The autoimmune response in various connective tissue diseases such as systemic lupus erythematosus (SLE), Sjogren’s syndrome (SS) and scleroderma is directed toward autoantigens that most often are large cellular complexes composed of proteins, DNA and small nuclear RNAs. Particular sets of autoantibody specificities, directed against these autoantigens, are associated with each disease and constitute an invaluable tool diagnostic markers. The portion of a protein which is recognized by antibodies, called an antigenic determinant or epitope, can be used as a reliable substrate in autoantibody detection tests, which are not only a confirmation of the diagnosis, but may also point to a subset of the disease with a particular prognosis. Furthermore, titers of antibody directed toward a particular epitope may correlate with disease severity, and thus may help in disease management. On the other hand, B and T cell epitopes can be coupled to synthetic carriers so that the prepared constructs could mimic reconstituted antigens. These macromolecular, well defined, constructs can be successfully applied in immunoassays, and also in developing animal models and studying the induction and evolution of autoimmunity. The availability of peptides has stimulated a great number of investigations about the mechanism of epitope spreading, a diversification of B and/or T-cell inter or intramolecular responses, which ultimately can improve our understanding of autoimmunity. Design of peptide models and/or peptide-mimetics that could interrupt the MHC/CD4 interaction, or T-cell epitope analogues that could inhibit the T-cell/TCR recognition is another promising aspect that deserves our attention. Such peptide models could be utilized as immunoregulators leading thus to the development of drugs in autoimmune diseases. Following the molecular recognition approach, complementary epitopes deriving from reverse RNA transcription and translation may offer an alternative approach in treating autoimmune diseases.
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