PXD004095

PXD004095 is an original dataset announced via ProteomeXchange.

Title	MS-based proteomics of Adeonvirus type 2 infected primary human cells
Description	To combat virus infections, which are major human killers, a deeper understanding of how viruses reprogram their hosts to create optimal production of progeny is needed. Most knowledge on the regulation of cellular gene expression during adenovirus infection is derived from studies of mRNA expression. Here, we investigated the changes in cellular protein expression during the late phase of adenovirus type 2 (Ad2) infection of primary human cells by stable isotope labeling in cell culture (SILAC) with subsequent liquid chromatography-high resolution tandem mass spectrometric (LC-MS/MS) analysis using a Q-Exactive Orbitrap instrument. Cells were in-depth evaluated 24 and 36 hours post infection (hpi) and two biological replicates were investigated using swapped labeling. In total, 2648 and 2394 proteins were quantified at 24 and 36 hpi, respectively. Among them, 659 and 645 were deregulated more than 1.6-fold at the two time points, and approximately 80% of them had sustained regulation from 24 to 36 hpi. For the deregulated genes the change in protein expression was compared with that of RNA expression using cDNA sequencing data from the same time points of infection. The comparison revealed a surprisingly low correlation (r = 0.3). Consistency between changes in RNA and protein expression was observed for approximately 30% of the genes, whereas a majority showed either divergent or opposite expression profiles. The deregulated proteins were subjected to pathway and biological function analysis using bioinformatics tools. A surprising observation was that proteins related to carbohydrate metabolism were up-regulated at the protein level but unchanged at the RNA level whereas histone proteins were down-regulated at the protein level but up-regulated at the RNA level. Our results show that regulation of cellular gene expression in the response to viral infection is more complex than hitherto believed and several examples of posttranscriptional regulation of gene expression were observed. The results contribute to our understanding of host cell gene regulation during infection at a deeper level.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:09.196.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sara Lind
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Human adenovirus C serotype 2 (HAdV-2) (Human adenovirus 2); NCBI TaxID: 10515;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-04 01:25:21	ID requested
1	2016-12-20 06:35:50	announced
⏵ 2	2023-11-14 08:49:09	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

curator keyword: Biomedical

submitter keyword: mass spectrometry, deregulation of host cell proteins,adenovirus type 2 infection, SILAC, IMR-90

Sara Lind
contact affiliation	Uppsala University, Department of Chemistry-BMC, Science for Life Laboratory, Analytical Chemistry.
contact email	sara.lind@kemi.uu.se
lab head
Sara Lind
contact affiliation	Uppsala University
contact email	sara.lind@kemi.uu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004095
     1. Label: PRIDE project
     2. Name: MS-based proteomics of Adeonvirus type 2 infected primary human cells