Grouping of carbonaceous nanomaterials based on association of patterns of inflammatory markers in BAL fluid with adverse outcomes in lungs

References

• Ahsen, M. E., T. P. Boren, N. K. Singh, B. Misganaw, D. G. Mutch, K. N. Moore, F. J. Backes, et al. 2017. “Sparse Feature Selection for Classification and Prediction of Metastasis in Endometrial Cancer.” BMC Genomics 18(S3): 233. doi:10.1186/s12864-017-3604-y.
   PubMedGoogle Scholar
• Arts, J. H., 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. E., M. Hadi, A. M. Keene, R. Kreiling, D. Lyon, M. Maier, K. Michel, et al. 2014. “A Critical Appraisal of Existing Concepts for the Grouping of Nanomaterials.” Regulatory Toxicology and Pharmacology 70(2): 492–506. doi:10.1016/j.yrtph.2014.07.025.
   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
• Belperio, J. A., M. Dy, M. D. Burdick, Y. Y. Xue, K. Li, J. A. Elias, and M. P. Keane. 2002. “Interaction of IL-13 and C10 in the Pathogenesis of Bleomycin-Induced Pulmonary Fibrosis.” American Journal of Respiratory Cell and Molecular Biology 27(4): 419. doi:10.1165/rcmb.2002-0009OC.
   PubMed Web of Science ®Google Scholar
• Bishop, L., L. Cena, M. Orandle, N. Yanamala, M. M. Dahm, M. E. Birch, D. E. Evans, et al. 2017. “In Vivo Toxicity Assessment of Occupational Components of the Carbon Nanotube Life Cycle to Provide Context to Potential Health Effects.” ACS Nano 11(9): 8849–8863. doi:10.1021/acsnano.7b03038.
   PubMed Web of Science ®Google Scholar
• Braakhuis, H. M., A. G. Oomen, and F. R. Cassee. 2016. “Grouping Nanomaterials to Predict Their Potential to Induce Pulmonary Inflammation.” Toxicology and Applied Pharmacology 299: 3–7. doi:10.1016/j.taap.2015.11.009.
   PubMed Web of Science ®Google Scholar
• Bradley, P. S., and O. L. Mangasarian. 1998. Feature Selection via Concave Minimization and Support Vector Machines. Proceedings of the Fifteenth International Conference on Machine Learning. San Francisco, CA: Morgan Kaufmann Publishers Inc., 82–90.
   Google Scholar
• Chensue, S. W. 2013. “Chemokines in Innate and Adaptive Granuloma Formation.” Frontiers in Immunology 4: 43.
   PubMed Web of Science ®Google Scholar
• Chiu, B. C., C. M. Freeman, V. R. Stolberg, E. Komuniecki, P. M. Lincoln, S. L. Kunkel, and S. W. Chensue. 2003. “Cytokine-Chemokine Networks in Experimental Mycobacterial and Schistosomal Pulmonary Granuloma Formation.” American Journal of Respiratory Cell and Molecular Biology 29(1): 106–116. doi:10.1165/rcmb.2002-0241OC.
   PubMed Web of Science ®Google Scholar
• Collins, L. M., and S. T. Lanza. 2010. The Latent Class Model. Latent Class and Latent Transition Analysis. Hoboken, NJ: Wiley.
   Google Scholar
• Dong, J., X. Yu, D. W. Porter, L. A. Battelli, M. L. Kashon, and Q. Ma. 2016. “Common and Distinct Mechanisms of Induced Pulmonary Fibrosis by Particulate and Soluble Chemical Fibrogenic Agents.” Archives of Toxicology 90(2): 385–402. doi:10.1007/s00204-015-1589-3.
   PubMed Web of Science ®Google Scholar
• Friedman-Birnbaum, R., A. Gilhar, S. Haim, and D. T. Golan. 1983. “Leukocyte Inhibitory Factor (LIF) in Granuloma Annulare: A Comparative Study between the Generalized and the Localized Types.” Acta Dermato-Venereologica 63: 242–243.
