PXD054443

PXD054443 is an original dataset announced via ProteomeXchange.

Title	Regulatory Role of the VCL/ICAM-1 Pathway in Inflammatory Exudative Damage to the Gas-Blood Barrier in SARS-CoV-2 Infection: New Insights from the Omicron Paradigm
Description	Infections by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), ranging from the initial Wildtype (WT) variant in Wuhan, China, to later variants including Omicron, have showcased a diverse spectrum of symptoms. This diversity underscores the need for ongoing exploration into the virus's elusive pathogenesis. This study employs multi-omics and collaborative validation methods to comprehensively understand SARS-CoV-2's pathology, offering insights that remain pertinent as the virus evolves. Through proteomic analysis, we have identified signaling pathways associated with damage to the vascular system. Importantly, the vinculin (VCL) pathway has been identified as a distinctive feature in Omicron infections, representing a key mechanism causing lung exudation. Metabolomic analysis uncovered disruptions in immune functions, cell membrane stability, and metabolic shifts. Integrated analysis highlighted the involvement of VCL in processes such as inflammation, cell adhesion, and extravasation. A validation cohort confirmed VCL and ICAM1 as Omicron-associated biomarkers. Our mouse model studies not only corroborated these findings but also indicated therapeutic potential of targeting VCL. In contrast to genomic studies highlighting host immunity and infection susceptibility in COVID-19, our research sheds light on the evolving physiological impacts induced by the Omicron variant via the VCL pathway. By our elucidation of key molecular mechanisms involved, provides a strategic direction for developing therapies to address emerging SARS-CoV-2 variants, emphasizing the need for continuous adaptation in combating viral challenges.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_23:07:42.137.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mingshan Xue
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-31 06:48:02	ID requested
⏵ 1	2025-05-06 23:07:42	announced

10.1038/s41467-025-59145-y;

Xue M, Lin Z, Wen Y, Fan S, Li Y, Qu HQ, Hu Q, Guo Q, Su L, Yang Q, Chen J, Jiang C, Huang H, Zheng P, Li N, Yuan Q, Zhang M, Zhao X, Wu Q, Hu F, Li L, Wang X, Liu P, Hakonarson H, Deng Z, Wang H, Tang X, Sun B, VCL/ICAM-1 pathway is associated with lung inflammatory damage in SARS-CoV-2 Omicron infection. Nat Commun, 16(1):3801(2025) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: Multi-Omics

SARS-CoV-2

Omicron

Protein modification

N-Glycosylation

Mingshan Xue
contact affiliation	Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China.
contact email	Frogms@163.com
lab head
Mingshan Xue
contact affiliation	Guangzhou Medical University
contact email	frogms@163.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/2025/05/PXD054443

PRIDE project URI

• PRIDE
  1. PXD054443
     1. Label: PRIDE project
     2. Name: Regulatory Role of the VCL/ICAM-1 Pathway in Inflammatory Exudative Damage to the Gas-Blood Barrier in SARS-CoV-2 Infection: New Insights from the Omicron Paradigm