PXD033392

PXD033392 is an original dataset announced via ProteomeXchange.

Title	Single-cell transcriptional profiling identifies a spectrum of unconventional intraepithelial T lineage cells in human cord blood
Description	Conventional CD4 and CD8 single positive T cell lineages constitute the main differentiation pathway in the thymus. In human thymus, a minor TCRαβ differentiation pathway diverges from the early double positive stage, consisting of CD10+ PD-1+ cells. These cells are phenotypically and functionally similar to murine agonist-selected intraepithelial T lymphocyte precursors (IELps) which home to the small intestine. Here, the progeny of the human agonist-selected IEL lineage was identified in antigen-inexperienced cord blood (CB) with a polyclonal T cell receptor (TCR) repertoire exhibiting a bias towards early TCR alpha chain rearrangements and elevated autoreactive indices. Single-cell RNA sequencing allowed further delineation of this unconventional lineage in CB. Trajectory analysis, along with TCR repertoire analysis, transcriptomics and proteomics, suggests a precursor-progeny relationship with the thymic IELps. The distinct, heterogeneous CB population can now be defined as CD3+ TCRαβ+ CD4- CCR7- CD26-. Besides recent thymic emigrants, this population also consists of newly identified effector clusters and previously described populations: the suppressive NK receptor expressing CD8+ Treg population, the KIR/NKG2A+ EOMES+ virtual memory population and the CD8αα+ T cell populations. The population shows a discriminating stable HELIOS expression and is exclusively able to downregulate CD8β expression, resulting in double negative T cells. The functional properties of this population suggest that the cells expand on inflammatory cues and exert cytotoxic and proinflammatory activity.
HostingRepository	PRIDE
AnnounceDate	2023-02-10
AnnouncementXML	Submission_2023-02-10_04:38:06.155.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	RupertMayer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-23 15:31:17	ID requested
⏵ 1	2023-02-10 04:38:06	announced

Dataset with its publication pending

submitter keyword: agonist-selection, T cell lineages, shotgun proteomics, Q Exactive HF, human,intraepithelial T cells, cord blood, label-free, thymus

BartVandekerckhove
contact affiliation	Department of Diagnostic Sciences, Ghent University, Ghent, Belgium. Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
contact email	Bart.Vandekerckhove@UGent.be
lab head
RupertMayer
contact affiliation	VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
contact email	rupert.mayer@vib-ugent.be
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/2023/02/PXD033392

PRIDE project URI

• PRIDE
  1. PXD033392
     1. Label: PRIDE project
     2. Name: Single-cell transcriptional profiling identifies a spectrum of unconventional intraepithelial T lineage cells in human cord blood