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.
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Acknowledgements
We thank Patricia Hrstic, Beate Pömmerl, Claudia Falkenburger, Katharina Graf and Nicole Zuschke for excellent technical support and Mathias Walzer for expert programming of in-house analytical scripts. This work was supported by the Deutsche Forschungsgesellschaft (DFG, SFB 685), the Fortüne Program of the University of Tübingen (Fortüne Number 2032-0-0) and the German Cancer Consortium (DKTK).
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Berlin, C., Kowalewski, D., Schuster, H. et al. Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy. Leukemia 29, 647–659 (2015). https://doi.org/10.1038/leu.2014.233
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DOI: https://doi.org/10.1038/leu.2014.233
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