In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over forty million patients worldwide. Although most coronavirus disease 2019 (COVID-19) patients have a good prognosis, some develop severe illness. Markers that define disease severity or predict clinical outcome need to be urgently developed as the mortality rate in critical cases is approximately 61.5%. In the present study, we performed in-depth proteome profiling of undepleted plasma from eight COVID-19 patients. Quantitative proteomic analysis using the BoxCar method revealed that 91 out of 1222 quantified proteins were differentially expressed depending on the severity of COVID-19. Importantly, we found 76 proteins, previously not reported, which could be novel prognostic biomarker candidates. Our plasma proteome signatures captured the host response to SARS-CoV-2 infection, thereby highlighting the role of neutrophil activation, complement activation, platelet function, and T cell suppression as well as proinflammatory factors upstream and downstream of interleukin-6, interleukin-1B, and tumor necrosis factor. Consequently, this study supports the development of blood biomarkers and potential therapeutic targets to aid clinical decision-making and subsequently improve prognosis of COVID-19.
Article activity feed
-
-
SciScore for 10.1101/2020.08.18.255315: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: All patients with positive results for SARS-CoV-2 infection, detected by analyzing the respiratory specimens via PCR, and willing to provide written informed consent were eligible for participation.
IRB: The Ethics Committee and Institutional Review Board of the National Medical Center (IRBRandomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Data processing for label-free quantification: Mass spectra were processed using MaxQuant version 1.6.1.0 [33] MaxQuantsuggested: (MaxQuant, RRID:SCR_014485)The MS proteomics data have been … SciScore for 10.1101/2020.08.18.255315: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: All patients with positive results for SARS-CoV-2 infection, detected by analyzing the respiratory specimens via PCR, and willing to provide written informed consent were eligible for participation.
IRB: The Ethics Committee and Institutional Review Board of the National Medical Center (IRBRandomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Data processing for label-free quantification: Mass spectra were processed using MaxQuant version 1.6.1.0 [33] MaxQuantsuggested: (MaxQuant, RRID:SCR_014485)The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [35] partner repository with the data set identifier PXD020354. PRIDEsuggested: (Pride-asap, RRID:SCR_012052)Statistical analysis: For pair-wise analysis in plasma experiments, data were statistically analyzed using Perseus software [36]. Perseussuggested: (Perseus, RRID:SCR_015753)Bioinformatics analysis: Funtional gene ontology (GO) and pathway enrichment analysis were performed using the EnrichR online tool (http://amp.pharm.mssm.edu/Enrichr/) [8]. EnrichRsuggested: (Enrichr, RRID:SCR_001575)Upstream regulation and protein networks were evaluated via Ingenuity Pathway Analysis (IPA, QIAGEN, Hilden, Germany) based on the DEPs in the plasma experiment. Ingenuity Pathway Analysissuggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
-