Towards a liquid self: How time, geography, and life experiences reshape the biological identity

Frontiers in Immunology

Volumn 5, Issue APR, 2014, Pages

  Grignolio, Andrea ^a   Mishto, Michele ^a,b   Caetano Faria, Ana Maria ^c   Garagnani, Paolo ^a   Franceschi, Claudio ^a,d,e   Tieri, Paolo ^e,f  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^c FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^d RIZZOLI ORTHOPAEDIC INSTITUTE   (Italy)

^e CNR   (Italy)

^f CNR   (Italy)

Author keywords

Antigen presentation; Gut microbiota; Host pathogen interaction; N glycan; Non self; Oral tolerance; Proteasome splicing; Self

Indexed keywords

ANTIGEN; GLYCAN; HEAT SHOCK PROTEIN; MITOCHONDRIAL DNA; SECRETORY IMMUNOGLOBULIN; T LYMPHOCYTE RECEPTOR; TOLL LIKE RECEPTOR 1;

ANTIGEN PRESENTATION; ARTICLE; COMMENSALISM; DNA METHYLATION; EPIGENETICS; EVOLUTION; GLYCOSYLATION; HOST PATHOGEN INTERACTION; HUMAN; IMMUNE RESPONSE; IMMUNOLOGICAL PARAMETERS; IMMUNOLOGICAL SELF; IMMUNOLOGY; IMMUNOREACTIVITY; INTESTINE FLORA; INTESTINE LYMPHATIC TISSUE; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR INTERACTION; MOLECULAR MIMICRY; REGULATORY T LYMPHOCYTE; SYMBIOSIS;

EID: 84900856809     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2014.00153     Document Type: Article

References (193)

1. Burnet FM. The Nobel Lectures in Immunology. The Nobel Prize for Physiology or Medicine, 1960. Immunologic recognition of self. Scand J Immunol (1991) 33:3-13.
2. Burnet FM, Fenner F. The Production of Antibodies. Melbourne: Macmillan (1949).
3. Janeway CA Jr. Approaching the asymptote? Evolution and revolution in immunology. Cold Spring Harb Symp Quant Biol (1989) 54(Pt 1):1-13. doi: 10.1101/SQB.1989.054.01.003.
4. Janeway CA Jr. The immune system evolved to discriminate infectious nonself from noninfectious self. Immunol Today (1992) 13:11-6. doi:10.1016/0167-5699(92)90198-G.
5. Matzinger P. Tolerance, danger, and the extended family. Annu Rev Immunol (1994) 12:991-1045. doi:10.1146/annurev.immunol.12.1.991.
6. Matzinger P. The evolution of the danger theory. Interview by Lauren constable, commissioning editor. Expert Rev Clin Immunol (2012) 8:311-7. doi:10.1586/eci.12.21.
7. Tauber A. The biological notion of self and non-self. In: Zalta EN, editor. The Stanford Encyclopedia of Philosophy (Summer 2012 Edition) (2012). Available from: http://plato.stanford.edu/archives/sum2012/entries/biology-self.
8. Loeb L, Wright S. Transplantation and Individuality differentials in inbred families of Guinea pigs. Am J Pathol (1927) 3:251-83.
9. Loeb L. The Biological Basis of Individuality. Springfield, IL, Baltimore, MD: C. C. Thomas (1945).
10. Zinkernagel RM, Doherty PC. MHC-restricted cytotoxic T cells: studies on the biological role of polymorphic major transplantation antigens determining T-cell restriction-specificity, function, and responsiveness. Adv Immunol (1979) 27:51-177. doi:10.1016/S0065-2776(08)60262-X.
11. Nossal GJ, Pike BL. Clonal anergy: persistence in tolerant mice of antigen-binding B lymphocytes incapable of responding to antigen or mitogen. Proc Natl Acad Sci U S A (1980) 77:1602-6. doi:10.1073/pnas.77.3.1602.
12. Chase MW. Inhibition of experimental drug allergy by prior feeding of the sensitizing agent. Proc Soc Exp Biol Med (1946) 61:257-9. doi:10.3181/00379727-61-15294P.
13. Bretscher P, Cohn M. A theory of self-nonself discrimination. Science (1970) 169:1042-9. doi:10.1126/science.169.3950.1042.
14. Lafferty KJ, Cunningham AJ. A new analysis of allogeneic interactions. Aust J Exp Biol Med Sci (1975) 53:27-42. doi:10.1038/icb.1975.3.
15. Coutinho A. Size and connectivity: a bit of the history of immune networks. J Theor Biol (1991) 149:425-7. doi:10.1016/S0022-5193(05)80314-5.
16. Coutinho A. The network theory: 21 years later. Scand J Immunol (1995) 42:3-8. doi:10.1111/j.1365-3083.1995.tb03619.x.
17. Coutinho A, Kazatchkine MD, Avrameas S. Natural autoantibodies. Curr Opin Immunol (1995) 7:812-8. doi:10.1016/0952-7915(95)80053-0.
18. Coutinho A. Beyond clonal selection and network. Immunol Rev (1989) 110:63-87. doi:10.1111/j.1600-065X.1989.tb00027.x.
19. Varela FJ, Coutinho A. Second generation immune networks. Immunol Today (1991) 12:159-66. doi:10.1016/S0167-5699(05)80046-5.
20. Cohen IR. Natural id-anti-id networks and the immunological homunculus. In: Atlan H, Cohen IR, editors. Theories of Immune Networks. Berlin: Springer-Verlag (1989). p. 6-12.
