Real and artificial immune systems: Computing the state of the body

Nature Reviews Immunology

Volumn 7, Issue 7, 2007, Pages 569-574

  Cohen, Irun R ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK PROTEIN; HEAT SHOCK PROTEIN 60; INTERLEUKIN 2 RECEPTOR ALPHA; MAJOR HISTOCOMPATIBILITY ANTIGEN;

B LYMPHOCYTE; CELLULAR IMMUNITY; HUMAN; HUMORAL IMMUNITY; IMMUNE SYSTEM; IMMUNOREGULATION; MATHEMATICAL MODEL; NATURAL KILLER CELL; NONHUMAN; PRIORITY JOURNAL; REVIEW; T LYMPHOCYTE;

ANIMALS; ANTIGENS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HEAT-SHOCK PROTEINS; HUMANS; IMMUNE SYSTEM;

EID: 34250890735     PISSN: 14741733     EISSN: None     Source Type: Journal    
DOI: 10.1038/nri2102     Document Type: Review

References (70)

1. th International Conference, ICARIS 2006. (eds Bersini, H. & Carneiro) (Springer-Verlag, Berlin, 2006).
2. Stepney, S. et al. Conceptual frameworks for artificial immune systems. Int. J. Unconventional Computing. 1, 315-338 (2005).
3. Hofmeyr, S. A. & Forrest, S. Architecture for an artificial immune system. Evol. Comput. 8, 443-73 (2000).
4. Timmis, J., Neal, M. & Hunt, J. An artificial immune system for data analysis. Biosystems 55, 143-150 (2000).
5. th International Conference, ICARIS 2006. (eds Bersini H and Carneiro J ) Preface (Springer-Verlag, Berlin, 2006).
6. Perelson, A. S. Modelling viral and immune system dynamics. Nature Rev. Immunol. 2, 28-36 (2002).
7. Garrett, S. How do we evaluate artificial immune systems? Evol. Comput. 13, 145-178 (2005).
8. Harel, D. Computers Ltd.: What They Really Can't Do, Revised paperback edition (Oxford Univ. Press, USA, 2003).
9. Harel, D. & Feldman, Y. Algorithmics: The Spirit of Computing 3rd edn (Addison-Wesley, 2004).
10. Ivanov, I. I., Diehl, G. E. & Littman, D. R. Lymphoid tissue inducer cells in intestinal immunity. Curr. Top. Microbiol. Immunol. 308, 59-82 (2006).
11. Sepehri, S., Kotlowski, R. Bernstein, C. N. & Krause, D. O. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm. Bowel Dis. 13, 675-683 (2007).
12. Rozenfeld, R. A., Liu, X., DePlaen, I. & Hsueh, W. Role of gut flora on intestinal group II phospholipase A2 activity and intestinal injury in shock. Am. J. Physiol. Gastrointest. Liver Physiol. 281, G957-G963 (2001).
13. Schaffer, M., Bongartz, M., Hoffmann, W. & Viebahn, R. MHC-class-II-deficiency impairs wound healing. J. Surg. Res. 138, 100-105 (2007).
14. Gillitzer, R. & Goebeler, M. Chemokines in cutaneous wound healing. J. Leukoc. Biol. 69, 513-521 (2001).
15. Ziv, Y., Avidan, H., Pluchino, S., Martino, G. & Schwartz, M. Synergy between immune cells and adult neural stem/progenitor cells promotes functional recovery from spinal cord injury. Proc. Natl Acad. Sci. USA 103, 13174-13179 (2006).
16. Zhang, Z. & Schluesener, H. J. Mammalian Toll-like receptors: from endogenous ligands to tissue regeneration. Cell. Mol. Life Sci. 63, 2901-2907 (2006).
17. Cursiefen, C. Immune privilege and angiogenic privilege of the cornea. Chem. Immunol. Allergy 92, 50-57 (2007).
18. Tettamanti, G. et al. Growth factors and chemokines: a comparative functional approach between invertebrates and vertebrates. Curr. Med. Chem. 13, 2737-2750 (2006).
19. Savill, J. Apoptosis in resolution of inflammation. J. Leukoc. Biol. 61, 375-380 (1997).
20. Krysko, D. V., D'Herde, K. & Vandenabeele, P. Clearance of apoptotic and necrotic cells and its immunological consequences. Apoptosis 11, 1709-1726 (2006).
21. Cohen, I. R. Discrimination and dialogue in the immune system. Semin. Immunol. 12, 215-9; 321-323 (2000).
22. Cohen, I. R. Tending Adam's Garden: Evolving the Cognitive Immune Self (Academic Press, London, UK 2000).
