PXD052223

PXD052223 is an original dataset announced via ProteomeXchange.

Title	Multi-level proteomics profiling of virus-restrictive and -permissive cellular environments reveal novel regulators of virus infection
Description	Virus proliferation inside host cells relies on a diverse range of host machineries and is also restricted by the host through expressions of antiviral factors. The configuration of virus-dependency and antiviral factors determine the permissiveness of host cells to virus infection, however, overall differences between highly permissive and restrictive cellular states remain largely unexplored. Here we employed an integrated omics analysis combining RNA-seq, proteomics, and phosphoproteomics to study determinants of virus permissiveness across cellular states. We focused on a model system comprising highly permissive cells (HEK293T), steady-state cells (HEK293), and highly restrictive cells (interferon alpha (IFN-a) stimulated HEK293) due to their similar genetic background and distinct virus permissiveness. Our dataset provides an in-depth proteomics map across these cellular states, which revealed pathway-level depletion of innate immune response and enrichment of anabolic processes in HEK293T cell. RNA-seq and proteomics results depicted dynamic regulations of IFN-a response across early/late timepoints and highlighted a group of robustly upregulated antiviral factors. In addition, phosphoproteomics uncovered extensive alterations of phosphorylation in IFN-a response. Integrated analysis of multi-level omics results identified putative regulators of infection that are previously under-described, and we experimentally verified 13 proteins with their regulatory roles in virus infection.
HostingRepository	PRIDE
AnnounceDate	2025-06-16
AnnouncementXML	Submission_2025-06-15_17:39:26.202.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Honglin Chen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; isotope labeled residue; iodoacetamide derivatized residue
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-13 08:06:13	ID requested
⏵ 1	2025-06-15 17:39:27	announced

10.1016/j.mcpro.2025.100966;

Chen H, Charles PD, Gu Q, Liberatori S, Robertson DL, Palmarini M, Wilson SJ, Mohammed S, Castello A, Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States. Mol Cell Proteomics, 24(5):100966(2025) [pubmed]

submitter keyword: Human, innate immunity, LC-MSMS, HEK293 cell line, proteomics, SILAC, phosphoproteomics, HEK293T cell line

Alfredo Castello
contact affiliation	Centre for Virues Research, University of Glasgow
contact email	alfredo.castello@glasgow.ac.uk
lab head
Honglin Chen
contact affiliation	Centre for Virus Research, University of Glasgow
contact email	2722555C@student.gla.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/2025/06/PXD052223

PRIDE project URI

• PRIDE
  1. PXD052223
     1. Label: PRIDE project
     2. Name: Multi-level proteomics profiling of virus-restrictive and -permissive cellular environments reveal novel regulators of virus infection