PXD046976-1

PXD046976 is an original dataset announced via ProteomeXchange.

Title	Differential contributions of interferon classes to driving host inflammatory responses and restricting virus progeny production
Description	The cornerstone of mammalian intrinsic and innate immune defense against pathogens is the production of interferons (IFN), cytokines that stimulate anti-pathogen signaling pathways through the simultaneous expression of hundreds of interferon-stimulated genes (ISG). We compared the effects of IFN classes on the cellular proteome and relative restriction of virus progeny production across multiple physiologically relevant cell types and viruses. We integrated global proteome analyses with targeted mass spectrometry (MS), thermal proximity coaggregation-MS (TPCA-MS), and molecular virology assays to determine how ISGs differentially contribute to host antiviral capacities between immune-modulatory cell types. In differentiated macrophage-like monocytic cells, we classified sets of both shared and distinct ISG proteins responsive to each IFN class. We orthogonally confirmed the relative protein alterations using parallel reaction monitoring (PRM) by developing a proteotypic peptide library for ISG markers induced by each IFN class. Additional comparison to stimulation with pro-inflammatory LPS helped to contextualize the observed IFN signatures. We further assessed ISG protein interactions upon IFN types I and II stimulation, observing maintenance of key ISG protein complexes across treatments. Subsequent comparison of macrophage-like monocytic cells to primary keratinocytes enabled us to identify relative ISG abundances, cytokine induction, and antiviral capacities of both cell types across infections with several ubiquitous human viruses. Infections with herpes simplex virus-1 (HSV-1), adenovirus (AdV), and human cytomegalovirus (HCMV) revealed cell type-dependent differences in virus progeny production.
HostingRepository	PRIDE
AnnounceDate	2024-02-28
AnnouncementXML	Submission_2024-02-28_11:28:37.973.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Krystal Lum
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-14 19:25:46	ID requested
⏵ 1	2024-02-28 11:28:38	announced
2	2024-10-22 06:31:54	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: macrophage, thermal proximity coaggregation,Interferon-beta, human cytomegalovirus, herpes simplex virus-1, interferon-gamma, adenovirus, parallel reaction monitoring, monocyte, interferon-stimulated gene, gingival keratinocyte

Ileana Cristea
contact affiliation	Princeton University
contact email	icristea@princeton.edu
lab head
Krystal Lum
contact affiliation	Princeton University
contact email	klum@princeton.edu
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/2024/02/PXD046976

PRIDE project URI

• PRIDE
  1. PXD046976
     1. Label: PRIDE project
     2. Name: Differential contributions of interferon classes to driving host inflammatory responses and restricting virus progeny production