21. Cohen IR. Kadishman's tree, Escher's angels, and the immunological homunculus. In: Coutinho A, Kazatchkine MD, editors. Autoimmunity: Physiology and Disease. New York: Wiley-Liss (1994). p. 7-18.
22. Cunliffe J. Morphostasis and immunity. Med Hypotheses (1995) 44:89-96. doi:10.1016/0306-9877(95)90076-4.
23. Dembic Z. Do we need integrity? Scand J Immunol (1996) 44:549-50. doi:10.1046/j.1365-3083.1996.d01-360.x.
24. Dembic Z. Immune system protects integrity of tissues. Mol Immunol (2000) 37:563-9. doi:10.1016/S0161-5890(00)00084-5.
25. Cohn M. The evolutionary context for a self-nonself discrimination. Cell Mol Life Sci (2010) 67:2851-62. doi:10.1007/s00018-010-0438-z.
26. Hood L, Talmage DW. Mechanism of antibody diversity: germ line basis for variability. Science (1970) 168:325-34. doi:10.1126/science.168.3929.325.
27. Watson JD. Recombinant DNA. New York: Scientific American Books (1992).
28. Waldmann H, Cobbold S, Benjamin R, Qin S. A theoretical framework for self-tolerance and its relevance to therapy of autoimmune disease. J Autoimmun (1988) 1:623-9. doi:10.1016/0896-8411(88)90053-4.
29. Zinkernagel RM, Pircher HP, Ohashi P, Oehen S, Odermatt B, Mak T, et al. T and B cell tolerance and responses to viral antigens in transgenic mice: implications for the pathogenesis of autoimmune versus immunopathological disease. Immunol Rev (1991) 122:133-71. doi:10.1111/j.1600-065X.1991.tb00601.x.
30. Mitchison NA. A walk round the edges of self tolerance. Ann Rheum Dis (1993) 52(Suppl 1):S3-5. doi:10.1136/ard.52.Suppl_1.S3.
31. Jerne NK. Towards a network theory of the immune system. Ann Immunol (Paris) (1974) 125C:373-89.
32. Salaun J, Bandeira A, Khazaal I, Calman F, Coltey M, Coutinho A, et al. Thymic epithelium tolerizes for histocompatibility antigens. Science (1990) 247:1471-4. doi:10.1126/science.2321009.
33. Tauber AI. The elusive immune self: a case of category errors. Perspect Biol Med (1999) 42:459-74.
34. Langman RE, Cohn M. Self-nonself discrimination revisited. Introduction. Semin Immunol (2000) 12:159-62. doi:10.1006/smim.2000.0227.
35. Ulvestad E. Defending Life: the Nature of Host-Parasite Relations. Dordrecht: Springer (2007).
36. Vance RE. Cutting edge: cutting edge commentary: a Copernican revolution? Doubts about the danger theory. J Immunol (2000) 165:1725-8.
37. Franceschi C, Grignolio A. Immunosenescence within an evolutionary perspective. In: Grignolio A, editor. Immunology Today: Three Historical Perspectives under Three Theoretical Horizons. Bologna: Bononia University Press (2010). p. 79-99.
38. Pradeu T, Cooper EL. The danger theory: 20 years later. Front Immunol (2012) 3:287. doi:10.3389/fimmu.2012.00287.
39. Zinkernagel RM. Localization dose and time of antigens determine immune reactivity. Semin Immunol (2000) 12:163-71. doi:10.1006/smim.2000.0253.
40. Meyer U, Feldon J, Dammann O. Schizophrenia and autism: both shared and disorder-specific pathogenesis via perinatal inflammation? Pediatr Res (2011) 69:26R-33R. doi:10.1203/PDR.0b013e318212c196.
41. Huurre A, Kalliomaki M, Rautava S, Rinne M, Salminen S, Isolauri E. Mode of delivery-effects on gut microbiota and humoral immunity. Neonatology (2008) 93:236-40. doi:10.1159/000111102.
42. Franceschi C, Bonafè M, Valensin S, Olivieri F, De Luca M, Ottaviani E, et al. Inflamm-aging. An evolutionary perspective on immunosenescence. Ann N Y Acad Sci (2000) 908:244-54. doi:10.1111/j.1749-6632.2000.tb06651.x.
43. Feinerman O, Germain RN, Altan-Bonnet G. Quantitative challenges in understanding ligand discrimination by alphabeta T cells. Mol Immunol (2008) 45:619-31. doi:10.1016/j.molimm.2007.03.028.
44. Bauman Z. Liquid Modernity. Cambridge: Polity (2000).
45. Bauman Z. Culture in a Liquid Modern World. Cambridge: Polity (2011).
46. Lee YC, Newport MJ, Goetghebuer T, Siegrist CA, Weiss HA, Pollard AJ, et al. Influence of genetic and environmental factors on the immunogenicity of Hib vaccine in Gambian twins. Vaccine (2006) 24:5335-40. doi:10.1016/j.vaccine.2006.04.021.
47. Pradeu T, Carosella E. On the definition of a criterion of immunogenicity. Proc Natl Acad Sci USA (2006) 103:17858-61. doi:10.1073/pnas.0608683103.
48. Pradeu T, Jaeger S, Vivier E. The speed of change: towards a discontinuity theory of immunity? Nat Rev Immunol (2013) 13:764-9. doi:10.1038/nri3521.
49. Grossman Z, Paul WE. Adaptive cellular interactions in the immune system: the tunable activation threshold and the significance of subthreshold responses. Proc Natl Acad Sci U S A (1992) 89:10365-9. doi:10.1073/pnas.89.21.10365.
