Critical role of glycosylation in determining the length and structure of T cell epitopes

Immunome Research BioMed Central Research Open Access Critical role of glycosylation in determining the length and structure of T cell epitopes Tamás G Szabó1, Robin Palotai2, Péter Antal3, Itay Tokatly1, László Tóthfalusi4, Ole Lund5, György Nagy1,6, András Falus1,7 and Edit I Buzás*1 Address: 1Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4, Budapest, Hungary, 2Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, 1094 Budapest, Tűzoltó u 37-47, Hungary, 3Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Pf 91, 1521 Budapest, Hungary, 4Department of Pharmacodynamics, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary, 5Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, DK-2800 Kongens Lyngby, Denmark, 6Department of Rheumatology, Semmelweis University, Árpád fejedelem u 7, 1022 Budapest, Hungary and 7Research Group for Inflammation Biology and Immunogenomics, Hungarian Academy of Sciences, Nagyvárad tér 4, 1089 Budapest, Hungary Email: Tamás G Szabó - ; Robin Palotai - ; Péter Antal - ; Itay Tokatly - ; László Tóthfalusi - ; Ole Lund - ; György Nagy - ; András Falus - ; Edit I Buzás* - * Corresponding author Published: 24 September 2009 Immunome Research 2009, 5:4 doi:10.1186/1745-7580-5-4 Received: 13 July 2009 Accepted: 24 September 2009 This article is available from: http://www.immunome-research.com/content/5/1/4 © 2009 Szabó et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Using a combined in silico approach, we investigated the glycosylation of T cell epitopes and autoantigens. The present systems biology analysis was made possible by currently available databases (representing full proteomes, known human T cell epitopes and autoantigens) as well as glycosylation prediction tools. Results: We analyzed the probable glycosylation of human T cell epitope sequences extracted from the ImmuneEpitope Database. Our analysis suggests that in contrast to full length SwissProt entries, only a minimal portion of experimentally verified T cell epitopes is potentially N- or Oglycosylated (2.26% and 1.22%, respectively). Bayesian analysis of entries extracted from the Autoantigen Database suggests a correlation between N-glycosylation and autoantigenicity. The analysis of random generated sequences shows that glycosylation probability is also affected by peptide length. Our data suggest that the lack of peptide glycosylation, a feature that probably favors effective recognition by T cells, might have resulted in a selective advantage for short peptides to become T cell epitopes. The length of T cell epitopes is at the intersection of curves determining specificity and glycosylation probability. Thus, the range of length of naturally occurring T cell epitopes may ensure the maximum specificity with the minimal glycosylation probability. Conclusion: The findings of this bioinformatical approach shed light on fundamental factors that might have shaped adaptive immunity during evolution. Our data suggest that amino acid sequencebased hypo/non-glycosylation of certain segments of proteins might be substantial for determining T cell immunity/autoimmunity. Page 1 of 12 (page number not for citation purposes) Immunome Research 2009, 5:4 Background Antigen recognition by the immune system is decisive in the fight against pathogens and tumors. T lymphocytes recognize short, linear peptide fragments (epitopes) of antigenic proteins in context with self MHC. Posttranslational protein modifications (PTMs) generate an enormous variety of modified protein-derived epitopes. However, the significance of the posttranslationally modified antigenic determinants in shaping the receptor repertoire and determining the outcome of an immune response, is poorly understood. Within the category of PTMs, glycosylation is the most frequent one, and N-glycosylation is the most abundant form of glycosylation in humans. The relative backlog in the understanding of glycoimmunology (as compared to anti-protein immunology) might be explained, at least partially, by the substantial technical difficulties of carbohydrate synthesis and sequencing. Fortunately, in the past years there has been an explosion of progress in glycobiology and also in glycoimmunology. However, despite the extensive work, fundamental questions (such as the role of epitope glycosylation in T cell recognition) remain to be answered. Glycosylation of a peptide increases its space-filling capacity, thus, altering its interactive surface with the TCR or with MHC. While it is obvious that glycosylation creates new ligands for different B cell receptors, it is yet unclear how it affects epitope recognition by T cells. The aim of this study was to investigate the impact of glycosylation on T cell recognition. According to our hypothesis, glycosylated peptides are less likely to be recognized by T cells because of the glycan moiety. Indeed, there are sporadic experimental data suggesting that peptide glycosylation may interfere with epitope recognition through TCR [1-3]. On the other hand, alterations in protein glycosylation may also play a role also in the pathogenesis of autoimmune diseases. The molecular mimicry theory predicts that a cross-reactive immune response to similar or identical antigen determinants of microbial and human origin, may result in a pathological immune response directed against self antigens. In line with this concept, self-nonself discrimination of exact sequence matches is possible as long as the peptides are differentially glycosylated. Removal of the glycan moiety in pathological conditions might, however, result in a facilitated recognition of a formerly tolerated epitope. In order to test this possibility, we compared the glycosylation frequency of the complete human proteome with that of the experimentally verified T cell epitopes and the bacterial proteins with mimicry potential. The relevance of epitope glycosylation in the development of autoimmunity has been recently suggested by the finding that an increased substrate flux through N-glycosyla- http://www.immunome-research.com/content/5/1/4 tion machinery has a therapeutic effect in some autoimmune diseases [4]. Publicly available T cell epitope prediction approaches focus on binding of a given peptide to HLA and not to TCR. Furthermore, it has also been described recently that the currently available in silico tools are rather limited in their prediction efficiency, which also differs from allele to allele [5]. This study was motivated by (...truncated)