Autoantibody repertoires, natural biomarkers, and system controllers

Trends in Immunology

Volumn 34, Issue 12, 2013, Pages 620-625

  Cohen, Irun R ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOANTIBODY; BIOLOGICAL MARKER; CHAPERONIN 60; CYCLOPHOSPHAMIDE; HEAT SHOCK PROTEIN 70; IMMUNOGLOBULIN A ANTIBODY; IMMUNOGLOBULIN G ANTIBODY; IMMUNOGLOBULIN M ANTIBODY; LYMPHOCYTE ANTIGEN RECEPTOR; TUMOR NECROSIS FACTOR ALPHA; TUMOR NECROSIS FACTOR ALPHA ANTIBODY;

ANTIGEN SPECIFICITY; AUTOIMMUNITY; EPIGENETICS; GENOMICS; HUMAN; IMMUNOCOMPETENT CELL; INSULIN DEPENDENT DIABETES MELLITUS; LYMPHOCYTE CLONE; MEMORY CELL; METABOLOMICS; MULTIPLE SCLEROSIS; NONHUMAN; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; RHEUMATOID ARTHRITIS; STEADY STATE; SYSTEMIC LUPUS ERYTHEMATOSUS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

AUTOANTIBODIES; BIOLOGICAL MARKERS; CHAPERONIN 60; HSP70 HEAT-SHOCK PROTEINS; HUMANS; IMMUNE SYSTEM;

EID: 84888434984     PISSN: 14714906     EISSN: 14714981     Source Type: Journal    
DOI: 10.1016/j.it.2013.05.003     Document Type: Review

References (55)

