Abstract
Major histocompatibility complexes (MHC) are expressed on antigen-presenting cells (APC) that display peptide antigens. This is a crucial step to activate a T-cell response. Since immunogenic ligand of MHC is closely related with autoimmunity, inflammatory diseases, and cancer, comprehensive analysis of MHC ligands (the so-called Ligandome) is essential to unveil disease pathogenesis. Recently, immunotherapies such as vaccination have been focused on as new therapies of cancer, HIV, and infectious diseases. Therefore, the importance of comprehensive analysis of MHC ligands is increasing. Mass spectrometry has been the core technology of ligand identification since the 1990s. The sensitivity of mass spectrometers has been improved dramatically in recent years; thus, it enables to identify MHC ligands in clinical materials. This chapter lays out the workflow of MHC ligand identification in clinical materials, especially human bronchoalveolar (BAL) cells. MHC-ligand complexes are enriched by immunoaffinity extraction and captured ligand peptides are identified by LC-MS/MS. MHC class II ligand in BAL cells is described in this text; however, this approach is applicable to MHC class I and other clinical materials such as tissues.
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References
Klein J (1986) Natural History of the Major Histocompatibility Complex, 99th edn. Wiley, New York
Rammensee HG (1995) Chemistry of peptides associated with MHC class I and class II molecules. Curr Opin Immunol 7:85–96
Chicz RM, Urban RG, Gorga JC, Vignali DA, Lane WS, Strominger JL (1993) Specificity and promiscuity among naturally processed peptides bound to HLA-DR alleles. J Exp Med 178:27–47
Dongre AR, Kovats S, deRoos P, McCormack AL, Nakagawa T, Paharkova-Vatchkova V, Eng J, Caldwell H, Yates JR 3rd, Rudensky AY (2001) In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. Eur J Immunol 31:1485–1494
Banchereau J, Palucka AK (2005) Dendritic cells as therapeutic vaccines against cancer. Nat Rev Immunol 5:296–306
Hunt DF, Michel H, Dickinson TA, Shabanowitz J, Cox AL, Sakaguchi K, Appella E, Grey HM, Sette A (1992) Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. Science 256:1817–1820
Kasuga K, Branca RM, Wahlstrom J, Wheelock AM, Eklund A, Grunewald J, Lehtio J (2011) High sensitivity approach for identification of MHC Class II-bound peptides from bronchoalveolar lavage cells in sarcoidosis patients. Am J Respir Crit Care Med 183:A6404
Horlock C, Stott B, Dyson J, Ogg G, McPherson T, Jones L, Sewell AK, Wooldridge L, Cole DK, Stebbing J, Savage P (2009) ELISPOT and functional T cell analyses using HLA mono-specific target cells. J Immunol Methods 350:150–160
Eklund A, Blaschke E (1986) Relationship between changed alveolar-capillary permeability and angiotensin converting enzyme activity in serum in sarcoidosis. Thorax 41:629–634
Wahlstrom J, Dengjel J, Winqvist O, Targoff I, Persson B, Duyar H, Rammensee HG, Eklund A, Weissert R, Grunewald J (2009) Autoimmune T cell responses to antigenic peptides presented by bronchoalveolar lavage cell HLA-DR molecules in sarcoidosis. Clin Immunol 133:353–363
Mano N, Abe K, Goto J (2006) Immunoaffinity extraction of a peptide modified by a small molecule. Anal Biochem 349:254–261
Friede T, Gnau V, Jung G, Keilholz W, Stevanovic S, Rammensee HG (1996) Natural ligand motifs of closely related HLA-DR4 molecules predict features of rheumatoid arthritis associated peptides. Biochim Biophys Acta 1316:85–101
Nag B, Passmore D, Deshpande SV, Clark BR (1992) In vitro maximum binding of antigenic peptides to murine MHC class II molecules does not always take place at the acidic pH of the in vivo endosomal compartment. J Immunol 148:369–372
Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G (2003) PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 17:2337–2342
Chen P, Rayner S, Hu KH (2011) Advances of bioinformatics tools applied in virus epitopes prediction. Virol Sin 26:1–7
Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50:213–219
Donnes P, Elofsson A (2002) Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3:25
Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101(26):9528–9533
Acknowledgments
Dr. Stefan Stevanović (Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany) and Dr. Rui Mamede Branca (Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory Stockholm) are gratefully acknowledged for helpful discussion. The author is a VINNMER fellow supported via VINNMER Marie Curie Chair—a VINNOVA programme cofounded by Marie Curie Actions.
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Kasuga, K. (2013). Comprehensive Analysis of MHC Ligands in Clinical Material by Immunoaffinity-Mass Spectrometry. In: Bäckvall, H., Lehtiö, J. (eds) The Low Molecular Weight Proteome. Methods in Molecular Biology, vol 1023. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7209-4_14
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DOI: https://doi.org/10.1007/978-1-4614-7209-4_14
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