50. Paul WE, Milner JD, Grossman Z. Pathogen-sensing, regulatory T Cells, and responsiveness-tuning collectively regulate foreign- and self-antigen mediated T-cell responses. Cold Spring Harb Symp Quant Biol (2013) LXXVIII:1-12. doi:10.1101/sqb.2013.78.020198.
51. Haldane JBS. Disease and evolution. Ric Sci (1949) 19:68-75.
52. Lederberg J. J. B. S. Haldane (1949) on infectious disease and evolution. Genetics (1999) 153:1-3.
53. Pozzoli U, Fumagalli M, Cagliani R, Comi GP, Bresolin N, Clerici M, et al. The role of protozoa-driven selection in shaping human genetic variability. Trends Genet (2010) 26:95-9. doi:10.1016/j.tig.2009.12.010.
54. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, et al. Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4:e1000144. doi:10.1371/journal.pgen.1000144.
55. Sironi M, Menozzi G, Comi GP, Cagliani R, Bresolin N, Pozzoli U. Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences. Hum Mol Genet (2005) 14:2533-46. doi:10.1093/hmg/ddi257.
56. Consortium TWTCC. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 447:661-78. doi:10.1038/nature05911.
57. Prugnolle F, Manica A, Charpentier M, Guegan JF, Guernier V, Balloux F. Pathogen-driven selection and worldwide HLA class I diversity. Curr Biol (2005) 15:1022-7. doi:10.1016/j.cub.2005.04.050.
58. Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, et al. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet (2007) 39:857-64. doi:10.1038/ng2068.
59. Sironi M, Clerici M. The hygiene hypothesis: an evolutionary perspective. Microbes Infect (2010) 12:421-7. doi:10.1016/j.micinf.2010.02.002.
60. Hemmingsen SM, Woolford C, van der Vies SM, Tilly K, Dennis DT, Georgopoulos CP, et al. Homologous plant and bacterial proteins chaperone oligomeric protein assembly. Nature (1988) 333:330-4. doi:10.1038/333330a0.
61. Karlin S, Brocchieri L. Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution. Proc Natl Acad Sci U S A (2000) 97:11348-53. doi:10.1073/pnas.97.21.11348.
62. Cohen IR, Young DB. Autoimmunity, microbial immunity and the immunological homunculus. Immunol Today (1991) 12:105-10. doi:10.1016/0167-5699(91)90093-9.
63. Cohen IR. Autoimmunity to hsp65 and the immunologic paradigm. Adv Intern Med (1992) 37:295-311.
64. Cohen IR. Real and artificial immune systems: computing the state of the body. Nat Rev Immunol (2007) 7:569-74. doi:10.1038/nri2102.
65. Kaufmann SH. Heat shock proteins and the immune response. Immunol Today (1990) 11:129-36. doi:10.1016/0167-5699(90)90050-J.
66. Kaufmann SH, Väth U, Thole JE, Van Embden JD, Emmrich F. Enumeration of T cells reactive with Mycobacterium tuberculosis organisms and specific for the recombinant mycobacterial 64-kDa protein. Eur J Immunol (1987) 17:351-7. doi:10.1002/eji.1830170308.
67. Sanchez-Campillo M, Bini L, Comanducci M, Raggiaschi R, Marzocchi B, Pallini V, et al. Identification of immunoreactive proteins of Chlamydia trachomatis by Western blot analysis of a two-dimensional electrophoresis map with patient sera. Electrophoresis (1999) 20:2269-79. doi:10.1002/(SICI)1522-2683(19990801)20:11<2269::AID-ELPS2269>3.0.CO;2-D.
68. Matthews RC, Maresca B, Burnie JP, Cardona A, Carratu L, Conti S, et al. Stress proteins in fungal diseases. Med Mycol (1998) 36(Suppl 1):45-51.
69. Kapp C. WHO warns of microbial threat. Lancet (1999) 353:2222. doi:10.1016/S0140-6736(05)76281-4.
70. Guarner F, Bourdet-Sicard R, Brandtzaeg P, Gill HS, McGuirk P, van Eden W, et al. Mechanisms of disease: the hygiene hypothesis revisited. Nat Clin Pract Gastroenterol Hepatol (2006) 3:275-84. doi:10.1038/ncpgasthep0471.
71. Strachan DP. Allergy and family size: a riddle worth solving. Clin Exp Allergy (1997) 27:235-6. doi:10.1111/j.1365-2222.1997.tb00699.x.
72. Strachan DP. Hay fever, hygiene, and household size. BMJ (1989) 299:1259-60. doi:10.1136/bmj.299.6710.1259.
73. Sakaguchi S, Wing K, Onishi Y, Prieto-Martin P, Yamaguchi T. Regulatory T cells: how do they suppress immune responses? Int Immunol (2009) 21:1105-11. doi:10.1093/intimm/dxp095.
74. Rook GA. Review series on helminths, immune modulation and the hygiene hypothesis: the broader implications of the hygiene hypothesis. Immunology (2009) 126:3-11. doi:10.1111/j.1365-2567.2008.03007.x.
75. Pennington R, Gatenbee C, Kennedy B, Harpending H, Cochran G. Group differences in proneness to inflammation. Infect Genet Evol (2009) 9:1371-80. doi:10.1016/j.meegid.2009.09.017.
76. Ward AE, Rosenthal BM. Evolutionary responses of innate immunity to adaptive immunity. Infect Genet Evol (2014) 21:492-6. doi:10.1016/j.meegid.2013.12.021.
77. Laayouni H, Oosting M, Luisi P, Ioana M, Alonso S, Ricano-Ponce I, et al. Convergent evolution in European and Rroma populations reveals pressure exerted by plague on toll-like receptors. Proc Natl Acad Sci U S A (2014) 111:2668-73. doi:10.1073/pnas.1317723111.
78. Fornarino S, Laval G, Barreiro LB, Manry J, Vasseur E, Quintana-Murci L. Evolution of the TIR domain-containing adaptors in humans: swinging between constraint and adaptation. Mol Biol Evol (2011) 28:3087-97. doi:10.1093/molbev/msr137.
79. Franceschi C, Bonafe M, Valensin S. Human immunosenescence: the prevailing of innate immunity, the failing of clonotypic immunity, and the filling of immunological space. Vaccine (2000) 18:1717-20. doi:10.1016/S0264-410X(99)00513-7.
80. + T cells. Exp Gerontol (2004) 39:1233-43. doi:10.1016/j.exger.2004.04.004.
81. + subsets. Int Immunol (1998) 10:1281-8. doi:10.1093/intimm/10.9.1281.
82. Tieri P, Grignolio A, Zaikin A, Mishto M, Remondini D, Castellani G, et al. Network, degeneracy and bow tie. Integrating paradigms and architectures to grasp the complexity of the immune system. Theor Biol Med Model (2010) 7:32. doi:10.1186/1742-4682-7-32.
83. Edelman G, Gally J. Degeneracy and complexity in biological systems. Proc Natl Acad Sci USA (2001) 98:13763-8. doi:10.1073/pnas.231499798.
84. Wucherpfennig K, Gagnon E, Call M, Huseby E, Call M. Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling. Cold Spring Harb Perspect Biol (2010) 2:a005140. doi:10.1101/cshperspect.a005140.
85. Wucherpfennig KW, Allen PM, Celada F I, Cohen R, De Boer R, Garcia KC, et al. Polyspecificity of T cell and B cell receptor recognition. Semin Immunol (2007) 19:216-24. doi:10.1016/j.smim.2007.02.012.
86. Zitvogel L, Kepp O, Kroemer G. Decoding cell death signals in inflammation and immunity. Cell (2010) 140:798-804. doi:10.1016/j.cell.2010.02.015.
87. Krysko DV, Agostinis P, Krysko O, Garg AD, Bachert C, Lambrecht BN, et al. Emerging role of damage-associated molecular patterns derived from mitochondria in inflammation. Trends Immunol (2011) 32:157-64. doi:10.1016/j.it.2011.01.005.
88. Zhang Q, Raoof M, Chen Y, Sumi Y, Sursal T, Junger W, et al. Circulating mitochondrial DAMPs cause inflammatory responses to injury. Nature (2010) 464:104-7. doi:10.1038/nature08780.
89. Jones DE. Autoantigens in primary biliary cirrhosis. J Clin Pathol (2000) 53:813-21. doi:10.1136/jcp.53.11.813.
90. Pinti M, Cevenini E, Nasi M, De Biasi S, Salvioli S, Monti D, et al. Circulating mitochondrial DNA increases with age and is a familiar trait: implications for "inflamm-aging". Eur J Immunol (2014). doi:10.1002/eji.201343921.
91. la Sala A, Ferrari D, Di Virgilio F, Idzko M, Norgauer J, Girolomoni G. Alerting and tuning the immune response by extracellular nucleotides. J Leukoc Biol (2003) 73:339-43. doi:10.1189/jlb.0802418.
92. Haskó G, Kuhel DG, Németh ZH, Mabley JG, Stachlewitz RF, Virág L, et al. Inosine inhibits inflammatory cytokine production by a posttranscriptional mechanism and protects against endotoxin-induced shock. J Immunol (2000) 164:1013-9.
93. la Sala A, Ferrari D, Corinti S, Cavani A, Di Virgilio F, Girolomoni G. Extracellular ATP induces a distorted maturation of dendritic cells and inhibits their capacity to initiate Th1 responses. J Immunol (2001) 166:1611-7.
94. la Sala A, Sebastiani S, Ferrari D, Di Virgilio F, Idzko M, Norgauer J, et al. Dendritic cells exposed to extracellular adenosine triphosphate acquire the migratory properties of mature cells and show a reduced capacity to attract type 1 T lymphocytes. Blood (2002) 99:1715-22. doi:10.1182/blood.V99.5.1715.
95. Hodgkinson CP, Patel K, Ye S. Functional toll-like receptor 4 mutations modulate the response to fibrinogen. Thromb Haemost (2008) 100:301-7. doi:10.1160/TH08-03-0179.
96. Kawai T, Akira S. The role of pattern-recognition receptors in innate immunity: update on toll-like receptors. Nat Immunol (2010) 11:373-84. doi:10.1038/ni.1863.
97. van der Heijden PJ, Stok W, Bianchi AT. Contribution of immunoglobulin-secreting cells in the murine small intestine to the total 'background' immunoglobulin production. Immunology (1987) 62:551-5.
98. Menezes JS, Mucida DS, Cara DC, Alvarez-Leite JI, Russo M, Vaz NM, et al. Stimulation by food proteins plays a critical role in the maturation of the immune system. Int Immunol (2003) 15:447-55. doi:10.1093/intimm/dxg043.
99. Husby S, Jensenius JC, Svehag SE. Passage of undegraded dietary antigen into the blood of healthy adults. Quantification, estimation of size distribution, and relation of uptake to levels of specific antibodies. Scand J Immunol (1985) 22:83-92. doi:10.1111/j.1365-3083.1985.tb01862.x.
100. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science (2006) 312:1355-9. doi:10.1126/science.1124234.
101. Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5:e156. doi:10.1371/journal.pbio.0050156.
102. Candela M, Maccaferri S, Turroni S, Carnevali P, Brigidi P. Functional intestinal microbiome, new frontiers in prebiotic design. Int J Food Microbiol (2010) 140:93-101. doi:10.1016/j.ijfoodmicro.2010.04.017.
103. Hill DA, Artis D. Intestinal bacteria and the regulation of immune cell homeostasis. Annu Rev Immunol (2010) 28:623-67. doi:10.1146/annurev-immunol-030409-101330.
104. Lee YK, Menezes JS, Umesaki Y, Mazmanian SK. Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci U S A (2011) 108(Suppl 1):4615-22. doi:10.1073/pnas.1000082107.
105. Moog F. The lining of the small intestine. Sci Am (1981) 245:154-8. doi:10.1038/scientificamerican1181-154.
106. Alpan O, Rudomen G, Matzinger P. The role of dendritic cells, B cells, and M cells in gut-oriented immune responses. J Immunol (2001) 166:4843-52.
107. Macpherson AJ, McCoy KD, Johansen FE, Brandtzaeg P. The immune geography of IgA induction and function. Mucosal Immunol (2008) 1:11-22. doi:10.1038/mi.2007.6.
108. Faria AM, Weiner HL. Oral tolerance. Immunol Rev (2005) 206:232-59. doi:10.1111/j.0105-2896.2005.00280.x.
109. Richman LK, Chiller JM, Brown WR, Hanson DG, Vaz NM. Enterically induced immunologic tolerance. I. Induction of suppressor T lymphoyctes by intragastric administration of soluble proteins. J Immunol (1978) 121:2429-34.
110. Faria AM, Weiner HL. Oral tolerance: therapeutic implications for autoimmune diseases. Clin Dev Immunol (2006) 13:143-57. doi:10.1080/17402520600876804.
111. Mestecky J, Husby S, Moldoveanu Z, Waldo FB, van den Wall Bake AW, Elson CO. Induction of tolerance in humans: effectiveness of oral and nasal immunization routes. Ann N Y Acad Sci (1996) 778:194-201. doi:10.1111/j.1749-6632.1996.tb21128.x.
112. Andrade MC, Menezes JS, Cassali GD, Martins-Filho OA, Cara DC, Faria AM. Alcohol-induced gastritis prevents oral tolerance induction in mice. Clin Exp Immunol (2006) 146:312-22. doi:10.1111/j.1365-2249.2006.03207.x.
113. Round JL, O'Connell RM, Mazmanian SK. Coordination of tolerogenic immune responses by the commensal microbiota. J Autoimmun (2010) 34:J220-5. doi:10.1016/j.jaut.2009.11.007.
114. Coombes JL, Siddiqui KR, Arancibia-Carcamo CV, Hall J, Sun CM, Belkaid Y, et al. A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-beta and retinoic acid-dependent mechanism. J Exp Med (2007) 204:1757-64. doi:10.1084/jem.20070590.
115. Mucida D, Park Y, Kim G, Turovskaya O, Scott I, Kronenberg M, et al. Reciprocal TH17 and regulatory T cell differentiation mediated by retinoic acid. Science (2007) 317:256-60. doi:10.1126/science.1145697.
116. Castro-Junior CJ, Milano J, Souza AH, Silva JF, Rigo FK, Dalmolin G, et al. Pha1β toxin prevents capsaicin-induced nociceptive behavior and mechanical hypersensitivity without acting on TRPV1 channels. Neuropharmacology (2013) 71:237-46. doi:10.1016/j.neuropharm.2013.04.001.
117. Martinez C, Pereira P, Bernabé R, Bandeira A, Larsson EL, Cazenave PA, et al. Internal complementarities in the immune system: regulation of the expression of helper T-cell idiotypes. Proc Natl Acad Sci U S A (1984) 81:4520-3. doi:10.1073/pnas.81.14.4520.
118. Avrameas S, Guilbert B, Dighiero G. Natural antibodies against tubulin, actin myoglobin, thyroglobulin, fetuin, albumin and transferrin are present in normal human sera, and monoclonal immunoglobulins from multiple myeloma and Waldenström's macroglobulinemia may express similar antibody specificities. Ann Immunol (Paris) (1981) 132C:231-6.
119. Avrameas S, Selmi C. Natural autoantibodies in the physiology and pathophysiology of the immune system. J Autoimmun (2013) 41:46-9. doi:10.1016/j.jaut.2013.01.006.
120. Casali P, Schettino EW. Structure and function of natural antibodies. Curr Top Microbiol Immunol (1996) 210:167-79.
121. Macpherson AJ, Gatto D, Sainsbury E, Harriman GR, Hengartner H, Zinkernagel RM. A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science (2000) 288:2222-6. doi:10.1126/science.288.5474.2222.
122. Sutherland DB, Fagarasan S. IgA synthesis: a form of functional immune adaptation extending beyond gut. Curr Opin Immunol (2012) 24:261-8. doi:10.1016/j.coi.2012.03.005.
123. Quan CP, Berneman A, Pires R, Avrameas S, Bouvet JP. Natural polyreactive secretory immunoglobulin A autoantibodies as a possible barrier to infection in humans. Infect Immun (1997) 65:3997-4004.
