093/toxsci/kfp100.
  • Musa, J., M. M. Aynaud, O. Mirabeau, O. Delattre, and T. G. Grunewald. 2017. “MYBL2 (B-Myb): a Central Regulator of Cell Proliferation, Cell Survival and Differentiation Involved in Tumorigenesis.” Cell Death & Disease 8 (6): e2895 doi:10.1038/cddis.2017.244.
  • Nahle, S., H. Cassidy, M. M. Leroux, R. Mercier, J. Ghanbaja, Z. Doumandji, D. Matallanas, B. H. Rihn, O. Joubert, and L. Ferrari. 2020. “Genes Expression Profiling of Alveolar Macrophages Exposed to Non-Functionalized, Anionic and Cationic Multi-Walled Carbon Nanotubes Shows Three Different Mechanisms of Toxicity.” Journal of Nanobiotechnology 18 (1): 36. doi:10.1186/s12951-020-0587-7.
  • Napolitano, G., and A. Ballabio. 2016. “TFEB at a Glance.” Journal of Cell Science 129 (13): 2475–2481. doi:10.1242/jcs.146365.
  • Nie, L., G. Wu, D. E. Culley, J. C. Scholten, and W. Zhang. 2007. “Integrative Analysis of Transcriptomic and Proteomic Data: Challenges, Solutions and Applications.” Critical Reviews in Biotechnology 27 (2): 63–75. doi:10.1080/07388550701334212.
  • Porter, D. W., A. F. Hubbs, B. T. Chen, W. Mckinney, R. R. Mercer, M. G. Wolfarth, L. Battelli, et al. 2013. “Acute Pulmonary Dose-Responses to Inhaled Multi-Walled Carbon Nanotubes.” Nanotoxicology 7 (7): 1179–1194. doi:10.3109/17435390.2012.719649.
  • Poulsen, S. S., P. Jackson, K. Kling, K. B. Knudsen, V. Skaug, Z. O. Kyjovska, B. L. Thomsen, et al. 2016. “Multi-Walled Carbon Nanotube Physicochemical Properties Predict Pulmonary Inflammation and Genotoxicity.” Nanotoxicology 10 (9): 1263–1275. doi:10.1080/17435390.2016.1202351.
  • Poulsen, S. S., K. B. Knudsen, P. Jackson, I. E. Weydahl, A. T. Saber, H. Wallin, and U. Vogel. 2017. “Multi-Walled Carbon Nanotube-Physicochemical Properties Predict the Systemic Acute Phase Response Following Pulmonary Exposure in Mice.” PLoS One 12 (4): e0174167. doi:10.1371/journal.pone.0174167.
  • Poulsen, S. S., A. T. Saber, A. Williams, O. Andersen, C. Kobler, R. Atluri, M. E. Pozzebon, et al. 2015. “MWCNTs of Different Physicochemical Properties Cause Similar Inflammatory Responses, but Differences in Transcriptional and Histological Markers of Fibrosis in Mouse lungs.” Toxicology and Applied Pharmacology 284 (1): 16–32. doi:10.1016/j.taap.2014.12.011.
  • Rahman, L., D. Wu, M. Johnston, A. William, and S. Halappanavar. 2017. “Toxicogenomics Analysis of Mouse Lung Responses Following Exposure to Titanium Dioxide Nanomaterials Reveal Their Disease Potential at High Doses.” Mutagenesis 32 (1): 59–76. doi:10.1093/mutage/gew048.
  • Rappsilber, J., M. Mann, and Y. Ishihama. 2007. “Protocol for Micro-Purification, Enrichment, Pre-Fractionation and Storage of Peptides for Proteomics Using StageTips.” Nature Protocols 2 (8): 1896–1906. doi:10.1038/nprot.2007.261.
  • Raudvere, U., L. Kolberg, I. Kuzmin, T. Arak, P. Adler, H. Peterson, and J. Vilo. 2019. “g:Profiler: A Web Server for Functional Enrichment Analysis and Conversions of Gene Lists (2019 Update).” Nucleic Acids Research 47 (W1): W191–W198. doi:10.1093/nar/gkz369.
  • Ritchie, M. E., B. Phipson, D. Wu, Y. Hu, C. W. Law, W. Shi, and G. K. Smyth. 2015. “Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies.” Nucleic Acids Research 43 (7): e47 doi:10.1093/nar/gkv007.
  • Rittinghausen, S., A. Hackbarth, O. Creutzenberg, H. Ernst, U. Heinrich, A. Leonhardt, and D. Schaudien. 2014. “The Carcinogenic Effect of Various Multi-Walled Carbon Nanotubes (MWCNTs) after Intraperitoneal Injection in Rats.” Particle and Fibre Toxicology 11: 59. doi:10.1186/s12989-014-0059-z.
