In autoimmune diseases, specific autoantibodies detected in patients’ sera areusually investigated by techniques using purified self-antigens and/or relevantpeptides from preselected targets. Such a restrictive view may be overcome by usingnew biological techniques to improve the diagnostic procedure. In a first step, weevaluated the impact of slight changes in target self-antigens related to posttranslationalmodifications, such as citrullination. In view of the weak resultsobtained, we further focused on some properties of the humoral response. Westudied the global self-reactive IgG antibody patterns against a large panel ofantigens derived from different target tissue extracts, especially brain antigens.Despite inter-individual differences, some reactivities allowed us to discriminatebetween the immune profiles of healthy individuals and those of patients. The selfreactivefootprints can also differentiate distinct autoimmune diseases and theirclinical forms. When we induced experimental autoimmune diseases, dynamicchanges occurred at the early phases with significant patterns related to pathogenicor protective events. A pathological distortion of the self-reactive antibodyrepertoire was also found in clinically isolated syndromes predictive of multiplesclerosis. Despite the predominant organ-specific symptoms in the clinical andexperimental situations studied, discriminant self-IgG reactivities mostly involvedubiquitous antigens rather than organ specific targets. Interestingly, discriminantIgM reactivities targeting both tissue-specific and ubiquitous antigens were alsospecifically observed in a T-dependent autoimmune disease (autoimmunepolyendocrinopathy syndrome), suggesting that T-cell-dependent but also T-cellindependentmechanisms might be involved in pathological changes in the selfreactiverepertoire. Although these footprints have allowed the identification ofuseful new biomarkers, their pathophysiological relevance remains to be defined.The molecular characterization of specific antigenic targets in autoimmune disease isa critical step towards understanding the pathological mechanisms and developinguseful diagnostic and therapeutic tools. In this perspective, we emphasize the needfor accurate methodological approaches. Our analysis of self-reactive footprintshighlights the potent role of complementary events related to putative dysfunctionin the innate/natural immune response in autoimmune diseases.
