- About this Journal ·
- Abstracting and Indexing ·
- Advance Access ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 505864, 17 pages
Systems Approaches to Modeling Chronic Mucosal Inflammation
1Sealy Center for Molecular Medicine, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
2Department of Internal Medicine, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
3Hamon Center for Therapeutic Oncology Research, Department of Internal Medicine Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
4Institute for Translational Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
5Departments of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
6Microbiology and Immunology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
Received 12 June 2013; Revised 8 August 2013; Accepted 9 August 2013
Academic Editor: Tao Huang
Copyright © 2013 Mridul Kalita et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- A. J. Polito and D. Proud, “Epithelial cells as regulators of airway inflammation,” Journal of Allergy and Clinical Immunology, vol. 102, no. 5, pp. 714–718, 1998.
- B. N. Lambrecht and H. Hammad, “The airway epithelium in asthma,” Nature Medicine, vol. 18, pp. 684–692, 2012.
- B. C. Willis, J. M. Liebler, K. Luby-Phelps et al., “Induction of epithelial-mesenchymal transition in alveolar epithelial cells by transforming growth factor-β1: potential role in idiopathic pulmonary fibrosis,” The American Journal of Pathology, vol. 166, no. 5, pp. 1321–1332, 2005.
- C. Ward, I. A. Forrest, D. M. Murphy et al., “Phenotype of airway epithelial cells suggests epithelial to mesenchymal cell transition in clinically stable lung transplant recipients,” Thorax, vol. 60, no. 10, pp. 865–871, 2005.
- S. G. Royce, L. Tan, A. A. Koek, and M. L. K. Tang, “Effect of extracellular matrix composition on airway epithelial cell and fibroblast structure: implications for airway remodeling in asthma,” Annals of Allergy, Asthma and Immunology, vol. 102, no. 3, pp. 238–246, 2009.
- D. E. Davies and S. T. Holgate, “Asthma: the importance of epithelial mesenchymal communication in pathogenesis: inflammation and the airway epithelium in asthma,” International Journal of Biochemistry and Cell Biology, vol. 34, no. 12, pp. 1520–1526, 2002.
- S. T. Holgate, J. Holloway, S. Wilson, F. Bucchieri, S. Puddicombe, and D. E. Davies, “Epithelial-mesenchymal communication in the pathogenesis of chronic asthma,” Proceedings of the American Thoracic Society, vol. 1, no. 2, pp. 93–98, 2004.
- R. Y. Huang, P. Guilford, and J. P. Thiery, “Early events in cell adhesion and polarity during epithelial-mesenchymal transition,” Journal of Cell Science, vol. 125, pp. 4417–4422, 2012.
- J. Lim and J. P. Thiery, “Epithelial-mesenchymal transitions: insights from development,” Development, vol. 139, pp. 3471–3486, 2012.
- B. C. Willis and Z. Borok, “TGF-β-induced EMT: mechanisms and implications for fibrotic lung disease,” American Journal of Physiology, vol. 293, no. 3, pp. L525–L534, 2007.
- R. Jain, P. W. Shaul, Z. Borok, and B. C. Willis, “Endothelin-1 induces alveolar epithelial-mesenchymal transition through endothelin type A receptor-mediated production of TGF-β1,” American Journal of Respiratory Cell and Molecular Biology, vol. 37, no. 1, pp. 38–47, 2007.
- B. C. Willis, R. M. DuBois, and Z. Borok, “Epithelial origin of myofibroblasts during fibrosis in the lung,” Proceedings of the American Thoracic Society, vol. 3, no. 4, pp. 377–382, 2006.
- T.-L. Hackett, S. M. Warner, D. Stefanowicz et al., “Induction of epithelial-mesenchymal transition in primary airway epithelial cells from patients with asthma by transforming growth factor-β1,” American Journal of Respiratory and Critical Care Medicine, vol. 180, no. 2, pp. 122–133, 2009.
- S. S. Sohal, D. Reid, A. Soltani et al., “Evaluation of epithelial mesenchymal transition in patients with chronic obstructive pulmonary disease,” Respiratory Research, vol. 12, p. 130, 2011.
- I. Y. Adamson, L. Young, and D. H. Bowden, “Relationship of alveolar epithelial injury and repair to the induction of pulmonary fibrosis,” The American Journal of Pathology, vol. 130, no. 2, pp. 377–383, 1988.
- S. Cannito, E. Novo, A. Compagnone et al., “Redox mechanisms switch on hypoxia-dependent epithelial-mesenchymal transition in cancer cells,” Carcinogenesis, vol. 29, no. 12, pp. 2267–2278, 2008.
- T. Vincent, E. P. Neve, J. R. Johnson et al., “A SNAIL1-SMAD3/4 transcriptional repressor complex promotes TGF-β mediated epithelial-mesenchymal transition,” Nature Cell Biology, vol. 11, no. 8, pp. 943–950, 2009.
- E. M. Minshall, D. Y. M. Leung, R. J. Martin et al., “Eosinophil-associated TGF-β1 mRNA Expression and airways fibrosis in bronchial asthma,” American Journal of Respiratory Cell and Molecular Biology, vol. 17, no. 3, pp. 326–333, 1997.
- J. Yang and R. A. Weinberg, “Epithelial-mesenchymal transition: at the crossroads of development and tumor metastasis,” Developmental Cell, vol. 14, no. 6, pp. 818–829, 2008.
- O. G. McDonald, H. Wu, W. Timp, A. Doi, and A. P. Feinberg, “Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition,” Nature Structural and Molecular Biology, vol. 18, no. 8, pp. 867–874, 2011.
- R. P. Garofalo and H. Haeberle, “Epithelial regulation of innate immunity to respiratory syncytial virus,” American Journal of Respiratory Cell and Molecular Biology, vol. 23, no. 5, pp. 581–585, 2000.
- S. Akira, S. Uematsu, and O. Takeuchi, “Pathogen recognition and innate immunity,” Cell, vol. 124, no. 4, pp. 783–801, 2006.
- A. R. Brasier, “The NF-k B signaling network: insights from systems approaches,” in Cellular Signaling and Innate Immune Responses to RNA Virus Infections, A. R. Brasier, S. M. Lemon, and A. Garcia-Sastre, Eds., pp. 119–135, American Society for Microbiology, 2008.
- S. Choudhary, M. Kalita, L. Fang et al., “Inducible TNF receptor associated factor 1 expression couples the canonical to the non-canonical NF-kB pathway in TNF stimulation,” The Journal of Biological Chemistry, vol. 288, pp. 14612–14623, 2013.
- A. R. Brasier, “The NF-kappaB regulatory network,” Cardiovascular Toxicology, vol. 6, no. 2, pp. 111–130, 2006.
- B. Tian, D. E. Nowak, M. Jamaluddin, S. Wang, and A. R. Brasier, “Identification of direct genomic targets downstream of the nuclear factor-κB transcription factor mediating tumor necrosis factor signaling,” The Journal of Biological Chemistry, vol. 280, no. 17, pp. 17435–17448, 2005.
- B. Tian, D. E. Nowak, and A. R. Brasier, “A TNF-induced gene expression program under oscillatory NF-κB control,” BMC Genomics, vol. 6, article 137, 2005.
- B. Tian and A. R. Brasier, “Identification of a nuclear factor KappaB-dependent gene network,” Recent Progress in Hormone Research, vol. 58, pp. 95–130, 2003.
- S. Thomson, F. Petti, I. Sujka-Kwok et al., “A systems view of epithelial-mesenchymal transition signaling states,” Clinical and Experimental Metastasis, vol. 28, no. 2, pp. 137–155, 2011.
- A. Schroeder, O. Mueller, S. Stocker et al., “The RIN: an RNA integrity number for assigning integrity values to RNA measurements,” BMC Molecular Biology, vol. 7, article 3, 2006.
- W. J. Kent, “BLAT—the BLAST-like alignment tool,” Genome Research, vol. 12, no. 4, pp. 656–664, 2002.
- K. J. Livak and T. D. Schmittgen, “Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method,” Methods, vol. 25, no. 4, pp. 402–408, 2001.
