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PXD022889

PXD022889 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteomic signature of host response to SARS-CoV-2 infection in the nasopharynx
DescriptionCoronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 infection has become a global health pandemic. COVID-19 severity ranges from asymptomatic infection to severe multi-organ disease. Although the inflammatory response has been implicated in the pathogenesis of COVID-19, the exact nature of dysregulation in signaling pathways has not yet been elucidated underscoring the need for further molecular characterization of SARS-CoV-2 infection in humans. Here, we characterize the host response directly at the point of viral entry through analysis of nasopharyngeal swabs. Multiplexed high resolution mass spectrometry-based proteomic analysis of confirmed COVID-19 cases and negative controls identified 7,682 proteins and revealed significant upregulation of interferon-mediated antiviral signaling in addition to multiple other proteins that are not interferon-stimulated genes (ISGs) or well-characterized during viral infections. Downregulation of several proteasomal subunits, E3 ubiquitin ligases, and components of protein synthesis machinery was significant upon SARS-CoV-2 infection. Targeted proteomics to measure abundance levels of MX1, ISG15, Stat1, RIG-I and CXCL10, permitted differentiation of COVID-19 positive from negative cases. Phosphoproteomic analysis revealed increased phosphorylation of several proteins with known antiviral properties and as well as several proteins including CEP131, CFAP57 and xxxx that have not previously been implicated in the context of viral (or coronavirus) infections. Additionally, decreased phosphorylation levels of AKT and PKC, which have been shown to play varying role in different viral infections, were observed in infected individuals relative to controls. These data provide novel insights that add depth to our understanding of SARS-CoV-2 infection in the upper airway and help characterize a signature for this viral infection.
HostingRepositoryPRIDE
AnnounceDate2021-08-09
AnnouncementXMLSubmission_2021-08-09_09:08:04.100.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAkhilesh Pandey
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Eclipse; Orbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-12-03 03:17:41ID requested
12021-08-09 09:08:04announced
Publication List
Dataset with its publication pending
Keyword List
ProteomeXchange project tag: Covid-19
submitter keyword: Phosphoproteomics, virus, infection, upper airway, COVID-19, interferon, host response
Contact List
Dr. Akhilesh Pandey
contact affiliationDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
contact emailpandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliationDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact emailpandey.akhilesh@mayo.edu
dataset submitter
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Dataset FTP location
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