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ORIGINAL RESEARCH article

Front. Immunol.
Sec. Cancer Immunity and Immunotherapy
Volume 15 - 2024 | doi: 10.3389/fimmu.2024.1490821
This article is part of the Research Topic Immunology and Immunotherapy of Skin Cancer View all 9 articles

SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells

Provisionally accepted
Melissa Bernhardt Melissa Bernhardt 1Anne Rech Anne Rech 2Marion Berthold Marion Berthold 2Melina Lappe Melina Lappe 3Jan-Niklas Herbel Jan-Niklas Herbel 3Florian Erhard Florian Erhard 4Annette Paschen Annette Paschen 5Bastian Schilling Bastian Schilling 6Andreas Schlosser Andreas Schlosser 1*
  • 1 Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
  • 2 Department of Dermatology, Venereology and Allergology, University Hospital Wuerzburg, Würzburg, Bavaria, Germany
  • 3 Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Würzburg, Würzburg, Bavaria, Germany
  • 4 Faculty of Computer Science and Data Science, University of Regensburg, Regensburg, Bavaria, Germany
  • 5 Department of Dermatology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
  • 6 Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Hesse, Germany

The final, formatted version of the article will be published soon.

    Background The immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It is highly dynamic and reflects the current cellular state, enabling the immune system to recognize abnormal cellular conditions, such as those present in cancer cells. To precisely determine how changes in cellular processes, such as those induced by drug treatment, affect the immunopeptidome, quantitative immunopeptidomics approaches are essential. Methods To meet this need, we developed a pulsed SILAC-based method for quantitative immunopeptidomics. Metabolic labeling with lysine, arginine, and leucine enabled isotopic labeling of nearly all HLA peptides across all allotypes (> 90% on average). We established a data analysis workflow that integrates the de novo sequencing-based tool Peptide-PRISM for comprehensive HLA peptide identification with MaxQuant for accurate quantification. Results We employed this strategy to explore the modulation of the immunopeptidome upon MAPK pathway inhibition (MAPKi) and to investigate alterations associated with early cellular responses to inhibitor treatment and acquired resistance to MAPKi. Our analyses demonstrated significant changes in the immunopeptidome early during MAPKi treatment and in the resistant state. Moreover, we identified putative tumor-specific cryptic HLA peptides linked to these processes that might represent exploitable targets for cancer immunotherapy. Conclusions We have developed a new mass spectrometric approach that allowed us to investigate the effects of common MAPK inhibitors on the immunopeptidome of melanoma cells. This finally led to the discovery of new potential targets for cancer immunotherapy.

    Keywords: Mass Spectrometry, stable isotope labeling, HLA-I peptides, T-cell epitopes, De novo peptide sequencing, cryptic HLA peptides, Melanoma, MAPK pathway inhibition

    Received: 03 Sep 2024; Accepted: 02 Dec 2024.

    Copyright: © 2024 Bernhardt, Rech, Berthold, Lappe, Herbel, Erhard, Paschen, Schilling and Schlosser. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Andreas Schlosser, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, 97080, Germany

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