124. Cebula A, Seweryn M, Rempala GA, Pabla SS, McIndoe RA, Denning TL, et al. Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota. Nature (2013) 497:258-62. doi:10.1038/nature12079.
125. Cebra JJ. Influences of microbiota on intestinal immune system development. Am J Clin Nutr (1999) 69:1046S-51S.
126. Guigoz Y, Doré J, Schiffrin EJ. The inflammatory status of old age can be nurtured from the intestinal environment. Curr Opin Clin Nutr Metab Care (2008) 11:13-20. doi:10.1097/MCO.0b013e3282f2bfdf.
127. Schiffrin EJ, Morley JE, Donnet-Hughes A, Guigoz Y. The inflammatory status of the elderly: the intestinal contribution. Mutat Res (2010) 690:50-6. doi:10.1016/j.mrfmmm.2009.07.011.
128. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One (2010) 5:e10667. doi:10.1371/journal.pone.0010667.
129. Eberl G. A new vision of immunity: homeostasis of the superorganism. Mucosal Immunol (2010) 3:450-60. doi:10.1038/mi.2010.20.
130. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol (2007) 5:e177. doi:10.1371/journal.pbio.0050177.
131. Biagi E, Candela M, Fairweather-Tait S, Franceschi C, Brigidi P. Aging of the human metaorganism: the microbial counterpart. Age (Dordr) (2012) 34:247-67. doi:10.1007/s11357-011-9217-5.
132. Cohn M. Degeneracy, mimicry and crossreactivity in immune recognition. Mol Immunol (2005) 42:651-5. doi:10.1016/j.molimm.2004.09.010.
133. Acuto O, Di Bartolo V, Michel F. Tailoring T-cell receptor signals by proximal negative feedback mechanisms. Nat Rev Immunol (2008) 8:699-712. doi:10.1038/nri2397.
134. Ishizuka J, Grebe K, Shenderov E, Peters B, Chen Q, Peng Y, et al. Quantitating T cell cross-reactivity for unrelated peptide antigens. J Immunol (2009) 183:4337-45. doi:10.4049/jimmunol.0901607.
135. Harkiolaki M, Holmes SL, Svendsen P, Gregersen JW, Jensen LT, McMahon R, et al. T cell-mediated autoimmune disease due to low-affinity crossreactivity to common microbial peptides. Immunity (2009) 30:348-57. doi:10.1016/j.immuni.2009.01.009.
136. Kanduc D, Stufano A, Lucchese G, Kusalik A. Massive peptide sharing between viral and human proteomes. Peptides (2008) 29:1755-66. doi:10.1016/j.peptides.2008.05.022.
137. Trost B, Kusalik A, Lucchese G, Kanduc D. Bacterial peptides are intensively present throughout the human proteome. Self Nonself (2010) 1:71-4. doi:10.4161/self.1.1.9588.
138. Schwartz AL, Ciechanover A. Targeting proteins for destruction by the ubiquitin system: implications for human pathobiology. Annu Rev Pharmacol Toxicol (2009) 49:73-96. doi:10.1146/annurev.pharmtox.051208.165340.
139. Li P, Gregg JL, Wang N, Zhou D, O'Donnell P, Blum JS, et al. Compartmentalization of class II antigen presentation: contribution of cytoplasmic and endosomal processing. Immunol Rev (2005) 207:206-17. doi:10.1111/j.0105-2896.2005.00297.x.
140. Sijts EJ, Kloetzel PM. The role of the proteasome in the generation of MHC class I ligands and immune responses. Cell Mol Life Sci (2011) 68:1491-502. doi:10.1007/s00018-011-0657-y.
141. Kloetzel PM. Antigen processing by the proteasome. Nat Rev Mol Cell Biol (2001) 2:179-87. doi:10.1038/35056572.
142. Basler M, Lauer C, Moebius J, Weber R, Przybylski M, Kisselev AF, et al. Why the structure but not the activity of the immunoproteasome subunit low molecular mass polypeptide 2 rescues antigen presentation. J Immunol (2012) 189:1868-77. doi:10.4049/jimmunol.1103592.
143. Chapiro J, Claverol S, Piette F, Ma W, Stroobant V, Guillaume B, et al. Destructive cleavage of antigenic peptides either by the immunoproteasome or by the standard proteasome results in differential antigen presentation. J Immunol (2006) 176:1053-61.
144. Guillaume B, Chapiro J, Stroobant V, Colau D, Van Holle B, Parvizi G, et al. Two abundant proteasome subtypes that uniquely process some antigens presented by HLA class I molecules. Proc Natl Acad Sci U S A (2010) 107:18599-604. doi:10.1073/pnas.1009778107.
145. Kincaid EZ, Che JW, York I, Escobar H, Reyes-Vargas E, Delgado JC, et al. Mice completely lacking immunoproteasomes show major changes in antigen presentation. Nat Immunol (2012) 13:129-35. doi:10.1038/ni.2203.
146. Dalet A, Stroobant V, Vigneron N, Van den Eynde BJ. Differences in the production of spliced antigenic peptides by the standard proteasome and the immunoproteasome. Eur J Immunol (2011) 41:39-46. doi:10.1002/eji.201040750.
147. Morel S, Levy F, Burlet-Schiltz O, Brasseur F, Probst-Kepper M, Peitrequin AL, et al. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells. Immunity (2000) 12:107-17. doi:10.1016/S1074-7613(00)80163-6.
148. Van den Eynde BJ, Morel S. Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome. Curr Opin Immunol (2001) 13:147-53. doi:10.1016/S0952-7915(00)00197-7.