   PubMed Web of Science ®Google Scholar
• Gabay, C. 2006. “Interleukin-6 and Chronic Inflammation.” Arthritis Research & Therapy 8: S3. doi:10.1186/ar1917.
   PubMed Web of Science ®Google Scholar
• Giannandrea, M., and W. C. Parks. 2014. “Diverse Functions of Matrix Metalloproteinases during Fibrosis.” Disease Models & Mechanisms 7(2): 193–203. doi:10.1242/dmm.012062.
   Google Scholar
• Godwin, H., C. Nameth, D. Avery, L. L. Bergeson, D. Bernard, E. Beryt, W. Boyes, et al. 2015. “Nanomaterial Categorization for Assessing Risk Potential to Facilitate Regulatory Decision-Making.” ACS Nano 9(4): 3409–3417. doi:10.1021/acsnano.5b00941.
   PubMed Web of Science ®Google Scholar
• Goodman, L. A. 2007. “On the Assignment of Individuals to Latent Classes.” Sociological Methodology 37(1): 1–22. doi:10.1111/j.1467-9531.2007.00184.x.
   Web of Science ®Google Scholar
• Guo, R. F., A. B. Lentsch, R. L. Warner, M. Huber-Lang, J. V. Sarma, T. Hlaing, M. M. Shi, N. W. Lukacs, and P. A. Ward. 2001. “Regulatory Effects of Eotaxin on Acute Lung Inflammatory Injury.” The Journal of Immunology 166(8): 5208–5218. doi:10.4049/jimmunol.166.8.5208.
   PubMed Web of Science ®Google Scholar
• Guyon, I., J. Weston, S. Barnhill, and V. Vapnik. 2002. “Gene Selection for Cancer Classification Using Support Vector Machines.” Machine Learning 46(1/3): 389–422. doi:10.1023/A:1012487302797.
   Web of Science ®Google Scholar
• Haugen, J., R. K. Chandyo, K. A. Brokstad, M. Mathisen, M. Ulak, S. Basnet, P. Valentiner-Branth, and T. A. Strand. 2015. “Cytokine Concentrations in Plasma from Children with Severe and Non-Severe Community Acquired Pneumonia.” PLoS One 10(9): e0138978. doi:10.1371/journal.pone.0138978.
   PubMed Web of Science ®Google Scholar
• Heinrich, U., R. Fuhst, S. Rittinghausen, O. Creutzenberg, B. Bellmann, W. Koch, and K. Levsen. 1995. “Chronic Inhalation Exposure of Wistar Rats and Two Different Strains of Mice to Diesel Engine Exhaust, Carbon Black, and Titanium Dioxide.” Inhalation Toxicology 7(4): 533–556. doi:10.3109/08958379509015211.
   Web of Science ®Google Scholar
• Huaux, F., M. Gharaee-Kermani, T. Liu, V. Morel, B. Mcgarry, M. Ullenbruch, S. L. Kunkel, J. Wang, Z. Xing, and S. H. Phan. 2005. “Role of Eotaxin-1 (CCL11) and CC Chemokine Receptor 3 (CCR3) in Bleomycin-induced Lung Injury and Fibrosis.” The American Journal of Pathology 167(6): 1485–1496. doi:10.1016/S0002-9440(10)61235-7.
   PubMed Web of Science ®Google Scholar
• Inoue, T., S. Fujishima, E. Ikeda, O. Yoshie, N. Tsukamoto, S. Aiso, N. Aikawa, A. Kubo, K. Matsushima, and K. Yamaguchi. 2004. “CCL22 and CCL17 in Rat Radiation Pneumonitis and in Human Idiopathic Pulmonary Fibrosis.” The European Respiratory Journal 24(1): 49–56. doi:10.1183/09031936.04.00110203.
   PubMed Web of Science ®Google Scholar
• Inoue, Y., T. E. King, S. S. Tinkle, K. Dockstader, and L. S. Newman. 1996. “Human Mast Cell Basic Fibroblast Growth Factor in Pulmonary Fibrotic Disorders.” The American Journal of Pathology 149: 2037–2054.