  • Rivero, S., M. Ceballos-Chavez, S. S. Bhattacharya, and J. C. Reyes. 2015. “HMG20A Is Required for SNAI1-Mediated Epithelial to Mesenchymal Transition.” Oncogene 34 (41): 5264–5276. doi:10.1038/onc.2014.446.
  • Serra, A., M. Fratello, L. Cattelani, I. Liampa, G. Melagraki, P. Kohonen, P. Nymark, et al. 2020. “Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment.” Nanomaterials 10 (4): 708. doi:10.3390/nano10040708.
  • Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. “Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.” Genome Research 13 (11): 2498–2504. doi:10.1101/gr.1239303.
  • Snyder-Talkington, B. N., J. Dymacek, D. W. Porter, M. G. Wolfarth, R. R. Mercer, M. Pacurari, J. Denvir, V. Castranova, Y. Qian, and N. L. Guo. 2013. “System-Based Identification of Toxicity Pathways Associated with Multi-Walled Carbon Nanotube-Induced Pathological Responses.” Toxicology and Applied Pharmacology 272 (2): 476–489. doi:10.1016/j.taap.2013.06.026.
  • Su, G., A. Kuchinsky, J. H. Morris, D. J. States, and F. Meng. 2010. “GLay: Community Structure Analysis of Biological Networks.” Bioinformatics (Oxford, England) 26 (24): 3135–3137. doi:10.1093/bioinformatics/btq596.
  • Suzui, M., M. Futakuchi, K. Fukamachi, T. Numano, M. Abdelgied, S. Takahashi, M. Ohnishi, et al. 2016. “Multiwalled Carbon Nanotubes Intratracheally Instilled into the Rat Lung Induce Development of Pleural Malignant Mesothelioma and Lung Tumors.” Cancer Science 107 (7): 924–935. doi:10.1111/cas.12954.
  • Taefehshokr, S., Y. A. Key, M. Khakpour, P. Dadebighlu, and A. Oveisi. 2017. “Early Growth Response 2 and Egr3 Are Unique Regulators in Immune System.” Central-European Journal of Immunology 42 (2): 205–209. doi:10.5114/ceji.2017.69363.
  • The Gene Ontology Consortium. 2019. “The Gene Ontology Resource: 20 Years and Still GOing Strong.” Nucleic Acids Research. 47: D330–D338.
  • Van Dam, S., U. Vosa, A. Van Der Graaf, L. Franke, and J. P. De Magalhaes. 2018. “Gene Co-Expression Analysis for Functional Classification and Gene-Disease Predictions.” Briefings in bioinformatics 19: 575–592.
  • Vizcaino, J. A., A. Csordas, N. Del-Toro, J. A. Dianes, J. Griss, I. Lavidas, G. Mayer, et al. 2016. “2016 Update of the PRIDE Database and Its Related Tools.” Nucleic Acids Research 44 (22): 11033. doi:10.1093/nar/gkw880.
  • Williams, K. L., I. Nanda, G. E. Lyons, C. T. Kuo, M. Schmid, J. M. Leiden, M. H. Kaplan, and E. J. Taparowsky. 2001. “Characterization of Murine BATF: A Negative Regulator of Activator Protein-1 Activity in the Thymus.” European Journal of Immunology 31 (5): 1620–1627. doi:10.1002/1521-4141(200105)31:5<1620::AID-IMMU1620>3.0.CO;2-3.
  • Yamamoto, M., E. Cid, S. Bru, and F. Yamamoto. 2011. “Rare and Frequent Promoter Methylation, Respectively, of TSHZ2 and 3 Genes That Are Both Downregulated in Expression in Breast and Prostate cancers.” PLoS One 6 (3): e17149. doi:10.1371/journal.pone.0017149.
  • Zhernovkov, V., T. Santra, H. Cassidy, O. Rukhlenko, D. Matallanas, A. Krstic, W. Kolch, V. Lobaskin, and B. N. Kholodenko. 2019. “An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated with Nanomaterial-Induced Toxicity.” Toxicological Sciences 171 (2): 303–314.
  • Zou, J., P. Guo, N. Lv, and D. Huang. 2015. “Lipopolysaccharide-Induced Tumor Necrosis Factor-α Factor Enhances Inflammation and Is Associated with Cancer (Review).” Molecular Medicine Reports 12 (5): 6399–6404. doi:10.3892/mmr.2015.4243.