PXD037265-3

PXD037265 is an original dataset announced via ProteomeXchange.

Title	Total Proteomics of SARS-CoV-2 variants
Description	The ancestral SARS-CoV-2 strain that initiated the Covid-19 pandemic at the end of 2019 has rapidly mutated into multiple variants of concern with variable pathogenicity and increasing immune escape strategies. However, differences in host cellular antiviral responses upon infection with SARS-CoV-2 variants remains elusive. Leveraging whole cell proteomics, we determined host signalling pathways that are differentially modulated upon infection with the clinical isolates of the ancestral SARS-CoV-2 B.1 and the variants of concern Delta and Omicron BA.1. Our findings illustrate alterations in the global host proteome landscape upon infection with SARS-CoV-2 variants and the resulting host immune responses. Additionally, viral proteome kinetics reveal declining levels of viral protein expression during Omicron BA.1 infection when compared to ancestral B.1 and Delta variants, consistent with its reduced replication rates. Moreover, molecular assays reveal deferral activation of specific host antiviral signalling upon Omicron BA.1 and BA.2 infection. Our study provides an overview of host proteome profile of multiple SARS-CoV-2 variants and brings forth a better understanding of the instigation of key immune signalling pathways causative for the differential pathogenicity of SARS-CoV-2 variants.
HostingRepository	PRIDE
AnnounceDate	2023-12-09
AnnouncementXML	Submission_2023-12-08_16:49:11.096.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD037265
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christian Münch
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-10 07:56:35	ID requested
1	2023-05-10 16:05:39	announced
2	2023-11-14 08:47:58	announced	2023-11-14: Updated project metadata.
⏵ 3	2023-12-08 16:49:11	announced	2023-12-09: Updated project metadata.

10.1016/j.mcpro.2023.100537;

Metzler M, Tharyan RG, Klann K, Grikscheit K, Bojkova D, Cinatl J, Tascher G, Ciesek S, M, ü, nch C, SARS-CoV-2 Variants Show Different Host Cell Proteome Profiles With Delayed Immune Response Activation in Omicron-Infected Cells. Mol Cell Proteomics, 22(5):100537(2023) [pubmed]

ProteomeXchange project tag: Covid-19, Sars-cov-2

submitter keyword: Delta, SARS-CoV-2,Omicron

Christian Münch
contact affiliation	Faculty of Medicine, Institute of Biochemistry II, Goethe University, 60590 Frankfurt am Main, Germany. Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany. Cardio-Pulmonary Institute, Goethe University, 60590 Frankfurt am Main, Germany
contact email	ch.muench@em.uni-frankfurt.de
lab head
Christian Münch
contact affiliation	Goethe University Frankfurt
contact email	ch.muench@em.uni-frankfurt.de
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/2023/05/PXD037265

PRIDE project URI

• PRIDE
  1. PXD037265
     1. Label: PRIDE project
     2. Name: Total Proteomics of SARS-CoV-2 variants