23. Cohen, I. R. in Lecture Notes in Computer Science 4199 MoDELS 2006, (eds O. Niestrasz et al.) 499-512 (Springer-Verlag, Berlin, 2006).
24. Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107-118 (2005).
25. Cohen, I. R. Regen und Auferstehung: Talmud und Naturwissenschaft im Dialog mit der Welt. (Vandenhoek & Ruprecht, Göttingen, Germany 2005).
26. Kuhn, T. The Structure of Scientific Revolutions, 2nd edn (Univ. Chicago Press, 1970).
27. Fleck, L. Genesis and Development of a Scientific Fact (Univ. Chicago Press, 1979).
28. Nobori, S. et al. Thymic rejuvenation and the induction of tolerance by adult thymic grafts. Proc. Natl Acad. Sci. USA 103, 19081-19086 (2006).
29. Li, Y., Louzoun, Y. & Weigert, M. Editing anti-DNA B cells by Vlambdax. J. Exp. Med. 199, 337-346 (2004).
30. Cabbage, S. E. et al. Regulatory T cells maintain long-term tolerance to myelin basic protein by inducing a novel, dynamic state of T cell tolerance. J. Immunol. 178, 887-896 (2007).
31. Cohen, I. R. The cognitive paradigm and the immunological homunculus. Immunol. Today 13, 490-494 (1992).
32. Nobrega, A. et al. Global analysis of antibody repertoires. II. Evidence for specificity, self-selection and the immunological 'homunculus' of antibodies in normal serum. Eur. J. Immunol. 23, 2851-2859 (1993).
33. Poletaev, A. B. The immunological homunculus (immunculus) in normal state and pathology. Biochemistry Mosc. 67, 600-608 (2002).
34. Avrameas, S. Natural autoantibodies: from 'horror autotoxicus' to 'gnothi seauton'. Immunol. Today 12, 154-159 (1991).
35. Merbl, Y., Zucker-Toledano, M., Quintana, F. J. & Cohen, I. R. Newborn humans manifest autoantibodies to defined self-molecules detected by antigen microarray informatics. J. Clin. Invest 117, 712-718 (2007).
36. Mouthon, L. et al. Invariance and restriction toward a limited set of self-antigens characterize neonatal IgM antibody repertoires and prevail in autoreactive repertoires of healthy adults. Proc. Natl Acad. Sci. USA 92, 3839-3843 (1995).
37. Mirilas, P., Fesel, C., Guilbert, B., Beratis, N. G. & Avrameas, S. Natural antibodies in childhood: development, individual stability, and injury effect indicate a contribution to immune memory. J. Clin. Immunol. 19, 109-115 (1999).
38. Srivastava, P. Roles of heat-shock proteins in innate and adaptive immunity. Nature Rev. Immunol. 2, 185-194 (2002).
39. Abulafia-Lapid, R. et al. T cell proliferative responses of type 1 diabetes patients and healthy individuals to human HSP60 and its peptides. J. Autoimmun. 12, 121-129 (1999).
40. Flohe, S. B. et al. Human heat shock protein 60 induces maturation of dendritic cells versus a Th1-promoting phenotype. J. Immunol. 170, 2340-2348 (2003).
41. + regulatory T cell function via innate TLR2 signaling. J. Clin. Invest. 116, 2022-2032 (2006).
42. Cohen-Sfady, M. et al. Heat shock protein 60 activates B cells via the TLR4-MyD88 Pathway. J. Immunol. 175, 3594-3602 (2005).
43. Amir-Kroll, H. et al. A conjugate vaccine composed of a heat shock protein 60 T-cell epitope peptide (p458) and Neisseria meningitidis type B capsular polysaccharide. Vaccine 24, 6555-6563 (2006).
44. Quintana, F. J. & Cohen, I. R. Heat shock proteins as endogenous adjuvants in sterile and septic inflammation. J. Immunol. 175, 2777-2782 (2005).
45. Kirwan, S. E. & Burshtyn, D. N. Regulation of natural killer cell activity. Curr. Opin. Immunol. 19, 46-54 (2007).
46. Zwirner, N. W., Fuertes, M. B., Girart, M. V., Domaica, C. I. & Rossi, L. E. Cytokine-driven regulation of NK cell functions in tumor immunity: Role of the MICA-NKG2D system. Cytokine Growth Factor Rev. 18, 159-170 (2007).
47. Gasser, S., Orsulic, S., Brown, E. J. & Raulet, D. H. The DNA damage pathway regulates innate immune system ligands of the NKG2D receptor. Nature 436, 1186-1190 (2005).
