The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02

Abstract

Mass-spectrometry based immunopeptidomics has provided unprecedented insights into antigen presentation, not only charting an enormous ligandome of self-antigens, but also cancer neoantigens and peptide antigens harbouring post-translational modifications. Here we concentrate on the latter, focusing on the small subset of HLA Class I peptides (less than 1%) that has been observed to be post-translationally modified (PTM) by a O-linked N-acetylglucosamine (GlcNAc). Just like neoantigens these modified antigens may have specific immunomodulatory functions. Here we compiled from literature, and a new dataset originating from the JY B cell lymphoblastoid cell line, a concise albeit comprehensive list of O-GlcNAcylated HLA class I peptides. This cumulative list of O-GlcNAcylated HLA peptides were derived from normal and cancerous origin, as well as tissue specimen. Remarkably, the overlap in detected O-GlcNAcylated HLA peptides as well as their source proteins is strikingly high. Most of the O-GlcNAcylated HLA peptides originate from nuclear proteins, notably transcription factors. From this list, we extract that O-GlcNAcylated HLA Class I peptides are preferentially presented by the HLA-B*07:02 allele. This allele loads peptides with a Proline residue anchor at position 2, and features a binding groove that can accommodate well the recently proposed consensus sequence for O-GlcNAcylation, P(V/A/T/S)g(S/T), essentially explaining why HLA-B*07:02 is a favoured binding allele. The observations drawn from the compiled list, may assist in the prediction of novel O-GlcNAcylated HLA antigens, which will be best presented by patients harbouring HLA-B*07:02 or related alleles that use Proline as anchoring residue.

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

“…The long-term aims of HiPP are to map the entire repertoire of peptides presented by HLA molecules using mass spectrometry technologies, and make its robust analysis accessible to immunologists, clinical investigators, and other researchers. Members of this team published three definitive articles on the peptidome of SARS-COV-2 in Cell , Cell Reports , and Nature Immunology − plus other landmark immunology publications identifying specific immuno-epitopes in Nature Communications , Journal of Clinical Investigation , and Frontiers in Immunology and Immunity . − …”

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“…Mass spectrometric detection of glycans and intact glycopeptides has emerged as an attractive glycoproteomics analytical platform. Recent progress in workflows, including glycopeptide extraction/enrichment, hybrid mass spectrometric fragmentation, and data analysis, have made detection of glycopeptides increasingly achievable ( 12 , 13 , 14 , 15 , 16 , 17 , 18 ). Notwithstanding these advances over the past decade, characterization and quantitation of intact glycopeptides from complex datasets remains a bottleneck because of their inherent glycan heterogeneity, ionization and separation characteristics, and their relative low abundance compared with nonmodified peptide counterparts ( 19 ).…”

HLA-Glyco: A large-scale interrogation of the glycosylated immunopeptidome

“…1 . While O-glycosylated MAPs are also of potential interest 25 , O-glycopeptide analysis typically requires electron-based activation to locate the glycosite(s) within the peptide. As the vast majority of available immunopeptidomics data lacks such activation, we focused exclusively on N-glycosylated MAPs for this analysis.…”