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A combined approach of human leukocyte antigen ligandomics and immunogenicity analysis to improve peptide-based cancer immunotherapy

  • Focussed Research Review
  • Published:
Cancer Immunology, Immunotherapy Aims and scope Submit manuscript

Abstract

The breakthrough development of immune checkpoint inhibitors as clinically effective novel therapies demonstrates the potential of cancer immunotherapy. The identification of suitable targets for specific immunotherapy, however, remains a challenging task. Most peptides previously used for vaccination in clinical trials were able to elicit strong immunological responses but failed with regard to clinical benefit. This might, at least partly, be caused by an inadequate peptide selection, usually derived from established tumor-associated antigens which are not necessarily presented as human leukocyte antigen (HLA) ligands. Recently, HLA ligandome analysis revealed cancer-associated peptides, which have been used in clinical trials showing encouraging impact on survival. To improve peptide-based cancer immunotherapy, our group established a combined approach of HLA ligandomics and immunogenicity analysis for the identification of vaccine peptides. This approach is based on the identification of naturally presented HLA ligands on tumor samples, the selection of tumor-associated/tumor-specific HLA ligands and their subsequent testing for immunogenicity in vitro. In this review, we want to present our pipeline for the identification of vaccine peptides, focusing on ovarian cancer, and want to discuss differences to other approaches. Furthermore, we want to give a short outlook of a potential multi-peptide vaccination trial using the novel identified peptides.

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Abbreviations

APC:

Antigen-presenting cell

aAPC:

Artificial antigen-presenting cell

CCL4:

C-C motive chemokine 4

cDNA:

Complementary DNA

CRA:

51Chromium release assay

CTLA-4:

Cytotoxic T lymphocyte-associated protein 4

DC:

Dendritic cells

HDAC1:

Histone deacetylase 1

HLA:

Human leukocyte antigen

IL:

Interleukin

IFN-γ:

Interferon gamma

LC-MS/MS:

Liquid chromatography-coupled tandem mass spectrometry

NY-ESO-1:

Cancer/testis antigen 1

OvCa:

Ovarian cancer

PAP:

Prostatic acid phosphatase

PBMCs:

Peripheral blood mononuclear cells

PD1:

Programmed cell death protein 1

PD-L1:

Programmed death-ligand 1

PSA:

Prostate-specific antigen

SEREX:

Serological analysis of recombinant cDNA expression libraries

SLP:

Synthetic long peptide

TAA:

Tumor-associated antigen

TAP:

Antigen peptide transporter

TCR:

T-cell receptor

TIL:

Tumor-infiltrating lymphocyte

TNFα:

Tumor necrosis factor alpha

References

  1. Hodi FS, O’Day SJ, McDermott DF, Weber RW, Sosman JA, Haanen JB, Gonzalez R, Robert C, Schadendorf D, Hassel JC, Akerley W, van den Eertwegh AJ, Lutzky J, Lorigan P, Vaubel JM, Linette GP, Hogg D, Ottensmeier CH, Lebbe C, Peschel C, Quirt I, Clark JI, Wolchok JD, Weber JS, Tian J, Yellin MJ, Nichol GM, Hoos A, Urba WJ (2010) Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med 363:711–723

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Herbst RS, Soria JC, Kowanetz M, Fine GD, Hamid O, Gordon MS, Sosman JA, McDermott DF, Powderly JD, Gettinger SN, Kohrt HE, Horn L, Lawrence DP, Rost S, Leabman M, Xiao Y, Mokatrin A, Koeppen H, Hegde PS, Mellman I, Chen DS, Hodi FS (2014) Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients. Nature 515:563–567

    Article  CAS  PubMed  Google Scholar 

  3. Kantoff PW, Higano CS, Shore ND, Berger ER, Small EJ, Penson DF, Redfern CH, Ferrari AC, Dreicer R, Sims RB, Xu Y, Frohlich MW, Schellhammer PF, Investigators IS (2010) Sipuleucel-T immunotherapy for castration-resistant prostate cancer. N Engl J Med 363:411–422

