Dataset Information

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection

ABSTRACT: We sought to build a catalog of epitopes presented by breast cancers using a renewable resource of well-characterized breast cancer cell lines. Starting from 70 breast cancer cell lines, we measured MHC class I abundance and used pre-existing RNAseq data to identify either HLA-A*02 or MHC class I-positive cell lines. For 20 of these cell lines, we used “reverse” immunogenetics, in which MHC class I-loaded peptides are recovered and their sequences are determined by mass spectrometry. We identified more than 2,700 unique MHC class I-bound peptides from a panel of basal, luminal, and claudin-low subtype of cell lines. HLA-A*02 binding prediction across all tested cell lines revealed a model which described the distribution of HLA-A*02-binding peptides and allowed us to identify those peptides most likely to be presented on HLA-A*02. Comparing the peptides that we identified to published literature found that more than 1500 peptides had been identified in previous studies and that 18 of these peptides have been shown to be immunogenic. Overall, this high throughput identification of MHC class I-loaded peptides is an effective strategy for systematic characterization of cancer epitopes and could be employed in a design of multipeptide-based anticancer vaccine.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Phillip Wilmarth

LAB HEAD: Paul Spellman

PROVIDER: PXD006406 | Pride | 2018-01-16

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	SPE1116_MHC_20120224_VE.RAW	Raw
	SPE1116_SPE1240_Rozanov_FASTA_files.zip	Other
	SPE1116_SPE1240_Rozanov_PEAK.zip	Other
	SPE1116_SPE1240_Rozanov_SEARCH.zip	Other
	SPE1116_SPE1240_Rozanov_file_listing.xlsx	Xlsx

Items per page:

1 - 5 of 29

Publications

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection.

Rozanov Dmitri V DV Rozanov Nikita D ND Chiotti Kami E KE Reddy Ashok A Wilmarth Phillip A PA David Larry L LL Cha Seung W SW Woo Sunghee S Pevzner Pavel P Bafna Vineet V Burrows Gregory G GG Rantala Juha K JK Levin Trevor T Anur Pavana P Johnson-Camacho Katie K Tabatabaei Shaadi S Munson Daniel J DJ Bruno Tullia C TC Slansky Jill E JE Kappler John W JW Hirano Naoto N Boegel Sebastian S Fox Bernard A BA Egelston Colt C Simons Diana L DL Jimenez Grecia G Lee Peter P PP Gray Joe W JW Spellman Paul T PT

Journal of proteomics 20180110

To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more ...[more]

PMID: 29331515

Similar Datasets

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.