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Purification and Identification of Naturally Presented MHC Class I and II Ligands

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Antigen Processing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1988))

Abstract

The large-scale and in-depth identification of MHC class I- and II-presented peptides is indispensable for gaining insight into the fundamental rules of immune recognition as well as for developing innovative immunotherapeutic approaches against cancer and other diseases. In this chapter we briefly review the existing strategies for the isolation of MHC-restricted peptides and provide a detailed protocol for the immunoaffinity purification of MHC class I- and II-presented peptides from primary tissues or cells.

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References

  1. Stevanovic S, Schild H (1999) Quantitative aspects of T cell activation—peptide generation and editing by MHC class I molecules. Semin Immunol 11(6):375–384

    Article  CAS  Google Scholar 

  2. Storkus WJ, Zeh HJ 3rd, Salter RD, Lotze MT (1993) Identification of T-cell epitopes: rapid isolation of class I-presented peptides from viable cells by mild acid elution. J Immunother Emphasis Tumor Immunol 14(2):94–103

    Article  CAS  Google Scholar 

  3. Lanoix J, Durette C, Courcelles M, Cossette E, Comtois-Marotte S, Hardy MP, Cote C, Perreault C, Thibault P (2018) Comparison of the MHC I immunopeptidome repertoire of B-cell lymphoblasts using two isolation methods. Proteomics:e1700251

    Google Scholar 

  4. Prilliman K, Lindsey M, Zuo Y, Jackson KW, Zhang Y, Hildebrand W (1997) Large-scale production of class I bound peptides: assigning a signature to HLA-B*1501. Immunogenetics 45(6):379–385

    Article  CAS  Google Scholar 

  5. Lazarus D, Weinstein-Marom H, Fishman S, Yossef R, Zuri D, Barnea E, Admon A, Margalit A, Gross G (2015) Efficient peptide recovery from secreted recombinant MHC-I molecules expressed via mRNA transfection. Immunol Lett 165(1):32–38

    Article  CAS  Google Scholar 

  6. Van Bleek GM, Nathenson SG (1990) Isolation of an endogenously processed immunodominant viral peptide from the class I H-2Kb molecule. Nature 348(6298):213–216

    Article  Google Scholar 

  7. Falk K, Rötzschke O, Stevanovic S, Jung G, Rammensee HG (1991) Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351(6324):290–296

    Article  CAS  Google Scholar 

  8. Di Marco M, Schuster H, Backert L, Ghosh M, Rammensee HG, Stevanovic S (2017) Unveiling the peptide motifs of HLA-C and HLA-G from naturally presented peptides and generation of binding prediction matrices. J Immunol 199(8):2639–2651

    Article  Google Scholar 

  9. Bassani-Sternberg M, Gfeller D (2016) Unsupervised HLA peptidome deconvolution improves ligand prediction accuracy and predicts cooperative effects in peptide-HLA interactions. J Immunol 197(6):2492–2499

    Article  CAS  Google Scholar 

  10. Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ (2017) Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction. Immunity 46(2):315–326

    Article  CAS  Google Scholar 

  11. Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50(3–4):213–219

    Article  CAS  Google Scholar 

  12. Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M (2017) NetMHCpan-4.0: improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. J Immunol 199(9):3360–3368

    Article  CAS  Google Scholar 

  13. Wahlström J, Dengjel J, Persson B, Duyar H, Rammensee HG, Stevanovic S, Eklund A, Weissert R, Grunewald J (2007) Identification of HLA-DR-bound peptides presented by human bronchoalveolar lavage cells in sarcoidosis. J Clin Invest 117(11):3576–3582

    Article  Google Scholar 

  14. Scholz E, Mestre-Ferrer A, Daura X, Garcia-Medel N, Carrascal M, James EA, Kwok WW, Canals F, Alvarez I (2016) A comparative analysis of the peptide repertoires of HLA-DR molecules differentially associated with rheumatoid arthritis. Arthritis Rheumatol 68(10):2412–2421