    Article  CAS  PubMed  Google Scholar 

  4. Mellman I, Coukos G, Dranoff G (2011) Cancer immunotherapy comes of age. Nature 480:480–489

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Norell H, Carlsten M, Ohlum T, Malmberg KJ, Masucci G, Schedvins K, Altermann W, Handke D, Atkins D, Seliger B, Kiessling R (2006) Frequent loss of HLA-A2 expression in metastasizing ovarian carcinomas associated with genomic haplotype loss and HLA-A2-restricted HER-2/neu-specific immunity. Cancer Res 66:6387–6394

    Article  CAS  PubMed  Google Scholar 

  6. Coleman RL, Monk BJ, Sood AK, Herzog TJ (2013) Latest research and treatment of advanced-stage epithelial ovarian cancer. Nat Rev Clin Oncol 10:211–224

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Zhang L, Conejo-Garcia JR, Katsaros D, Gimotty PA, Massobrio M, Regnani G, Makrigiannakis A, Gray H, Schlienger K, Liebman MN, Rubin SC, Coukos G (2003) Intratumoral T cells, recurrence, and survival in epithelial ovarian cancer. N Engl J Med 348:203–213

    Article  CAS  PubMed  Google Scholar 

  8. Hwang WT, Adams SF, Tahirovic E, Hagemann IS, Coukos G (2012) Prognostic significance of tumor-infiltrating T cells in ovarian cancer: a meta-analysis. Gynecol Oncol 124:192–198

    Article  PubMed Central  PubMed  Google Scholar 

  9. Coulie PG, Lehmann F, Lethe B, Herman J, Lurquin C, Andrawiss M, Boon T (1995) A mutated intron sequence codes for an antigenic peptide recognized by cytolytic T lymphocytes on a human melanoma. Proc Natl Acad Sci USA 92:7976–7980

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen YS, Shea LK, Hundal J, Wendl MC, Demeter R, Wylie T, Allison JP, Smyth MJ, Old LJ, Mardis ER, Schreiber RD (2012) Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature 482:400–404

    Article  CAS  PubMed  Google Scholar 

  11. Odunsi K, Jungbluth AA, Stockert E, Qian F, Gnjatic S, Tammela J, Intengan M, Beck A, Keitz B, Santiago D, Williamson B, Scanlan MJ, Ritter G, Chen YT, Driscoll D, Sood A, Lele S, Old LJ (2003) NY-ESO-1 and LAGE-1 cancer-testis antigens are potential targets for immunotherapy in epithelial ovarian cancer. Cancer Res 63:6076–6083

    CAS  PubMed  Google Scholar 

  12. Dutoit V, Herold-Mende C, Hilf N, Schoor O, Beckhove P, Bucher J, Dorsch K, Flohr S, Fritsche J, Lewandrowski P, Lohr J, Rammensee HG, Stevanovic S, Trautwein C, Vass V, Walter S, Walker PR, Weinschenk T, Singh-Jasuja H, Dietrich PY (2012) Exploiting the glioblastoma peptidome to discover novel tumour-associated antigens for immunotherapy. Brain 135:1042–1054

    Article  PubMed  Google Scholar 

  13. Walter S, Weinschenk T, Stenzl A, Zdrojowy R, Pluzanska A, Szczylik C, Staehler M, Brugger W, Dietrich PY, Mendrzyk R, Hilf N, Schoor O, Fritsche J, Mahr A, Maurer D, Vass V, Trautwein C, Lewandrowski P, Flohr C, Pohla H, Stanczak JJ, Bronte V, Mandruzzato S, Biedermann T, Pawelec G, Derhovanessian E, Yamagishi H, Miki T, Hongo F, Takaha N, Hirakawa K, Tanaka H, Stevanovic S, Frisch J, Mayer-Mokler A, Kirner A, Rammensee HG, Reinhardt C, Singh-Jasuja H (2012) Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival. Nat Med 18:1254–1261

