PXD014062

PXD014062 is an original dataset announced via ProteomeXchange.

Title	LC-MSMS of primary HGSC class I immunopeptidom
Description	High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecological malignancies in the world, has not significantly benefited from recent progress in cancer immunotherapy. While HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSAs) using a mass spectrometry pipeline that interrogates all reading frames of all genomic regions. In 23 HGSC tumors, we identified 113 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only seven of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation or from non-exonic sequences. The most interesting group of TSAs (n = 94) derived from aberrantly expressed unmutated genomic sequences which are not expressed in normal tissues. These aberrantly expressed TSAs (aeTSAs) derived primarily from non-exonic sequences, in particular intronic (31%) and intergenic (22%). Their expression was regulated at the transcriptional level by variations in gene copy number and DNA methylation. While mutated TSAs were unique to individual tumors, aeTSAs were shared by a large proportion of HGSCs. We conclude that, in view of their number and the fact that they are shared by many tumors, aeTSAs may be the most attractive targets for HGSC immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2020-02-19
AnnouncementXML	Submission_2020-02-19_05:07:14.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD014062
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Courcelles Mathieu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Deamidated; Oxidation
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-29 04:20:46	ID requested
⏵ 1	2020-02-19 05:07:16	announced

Zhao Q, Laverdure JP, Lanoix J, Durette C, C, ô, t, é C, Bonneil É, Laumont CM, Gendron P, Vincent K, Courcelles M, Lemieux S, Millar DG, Ohashi PS, Thibault P, Perreault C, Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer. Cancer Immunol Res, 8(4):544-555(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: HGSC, LC-MSMS, MHC class I, immunopeptidome

Pierre Thibault
contact affiliation	Institute for Research in Immunology and Cancer, Department of Biochemistry, Department of Chemistry, Université de Montréal, Québec, Canada H3T 1J4
contact email	pierre.thibault@umontreal.ca
lab head
Courcelles Mathieu
contact affiliation	IRIC
contact email	mathieu.courcelles@umontreal.ca
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/02/PXD014062

PRIDE project URI

• PRIDE
  1. PXD014062
     1. Label: PRIDE project
     2. Name: LC-MSMS of primary HGSC class I immunopeptidom