    Article  CAS  Google Scholar 

  15. Shiga H, Shioda T, Tomiyama H, Takamiya Y, Oka S, Kimura S, Yamaguchi Y, Gojoubori T, Rammensee HG, Miwa K, Takiguchi M (1996) Identification of multiple HIV-1 cytotoxic T-cell epitopes presented by human leukocyte antigen B35 molecules. AIDS 10(10):1075–1083

    CAS  PubMed  Google Scholar 

  16. Günther PS, Peper JK, Faist B, Kayser S, Hartl L, Feuchtinger T, Jahn G, Neuenhahn M, Busch DH, Stevanovic S, Dennehy KM (2015) Identification of a Novel Immunodominant HLA-B*07: 02-restricted adenoviral peptide epitope and its potential in adoptive transfer immunotherapy. J Immunother 38(7):267–275

    Article  Google Scholar 

  17. Berlin C, Kowalewski DJ, Schuster H, Mirza N, Walz S, Handel M, Schmid-Horch B, Salih HR, Kanz L, Rammensee HG, Stevanovic S, Stickel JS (2016) Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy. Leukemia 30(4):1003–1004

    Article  CAS  Google Scholar 

  18. Neidert MC, Schoor O, Trautwein C, Trautwein N, Christ L, Melms A, Honegger J, Rammensee HG, Herold-Mende C, Dietrich PY, Stevanovic S (2013) Natural HLA class I ligands from glioblastoma: extending the options for immunotherapy. J Neuro-Oncol 111(3):285–294

    Article  CAS  Google Scholar 

  19. Schuster H, Peper JK, Bösmüller HC, Röhle K, Backert L, Bilich T, Ney B, Löffler MW, Kowalewski DJ, Trautwein N, Rabsteyn A, Engler T, Braun S, Haen SP, Walz JS, Schmid-Horch B, Brucker SY, Wallwiener D, Kohlbacher O, Fend F, Rammensee HG, Stevanovic S, Staebler A, Wagner P (2017) The immunopeptidomic landscape of ovarian carcinomas. Proc Natl Acad Sci U S A 114(46):E9942–E9951

    Article  CAS  Google Scholar 

  20. Kowalewski DJ, Schuster H, Backert L, Berlin C, Kahn S, Kanz L, Salih HR, Rammensee HG, Stevanovic S, Stickel JS (2015) HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). Proc Natl Acad Sci U S A 112(2):E166–E175

    Article  CAS  Google Scholar 

  21. Walz S, Stickel JS, Kowalewski DJ, Schuster H, Weisel K, Backert L, Kahn S, Nelde A, Stroh T, Handel M, Kohlbacher O, Kanz L, Salih HR, Rammensee HG, Stevanovic S (2015) The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy. Blood 126(10):1203–1213

    Article  CAS  Google Scholar 

  22. Heidenreich F, Rucker-Braun E, Walz JS, Eugster A, Kuhn D, Dietz S, Nelde A, Tunger A, Wehner R, Link CS, Middeke JM, Stolzel F, Tonn T, Stevanovic S, Rammensee HG, Bonifacio E, Bachmann M, Zeis M, Ehninger G, Bornhauser M, Schetelig J, Schmitz M (2017) Mass spectrometry-based identification of a naturally presented receptor tyrosine kinase-like orphan receptor 1-derived epitope recognized by CD8(+) cytotoxic T cells. Haematologica 102(11):e460–e464

    Article  CAS  Google Scholar 

  23. Löffler MW, Chandran PA, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yanez VA, Mohr C, Sturm M, Nguyen HP, Riess O, Bauer P, Nahnsen S, Nadalin S, Zieker D, Glatzle J, Thiel K, Schneiderhan-Marra N, Clasen S, Bösmüller H, Fend F, Kohlbacher O, Gouttefangeas C, Stevanovic S, Königsrainer A, Rammensee HG (2016) Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient. J Hepatol 65(4):849–855

    Article  Google Scholar 

  24. Bassani-Sternberg M, Braunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, HB D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM (2016) Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun 7:13404

