Modulating temporal control of NF-κB activation: Implications for therapeutic and assay selection

Biophysical Journal

Volumn 94, Issue 11, 2008, Pages 4249-4259

  Klinke II, David J ^a,b   Ustyugova, Irina V ^b   Brundage, Kathleen M ^b   Barnett, John B ^b  

^a West Virginia University   (United States)

^b WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LIPOPOLYSACCHARIDE;

ANIMAL; ARTICLE; BIOASSAY; BIOLOGICAL MODEL; CELL LINE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; DRUG EFFECT; MACROPHAGE; METABOLISM; METHODOLOGY; MOUSE; PHYSIOLOGY; TIME; TRANSACTIVATION;

ANIMALS; BIOLOGICAL ASSAY; CELL LINE; COMPUTER SIMULATION; DNA; LIPOPOLYSACCHARIDES; MACROPHAGES; MICE; MODELS, BIOLOGICAL; MODELS, CHEMICAL; NF-KAPPA B; TIME FACTORS; TRANS-ACTIVATION (GENETICS);

EID: 44849085131     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.120451     Document Type: Article

References (43)

1. Ghosh, S., M. J. May, and E. B. Kopp. 1998. NF-κB and Rel proteins: evolutionarily conserved mediators of immune responses. Annu. Rev. Immunol. 16:225-260.
2. Baldwin, A. S., Jr. 1996. The NF-κB and I κB proteins: new discoveries and insights. Annu. Rev. Immunol. 14:649-683.
3. Wallach, D., E. E. Varfolomeev, N. L. Malinin, Y. V. Goltsev, A. V. Kovalenko, and M. P. Boldin. 1999. Tumor necrosis factor receptor and Fas signaling mechanisms. Annu. Rev. Immunol. 17:331-367.
4. Hayden, M. S., and S. Ghosh. 2004. NF-κB and Rel proteins: evolutionarily conserved mediators of immune responses. Genes Dev. 18:2195-2224.
5. Hoffmann, A., A. Levchenko, M. L. Scott, and D. Baltimore. 2002. The IκB-NF-κB signaling module: temporal control and selective gene activation. Science. 298:1241-1245.
6. Gilmore, T. D., and M. Herscovitch. 2006. Inhibitors of NF-κB signaling: 785 and counting. Oncogene. 25:6887-6899.
7. Hoffmann, A., and D. Baltimore. 2006. Circuitry of nuclear factor κB signaling. Immunol. Rev. 210:171-186.
8. Nathan, C. F., and J. B. Jr. Hibbs. 1991. Role of nitric oxide synthesis in macrophage antimicrobial activity. Curr. Opin. Immunol. 3:65-70.
9. Miller, R. A., and B. E. Britigan. 1997. Role of oxidants in microbial pathophysiology. Clin. Microbiol. Rev. 10:1-18.
10. Unanue, E. R. 1981. The regulatory role of macrophages in antigenic stimulation. Part Two: symbiotic relationship between lymphocytes and macrophages. Adv. Immunol. 31:1-136.
11. Unanue, E. R. 1984. Antigen-presenting function of the macrophage. Annu. Rev. Immunol. 2:395-428.
12. Adams, D. O., and T. A. Hamilton. 1984. The cell biology of macrophage activation. Annu. Rev. Immunol. 2:283-318.
13. Ustyugova, I. V., L. L. Frost, K. Vandyke, K. M. Brundage, R. Schafer, and J. B. Barnett. 2007. 3,4-Dichloropropionaniline suppresses normal macrophage function. Toxicol. Sci. 97:364-374.
14. Xie, Y. C., R. Schafer, and J. B. Barnett. 1997. Inhibitory effect of 3,4-dichloro-propionaniline on cytokine production by macrophages is associated with LPS-mediated signal transduction. J. Leukoc. Biol. 61:745-752.
15. Xie, Y. C., R. Schafer, and J. B. Barnett. 1997. The immunomodulatory effects of the herbicide propanil on murine macrophage interleukin-6 and tumor necrosis factor-α production. Toxicol. Appl. Pharmacol. 145:184-191.
16. Frost, L. L., Y. X. Neeley, R. Schafer, L. F. Gibson, and J. B. Barnett. 2001. Propanil inhibits tumor necrosis factor-α production by reducing nuclear levels of the transcription factor nuclear factor-κb in the macrophage cell line IC-21. Toxicol. Appl. Pharmacol. 172:186-193.
17. Hendrickson, W. 1985. Protein-DNA interactions studied by the gel electrophoresis-DNA binding assay. Biotechniques. 3:198-207.
18. Revzin, A. 1989. Gel electrophoresis assays for DNA-protein interactions. Biotechniques. 7:346-355.
19. Fried, M. G., and D. M. Crothers. 1981. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9:6505-6525.