    Article  CAS  PubMed  Google Scholar 

  14. Hailemichael Y, Dai Z, Jaffarzad N, Ye Y, Medina MA, Huang XF, Dorta-Estremera SM, Greeley NR, Nitti G, Peng W, Liu C, Lou Y, Wang Z, Ma W, Rabinovich B, Sowell RT, Schluns KS, Davis RE, Hwu P, Overwijk WW (2013) Persistent antigen at vaccination sites induces tumor-specific CD8(+) T cell sequestration, dysfunction and deletion. Nat Med 19:465–472

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Kenter GG, Welters MJ, Valentijn AR, Lowik MJ, Berends-van der Meer DM, Vloon AP, Essahsah F, Fathers LM, Offringa R, Drijfhout JW, Wafelman AR, Oostendorp J, Fleuren GJ, van der Burg SH, Melief CJ (2009) Vaccination against HPV-16 oncoproteins for vulvar intraepithelial neoplasia. N Engl J Med 361:1838–1847

    Article  CAS  PubMed  Google Scholar 

  16. Kessler JH, Beekman NJ, Bres-Vloemans SA, Verdijk P, van Veelen PA, Kloosterman-Joosten AM, Vissers DC, ten Bosch GJ, Kester MG, Sijts A, Wouter Drijfhout J, Ossendorp F, Offringa R, Melief CJ (2001) Efficient identification of novel HLA-A(*)0201-presented cytotoxic T lymphocyte epitopes in the widely expressed tumor antigen PRAME by proteasome-mediated digestion analysis. J Exp Med 193:73–88

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. van der Bruggen P, Traversari C, Chomez P, Lurquin C, De Plaen E, Van den Eynde B, Knuth A, Boon T (1991) A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma. Science 254:1643–1647

    Article  PubMed  Google Scholar 

  18. Sahin U, Türeci O, Schmitt H, Cochlovius B, Johannes T, Schmits R, Stenner F, Luo G, Schobert I, Pfreundschuh M (1995) Human neoplasms elicit multiple specific immune responses in the autologous host. Proc Natl Acad Sci USA 92:11810–11813

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. 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 351:290–296

    Article  CAS  PubMed  Google Scholar 

  20. Lundegaard C, Hoof I, Lund O, Nielsen M (2010) State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res 6(Suppl 2):S3

    Article  PubMed Central  PubMed  Google Scholar 

  21. Schirle M, Keilholz W, Weber B, Gouttefangeas C, Dumrese T, Becker HD, Stevanovic S, Rammensee HG (2000) Identification of tumor-associated MHC class I ligands by a novel T cell-independent approach. Eur J Immunol 30:2216–2225

    Article  CAS  PubMed  Google Scholar 

  22. Weinzierl AO, Lemmel C, Schoor O, Müller M, Krüger T, Wernet D, Hennenlotter J, Stenzl A, Klingel K, Rammensee HG, Stevanovic S (2007) Distorted relation between mRNA copy number and corresponding major histocompatibility complex ligand density on the cell surface. Mol Cell Proteomics 6:102–113

    Article  CAS  PubMed  Google Scholar 

  23. Kowalewski DJ, Stevanovic S (2013) Biochemical large-scale identification of MHC class I ligands. Methods Mol Biol 960:145–157

    Article  CAS  PubMed  Google Scholar 

  24. Kowalewski DJ, Schuster H, Backert L, Berlin C, Kahn S, Kanz L, Salih HR, Rammensee H, Stevanovic S, Stickel JS (2014) HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). Proc Natl Acad Sci USA 112:166–175

    Article  Google Scholar 

  25. 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 (2014) Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy. Leukemia 29:647–659

    Article  PubMed  Google Scholar 

  26. Neumann A, Hörzer H, Hillen N, Klingel K, Schmid-Horch B, Bühring HJ, Rammensee HG, Aebert H, Stevanovic S (2013) Identification of HLA ligands and T-cell epitopes for immunotherapy of lung cancer. Cancer Immunol Immunother 62:1485–1497

    Article  CAS  PubMed  Google Scholar 

  27. 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 Neurooncol 111:285–294

    Article  CAS  PubMed  Google Scholar 

  28. Campoli M, Ferrone S (2008) HLA antigen changes in malignant cells: epigenetic mechanisms and biologic significance. Oncogene 27:5869–5885