   PubMed Web of Science ®Google Scholar
• Jones, C. V., and S. D. Ricardo. 2013. “Macrophages and CSF-1: Implications for Development and beyond.” Organogenesis 9(4): 249–260. doi:10.4161/org.25676.
   PubMed Web of Science ®Google Scholar
• Kasai, T., Y. Umeda, M. Ohnishi, H. Kondo, T. Takeuchi, S. Aiso, T. Nishizawa, M. Matsumoto, and S. Fukushima. 2015a. “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.
   PubMed Web of Science ®Google Scholar
• Kasai, T., Y. Umeda, M. Ohnishi, T. Mine, H. Kondo, T. Takeuchi, M. Matsumoto, and S. Fukushima. 2015b. “Lung Carcinogenicity of Inhaled Multi-Walled Carbon Nanotube in Rats.” Particle and Fibre Toxicology 13(1): 53. doi:10.1186/s12989-016-0164-2.
   Google Scholar
• Kim, K. H., K. Burkhart, P. Chen, C. W. Frevert, J. Randolph-Habecker, R. C. Hackman, P. D. Soloway, and D. K. Madtes. 2005. “Tissue Inhibitor of Metalloproteinase-1 Deficiency Amplifies Acute Lung Injury in Bleomycin-Exposed Mice.” American Journal of Respiratory Cell and Molecular Biology 33(3): 271–279. doi:10.1165/rcmb.2005-0111OC.
   PubMed Web of Science ®Google Scholar
• Krafts, K. P. 2010. “Tissue Repair: The Hidden Drama.” Organogenesis 6(4): 225–233. doi:10.4161/org.6.4.12555.
   PubMed Web of Science ®Google Scholar
• Kuempel, E. D., V. Castranova, C. L. Geraci, and P. A. Schulte. 2012. “Development of Risk-Based Nanomaterial Groups for Occupational Exposure Control.” Journal of Nanoparticle Research 14(9): 1029. doi:10.1007/s11051-012-1029-8.
   PubMed Web of Science ®Google Scholar
• Lanza, S. T., J. J. Dziak, L. Huang, A. T. Wagner, and L. M. Collins. 2015. Proc LCA & Proc LTA users' guide (Version 1.3.2). University Park: The Methodology Center. Penn State.
   Google Scholar
• Lynch, I., C. Weiss, and E. Valsami-Jones. 2014. “A Strategy for Grouping of Nanomaterials Based on Key Physico-Chemical Descriptors as a Basis for Safer-by-Design NMs.” Nano Today 9(3): 266–270. doi:10.1016/j.nantod.2014.05.001.
   Web of Science ®Google Scholar
• Manoury, B., S. Caulet-Maugendre, I. Guenon, V. Lagente, and E. Boichot. 2006. “TIMP-1 Is a Key Factor of Fibrogenic Response to Bleomycin in Mouse Lung.” International Journal of Immunopathology and Pharmacology 19(3): 471–487. doi:10.1177/039463200601900303.
   PubMed Web of Science ®Google Scholar
• Mclachlan, G., and K. Basford. 1988. Mixture Models: Inference and Applications to Clustering. New York, USA: Marcel Dekker.
   Google Scholar
• Meinshausen, N., and P. Bühlmann. 2010. “Stability Selection.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 72(4): 417–473. doi:10.1111/j.1467-9868.2010.00740.x.
   Web of Science ®Google Scholar
• Meloni, F., N. Solari, S. Miserere, M. Morosini, A. Cascina, C. Klersy, E. Arbustini, C. Pellegrini, M. Viganò, and A. M. Fietta. 2008. “Chemokine Redundancy in BOS Pathogenesis. A Possible Role Also for the CC Chemokines: MIP3-Beta, MIP3-Alpha, MDC and Their Specific Receptors.” Transplant Immunology 18(3): 275–280. doi:10.1016/j.trim.2007.08.004.