149. Vigneron N, Van den Eynde BJ. Proteasome subtypes and the processing of tumor antigens: increasing antigenic diversity. Curr Opin Immunol (2011) 24:84-91. doi:10.1016/j.coi.2011.12.002.
150. Kniepert A, Groettrup M. The unique functions of tissue-specific proteasomes. Trends Biochem Sci (2014) 39:17-24. doi:10.1016/j.tibs.2013.10.004.
151. Bellavista E, Andreoli F, Parenti MD, Martucci M, Santoro A, Salvioli S, et al. Immunoproteasome in cancer and neuropathologies: a new therapeutic target? Curr Pharm Des (2013) 19:702-18. doi:10.2174/1381612811306040702.
152. Dalet A, Vigneron N, Stroobant V, Hanada K, Van den Eynde BJ. Splicing of distant peptide fragments occurs in the proteasome by transpeptidation and produces the spliced antigenic peptide derived from fibroblast growth factor-5. J Immunol (2010) 184:3016-24. doi:10.4049/jimmunol.0901277.
153. Liepe J, Mishto M, Textoris-Taube K, Janek K, Keller C, Henklein P, et al. The 20S proteasome splicing activity discovered by SpliceMet. PLoS Comput Biol (2010) 6:e1000830. doi:10.1371/journal.pcbi.1000830.
154. Dalet A, Robbins PF, Stroobant V, Vigneron N, Li YF, El-Gamil M, et al. An antigenic peptide produced by reverse splicing and double asparagine deamidation. Proc Natl Acad Sci U S A (2011) 108:E323-31. doi:10.1073/pnas.1101892108.
155. Hanada K, Yewdell JW, Yang JC. Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature (2004) 427:252-6. doi:10.1038/nature02240.
156. Vigneron N, Stroobant V, Chapiro J, Ooms A, Degiovanni G, Morel S, et al. An antigenic peptide produced by peptide splicing in the proteasome. Science (2004) 304:587-90. doi:10.1126/science.1095522.
157. Warren EH, Vigneron NJ, Gavin MA, Coulie PG, Stroobant V, Dalet A, et al. An antigen produced by splicing of noncontiguous peptides in the reverse order. Science (2006) 313:1444-7. doi:10.1126/science.1130660.
158. Mishto M, Goede A, Taube KT, Keller C, Janek K, Henklein P, et al. Driving forces of proteasome-catalyzed peptide splicing in yeast and humans. Mol Cell Proteomics (2012) 11:1008-23. doi:10.1074/mcp.M112.020164.
159. Rammensee HG. Immunology: protein surgery. Nature (2004) 427:203-4. doi:10.1038/427203a.
160. Rachmilewitz J. Glycosylation: an intrinsic sign of "danger". Self Nonself (2010) 1:250-4. doi:10.4161/self.1.3.12330.
161. Parekh R, Roitt I, Isenberg D, Dwek R, Rademacher T. Age-related galactosylation of the N-linked oligosaccharides of human serum IgG. J Exp Med (1988) 167:1731-6. doi:10.1084/jem.167.5.1731.
162. Shikata K, Yasuda T, Takeuchi F, Konishi T, Nakata M, Mizuochi T. Structural changes in the oligosaccharide moiety of human IgG with aging. Glycoconj J (1998) 15:683-9. doi:10.1023/A:1006936431276.
163. Yamada E, Tsukamoto Y, Sasaki R, Yagyu K, Takahashi N. Structural changes of immunoglobulin G oligosaccharides with age in healthy human serum. Glycoconj J (1997) 14:401-5. doi:10.1023/A:1018582930906.
164. Vanhooren V, Desmyter L, Liu XE, Cardelli M, Franceschi C, Federico A, et al. N-glycomic changes in serum proteins during human aging. Rejuvenation Res (2007) 10:521a-31a. doi:10.1089/rej.2007.0556.
165. Vanhooren V, Dewaele S, Libert C, Engelborghs S, De Deyn PP, Toussaint O, et al. Serum N-glycan profile shift during human ageing. Exp Gerontol (2010) 45:738-43. doi:10.1016/j.exger.2010.08.009.
166. Dall'Olio F, Vanhooren V, Chen CC, Slagboom PE, Wuhrer M, Franceschi C. N-glycomic biomarkers of biological aging and longevity: a link with inflammaging. Ageing Res Rev (2013) 12:685-98. doi:10.1016/j.arr.2012.02.002.
167. Ezekowitz RA. Agalactosyl IgG and mannose-binding proteins: biochemical nicety or pathophysiological paradigm? Nat Med (1995) 1:207-8. doi:10.1038/nm0395-207.
168. Malhotra R, Wormald MR, Rudd PM, Fischer PB, Dwek RA, Sim RB. Glycosylation changes of IgG associated with rheumatoid arthritis can activate complement via the mannose-binding protein. Nat Med (1995) 1:237-43. doi:10.1038/nm0395-237.
169. Dong X, Storkus WJ, Salter RD. Binding and uptake of agalactosyl IgG by mannose receptor on macrophages and dendritic cells. J Immunol (1999) 163:5427-34.
170. Yabe R, Tateno H, Hirabayashi J. Frontal affinity chromatography analysis of constructs of DC-SIGN, DC-SIGNR and LSECtin extend evidence for affinity to agalactosylated N-glycans. FEBS J (2010) 277:4010-26. doi:10.1111/j.1742-4658.2010.07792.x.
171. Dall'olio F, Vanhooren V, Chen CC, Slagboom PE, Wuhrer M, Franceschi C. N-glycomic biomarkers of biological aging and longevity: a link with inflammaging. Ageing Res Rev (2012) 12:685-98. doi:10.1016/j.arr.2012.02.002.