- R. D. Ramirez, S. Sheridan, L. Girard et al., “Immortalization of human bronchial epithelial cells in the absence of viral oncoproteins,” Cancer Research, vol. 64, no. 24, pp. 9027–9034, 2004.
- B. Tian, J. Yang, and A. R. Brasier, “Two-step cross-linking for analysis of protein-chromatin interactions,” Methods in Molecular Biology, vol. 809, pp. 105–120, 2012.
- D. E. Nowak, B. Tian, and A. R. Brasier, “Two-step cross-linking method for identification of NF-κB gene network by chromatin immunoprecipitation,” BioTechniques, vol. 39, no. 5, pp. 715–724, 2005.
- S. Basak, H. Kim, J. D. Kearns et al., “A fourth IκB protein within the NF-κB signaling module,” Cell, vol. 128, no. 2, pp. 369–381, 2007.
- C. Cheadle, M. P. Vawter, W. J. Freed, and K. G. Becker, “Analysis of microarray data using Z score transformation,” Journal of Molecular Diagnostics, vol. 5, no. 2, pp. 73–81, 2003.
- D. E. Nowak, B. Tian, M. Jamaluddin et al., “RelA Ser276 phosphorylation is required for activation of a subset of NF-κB-dependent genes by recruiting cyclin-dependent kinase 9/cyclin t1 complexes,” Molecular and Cellular Biology, vol. 28, no. 11, pp. 3623–3638, 2008.
- D. E. Nelson, A. E. C. Ihekwaba, M. Elliott et al., “Oscillations in NF-κB signaling control the dynamics of gene expression,” Science, vol. 306, no. 5696, pp. 704–708, 2004.
- K. Chiba, J. Yamamoto, Y. Yamaguchi, and H. Handa, “Promoter-proximal pausing and its release: molecular mechanisms and physiological functions,” Experimental Cell Research, vol. 316, no. 17, pp. 2723–2730, 2010.
- A. R. Brasier, B. Tian, M. Jamaluddin, M. K. Kalita, R. P. Garofalo, and M. Lu, “RelA Ser276 phosphorylation-coupled Lys310 acetylation controls transcriptional elongation of inflammatory cytokines in respiratory syncytial virus infection,” Journal of Virology, vol. 85, no. 22, pp. 11752–11769, 2011.
- B. Tian, Y. Zhao, M. Kalita et al., “CDK9-dependent transcriptional elongation in the innate ISG response to RSV infection in airway epithelial cells,” Journal of Virology, vol. 87, no. 12, pp. 7075–7092, 2013.
- J. Yang, A. Mitra, N. Dojer, S. Fu, M. Rowicka, and A. R. Brasier, “A probabilistic approach to learn chromatin architecture and accurate inference of the NF-kappaB/RelA regulatory network using ChIP-Seq,” Nucleic Acids Research, vol. 41, no. 15, pp. 7240–7259, 2013.
- L. Yang, L. Gu, Z. Li, and M. Zhou, “Translation of TRAF1 is regulated by IRES-dependent mechanism and stimulated by vincristine,” Nucleic Acids Research, vol. 38, no. 13, pp. 4503–4513, 2010.
- S. Choudhary, S. Boldogh, R. Garofalo, M. Jamaluddin, and A. R. Brasier, “Respiratory syncytial virus influences NF-κB-dependent gene expression through a novel pathway involving MAP3K14/NIK expression and nuclear complex formation with NF-κB2,” Journal of Virology, vol. 79, no. 14, pp. 8948–8959, 2005.
- Y.-J. Chen, S.-J. Zeng, J. T. Hsu et al., “Amantadine as a regulator of internal ribosome entry site,” Acta Pharmacologica Sinica, vol. 29, no. 11, pp. 1327–1333, 2008.
- K. K. Kim, M. C. Kugler, P. J. Wolters et al., “Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 35, pp. 13180–13185, 2006.
- Y. C. Yang, N. Zhang, K. van Crombruggen, G. H. Hu, S. L. Hong, and C. Bachert, “Transforming growth factor-beta1 in inflammatory airway disease: a key for understanding inflammation and remodeling,” Allergy, vol. 67, no. 10, pp. 1193–1202, 2012.
