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MHC-I peptidome analysis of human cancer cell lines

ABSTRACT: In this study, we sought to identify naturally presented MHC peptides in 3 human cancer cell lines: A431, Colo668, HuCCT1. Peptides identified were 8-15 amino acid long with the majority between 8 to 11 amino acids which match known properties of MHC-I presented peptides.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Dora Warshaviak

LAB HEAD: Agi Hamburger

PROVIDER: PXD033685 | Pride | 2022-05-09

REPOSITORIES: Pride

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			Action	DRS
	A431-budv901421a21101xms1.raw	Raw
	Colo668-budv901621a21101xms1.raw	Raw
	HuCCT1-budv901521a21101xms1.raw	Raw
	SEARCH-Peptide_Report_Table.csv	Csv
	checksum.txt	Txt

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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-I peptidome analysis of human cancer cell lines

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