Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors
| Autor: | Sri H. Ramarathinam, Nathan P. Croft, Shutao Mei, Pouya Faridi, Rochelle Ayala, Jiangning Song, Patricia T. Illing, Anthony W. Purcell |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Proteomics
Glycan Glycosylation Amino Acid Motifs Epitopes T-Lymphocyte Peptide Protein degradation Biochemistry Amino Acid Chloromethyl Ketones Cell Line Analytical Chemistry 03 medical and health sciences chemistry.chemical_compound N-linked glycosylation Tandem Mass Spectrometry Humans Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase Asparagine Deamidation Molecular Biology Glycoproteins 030304 developmental biology chemistry.chemical_classification 0303 health sciences biology Histocompatibility Antigens Class I 030302 biochemistry & molecular biology Histocompatibility Antigens Class II Technological Innovation and Resources Endoplasmic Reticulum-Associated Degradation chemistry Deamination biology.protein Peptides Glycoprotein Protein Processing Post-Translational Chromatography Liquid |
| Zdroj: | Mol Cell Proteomics |
| ISSN: | 1535-9476 |
| DOI: | 10.1074/mcp.ra119.001846 |
| Popis: | The presentation of post-translationally modified (PTM) peptides by cell surface HLA molecules has the potential to increase the diversity of targets for surveilling T cells. Although immunopeptidomics studies routinely identify thousands of HLA-bound peptides from cell lines and tissue samples, in-depth analyses of the proportion and nature of peptides bearing one or more PTMs remains challenging. Here we have analyzed HLA-bound peptides from a variety of allotypes and assessed the distribution of mass spectrometry-detected PTMs, finding deamidation of asparagine or glutamine to be highly prevalent. Given that asparagine deamidation may arise either spontaneously or through enzymatic reaction, we assessed allele-specific and global motifs flanking the modified residues. Notably, we found that the N-linked glycosylation motif NX(S/T) was highly abundant across asparagine-deamidated HLA-bound peptides. This finding, demonstrated previously for a handful of deamidated T cell epitopes, implicates a more global role for the retrograde transport of nascently N-glycosylated polypeptides from the ER and their subsequent degradation within the cytosol to form HLA-ligand precursors. Chemical inhibition of Peptide:N-Glycanase (PNGase), the endoglycosidase responsible for the removal of glycans from misfolded and retrotranslocated glycoproteins, greatly reduced presentation of this subset of deamidated HLA-bound peptides. Importantly, there was no impact of PNGase inhibition on peptides not containing a consensus NX(S/T) motif. This indicates that a large proportion of HLA-I bound asparagine deamidated peptides are generated from formerly glycosylated proteins that have undergone deglycosylation via the ER-associated protein degradation (ERAD) pathway. The information herein will help train deamidation prediction models for HLA-peptide repertoires and aid in the design of novel T cell therapeutic targets derived from glycoprotein antigens. |
| Databáze: | OpenAIRE |
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