PXD024087

PXD024087 is an original dataset announced via ProteomeXchange.

Title	Kinome and phosphoproteome reprogramming underlie the immunological abnormalities in severe COVID-19
Description	The SARS-CoV-2 infection elicits widespread immunological reactions and causes severe diseases in some individuals. However, the molecular basis behind the excessive, yet non-productive immune response in COVID-19 patients with severe diseases is not fully understood. Nor is it fully known of the molecular and cellular discrepancies between severe COVID-19 and sepsis caused by other infections. To gain systems-level insights into the pathogenesis of COVID-19, we compared the blood proteome and phosphoproteome of patients under intensive care with or without SARS-CoV-2 infection, and healthy control subjects by quantitative mass spectrometry. SARS-CoV-2 infection causes global reprogramming of the kinome and the phosphoproteome, resulting in incomplete adaptive immune responses mediated by B cells and T cells, compromised innate immune response via inhibitory SIGLEC and SLAM family receptor signaling, and excessive JAK/STAT signaling. Our work identifies the kinases CK2, SYK, JAK2/3, TYK2, and the cytokine IL-12 as potential targets for the immunomodulatory treatment of severe COVID-19 and provides a valuable resource for deciphering the mechanism of pathogen-host interactions.
HostingRepository	PRIDE
AnnounceDate	2024-05-24
AnnouncementXML	Submission_2024-05-24_03:21:30.301.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tomonori Kaneko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-09 08:57:42	ID requested
⏵ 1	2024-05-24 03:21:31	announced

10.1186/s12014-024-09457-w;

Kaneko T, Ezra S, Abdo R, Voss C, Zhong S, Liu X, Hovey O, Slessarev M, Van Nynatten LR, Ye M, Fraser DD, Li SS, Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients. Clin Proteomics, 21(1):13(2024) [pubmed]

submitter keyword: T cell, immune regulation, phosphoproteome, inhibitory receptor, CK2, SARS-CoV-2, IL-12, SYK,COVID-19, cytokine, natural killer cells, immunoreceptor Tyr-based motifs, signal transduction, B cell, kinase, JAK-STAT, proteome

Shawn SC Li
contact affiliation	Department of Biochemistry, Western University, Canada
contact email	sli@uwo.ca
lab head
Tomonori Kaneko
contact affiliation	Western University
contact email	tkaneko@uwo.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/2024/05/PXD024087

PRIDE project URI

• PRIDE
  1. PXD024087
     1. Label: PRIDE project
     2. Name: Kinome and phosphoproteome reprogramming underlie the immunological abnormalities in severe COVID-19