Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design

Emma C. Jappe, Christian Garde, Sri H. Ramarathinam, Ethan Passantino, Patricia T. Illing, Nicole A. Mifsud, Thomas Trolle, Jens V. Kringelum (), Nathan P. Croft () and Anthony W. Purcell ()
Additional contact information
Emma C. Jappe: Evaxion Biotech
Christian Garde: Evaxion Biotech
Sri H. Ramarathinam: Monash University
Ethan Passantino: Monash University
Patricia T. Illing: Monash University
Nicole A. Mifsud: Monash University
Thomas Trolle: Evaxion Biotech
Jens V. Kringelum: Evaxion Biotech
Nathan P. Croft: Monash University
Anthony W. Purcell: Monash University

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: Abstract The features of peptide antigens that contribute to their immunogenicity are not well understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a method that provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra-allelic and inter-allelic differences in pMHC stability and reveals profiles of stability that are broader than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improves the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.

Date: 2020
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DOI: 10.1038/s41467-020-20166-4

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