PXD024846

PXD024846 is an original dataset announced via ProteomeXchange.

Title	Antiviral HCV Treatment Induces Rapid Proteomic and Phospho-proteomic Changes in Hepatic Interferon and ERK1/2 Signaling Pathways
Description	Although treatment of chronic hepatitis C virus (HCV) infection with direct acting antivirals (DAAs) results in high rates of cure, liver fibrosis does not resolve immediately after HCV eradication. Resolution of fibrosis occurs in some, but not all patients, after HCV cure, and hepatic decompensation and hepatocellular carcinoma can still occur in patients with pre-existing cirrhosis. We hypothesized that evaluation of the host liver proteome in the context of HCV treatment would provide insight into how inflammatory and fibrinogenic pathways change upon HCV eradication. We evaluated the whole liver proteome and phosphoproteome using paired liver biopsies from 8 HCV-infected patients collected before or immediately after treatment with DAAs in clinical trials. We identify interferon stimulated proteins as the predominant pathways that decrease with HCV treatment, which is consistent with previous analyses of the liver transcriptome during DAA therapy. While there was no change in the proteome of pathways associated with liver fibrosis, we identified a decrease in the phosphoproteome signature for ERK1/ERK2 as a result of HCV treatment. Conclusion: There is a reduction in the endogenous interferon-mediated antiviral response and alterations in the phosphoproteome that may precede resolution of fibrosis in the liver immediately after treatment of HCV with DAAs.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:37:19.382.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024846
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jennifer Bethard
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-18 23:43:01	ID requested
1	2023-03-10 21:10:23	announced
⏵ 2	2023-11-14 08:37:21	announced	2023-11-14: Updated project metadata.

Ball LE, Agana B, Comte-Walters S, Rockey DC, Masur H, Kottilil S, Meissner EG, Hepatitis C virus treatment with direct-acting antivirals induces rapid changes in the hepatic proteome. J Viral Hepat, 28(11):1614-1623(2021) [pubmed]

10.6019/PXD024846;

submitter keyword: Phosphoproteomics, HCV, liver biopsy,Proteomics, DAA

Eric Meissner, M.D., Ph.D.
contact affiliation	Medical Univeristy of South Carolina Division of Infectious Diseases Department of Microbiology and Immunology
contact email	meissner@musc.edu
lab head
Jennifer Bethard
contact affiliation	Medical University of SC
contact email	bethard@musc.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/2023/03/PXD024846

PRIDE project URI

• PRIDE
  1. PXD024846
     1. Label: PRIDE project
     2. Name: Antiviral HCV Treatment Induces Rapid Proteomic and Phospho-proteomic Changes in Hepatic Interferon and ERK1/2 Signaling Pathways