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

ABSTRACT: 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. 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 HLA 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. We employed this strategy to explore the modulation of the immunopeptidome upon MAPK pathway inhibition and to investigate alterations associated with acquired resistance to BRAF and MEK inhibitors. Our analyses demonstrated significant changes in the immunopeptidome following MAPK pathway inhibition, as well as in cells resistant to BRAF/MEK inhibitors. Moreover, we identified putative tumor-specific cryptic HLA peptides linked to these processes.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

DISEASE(S): Skin Melanoma

SUBMITTER: Melissa Bernhardt  

LAB HEAD: Andreas Schlosser

PROVIDER: PXD054097 | Pride | 2025-05-07

REPOSITORIES: Pride