PXD023140

PXD023140 is an original dataset announced via ProteomeXchange.

Title	Tissue adaptation is the dominant driver of the proteomic landscape of intestinal intraepithelial lymphocytes
Description	Intestinal intraepithelial T lymphocytes (T-IEL) patrol the single layer of epithelial cells lining the gut, and consist of both induced T-IEL, derived from systemic antigen-experienced lymphocytes, and natural IEL, that are developmentally targeted to the intestine. To gain functional insights into these enigmatic cells, we used high-resolution quantitative mass spectrometry to investigate the proteomic landscape of the main T-IEL populations in the gut. Comparing the proteomes of induced T-IEL, tissue-resident memory TCRαβ+ CD8αβ+ cells and natural TCRγδ+ CD8αα+ and TCRαβ+ CD8αα+ T-IEL, with naive CD8+ T cells from lymph nodes reveals striking similarities between T-IEL subsets and the dominant effect of the gut environment on T-IEL phenotypes. Analysis of copy numbers/cell of >7000 proteins provides new understanding of the differences in composition of T cell antigen receptor signal transduction pathways in T-IEL versus conventional T cells and reveals skewing of the metabolic machinery towards an exhausted T cell phenotype adapted to the intestinal environment. This study provides a resource for exploring and understanding how multiple inputs are integrated into T-IEL function.
HostingRepository	PRIDE
AnnounceDate	2021-03-15
AnnouncementXML	Submission_2021-09-20_06:07:43.322.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alejandro Brenes
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-15 03:12:06	ID requested
1	2021-03-15 08:59:29	announced
⏵ 2	2021-09-20 06:07:44	announced	2021-09-20: Updated publication reference for PubMed record(s): 34473623.

Brenes AJ, Vandereyken M, James OJ, Watt H, Hukelmann J, Spinelli L, Dikovskaya D, Lamond AI, Swamy M, Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes. Elife, 10():(2021) [pubmed]

submitter keyword: TMT, IEL, T cells, lymphocytes, lymph nodes

Angus I. Lamond
contact affiliation	Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee
contact email	a.i.lamond@dundee.ac.uk
lab head
Alejandro Brenes
contact affiliation	University of Dundee
contact email	ajbrenesmurillo@dundee.ac.uk
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/2021/03/PXD023140

PRIDE project URI

• PRIDE
  1. PXD023140
     1. Label: PRIDE project
     2. Name: Tissue adaptation is the dominant driver of the proteomic landscape of intestinal intraepithelial lymphocytes