172. Gentilini D, Mari D, Castaldi D, Remondini D, Ogliari G, Ostan R, et al. Role of epigenetics in human aging and longevity: genome-wide DNA methylation profile in centenarians and centenarians' offspring. Age (Dordr) (2013) 35:1961-73. doi:10.1007/s11357-012-9463-1.
173. Bollati V, Schwartz J, Wright R, Litonjua A, Tarantini L, Suh H, et al. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mech Ageing Dev (2009) 130:234-9. doi:10.1016/j.mad.2008.12.003.
174. Fraga MF, Agrelo R, Esteller M. Cross-talk between aging and cancer: the epigenetic language. Ann N Y Acad Sci (2007) 1100:60-74. doi:10.1196/annals.1395.005.
175. Kim M, Long TI, Arakawa K, Wang R, Yu MC, Laird PW. DNA methylation as a biomarker for cardiovascular disease risk. PLoS One (2010) 5:e9692. doi:10.1371/journal.pone.0009692.
176. Moore LE, Pfeiffer RM, Poscablo C, Real FX, Kogevinas M, Silverman D, et al. Genomic DNA hypomethylation as a biomarker for bladder cancer susceptibility in the Spanish Bladder Cancer Study: a case-control study. Lancet Oncol (2008) 9:359-66. doi:10.1016/S1470-2045(08)70038-X.
177. Marchant A, Pihlgren M, Goetghebuer T, Weiss HA, Ota MO, Schlegel-Hauter SE, et al. Predominant influence of environmental determinants on the persistence and avidity maturation of antibody responses to vaccines in infants. J Infect Dis (2006) 193:1598-605. doi:10.1086/503775.
178. Nair N, Gans H, Lew-Yasukawa L, Long-Wagar AC, Arvin A, Griffin DE. Age-dependent differences in IgG isotype and avidity induced by measles vaccine received during the first year of life. J Infect Dis (2007) 196:1339-45. doi:10.1086/522519.
179. Ballestar E. Epigenetics lessons from twins: prospects for autoimmune disease. Clin Rev Allergy Immunol (2010) 39:30-41. doi:10.1007/s12016-009-8168-4.
180. Greer JM, McCombe PA. The role of epigenetic mechanisms and processes in autoimmune disorders. Biologics (2012) 6:307-27. doi:10.2147/BTT.S24067.
181. Hauch A, Heneghan J, Killackey M, Zhang R, Wands E, Buell J, et al. Living-related kidney transplant in two sets of Hla-identical twins. J Surg Transplant Sci (2013) 1:1003.
182. Mortensen LH, Maier AB, Slagbom PE, Pawelec G, Derhovanessian E, Petersen I, et al. Early-life environment influencing susceptibility to cytomegalovirus infection: evidence from the Leiden Longevity Study and the Longitudinal Study of Aging Danish Twins. Epidemiol Infect (2012) 140:835-41. doi:10.1017/S0950268811001397.
183. Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Perez-Losada M, et al. HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol (2011) 11:62. doi:10.1186/1471-2148-11-62.
184. Bisgard KM, Kao A, Leake J, Strebel PM, Perkins BA, Wharton M. Haemophilus influenzae invasive disease in the United States, 1994-1995: near disappearance of a vaccine-preventable childhood disease. Emerg Infect Dis (1998) 4:229-37. doi:10.3201/eid0402.980210.
185. Galil K, Singleton R, Levine OS, Fitzgerald MA, Bulkow L, Getty M, et al. Reemergence of invasive Haemophilus influenzae type b disease in a well-vaccinated population in remote Alaska. J Infect Dis (1999) 179:101-6. doi:10.1086/314569.
186. Heath PT. Haemophilus influenzae type b conjugate vaccines: a review of efficacy data. Pediatr Infect Dis J (1998) 17:S117-22. doi:10.1097/00006454-199809001-00005.
187. Krstic D, Madhusudan A, Doehner J, Vogel P, Notter T, Imhof C, et al. Systemic immune challenges trigger and drive Alzheimer-like neuropathology in mice. J Neuroinflammation (2012) 9:151. doi:10.1186/1742-2094-9-151.
188. Medzhitov R. Origin and physiological roles of inflammation. Nature (2008) 454:428-35. doi:10.1038/nature07201.
189. Gregor MF, Hotamisligil GS. Inflammatory mechanisms in obesity. Annu Rev Immunol (2011) 29:415-45. doi:10.1146/annurev-immunol-031210-101322.
190. Franceschi C, Capri M, Monti D, Giunta S, Olivieri F, Sevini F, et al. Inflammaging and anti-inflammaging: a systemic perspective on aging and longevity emerged from studies in humans. Mech Ageing Dev (2007) 128:92-105. doi:10.1016/j.mad.2006.11.016.
191. Martin OA, Redon CE, Dickey JS, Nakamura AJ, Bonner WM. Para-inflammation mediates systemic DNA damage in response to tumor growth. Commun Integr Biol (2011) 4:78-81. doi:10.4161/cib.4.1.13942.
192. Waddington CH. The epigenotype. 1942. Int J Epidemiol (2012) 41:10-3. doi:10.1093/ije/dyr184.
193. Baedke J. The epigenetic landscape in the course of time: Conrad Hal Waddington's methodological impact on the life sciences. Stud Hist Philos Biol Biomed Sci (2013) 44:756-73. doi:10.1016/j.shpsc.2013.06.001.