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Weinschenk T, Gouttefangeas C, Schirle M, Obermayr F, Walter S, Schoor O, Kurek R, Loeser W, Bichler KH, Wernet D, Stevanovic S, Rammensee HG (2002) Integrated functional genomics approach for the design of patient-individual antitumor vaccines. Cancer Res 62:5818–5827

    CAS  PubMed  Google Scholar 

  30. Glozak MA, Seto E (2007) Histone deacetylases and cancer. Oncogene 26:5420–5432

    Article  CAS  PubMed  Google Scholar 

  31. Jin KL, Pak JH, Park JY, Choi WH, Lee JY, Kim JH, Nam JH (2008) Expression profile of histone deacetylases 1, 2 and 3 in ovarian cancer tissues. J Gynecol Oncol 19:185–190

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Mann BS, Johnson JR, Cohen MH, Justice R, Pazdur R (2007) FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist 12:1247–1252

    Article  CAS  PubMed  Google Scholar 

  33. Lanzavecchia A, Iezzi G, Viola A (1999) From TCR engagement to T cell activation: a kinetic view of T cell behavior. Cell 96:1–4

    Article  CAS  PubMed  Google Scholar 

  34. Inzkirweli N, Gückel B, Sohn C, Wallwiener D, Bastert G, Lindner M (2007) Antigen loading of dendritic cells with apoptotic tumor cell-preparations is superior to that using necrotic cells or tumor lysates. Anticancer Res 27:2121–2129

    CAS  PubMed  Google Scholar 

  35. Schultze JL, Michalak S, Seamon MJ, Dranoff G, Jung K, Daley J, Delgado JC, Gribben JG, Nadler LM (1997) CD40-activated human B cells: an alternative source of highly efficient antigen presenting cells to generate autologous antigen-specific T cells for adoptive immunotherapy. J Clin Invest 100:2757–2765

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Suhoski MM, Golovina TN, Aqui NA, Tai VC, Varela-Rohena A, Milone MC, Carroll RG, Riley JL, June CH (2007) Engineering artificial antigen-presenting cells to express a diverse array of co-stimulatory molecules. Mol Ther 15:981–988

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Walter S, Herrgen L, Schoor O, Jung G, Wernet D, Bühring HJ, Rammensee HG, Stevanovic S (2003) Cutting edge: predetermined avidity of human CD8 T cells expanded on calibrated MHC/anti-CD28-coated microspheres. J Immunol 171:4974–4978

    Article  CAS  PubMed  Google Scholar 

  38. Maus MV, Thomas AK, Leonard DG, Allman D, Addya K, Schlienger K, Riley JL, June CH (2002) Ex vivo expansion of polyclonal and antigen-specific cytotoxic T lymphocytes by artificial APCs expressing ligands for the T-cell receptor, CD28 and 4-1BB. Nat Biotechnol 20:143–148

    Article  CAS  PubMed  Google Scholar 

  39. Rudolf D, Silberzahn T, Walter S, Maurer D, Engelhard J, Wernet D, Bühring HJ, Jung G, Kwon BS, Rammensee HG, Stevanovic S (2008) Potent costimulation of human CD8 T cells by anti-4-1BB and anti-CD28 on synthetic artificial antigen presenting cells. Cancer Immunol Immunother 57:175–183

    Article  CAS  PubMed  Google Scholar 

  40. Altman JD, Moss PA, Goulder PJ, Barouch DH, McHeyzer-Williams MG, Bell JI, McMichael AJ, Davis MM (1996) Phenotypic analysis of antigen-specific T lymphocytes. Science 274:94–96

    Article  CAS  PubMed  Google Scholar 

  41. Jung T, Schauer U, Heusser C, Neumann C, Rieger C (1993) Detection of intracellular cytokines by flow cytometry. J Immunol Methods 159:197–207

    Article  CAS  PubMed  Google Scholar 

  42. Czerkinsky C, Andersson G, Ekre HP, Nilsson LA, Klareskog L, Ouchterlony O (1988) Reverse ELISPOT assay for clonal analysis of cytokine production. I. Enumeration of gamma-interferon-secreting cells. J Immunol Methods 110:29–36

