PXD018124

PXD018124 is an original dataset announced via ProteomeXchange.

Title	LC-MSMS of OVCAR-3 class I immunopeptidome
Description	Endogenous retroelements (ERE) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a systems-level evaluation of their expression in human tissues is lacking. We report that all human tissues express EREs but the breadth and magnitude of ERE expression are very heterogeneous from one tissue to another. ERE expression was particularly high in two MHC-I-deficient tissues (ESCs and testis) and one MHC-I-expressing tissue, mTECs. In mutant mice, we report that the exceptional expression of EREs in mTECs was AIRE-independent. MS analyses identified 103 non-redundant ERE-derived MAPs (ereMAPs) in B-LCLs. These ereMAPs preferentially derived from sense translation of intronic EREs. Notably, detailed analyses of their amino acid composition revealed that ERE-derived MAPs presented homology to viral MAPs. This study shows that ERE expression in somatic tissues is more pervasive and heterogeneous than anticipated. The high and diversified expression of EREs in mTECs and their ability to generate MAPs suggest that EREs may play an important role in the establishment of self-tolerance. The viral-like properties of ERE-derived MAPs suggest that those not expressed in mTECs can be highly immunogenic.
HostingRepository	PRIDE
AnnounceDate	2020-05-26
AnnouncementXML	Submission_2020-05-26_02:57:36.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD018124
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; monohydroxylated residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-20 07:33:34	ID requested
⏵ 1	2020-05-26 02:57:37	announced

Larouche JD, Trofimov A, Hesnard L, Ehx G, Zhao Q, Vincent K, Durette C, Gendron P, Laverdure JP, Bonneil É, C, ô, t, é C, Lemieux S, Thibault P, Perreault C, Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues. Genome Med, 12(1):40(2020) [pubmed]

submitter keyword: OVCAR-3, 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/2020/05/PXD018124

PRIDE project URI

• PRIDE
  1. PXD018124
     1. Label: PRIDE project
     2. Name: LC-MSMS of OVCAR-3 class I immunopeptidome