PXD052229-1

PXD052229 is an original dataset announced via ProteomeXchange.

Title	Multi-omics analysis reveals the impact of influenza A virus host adaptation on immune signatures in pig tracheal tissue
Description	Influenza A virus (IAV) infection is a global respiratory disease, which annually leads to 3-5 million cases of severe illness, resulting in 290,000-650,000 deaths. Additionally, during the past century, four global IAV pandemics have claimed millions of human lives. The epithelial lining of the trachea plays a vital role during IAV infection, both as point of viral entry and replication as well as in the antiviral immune response. Tracheal tissue is generally inaccessible from human patients, which makes animal models crucial for the study of the tracheal host immune response. In this study, pigs were inoculated with swine- or human-adapted H1N1 IAV to gain insight into how host adaptation of IAV shapes the innate immune response during infection. In-depth multi-omics analysis (global proteomics and RNA sequencing) of the host response in upper and lower tracheal tissue was conducted, and results were validated by microfluidic qPCR. Additionally, a subset of samples was selected for histopathological examination. A classical innate antiviral immune response was induced in both upper and lower trachea after infection with either swine- or human-adapted IAV with upregulation of genes and higher abundance of proteins associated with viral infection and recognition, accompanied by a significant induction of interferon stimulated genes with corresponding higher proteins concentrations. Infection with the swine-adapted virus induced a much stronger immune response compared to infection with a human-adapted IAV strain in the lower trachea, which could be a consequence of a higher viral load and a higher degree of inflammation. Central components of the JAK-STAT pathway, apoptosis, pyrimidine metabolism, and the cytoskeleton were significantly altered depending on infection with swine- or human-adapted virus and might be relevant mechanisms in relation to antiviral immunity against putative zoonotic IAV. Based on our findings, we hypothesize that during host adaptation, IAV evolve to modulate important host cell elements to favor viral infectivity and replication.
HostingRepository	PRIDE
AnnounceDate	2024-08-08
AnnouncementXML	Submission_2024-08-08_04:48:51.005.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Konstantinos Kalogeropoulos
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-13 09:55:18	ID requested
⏵ 1	2024-08-08 04:48:51	announced
2	2024-10-22 06:52:58	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: immune regulation,Influenza A virus, global proteomics, host adaptation, RNA-seq, host metabolism

Kerstin Skovgaard
contact affiliation	Technical University of Denmark, Department of Biotechnology and Biomedicine
contact email	kesk@dtu.dk
lab head
Konstantinos Kalogeropoulos
contact affiliation	Technical University of Denmark
contact email	konskalogero@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD052229
     1. Label: PRIDE project
     2. Name: Multi-omics analysis reveals the impact of influenza A virus host adaptation on immune signatures in pig tracheal tissue