- H. Kasai, J. T. Allen, R. M. Mason, T. Kamimura, and Z. Zhang, “TGF-β1 induces human alveolar epithelial to mesenchymal cell transition (EMT),” Respiratory Research, vol. 6, article 56, 2005.
- C. G. Lee, B. Ma, S. Takyar et al., “Studies of vascular endothelial growth factor in asthma and chronic obstructive pulmonary disease,” Proceedings of the American Thoracic Society, vol. 8, no. 6, pp. 512–515, 2011.
- S. S. Sidhu, S. Yuan, A. L. Innes et al., “Roles of epithelial cell-derived periostin in TGF-β activation, collagen production, and collagen gel elasticity in asthma,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 32, pp. 14170–14175, 2010.
- S. Al-Muhsen, J. R. Johnson, and Q. Hamid, “Remodeling in asthma,” Journal of Allergy and Clinical Immunology, vol. 128, no. 3, pp. 451–462, 2011.
- H. L. Chua, P. Bhat-Nakshatri, S. E. Clare, A. Morimiya, S. Badve, and H. Nakshatri, “NF-κB represses E-cadherin expression and enhances epithelial to mesenchymal transition of mammary epithelial cells: potential involvement of ZEB-1 and ZEB-2,” Oncogene, vol. 26, no. 5, pp. 711–724, 2007.
- H. J. Kim, B. C. Litzenburger, X. Cui et al., “Constitutively active type I insulin-like growth factor receptor causes transformation and xenograft growth of immortalized mammary epithelial cells and is accompanied by an epithelial-to-mesenchymal transition mediated by NF-κB and snail,” Molecular and Cellular Biology, vol. 27, no. 8, pp. 3165–3175, 2007.
- M. J. Barberà, I. Puig, D. Domínguez et al., “Regulation of Snail transcription during epithelial to mesenchymal transition of tumor cells,” Oncogene, vol. 23, no. 44, pp. 7345–7354, 2004.
- Y. Wu, J. Deng, P. G. Rychahou, S. Qiu, B. M. Evers, and B. P. Zhou, “Stabilization of Snail by NF-κB Is Required for inflammation-induced cell migration and invasion,” Cancer Cell, vol. 15, no. 5, pp. 416–428, 2009.
- A. R. Brasier, A. Garcia-Sastre, and S. M. Lemon, Cellular Signaling and Innate Immune Response to RNA Virus Infections, ASM Press, Washington, DC, USA, 2008.
- R. J. Sims III, R. Belotserkovskaya, and D. Reinberg, “Elongation by RNA polymerase II: the short and long of it,” Genes and Development, vol. 18, no. 20, pp. 2437–2468, 2004.
- B. M. Peterlin and D. H. Price, “Controlling the elongation phase of transcription with P-TEFb,” Molecular Cell, vol. 23, no. 3, pp. 297–305, 2006.
- S. Tourdot, S. Mathie, T. Hussell et al., “Respiratory syncytial virus infection provokes airway remodelling in allergen-exposed mice in absence of prior allergen sensitization,” Clinical and Experimental Allergy, vol. 38, no. 6, pp. 1016–1024, 2008.
- L. S. van Rijt, N. Vos, M. Willart et al., “Persistent activation of dendritic cells after resolution of allergic airway inflammation breaks tolerance to inhaled allergens in mice,” American Journal of Respiratory and Critical Care Medicine, vol. 184, no. 3, pp. 303–311, 2011.
- E. Kaltenborn, S. Kern, S. Frixel et al., “Respiratory syncytial virus potentiates ABCA3 mutation-induced loss of lung epithelial cell differentiation,” Human Molecular Genetics, vol. 21, pp. 2793–2806, 2012.
- C. Palena, D. E. Polev, K. Y. Tsang et al., “The human T-box mesodermal transcription factor Brachyury is a candidate target for T-cell—mediated cancer immunotherapy,” Clinical Cancer Research, vol. 13, no. 8, pp. 2471–2478, 2007.