    Article  CAS  PubMed  Google Scholar 

  43. Betts MR, Brenchley JM, Price DA, De Rosa SC, Douek DC, Roederer M, Koup RA (2003) Sensitive and viable identification of antigen-specific CD8+ T cells by a flow cytometric assay for degranulation. J Immunol Methods 281:65–78

    Article  CAS  PubMed  Google Scholar 

  44. Brunner KT, Mauel J, Cerottini JC, Chapuis B (1968) Quantitative assay of the lytic action of immune lymphoid cells on 51-Cr-labelled allogeneic target cells in vitro; inhibition by isoantibody and by drugs. Immunology 14:181–196

    PubMed Central  CAS  PubMed  Google Scholar 

  45. Jedema I, van der Werff NM, Barge RM, Willemze R, Falkenburg JH (2004) New CFSE-based assay to determine susceptibility to lysis by cytotoxic T cells of leukemic precursor cells within a heterogeneous target cell population. Blood 103:2677–2682

    Article  CAS  PubMed  Google Scholar 

  46. Peper JK, Schuster H, Löffler MW, Schmid-Horch B, Rammensee HG, Stevanovic S (2014) An impedance-based cytotoxicity assay for real-time and label-free assessment of T-cell-mediated killing of adherent cells. J Immunol Methods 405:192–198

    Article  CAS  PubMed  Google Scholar 

  47. Suresh M, Whitmire JK, Harrington LE, Larsen CP, Pearson TC, Altman JD, Ahmed R (2001) Role of CD28-B7 interactions in generation and maintenance of CD8 T cell memory. J Immunol 167:5565–5573

    Article  CAS  PubMed  Google Scholar 

  48. Diefenbach CS, Gnjatic S, Sabbatini P, Aghajanian C, Hensley ML, Spriggs DR, Iasonos A, Lee H, Dupont B, Pezzulli S, Jungbluth AA, Old LJ, Dupont J (2008) Safety and immunogenicity study of NY-ESO-1b peptide and montanide ISA-51 vaccination of patients with epithelial ovarian cancer in high-risk first remission. Clin Cancer Res 14:2740–2748

    Article  CAS  PubMed  Google Scholar 

  49. Rahma OE, Ashtar E, Czystowska M, Szajnik ME, Wieckowski E, Bernstein S, Herrin VE, Shams MA, Steinberg SM, Merino M, Gooding W, Visus C, Deleo AB, Wolf JK, Bell JG, Berzofsky JA, Whiteside TL, Khleif SN (2012) A gynecologic oncology group phase II trial of two p53 peptide vaccine approaches: subcutaneous injection and intravenous pulsed dendritic cells in high recurrence risk ovarian cancer patients. Cancer Immunol Immunother 61:373–384

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  50. Hamilton SE, Wolkers MC, Schoenberger SP, Jameson SC (2006) The generation of protective memory-like CD8+ T cells during homeostatic proliferation requires CD4+ T cells. Nat Immunol 7:475–481

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This research was supported by the DFG (Deutsche Forschungsgemeinschaft; Collaborative Research Center 685) and the German Cancer Consortium. The authors thank Dr. Markus Löffler for proof reading.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Immunology, Institute of Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany

    Janet Kerstin Peper & Stefan Stevanović

  2. German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany

    Stefan Stevanović

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  1. Janet Kerstin Peper
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  2. Stefan Stevanović
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Correspondence to Janet Kerstin Peper.

Additional information

This paper is a Focussed Research Review based on a presentation given at the Fourteenth International Conference on Progress in Vaccination against Cancer (PIVAC 14), held in Rome, Italy, 24th – 26th September, 2014. It is part of a Cancer Immunology, Immunotherapy series of Focussed Research Reviews and meeting report.

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Peper, J.K., Stevanović, S. A combined approach of human leukocyte antigen ligandomics and immunogenicity analysis to improve peptide-based cancer immunotherapy. Cancer Immunol Immunother 64, 1295–1303 (2015). https://doi.org/10.1007/s00262-015-1682-8

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  • DOI: https://doi.org/10.1007/s00262-015-1682-8

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