    Article  CAS  Google Scholar 

  25. Nelde A, Kowalewski DJ, Backert L, Schuster H, Werner JO, Klein R, Kohlbacher O, Kanz L, Salih HR, Rammensee HG, Stevanovic S, Walz JS (2018) HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy. Oncoimmunology 7(4):e1316438

    Article  Google Scholar 

  26. Barth SM, Schreitmüller CM, Proehl F, Oehl K, Lumpp LM, Kowalewski DJ, Di Marco M, Sturm T, Backert L, Schuster H, Stevanovic S, Rammensee HG, Planz O (2016) Characterization of the canine MHC Class I DLA-88*50101 peptide binding motif as a prerequisite for canine T cell immunotherapy. PLoS One 11(11):e0167017

    Article  Google Scholar 

  27. Chong C, Marino F, Pak H, Racle J, Daniel RT, Muller M, Gfeller D, Coukos G, Bassani-Sternberg M (2018) High-throughput and sensitive immunopeptidomics platform reveals profound interferongamma-mediated remodeling of the human leukocyte antigen (HLA) ligandome. Mol Cell Proteomics 17(3):533–548

    Article  CAS  Google Scholar 

  28. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372

    Article  CAS  Google Scholar 

  29. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10(4):1794–1805

    Article  CAS  Google Scholar 

  30. Eyrich B, Sickmann A, Zahedi RP (2011) Catch me if you can: mass spectrometry-based phosphoproteomics and quantification strategies. Proteomics 11(4):554–570

    Article  CAS  Google Scholar 

  31. Abelin JG, Trantham PD, Penny SA, Patterson AM, Ward ST, Hildebrand WH, Cobbold M, Bai DL, Shabanowitz J, Hunt DF (2015) Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry. Nat Protoc 10(9):1308–1318

    Article  CAS  Google Scholar 

  32. Barnstable CJ, Bodmer WF, Brown G, Galfre G, Milstein C, Williams AF, Ziegler A (1978) Production of monoclonal antibodies to group A erythrocytes, HLA and other human cell surface antigens-new tools for genetic analysis. Cell 14(1):9–20

    Article  CAS  Google Scholar 

  33. Parham P, Brodsky FM (1981) Partial purification and some properties of BB7.2. A cytotoxic monoclonal antibody with specificity for HLA-A2 and a variant of HLA-A28. Hum Immunol 3(4):277–299

    Article  CAS  Google Scholar 

  34. Rebai N, Malissen B (1983) Structural and genetic analyses of HLA class I molecules using monoclonal xenoantibodies. Tissue Antigens 22(2):107–117

    Article  CAS  Google Scholar 

  35. Berger AE, Davis JE, Cresswell P (1982) Monoclonal antibody to HLA-A3. Hybridoma 1(2):87–90

    Article  CAS  Google Scholar 

  36. Goldman JM, Hibbin J, Kearney L, Orchard K, Th'ng KH (1982) HLA-DR monoclonal antibodies inhibit the proliferation of normal and chronic granulocytic leukaemia myeloid progenitor cells. Br J Haematol 52(3):411–420

    Article  CAS  Google Scholar 

  37. Pawelec G, Ziegler A, Wernet P (1985) Dissection of human allostimulatory determinants with cloned T cells: stimulation inhibition by monoclonal antibodies TU22, 34, 35, 36, 37, 39, 43, and 58 against distinct human MHC class II molecules. Hum Immunol 12(3):165–176

    Article  CAS  Google Scholar 

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Correspondence to Stefan Stevanović .

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Nelde, A., Kowalewski, D.J., Stevanović, S. (2019). Purification and Identification of Naturally Presented MHC Class I and II Ligands. In: van Endert, P. (eds) Antigen Processing. Methods in Molecular Biology, vol 1988. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9450-2_10

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  • DOI: https://doi.org/10.1007/978-1-4939-9450-2_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9449-6

  • Online ISBN: 978-1-4939-9450-2

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