Abstract
Autoimmune diseases affect approximately 1 in 21 persons in the United States. Treatment often requires long-term cytotoxic therapy. How and why these deleterious diseases occur is unclear. A serendipitous finding in our laboratory using serum from patients with autoimmune vasculitis led us to develop the theory of autoantigen complementarity, a novel concept that may elucidate the etiological and pathogenetic mechanisms underlying autoimmune disease in general. The theory proposes that the inciting immunogen that elicits a cascade of immunological events is not the self-antigen (the autoantigen) or its mimic but rather a protein that is complementary in surface structure to the autoantigen; that is, a protein homologous or identical to the amino acid sequence of translated antisense RNA from the noncoding strand of the autoantigen gene. The cascade begins when this complementary protein initiates the production of antibodies that in turn elicit an anti-antibody or anti-idiotypic response. These anti-idiotypic antibodies can now react with the autoantigen. Strikingly, homology search of complementary proteins yields microbial and fungal proteins, thus indicating that invading micro-organisms can deliver the inciting immunogen. Curiously, approximately 50% of our patients transcribe the complementary protein’s antisense RNA. If it transpires that these aberrant RNAs are translated, the complementary protein would be produced by the individual. Here we review published research investigating complementary proteins, anti-idiotypic immune responses, and antisense transcripts, all of which support complementary proteins as initiators of autoimmune disease. In addition, we provide possible microbial and/or fungal organisms that may incite some of the most studied autoimmune diseases. Lastly, we propose mechanisms by which cell-mediated autoimmunity can be triggered by autoantigen complementarity. Based on our data and the contributions of the researchers described in this review, identification of proteins complementary to autoantigens is likely to be informative in most autoimmune diseases. This vein of study is in the early phases; however, we expect “autoantigen complementarity” is an underlying mechanism in many autoimmune diseases.


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Abbreviations
- ANCA :
-
Anti-neutrophil cytoplasmic autoantibody
- APC :
-
Antigen-presenting cell
- BCR :
-
B-cell receptor
- BP :
-
Bullous pemphigoid
- CDR :
-
Complementarity-determining region
- GBM :
-
Glomerular basement membrane
- GD :
-
Graves’ disease
- HT :
-
Hashimoto’s thyroiditis
- MPO :
-
Myeloperoxidase
- NAT :
-
Natural antisense transcript
- PAT :
-
Pathologic antisense transcript
- PR3 :
-
Proteinase 3
- SLE :
-
Systemic lupus erythematosus
- TCR :
-
T-cell receptor
- T H :
-
T-helper cell
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Acknowledgements
The authors thank the collaborators involved in those studies described here and those that are ongoing in our laboratory, including Alex Tropsha, Ph.D., Ruchir Shah, Thomas Hellmark, Ph.D., Marten Segelmark, M.D., Ph.D., Jorgen Wieslander, Ph.D., Anna Sediva, M.D., Ph.D., and Charles Carter, Ph.D. We also thank the many investigators referenced in this review that contributed to advancements in the field of complementary proteins, the idiotypic network, antisense transcripts, and autoimmunity.
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This review is based on information from our own laboratory and that of others obtained by a recent Medline search with “complementary peptide/protein,” “antisense transcript,” and “autoimmunity” with or without “epitope” as keywords
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Pendergraft, W.F., Pressler, B.M., Jennette, J.C. et al. Autoantigen complementarity: a new theory implicating complementary proteins as initiators of autoimmune disease. J Mol Med 83, 12–25 (2005). https://doi.org/10.1007/s00109-004-0615-3
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DOI: https://doi.org/10.1007/s00109-004-0615-3

