Summary
CD4+ T-helper cells recognize antigenic peptides presented by MHC class II molecules. The binding of the nominal peptide to the MHC class II allele is dependent on the amino acid sequence of the peptide as well as on amino acid (aa) residues in the peptide binding groove of the MHC class II allele. MHC class II alleles can either be associated with protection or susceptibility to disease (coined as “MHC class II-associated diseases”). A detailed knowledge about the nature, composition, and biochemical interaction of peptides with MHC class II molecules aids to link individual peptide species with MHC class II presentation and ultimately with CD4+ T-cell recognition. Several methods have been described to identify potential MHC class II candidate binding peptides. We present here a high content screening for MHC class II (HLA-DR) binding to a peptide library in a chip-format. Binding of soluble MHC class II molecules to individual peptides can be visualized using an anti-DR directed monoclonal antibody (mAb). Positive events (MHC class II/peptide complexes) are normalized and available for pattern analysis.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Topalian, S. L. (1994) MHC class II restricted tumor antigens and the role of CD4+ T-cells in cancer immunotherapy. Curr. Opin. Immunol. 6, 741–745.
Southwood, S., Sidney, J., Kondo, A., del Guercio, M. F., Appella, E., Hoffman, S., Kubo, R. T., Chesnut, R. W., Grey, H. M., and Sette, A. (1998) Several common HLA-DR types share largely overlapping peptide binding repertoires. J. Immunol. 160, 3363–3373.
Sinigaglia, F. and Hammer, J. (1994) Defining rules for the peptide-MHC class II interaction. Curr. Opin. Immunol. 6, 52–56.
Sette, A., Adorini, L., Colon, S. M., Buus, S., and Grey, H. M. (1989) Capacity of intact proteins to bind to MHC class II molecules. J. Immunol. 143, 1265–1267.
Stern, L. J., Brown, J. H., Jardetzky, T. S., Gorga, J. C., Urban, R. G., Strominger, J. L., and Wiley, D. C. (1994) Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368, 215–221.
Sercarz, E. E. and Maverakis, E. (2003) Mhc-guided processing: binding of large antigen fragments. Nat. Rev. Immunol. 3, 621–629.
Gaudebout, P., Zeliszewski, D., Golvano, J. J., Pignal, C., Le Gac, S., Borras-Cuesta, F., and Sterkers, G. (1997) Binding analysis of 95 HIV gp120 peptides to HLA-DR1101 and -DR0401 evidenced many HLA-class II binding regions on gp120 and suggested several promiscuous regions. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 14, 91–101.
Kobayashi, H., Wood, M., Song, Y., Appella, E., and Celis, E. (2000) Defining promiscuous MHC class II helper T-cell epitopes for the HER2/neu tumor antigen. Cancer Res. 60, 5228–5236.
Panina-Bordignon, P., Tan, A., Termijtelen, A., Demotz, S., Corradin, G., and Lanzavecchia, A. (1989) Universally immunogenic T-cell epitopes: promiscuous binding to human MHC class II and promiscuous recognition by T-cells. Eur. J. Immunol. 19, 2237–2242.
Sinigaglia, F., Guttinger, M., Kilgus, J., Doran, D. M., Matile, H., Etlinger, H., Trzeciak, A., Gillessen, D., and Pink, J. R. (1988) A malaria T-cell epitope recognized in association with most mouse and human MHC class II molecules. Nature 336, 778–780.
Hammer, J., Valsasnini, P., Tolba, K., Bolin, D., Higelin, J., Takacs, B., and Sinigaglia, F. (1993) Promiscuous and allele-specific anchors in HLA-DR-binding peptides. Cell 74, 197–203.
Hammer, J., Takacs, B., and Sinigaglia, F. (1992) Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. J. Exp. Med. 176, 1007–1013.
Siebold, C., Hansen, B. E., Wyer, J. R., Harlos, K., Esnouf, R. E., Svejgaard, A., Bell, J. I., Strominger, J. L., Jones, E. Y., and Fugger, L.(2004) Crystal structure of HLA-DQ0602 that protects against type 1 diabetes and confers strong susceptibility to narcolepsy. Proc. Natl. Acad. Sci. U. S. A. 101, 1999–2004.
Dengjel, J., Rammensee, H. G., and Stevanovic, S. (2005) Glycan side chains on naturally presented MHC class II ligands. J. Mass Spectrom. 40, 100–104.
