Proteomics

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The landscape of phosphorylated HLA-I ligands

ABSTRACT: The identification and prediction of HLA-I–peptide interactions play an important role in our understanding of antigen recognition in infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. In this study, we collected in-depth phosphorylated HLA-I peptidomics data (1,920 unique phosphorylated peptides) from several studies covering 67 HLA-I alleles and expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands for several alleles. In addition to the previously observed preferences for phosphorylation at P4, for proline next to the phosphosite and for arginine at P1, we could detect a clear enrichment of phosphorylated peptides among HLA-C ligands and among longer peptides. Binding assays were used to validate and interpret these observations. We then used these data to develop the first predictor of HLA-I– phosphorylated peptide interactions and demonstrated that combining phosphorylated and unmodified HLA-I ligands in the training of the predictor led to highest accuracy.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Michal Bassani-Sternberg  

LAB HEAD: Michal Bassani-Sternberg

PROVIDER: PXD013831 | Pride | 2019-12-18

REPOSITORIES: Pride

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Publications

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.

Solleder Marthe M   Guillaume Philippe P   Racle Julien J   Michaux Justine J   Pak Hui-Song HS   Müller Markus M   Coukos George G   Bassani-Sternberg Michal M   Gfeller David D  

Molecular & cellular proteomics : MCP 20191217 2

The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for <i>in vivo</i> identificati  ...[more]

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