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MHC-IP MS of EpiScan A02 SARS-CoV-2 library

ABSTRACT: Identification of CD8+ T-cell epitopes is critical for the development of immunotherapeutics. Existing methods for MHC-I ligand discovery are time-intensive, specialized and unable to interrogate specific proteins on a large scale. Here we present EpiScan, which uses surface MHC-I levels as a readout for whether a genetically encoded peptide is an MHC-I ligand. Oligonucleotide synthesis permits facile screening for MHC-I ligands amongst predetermined starting pools comprising >100,000 peptides. We exploit this programmability of EpiScan to uncover an unappreciated role for cysteine that increases the number of predicted ligands by 12-21%, reveal affinity hierarchies by analysis of biased-anchor peptide libraries, and screen viral proteomes for MHC-I ligands. Using these data, we generate and iteratively refine peptide binding prediction predictions to create EpiScan Predictor, or ESP. ESP performed comparably to other state-of-the-art MHC-I peptide binding prediction algorithms while not suffering from underrepresentation of cysteine-containing peptides. Thus, targeted immunopeptidomics using EpiScan will accelerate CD8+ T-cell epitope discovery towards the goal of patient-specific immunotherapeutics.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Severe Acute Respiratory Syndrome Coronavirus 2

SUBMITTER: Peter Bruno

LAB HEAD: Stephen Elledge

PROVIDER: PXD036939 | Pride | 2022-10-13

REPOSITORIES: Pride

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Project description:The majority of peptides presented by MHC class I results from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, either alone or together with the proteasome, contribute peptides for MHC class I loading non-canonically. We used an im-munopeptidomics workflow combined with a prediction software for proteasomal cleavage probabilities to analyze how inflammatory conditions affect proteasomal processing of immune epitopes presented by A549 cells. Treatment of A549 cells with IFNγ enhanced proteasomal cleavage probability of MHC class I ligands for both, the constitutive proteasome and the im-munoproteasome. Furthermore, IFNγ alters the contribution of the different HLA allotypes to the immunopeptidome. When we calculated HLA allotype-specific proteasomal cleavage probabili-ties for MHC class I ligands, peptides presented by HLA-A*30:01 showed characteristics hinting at a reduced C-terminal proteasomal cleavage probability independently of the type of proteasome. This was confirmed by HLA-A*30:01 ligands from the immune epitope database, which also showed this effect. Furthermore, two additional HLA allotypes, namely HLA-A*03:01 and HLA-A*11:01, presented peptides with a markedly reduced C-terminal proteasomal cleavage probability. Peptides eluted from all three HLA allotypes shared a peptide binding motif with a C-terminal lysine residue suggesting that this lysine residue impairs proteasome-dependent HLA ligand production and might, in turn, favor peptide generation by other cellular proteases. The mass spectrometry raw files used in this study were originally produced for a previous publication, where they were utilized to address the influence of cigarette smoke on the antiviral T-cell immune response. Here, we have reanalyzed the data to investigate processing of MHC class I ligands by c20S or i20S, respectively. Original publication: Chen, J.; Wang, X.; Schmalen, A.; Haines, S.; Wolff, M.; Ma, H.; Zhang, H.; Stoleriu, M.G.; Nowak, J.; Nakayama, M.; et al. Antiviral CD8(+) T cell immune responses are impaired by cigarette smoke and in COPD. Eur Respir J 2023, doi:10.1183/13993003.01374-2022.

Project description:Peptides displayed by MHC molecules on a cell’s surface, referred to as its immunopeptidome, play an important role in the adaptive the immune response. Antigen processing for MHC class I presentation is a ubiquitous pathway present in all nucleated cells which generate and present peptides of both self and non-self origin. Peptides with post-translational modifications (PTMs) are one of the classes of peptides presented by MHC class I molecules. However, due to the high background of self-peptides presented by the cells, the diversity of peptides with post-translational modifications is not well reported. In this study, we have carried out MHC Class I immunopeptidomics analysis on Jurkat and A375 cell lines to characterize the diversity of post-translational modifications among MHC class I peptides. Using high resolution mass spectrometry, we identified 25,761 MHC-bound peptides across both the cell lines using Bolt and Sequest search engines. High specificity of the enrichment method is demonstrated by identifying ~90% of the peptides with typical length distribution of 8-12 aa and enriched motifs within those peptides similar to the binding motifs of MHC alleles. Among the MHC-bound peptides, we identified phosphorylation as a major post-translational modification followed by deamidation. We observed site-specific localization of these post-translational modifications, at position P4 for phosphorylated peptides and position P3 for deamidated peptides. We identified a smaller number of peptides with acetylated and methylated lysine, possibly due to very low stoichiometric levels of these post-translational modifications compared to phosphorylation and deamidation. Using PEAKS de novo sequencing algorithm, we identified spliced peptides that account for ~5-7% of MHC-bound peptides across the two cell lines. These peptides share similar features with respect to normal MHC-bound peptides such as peptide length distribution and binding motifs. We validated the identification of several post-translationally modified peptides and spliced peptides using synthetic peptide sequences. In conclusion, our study demonstrates unbiased identification of these low stoichiometric PTMs and unusual spliced peptides using high resolution mass spectrometry.

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MHC-IP MS of EpiScan A02 SARS-CoV-2 library

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