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N-glycosylated HLA class I peptides

Peptidomics and small proteins PTM & Glycoproteomics

Abstract #36 Posted on24 February 20259 May 2025 9 May 2025 14h18

Abstract

HLA-presented peptides are known to display a large variety of post-translational modifications. Examples include oxidation, deamidation, methylation, phosphorylation, and glycosylation. The latter has been reported on HLA class II-presented peptides, which is logical considering the source of HLA class II-presented peptides. In addition, some HLA class I-presented extended O-GlcNAc peptides have been observed.
Here we report on the identification of large N-linked glycan structures on HLA class I-presented peptides, including high mannose as well as complex type N-glycans. Moreover, based on glycan signature ions, we witnessed additional glycopeptides of which the peptide sequence could not be assigned. Collectively, these data point to the existence of a substantial HLA class I glycosylated peptidome subset.
In the identified glycopeptides, the glycan modification occurs mostly at position 4, which is in line with a previous report, and can be explained by structural constraints, in which the glycan structure has to point away from the groove towards the T cell receptor. Peptides stem mostly from cytosolic and nuclear proteins, a location where proteins are thought not to be glycosylated. Therefore, these HLA-ligands are assumed to be artificially N-glycosylated in the ER/Golgi, which involves many processing steps. Several aspects of these N-glycan carrying HLA-peptides will be discussed.

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HLA-presented peptides are known to display a large variety of post-translational modifications. Examples include oxidation, deamidation, methylation, phosphorylation, and glycosylation. The latter has been reported on HLA class II-presented peptides, which is logical considering the source of HLA class II-presented peptides. In addition, some HLA class I-presented extended O-GlcNAc peptides have been observed. 
Here we report on the identification of large N-linked glycan structures on HLA class I-presented peptides, including high mannose as well as complex type N-glycans. Moreover, based on glycan signature ions, we witnessed additional glycopeptides of which the peptide sequence could not be assigned. Collectively, these data point to the existence of a substantial HLA class I glycosylated peptidome subset.
In the identified glycopeptides, the glycan modification occurs mostly at position 4, which is in line with a previous report, and can be explained by structural constraints, in which the glycan structure has to point away from the groove towards the T cell receptor. Peptides stem mostly from cytosolic and nuclear proteins, a location where proteins are thought not to be glycosylated. Therefore, these HLA-ligands are assumed to be artificially N-glycosylated in the ER/Golgi, which involves many processing steps. Several aspects of these N-glycan carrying HLA-peptides will be discussed.

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