20. Garner, M. M., and A. Revzin. 1981. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 9:3047-3060.
21. Benotmane, A. M., M. F. Hoylaerts, D. Collen, and A. Belayew. 1997. Nonisotopic quantitative analysis of protein-DNA interactions at equilibrium. Anal. Biochem. 250:181-185.
22. McKay, I. A., L. Kirby, E. V. Volyanik, V. Kumar, P. W. Wong, and S. A. Bustin. 1998. An enzyme-linked immunosorbent assay for the detection of agents which interfere with the DNA binding activities of transcription factors-exemplified by NF-IL6. Anal. Biochem. 265:28-34.
23. Renard, P., I. Ernest, A. Houbion, M. Art, H. Le Calvez, M. Raes, and J. Remacle. 2001. Development of a sensitive multi-well colorimetric assay for active NFκB. Nucleic Acids Res. 29:e21.
24. Poltorak, A., X. He, I. Smirnova, M. Y. Liu, H. C. Van, X. Du, D. Birdwell, E. Alejos, M. Silva, C. Galanos, M. Freudenberg, P. Ricciardi-Castagnoli, B. Layton, and B. Beutler. 1998. Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science. 282:2085-2088.
25. Efron, B., and R. Tibshirani. 1986. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat. Sci. 1:54-77.
26. Chernick, M. R. 1999. Bootstrap Methods: A Practitioner's Guide. Wiley, New York. 150-151.
27. Covert, M. W., T. H. Leung, J. E. Gaston, and D. Baltimore. 2005. Achieving stability of lipopolysaccharide-induced NF-κB activation. Science. 309:1854-1857.
28. Reference deleted in proof.
29. Schulze-Luehrmann, J., and S. Ghosh. 2006. Antigen-receptor signaling to nuclear factor κB. Immunity. 25:701-715.
30. Akira, S., and K. Takeda. 2004. Toll-like receptor signalling. Nat. Rev. Immunol. 4:499-511.
31. Kearns, J. D., S. Basak, S. L. Werner, C. S. Huang, and A. Hoffmann. 2006. IκBε provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expression. J. Cell Biol. 173:659-664.
32. Dong, W., Y. Liu, J. Peng, L. Chen, T. Zou, H. Xiao, Z. Liu, W. Li, Y. Bu, and Y. Qi. 2006. The IRAK-1-BCL10-MALT1-TRAF6-TAK1 cascade nediates signaling to NF-κB from toll-like receptor 4. J. Biol. Chem. 281:26029-26040.
33. Sun, L., L. Deng, C.-K. Ea, Z.-P. Xia, and Z. J. Chen. 2004. The TRAF6 ubiquitin ligase and TAK1 kinase mediate IKK activation by BCL10 and MALT1 in T lymphocytes. Mol. Cell. 14:289-301.
34. Kopp, E. B., and S. Ghosh. 1995. NF-κB and rel proteins in innate immunity. Adv. Immunol. 58:1-27.
35. Werner, S. L., D. Barken, and A. Hoffmann. 2005. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science. 309:1857-1861.
36. Wright, S. D., R. A. Ramos, P. S. Tobias, R. J. Ulevitch, and J. C. Mathison. 1990. CD14, a receptor for complexes of lipopolysaccharide (LPS) and LPS binding protein. Science. 249:1431-1433.
37. Nelson, D. E., A. E. Ihekwaba, M. Elliott, J. R. Johnson, C. A. Gibney, B. E. Foreman, G. Nelson, V. See, C. A. Horton, D. G. Spiller, S. W. Edwards, H. P. McDowell, J. F. Unitt, E. Sullivan, R. Grimley, N. Benson, D. Broomhead, D. B. Kell, and M. R. White. 2004. Oscillations in NF-κB signaling control the dynamics of gene expression. Science. 306:704-708.
38. Lipniacki, T., P. Paszek, A. R. Brasier, B. A. Luxon, and M. Kimmel. 2006. Stochastic regulation in early immune response. Biophys. J. 90:725-742.
39. Maddox, J. 1992. Is molecular biology yet a science? Nature. 355:201.
40. Maddox, J. 1994. Towards more measurement in biology. Nature. 368:95. (Abstr.)
41. Jacquez, J. A., and T. Perry. 1990. Parameter estimation: local identifiability of parameters. Am. J. Physiol. 258:E727-E736.
42. Audoly, S., G. Bellu, L. D'Angio, M. P. Saccomani, and C. Cobelli. 2001. Global identifiability of nonlinear models of biological systems. IEEE Trans. Biomed. Eng. 48:55-65.
43. Turanyi, T., and H. Rabitz. 2000. Local methods. In Sensitivity Analysis. A. Saltelli, K. Chan, and E. M. Scott, editors. John Wiley, New York. 81-100.