Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy

C Berlin; D J Kowalewski; H Schuster; N Mirza; S Walz; M Handel; B Schmid-Horch; H R Salih; L Kanz; H-G Rammensee; S Stevanović; J S Stickel

doi:10.1038/leu.2014.233

Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy

Leukemia. 2015 Mar;29(3):647-59. doi: 10.1038/leu.2014.233. Epub 2014 Aug 5.

Authors

C Berlin¹, D J Kowalewski², H Schuster², N Mirza¹, S Walz¹, M Handel³, B Schmid-Horch⁴, H R Salih⁵, L Kanz⁶, H-G Rammensee⁷, S Stevanović⁷, J S Stickel¹

Affiliations

¹ 1] Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany [2] Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.
² Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
³ Hospital Group South-West, Department of Orthopedics, Calw, Germany.
⁴ Institute for Clinical and Experimental Transfusion Medicine, University of Tübingen, Tübingen, Germany.
⁵ 1] Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany [2] Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
⁶ Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.
⁷ 1] Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany [2] Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.

PMID: 25092142
DOI: 10.1038/leu.2014.233

Abstract

Identification of physiologically relevant peptide vaccine targets calls for the direct analysis of the entirety of naturally presented human leukocyte antigen (HLA) ligands, termed the HLA ligandome. In this study, we implemented this direct approach using immunoprecipitation and mass spectrometry to define acute myeloid leukemia (AML)-associated peptide vaccine targets. Mapping the HLA class I ligandomes of 15 AML patients and 35 healthy controls, more than 25 000 different naturally presented HLA ligands were identified. Target prioritization based on AML exclusivity and high presentation frequency in the AML cohort identified a panel of 132 LiTAAs (ligandome-derived tumor-associated antigens), and 341 corresponding HLA ligands (LiTAPs (ligandome-derived tumor-associated peptides)) represented subset independently in >20% of AML patients. Functional characterization of LiTAPs by interferon-γ ELISPOT (Enzyme-Linked ImmunoSpot) and intracellular cytokine staining confirmed AML-specific CD8(+) T-cell recognition. Of note, our platform identified HLA ligands representing several established AML-associated antigens (e.g. NPM1, MAGED1, PRTN3, MPO, WT1), but found 80% of them to be also represented in healthy control samples. Mapping of HLA class II ligandomes provided additional CD4(+) T-cell epitopes and potentially synergistic embedded HLA ligands, allowing for complementation of a multipeptide vaccine for the immunotherapy of AML.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
CD4-Positive T-Lymphocytes / immunology
CD4-Positive T-Lymphocytes / metabolism
CD4-Positive T-Lymphocytes / pathology
CD8-Positive T-Lymphocytes / immunology
CD8-Positive T-Lymphocytes / metabolism
CD8-Positive T-Lymphocytes / pathology
Cancer Vaccines / administration & dosage
Cancer Vaccines / genetics
Cancer Vaccines / immunology*
Case-Control Studies
Epitopes, T-Lymphocyte / chemistry
Epitopes, T-Lymphocyte / genetics
Epitopes, T-Lymphocyte / immunology
Gene Expression
Histocompatibility Antigens Class I / chemistry
Histocompatibility Antigens Class I / genetics*
Histocompatibility Antigens Class I / immunology
Histocompatibility Antigens Class II / chemistry
Histocompatibility Antigens Class II / genetics*
Histocompatibility Antigens Class II / immunology
Humans
Immunoprecipitation
Immunotherapy, Active / methods*
Leukemia, Myeloid, Acute / genetics
Leukemia, Myeloid, Acute / immunology
Leukemia, Myeloid, Acute / pathology
Leukemia, Myeloid, Acute / therapy*
Ligands
Mass Spectrometry
Molecular Sequence Data
Neoplasm Proteins / genetics
Neoplasm Proteins / immunology*
Nucleophosmin
Peptide Mapping
Peptides / chemistry
Peptides / genetics
Peptides / immunology*

Substances

Cancer Vaccines
Epitopes, T-Lymphocyte
Histocompatibility Antigens Class I
Histocompatibility Antigens Class II
Ligands
NPM1 protein, human
Neoplasm Proteins
Peptides
Nucleophosmin