PXD006406

PXD006406 is an original dataset announced via ProteomeXchange.

Title	MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection
Description	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.
HostingRepository	PRIDE
AnnounceDate	2018-01-16
AnnouncementXML	Submission_2018-01-16_01:58:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Phillip Wilmarth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-28 01:47:39	ID requested
⏵ 1	2018-01-16 01:59:00	announced

Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT, MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics, 176():13-23(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Breast cancer, cell lines, human, HLA typing, RNA-seq, MHC class 1 ligands, immunoprecipitation, immune system, mass spectrometry, peptide sequencing

Paul Spellman
contact affiliation	Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR USA
contact email	spellmap@ohsu.edu
lab head
Phillip Wilmarth
contact affiliation	OHSU
contact email	wilmarth@ohsu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006406
     1. Label: PRIDE project
     2. Name: MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection