PXD032333-1

PXD032333 is an original dataset announced via ProteomeXchange.

Title	Proteomic snapshot of saliva samples reveals new pathways implicated in SARS-CoV-2 pathogenesis
Description	Variations in the susceptibility to SARS-CoV-2 infection and risk of severe disease are yet not well understood. The information on the human pathways and active members of the microbiome that can affect SARS-CoV-2 susceptibility and disease progression in the saliva is very scarce. Here, we studied 10 hospitalized patients with severe and moderate COVID-19 (Scov and Mcov) at an early stage of the disease during April to June 2020, compared to 10 uninfected individuals, including healthcare workers with repeated high-risk exposures to the virus but not infected (Non-susceptible, Nsus) and subjects who became infected during the follow-up (susceptible, Non-COVID, Ncov). We performed high-throughput proteomic profiling in saliva to determine the human pathways and active members of the microbiome across individuals. We detected differentially expressed proteins between groups, being the differences especially remarkable in the comparison between the non-infected vs the non-susceptible groups. In a functional analysis to correlate the putative protein biomarkers with relevant biological functions, we found increased expression of proteins related to inflammatory responses and central cellular processes and decreased expression of molecules involved in antiviral activity. The most noteworthy are the Cystatin family, protective molecules present at the oral cavity, the Calprotectin family involved in cell cycle progression, or the Histone family related to nucleosome functions. Furthermore, since proteomics allows checking microbiome functionality, we explored bacterial products and found in the COVID-19+ group 4 overrepresented genera and 2 phyla together with 4 main functional features (KOs) related to ribosomal proteins. Finally, we studied correlations with the plasma activity of the molecular target of SARS-CoV-2, ACE2, and found a link with two proteins related to protein transport through the microtubules in the cytoplasm (DYBC1 and MAPR1). Our study delineates new mechanisms of SARS-CoV-2 susceptibility and progression to severe disease that may help find better therapies for COVID-19.
HostingRepository	PRIDE
AnnounceDate	2024-05-31
AnnouncementXML	Submission_2024-05-31_09:16:00.697.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD032333
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sergio Ciordia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-16 09:17:56	ID requested
⏵ 1	2024-05-31 09:16:01	announced

10.1186/s12014-024-09482-9;

Moreno E, Ciordia S, F, á, tima SM, Jim, é, nez D, Mart, í, nez-Sanz J, Vizcarra P, Ron R, S, á, nchez-Conde M, Bargiela R, Sanchez-Carrillo S, Moreno S, Corrales F, Ferrer M, Serrano-Villar S, Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis. Clin Proteomics, 21(1):37(2024) [pubmed]

10.6019/PXD032333;

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

submitter keyword: functional analysis,proteomics, SARS-CoV-2, saliva, pathogenesis

Sergio Serrano-Villar
contact affiliation	Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, IRYCIS. AND CIBERInf, Instituto de Salud Carlos III. Madrid, Spain
contact email	sergio.serrano@salud.madrid.org
lab head
Sergio Ciordia
contact affiliation	Spanish National Center for Biotechnology
contact email	sciordia@cnb.csic.es
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/2024/05/PXD032333

PRIDE project URI

• PRIDE
  1. PXD032333
     1. Label: PRIDE project
     2. Name: Proteomic snapshot of saliva samples reveals new pathways implicated in SARS-CoV-2 pathogenesis