Wahlstrom, J., Dengjel, J., Persson, B., Duyar, H., Rammensee, H. G., Stevanovic, S., Eklund, A., Weissert, R., and Grunewald, J. (2007) Identification of HLA-DR-bound peptides presented by human bronchoalveolar lavage cells in sarcoidosis. J. Clin. Invest. 117, 3576–3582.
Newman, M. J., Livingston, B., McKinney, D. M., Chesnut, R. W., and Sette, A. (2002) T-lymphocyte epitope identification and their use in vaccine development for HIV-1. Front. Biosci. 7, d1503–d1515.
Schaeffer, E. B., Sette, A., Johnson, D. L., Bekoff, M. C., Smith, J. A., Grey, H. M., and Buus, S. (1989) Relative contribution of “determinant selection” and “holes in the T-cell repertoire” to T-cell responses. Proc. Natl. Acad. Sci. U. S. A. 86, 4649–4653.
Sette, A. and Grey, H. M. (1992) Chemistry of peptide interactions with MHC proteins. Curr. Opin. Immunol. 4, 79–86.
Altfeld, M. A., Livingston, B., Reshamwala, N., Nguyen, P. T., Addo, M. M., Shea, A., Newman, M., Fikes, J., Sidney, J., Wentworth, P., Chesnut, R., Eldridge, R. L., Rosenberg, E. S., Robbins, G. K., Brander, C., Sax, P. E., Boswell, S., Flynn, T., Buchbinder, S., Goulder, P. J., Walker, B. D., Sette, A., and Kalams, S. A. (2001) Identification of novel HLA-A2-restricted human immunodeficiency virus type 1-specific cytotoxic T-lymphocyte epitopes predicted by the HLA-A2 supertype peptide-binding motif. J. Virol. 75, 1301–1311.
Tong, J. C., Tan, T. W., and Ranganathan, S. (2007) Methods and protocols for prediction of immunogenic epitopes. Brief. Bioinform. 8, 96–108.
Zhu, S., Udaka, K., Sidney, J., Sette, A., Aoki-Kinoshita, K. F., and Mamitsuka, H. (2006) Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics 22, 1648–1655.
DeLuca, D. S., Khattab, B., and Blasczyk, R. (2007) A modular concept of HLA for comprehensive peptide binding prediction. Immunogenetics 59, 25–35.
Mallios, R. R. (2003) A consensus strategy for combining HLA-DR binding algorithms. Hum. Immunol. 64, 852–856.
Novak, E. J., Liu, A. W., Nepom, G. T., and Kwok, W. W. (1999) MHC class II tetramers identify peptide-specific human CD4(+) T-cells proliferating in response to influenza A antigen. J. Clin. Invest. 104, R63–R67.
Ye, M., Kasey, S., Khurana, S., Nguyen, N. T., Schubert, S., Nugent, C. T., Kuus-Reichel, K., and Hampl, J. (2004) MHC class II tetramers containing influenza hemagglutinin and EBV EBNA1 epitopes detect reliably specific CD4(+) T-cells in healthy volunteers. Hum. Immunol. 65, 507–513.
Nahtman, T., Jernberg, A., Mahdavifar, S., Zerweck, J., Schutkowski, M., Maeurer, M., and Reilly, M. (2007) Validation of peptide epitope microarray experiments and extraction of quality data. J. Immunol. Methods 328, 1–13.
Acknowledgements
We thank Marie Reilly, Davide Valentini and Yen Ngo, MEB, Karolinska Institutet for statistical analysis, Emmanuel Gautherot and Felix Montero at Beckman Coulter Marseille, for HLA-DR molecules and JPT Peptide Technologies for peptide microarrays.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Gaseitsiwe, S., Maeurer, M.J. (2009). Identification of MHC Class II Binding Peptides: Microarray and Soluble MHC Class II Molecules. In: Schutkowski, M., Reineke, U. (eds) Epitope Mapping Protocols. Methods in Molecular Biology™, vol 524. Humana Press. https://doi.org/10.1007/978-1-59745-450-6_30
Download citation
DOI: https://doi.org/10.1007/978-1-59745-450-6_30
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-934115-17-6
Online ISBN: 978-1-59745-450-6
eBook Packages: Springer Protocols