PXD038810

PXD038810 is an original dataset announced via ProteomeXchange.

Title	Integrative proteomics and transcriptomics of human T-cells reveals temporal changes in metabolic pathways following TCR-mediated activation
Description	T-cells are a critical component of the adaptive immune system and play a key role in immunological surveillance. Upon engagement of T-cell receptor (TCR), CD4+ and CD8+ T-cells acquire effector functions through a complex interplay between mRNA and proteins yet to be fully understood. In this study we explored the temporal transcriptomic and proteomic changes mediated by TCR engagement in both CD4+ and CD8+ T-cells. T-cells isolated from peripheral blood mononuclear cells of three healthy volunteers over 90% purity as assessed by fluorescence-labeled flow cytometry (FACS) and monoclonal antibodies were in vitro activated using anti-CD3/CD28 Dynabeads. Samples obtained before the activation, and 6h, 12h, 24h, 3 days (d), and 7d following activation were analyzed using label-free data-dependent acquisition mass spectrometry-based proteomics (DDA-proteomics), to identify the temporal dynamics in CD4+ and CD8+ T-cell proteomes during activation. A parallel analysis was performed to explore the transcriptomic dynamics during T-cell activation. Our data revealed a time-dependent dissociation between the T-cell transcriptome and proteome: the onset of activation was driven by rapid changes of the mRNA content with sluggish increase in protein synthesis, ultimately leading to rewired transcriptome and proteome. We surprisingly found that CD4+ and CD8+ T-cells became transcriptionally more divergent while their proteome became more similar over the time course of activation. Several changes in the content of mRNAs and proteins associated with metabolic pathways were detected through KEGG pathway analysis, revealing a transient disconnection between the aerobic glycolysis and glutaminolysis pathways in activated T-cells. This dataset provides a comprehensive framework for understanding the main temporal changes that regulate metabolic pathways governing the acquisition of effector functions by CD4+ and CD8+ T-cells.
HostingRepository	PRIDE
AnnounceDate	2024-03-18
AnnouncementXML	Submission_2024-03-18_16:20:21.969.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Harshi Weerakoon
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-13 22:57:28	ID requested
1	2023-12-28 12:01:05	announced
⏵ 2	2024-03-18 16:20:23	announced	2024-03-18: Updated project metadata.

10.1038/s41540-024-00346-4;

Weerakoon H, Mohamed A, Wong Y, Chen J, Senadheera B, Haigh O, Watkins TS, Kazakoff S, Mukhopadhyay P, Mulvenna J, Miles JJ, Hill MM, Lepletier A, Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation. NPJ Syst Biol Appl, 10(1):21(2024) [pubmed]

submitter keyword: Human T cell activation, DDA proteomics, CD8+ T cells,CD4+ T cells

Dr. Ailin Lepletier
contact affiliation	Laboratory of Vaccines for the Developing World, Institute for Glycomics, Southport, QLD, Australia
contact email	a.lepletierdeoliveira@griffith.edu.au
lab head
Harshi Weerakoon
contact affiliation	Senior lecturer, Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka Visiting Scientists, Precision and Systems Biomedicine group, QIMR Berghofer Medical Reserach Institute, Brisbane, Australia
contact email	harshitw83@yahoo.com
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/2023/12/PXD038810

PRIDE project URI

• PRIDE
  1. PXD038810
     1. Label: PRIDE project
     2. Name: Integrative proteomics and transcriptomics of human T-cells reveals temporal changes in metabolic pathways following TCR-mediated activation