SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells
BackgroundThe 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 determi...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1490821/full |
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| author | Melissa Bernhardt Anne Rech Marion Berthold Melina Lappe Jan-Niklas Herbel Florian Erhard Annette Paschen Bastian Schilling Bastian Schilling Andreas Schlosser |
| author_facet | Melissa Bernhardt Anne Rech Marion Berthold Melina Lappe Jan-Niklas Herbel Florian Erhard Annette Paschen Bastian Schilling Bastian Schilling Andreas Schlosser |
| author_sort | Melissa Bernhardt |
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| description | BackgroundThe 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.MethodsTo 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.ResultsWe 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.ConclusionsWe 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. |
| format | Article |
| id | doaj-art-bc3052f061af4e45ae1aac038494bcd7 |
| institution | Kabale University |
| issn | 1664-3224 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj-art-bc3052f061af4e45ae1aac038494bcd72025-01-06T10:36:54ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-01-011510.3389/fimmu.2024.14908211490821SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cellsMelissa Bernhardt0Anne Rech1Marion Berthold2Melina Lappe3Jan-Niklas Herbel4Florian Erhard5Annette Paschen6Bastian Schilling7Bastian Schilling8Andreas Schlosser9Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität of Würzburg, Würzburg, GermanyDepartment of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, GermanyDepartment of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, GermanyInstitute for Pharmacology and Toxicology, Julius-Maximilians-Universität of Würzburg, Würzburg, GermanyInstitute for Pharmacology and Toxicology, Julius-Maximilians-Universität of Würzburg, Würzburg, GermanyFaculty for Informatics and Data Science, University of Regensburg, Regensburg, GermanyDepartment of Dermatology, University Hospital Essen, University Duisburg-Essen and German Cancer Consortium (DKTK), Essen, GermanyDepartment of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, GermanyDepartment of Dermatology, Venerology and Allergology, Goethe University Frankfurt, University Hospital, Frankfurt, GermanyRudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität of Würzburg, Würzburg, GermanyBackgroundThe 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.MethodsTo 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.ResultsWe 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.ConclusionsWe 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.https://www.frontiersin.org/articles/10.3389/fimmu.2024.1490821/fullmass spectrometrystable isotope labelingHLA-I peptidesT-cell epitopesde novo peptide sequencingcryptic HLA peptides |
| spellingShingle | Melissa Bernhardt Anne Rech Marion Berthold Melina Lappe Jan-Niklas Herbel Florian Erhard Annette Paschen Bastian Schilling Bastian Schilling Andreas Schlosser SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells Frontiers in Immunology mass spectrometry stable isotope labeling HLA-I peptides T-cell epitopes de novo peptide sequencing cryptic HLA peptides |
| title | SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells |
| title_full | SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells |
| title_fullStr | SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells |
| title_full_unstemmed | SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells |
| title_short | SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells |
| title_sort | silac based quantification reveals modulation of the immunopeptidome in braf and mek inhibitor sensitive and resistant melanoma cells |
| topic | mass spectrometry stable isotope labeling HLA-I peptides T-cell epitopes de novo peptide sequencing cryptic HLA peptides |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1490821/full |
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