1. Cohen I.R. Tending Adam's Garden: Evolving the Cognitive Immune Self 2000, Academic Press.
2. Structure, function and diversity of the healthy human microbiome. Nature 2012, 487:207-214. Human Microbiome Project Consortium.
3. Bakhtiar S.M., et al. Implications of the human microbiome in inflammatory bowel diseases. FEMS Microbiol. Lett. 2013, 342:10-17.
4. Cohen I.R., Harel D. Explaining a complex living system: dynamics, multi-scaling and emergence. J. R. Soc. Interface 2007, 4:175-182.
5. Purvis J.E., Lahav G. Encoding and decoding cellular information through signaling dynamics. Cell 2013, 152:945-956.
6. Vainas O., et al. Reactive animation: from piecemeal experimentation to reactive biological systems. Autoimmunity 2011, 44:271-281.
7. Idris S.F. The role of high-throughput technologies in clinical cancer genomics. Expert Rev. Mol. Diagn. 2013, 13:167-181.
8. Teperino R., et al. Bridging epigenomics and complex disease: the basics. Cell. Mol. Life Sci. 2013, 70:1609-1621.
9. Choi D.S., et al. Proteomics, transcriptomics and lipidomics of exosomes and ectosomes. Proteomics 2013, 10.1002/pmic.201200329.
10. Russell C., et al. Application of genomics, proteomics and metabolomics in drug discovery, development and clinic. Ther. Deliv. 2013, 4:395-413.
11. Putri S.P., et al. Current metabolomics: practical applications. J. Biosci. Bioeng. 2013, 115:579-589.
12. Derouiche A., et al. Protein phosphorylation from the perspective of systems biology. Curr. Opin. Biotechnol. 2012, 23:585-590.
13. Rogne M., Taskén K. Cell signalling analyses in the functional genomics era. N. Biotechnol. 2013, 30:333-338.
14. Efroni S., et al. Toward rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic T-cell maturation. Genome Res. 2003, 13:2485-2497.
15. Sade-Feldman M., et al. Tumor necrosis factor-α blocks differentiation and enhances suppressive activity of immature myeloid cells during chronic inflammation. Immunity 2013, 38:541-554.
16. Herenius M.M., et al. Anti-TNF therapy reduces serum levels of chemerin in rheumatoid arthritis: a new mechanism by which anti-TNF might reduce inflammation. JAMA 2013, 309:887-895.
17. Gregory A.P., et al. TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis. Nature 2012, 488:508-511.
18. Burnet F.M. The Clonal Selection Theory of Acquired Immunity 1959, Cambridge University Press.
19. Brooks-Worrell B., et al. Biomarkers and immune-modulating therapies for type 2 diabetes. Trends Immunol. 2012, 33:546-553.
20. Cohen I.R. Biomarkers, self-antigens and the immunological homunculus. J. Autoimmun. 2007, 29:246-249.
21. Cohen I.R. Biomarker vaccines. Hum. Vaccin. 2009, 5:637-639.
22. Cohen I.R. Real and artificial immune systems: computing the state of the body. Nat. Rev. Immunol. 2007, 7:569-574.
23. Quintana J.F., et al. Antigen-chip technology for accessing global information about the state of the body. Lupus 2006, 15:428-430.
24. Merbl Y., et al. Newborn humans manifest autoantibodies to defined self molecules detected by antigen microarray informatics. J. Clin. Invest. 2007, 117:712-718.
25. Cohen I.R. The cognitive paradigm and the immunological homunculus. Immunol. Today 1992, 13:490-494.
26. Madi A., et al. The natural autoantibody repertoire in newborns and adults: a current overview. Adv. Exp. Med. Biol. 2012, 750:198-212.
27. Cohen I.R., Young D.B. Autoimmunity, microbial immunity and the immunological homunculus. Immunol. Today 1991, 12:105-110.
28. Madi A., et al. Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:14484-14489.
29. Madi A., et al. Network theory analysis of antibody-antigen reactivity data: the immune trees at birth and adulthood. PLoS ONE 2011, 6:e17445.
30. Robinson W.H., et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 2002, 8:295-301.
31. Quintana F.J., et al. Antigen microarrays identify unique serum autoantibody signatures associated with different clinical forms and pathologic subtypes of multiple sclerosis. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:18889-18894.
32. Quintana F.J., et al. Antigen microarrays identify CNS-produced autoantibodies in RRMS. Neurology 2012, 78:532-539.
33. Graham K.L., et al. High-throughput methods for measuring autoantibodies in systemic lupus erythematosus and other autoimmune diseases. Autoimmunity 2004, 37:269-272.
34. Fattal I., et al. An antibody profile of systemic lupus erythematosus detected by antigen microarray. Immunology 2010, 130:337-343.
35. Li Q.Z., et al. Identification of autoantibody clusters that best predict lupus disease activity using glomerular proteome arrays. J. Clin. Invest. 2005, 115:3428-3439.
36. Hagedorn P.H., et al. Chronic rejection of a lung transplant is marked by a profile of specific autoantibodies. Immunology 2010, 130:427-435.
37. Hagedorn P.H., et al. Integrative analysis correlates donor transcripts to recipient autoantibodies in primary graft dysfunction after lung transplantation. Immunology 2010, 132:394-400.
38. Merbl Y., et al. A systems immunology approach to the host-tumor interaction: large-scale patterns of natural autoantibodies distinguish healthy and tumor-bearing mice. PLoS ONE 2009, 4:e6053.
39. Elias D., et al. Vaccination against autoimmune mouse diabetes with a T-cell epitope of the human 65-kDa heat shock protein. Proc. Natl. Acad. Sci. U.S.A. 1991, 88:3088-3091.
40. van Eden W., et al. Cloning of the mycobacterial epitope recognized by T lymphocytes in adjuvant arthritis. Nature 1988, 331:171-173.
41. Quintana F.J., et al. 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. 2004, 50:3712-3720.
42. Almanzar G., et al. Autoreactive HSP60 epitope-specific T-cells in early human atherosclerotic lesions. J. Autoimmun. 2012, 39:441-450.
43. Rizzo M., et al. Heat shock protein-60 and risk for cardiovascular disease. Curr. Pharm. Des. 2011, 17:3662-3668.
44. Ablamunits V., et al. Acceleration of autoimmune diabetes by cyclophosphamide is associated with an enhanced IFN-γ secretion pathway. J. Autoimmun. 1999, 13:383-392.
45. 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. U.S.A. 2004, 101(Suppl. 2):14615-14621.
46. Elias D., Cohen I.R. Peptide therapy for diabetes in NOD mice. Lancet 1994, 343:704-706.
47. Raz I., et al. β-cell function in new-onset type 1 diabetes and immunomodulation with a heat-shock protein peptide (DiaPep277): a randomised, double-blind, phase II trial. Lancet 2001, 358:1749-1753.
48. Quintana F.J., et al. DNA fragments of the human 60-kDa heat shock protein (HSP60) vaccinate against adjuvant arthritis: identification of a regulatory HSP60 peptide. J. Immunol. 2003, 171:3533-3541.
49. van Herwijnen M.J., et al. Regulatory T cells that recognize a ubiquitous stress-inducible self-antigen are long-lived suppressors of autoimmune arthritis. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:14134-14139.
50. + regulatory T cell function via innate TLR2 signaling. J. Clin. Invest. 2006, 116:2022-2032.
51. Quintana F.J., Cohen I.R. The HSP60 immune system network. Trends Immunol. 2011, 32:89-95.
52. Cohen I.R. Peptide therapy for type I diabetes: the immunological homunculus and the rationale for vaccination. Diabetologia 2002, 45:1468-1474.
53. Harel D. A Turing-like test for biological modeling. Nat. Biotechnol. 2005, 23:495-496.
54. Efroni S., et al. Emergent dynamics of thymocyte development and lineage determination. PLoS Comput. Biol. 2007, 3:e13.
55. Efroni S., et al. A theory for complex systems: reactive animation. Multidisciplinary Approaches to Theory in Medicine (Studies in Multidisciplinarity, Vol. 3) 2005, 309-324. Elsevier. R. Paton, L. McNamara (Eds.).