48. Quintana, F. J., Carmi, P., Mor, F. & Cohen, I. R. DNA fragments of the human 60-kDa heat shock protein (HSP60) vaccinate against adjuvant arthritis: identification of a regulatory HSP60 peptide. J. Immunol. 171, 3533-3541 (2003).
49. Cohen, I. R. Peptide therapy for Type I diabetes: the immunological homunculus and the rationale for vaccination. Diabetologia 45, 1468-1474 (2002).
50. Quintana, F. J., Carmi, P., Mor, F. & Cohen, I. R. Inhibition of adjuvant-induced arthritis by DNA vaccination with the 70-kd or the 90-kd human heat-shock protein immune cross-regulation with the 60-kd heat-shock protein. Arthritis Rheum. 50, 3712-3720 (2004).
51. Oki, Y. et al. Experience with heat shock protein-peptide complex 96 vaccine therapy in patients with indolent non-Hodgkin lymphoma. Cancer 109, 77-83 (2007).
52. van Eden. W., van der Zee, R. & Prakken, B. Heatshock proteins induce T-cell regulation of chronic inflammation. Nature Rev. Immunol. 5, 318-330 (2005).
53. Lohse, A. W., Mor, F., Karin, N. & Cohen, I. R. Control of experimental autoimmune encephalomyelitis by T cells responding to activated T cells. Science 244, 820-822 (1989).
54. Mimran, A. et al. DNA vaccination with CD25 protects rats from adjuvant arthritis and induces an antiergotypic response. J. Clin. Invest. 113, 924-932 (2004).
55. Cohen, I. R., Quintana, F. J. & Mimran, A. Tregs in T cell vaccination: exploring the regulation of regulation. J. Clin. Invest. 114, 1227-1232 (2004).
56. Zhang, X. Y., Liu, X. G., Wand, W., Wang, W. C. & Gao, X. M. Anti-T-cell humoral and cellular responses in healthy BALB/c mice following immunization with ovalbumin or ovalbumin-specific T cells. Immunol. 108, 465-473 (2003).
57. Quintana, F. J. & Cohen, I. R. Anti-ergotypic immunoregulation. Scand. J. Immunol. 64, 205-210 (2006).
58. + T-cells by different mechanisms. J. Neuroimmunol. 80, 47-64 (1997).
59. Heinemann, M. & Panke, S. Synthetic biology - putting engineering into biology. Bioinformatics 22, 2790-2799 (2006).
60. Quintana, F. J. et al. Functional immunomics: microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proc. Natl Acad. Sci. USA 101 (Suppl. 2), 14615-14621 (2004).
61. Quintana, J. F., Merbl, Y., Sahar, E., Domany, E. & Cohen, I. R. Antigen-chip technology for accessing global information about the state of the body. Lupus 15, 428-430 (2006).
62. Orimo, A. & Weinberg, R. A. Stromal fibroblasts in cancer: a novel tumor-promoting cell type. Cell Cycle 5, 1597-1601 (2006).
63. Witz, I. P. Tumor-microenvironment interactions: the selectin-selectin ligand axis in tumor-endothelium cross talk. Cancer Treat. Res. 130, 125-140 (2006).
64. Whiteside, T. L. The role of immune cells in the tumor microenvironment. Cancer Treat. Res. 130, 103-124 (2006).
65. Tan, T. T. & Coussens, L. M. Humoral immunity, inflammation and cancer. Curr. Opin. Immunol. 19, 209-216 (2007).
66. Elaraj, D. M. et al. The role of interleukin 1 in growth and metastasis of human cancer xenografts. Clin. Cancer Res. 12, 1088-1096 (2006).
67. Bergmann, C., van Hemmen. J. L. & Segel, L. A. How instruction and feedback can select the appropriate T helper response. Bull. Math. Biol. 64, 425-446 (2002).
68. Meier-Schellersheim M., Xu X., Angermann B., Kunkel E. J., Jin T., Germain R.N. Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput. Biol. 2, e82 (2006).
69. Cohen, I. R. & Harel, D. Explaining a complex living system: dynamics, multi-scaling and emergence. J. R. Soc. Interface 4, 175-182 (2007).
70. Efroni, S., Harel, D. & Cohen, I. R. Emergent dynamics of thymocyte development and lineage determination. PLoS Comput. Biol. 3, e13 (2007).