   PubMed Web of Science ®Google Scholar
• Mercer, R. R., A. F. Hubbs, J. F. Scabilloni, L. Wang, L. A. Battelli, S. Friend, V. Castranova, and D. W. Porter. 2011. “Pulmonary Fibrotic Response to Aspiration of Multi-Walled Carbon Nanotubes.” Particle and Fibre Toxicology 8(1): 21. doi:10.1186/1743-8977-8-21.
   PubMedGoogle Scholar
• Misganaw, B., E. Ahsen, N. Singh, K. A. Baggerly, A. Unruh, M. A. White, and M. Vidyasagar. 2015. “Optimized Prediction of Extreme Treatment Outcomes in Ovarian Cancer.” Cancer Informatics 14: 45–55. doi:10.4137/CIN.S30803.
   PubMed Web of Science ®Google Scholar
• Mohr, U., H. Ernst, M. Roller, and F. Pott. 2006. “Pulmonary Tumor Types Induced in Wistar Rats of the So-called "19-dust study.” Experimental and Toxicologic Pathology 58(1): 13–20. doi:10.1016/j.etp.2006.06.001.
   PubMedGoogle Scholar
• Niosh-Cib-65. 2013. Occupational Exposure to Carbon Nanotubes and Nanofibers. Current Intelligence Bulletin. Cincinnati, OH: Department of Health and Human Services, Centers for Disease and Prevention, National Institute for Occupational Safety and Health, 156 pages.
   Google Scholar
• Nolan, A., B. Naveed, A. L. Comfort, N. Ferrier, C. B. Hall, S. Kwon, K. J. Kasturiarachchi, et al. 2012. “Inflammatory Biomarkers Predict Airflow Obstruction after Exposure to World Trade Center Dust.” Chest 142(2): 412–418. doi:10.1378/chest.11-1202.
   PubMed Web of Science ®Google Scholar
• Oomen, A. G., P. M. Bos, T. F. Fernandes, K. Hund-Rinke, D. Boraschi, H. J. Byrne, K. Aschberger, et al. 2014. “Concern-Driven Integrated Approaches to Nanomaterial Testing and Assessment–Report of the NanoSafety Cluster Working Group 10.” Nanotoxicology 8(3): 334–348. doi:10.3109/17435390.2013.802387.
   PubMed Web of Science ®Google Scholar
• Poland, C. A., R. Duffin, I. Kinloch, A. Maynard, W. A. Wallace, A. Seaton, V. Stone, S. Brown, W. Macnee, and K. Donaldson. 2008. “Carbon Nanotubes Introduced into the Abdominal Cavity of Mice Show Asbestos-like Pathogenicity in a Pilot Study.” Nature Nanotechnology 3(7): 423–428. doi:10.1038/nnano.2008.111.
   PubMed Web of Science ®Google Scholar
• R Core Team. 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
   Google Scholar
• Reinert, T., C. S. D. R. Baldotto, F. A. P. Nunes, and A. A. D. S. Scheliga. 2013. “Bleomycin-Induced Lung Injury.” Journal of Cancer Research 2013: 1.
   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
• Ritter, M., R. Goggel, N. Chaudhary, A. Wiedenmann, B. Jung, A. Weith, and P. Seither. 2005. “Elevated Expression of TARC (CCL17) and MDC (CCL22) in Models of Cigarette Smoke-Induced Pulmonary Inflammation.” Biochemical and Biophysical Research Communications 334(1): 254–262. doi:10.1016/j.bbrc.2005.06.084.
   PubMed Web of Science ®Google Scholar
• Roberts, J. R., R. R. Mercer, A. B. Stefaniak, M. S. Seehra, U. K. Geddam, I. S. Chaudhuri, A. Kyrlidis, et al. 2015. “Evaluation of Pulmonary and Systemic Toxicity following Lung Exposure to Graphite Nanoplates: A Member of the Graphene-Based Nanomaterial Family.” Particle and Fibre Toxicology 13(1): 34. doi:10.1186/s12989-016-0145-5.
   Web of Science ®Google Scholar
• Roberts, J., M. Barger, K. Roach, W. Mckinney, T. Chen, S. Friend, R. Mercer, et al. 2018. Toxicological evaluation of graphene nanomaterials that differ in size and oxidative form following pharyngeal aspiration in mice. 9th International Conference on Nanotoxicology, Neuss, Germany: Nanotox.
   Google Scholar
• Sandler, N. G., M. M. Mentink-Kane, A. W. Cheever, and T. A. Wynn. 2003. “Global Gene Expression Profiles during Acute Pathogen-Induced Pulmonary Inflammation Reveal Divergent Roles for Th1 and Th2 Responses in Tissue Repair.” The Journal of Immunology 171(7): 3655–3667. doi:10.4049/jimmunol.171.7.3655.
   PubMed Web of Science ®Google Scholar
• Sargent, L. M., D. W. Porter, L. M. Staska, A. F. Hubbs, D. T. Lowry, L. Battelli, K. J. Siegrist, et al. 2014. “Promotion of Lung Adenocarcinoma following Inhalation Exposure to Multi-Walled Carbon Nanotubes.” Particle and Fibre Toxicology 11(1): 3. doi:10.1186/1743-8977-11-3.
   PubMed Web of Science ®Google Scholar
• Sas-Institute. 2004. SAS/STAT® User’s Guide. Cary, NC: SAS Institute Inc.
   Google Scholar
• Shibata, Y., S. Abe, S. Inoue, A. Igarashi, K. Yamauchi, Y. Aida, H. Kishi, et al. 2013. “Relationship between Plasma Fibrinogen Levels and Pulmonary Function in the Japanese Population: The Takahata Study.” International Journal of Medical Sciences 10(11): 1530–1536. doi:10.7150/ijms.7256.
   PubMed Web of Science ®Google Scholar
• Vidyasagar, M. 2014. “Machine Learning Methods in the Computational Biology of Cancer.” Proceedings. Mathematical, Physical, and Engineering Sciences 470(2167): 20140081. doi:10.1098/rspa.2014.0081.
   PubMed Web of Science ®Google Scholar
• Winder, N. C., G. Grunig, M. Hermann, and R. Von Fellenberg. 1990. “Fibrin/Fibrinogen in Lungs and Respiratory Secretions of Horses with Chronic Pulmonary Disease.” American Journal of Veterinary Research 51: 945–949.
   PubMed Web of Science ®Google Scholar
• Wynn, T. A. 2004. “Fibrotic Disease and the T(H)1/T(H)2 Paradigm.” Nature Reviews. Immunology 4(8): 583–594. doi:10.1038/nri1412.
   PubMed Web of Science ®Google Scholar
• Wynn, T. A. 2008. “Cellular and Molecular Mechanisms of Fibrosis.” The Journal of Pathology 214(2): 199–210. doi:10.1002/path.2277.
   PubMed Web of Science ®Google Scholar
• Wynn, T. A., and T. R. Ramalingam. 2012. “Mechanisms of Fibrosis: Therapeutic Translation for Fibrotic Disease.” Nature Medicine 18: 1028–1040. doi:10.1038/nm.2807.
   PubMed Web of Science ®Google Scholar
• Yanamala, N., M. S. Orandle, V. K. Kodali, L. Bishop, P. C. Zeidler-Erdely, J. R. Roberts, V. Castranova, and A. Erdely. 2018. “Sparse Supervised Classification Methods Predict and Characterize Nanomaterial Exposures: Independent Markers of MWCNT Exposures.” Toxicologic Pathology 46(1): 14–27. doi:10.1177/0192623317730575.
   PubMed Web of Science ®Google Scholar
• Zhou, J., J.-O. Jin, J. Du, and Q. Yu. 2015. “Innate Immune Signaling Induces IL-7 Production, Early Inflammatory Responses, and Sjögren's-Like Dacryoadenitis in C57BL/6 Mice.” Investigative Opthalmology & Visual Science 56: 7831–7838. doi:10.1167/iovs.15-17368.
   PubMed Web of Science ®Google Scholar