ABSTRACT
Coronavirus disease 2019 (COVID-19) is a highly contagious infection and threating the human lives in the world. The elevation of cytokines in blood is crucial to induce cytokine storm and immunosuppression in the transition of severity in COVID-19 patients. However, the comprehensive changes of serum proteins in COVID-19 patients throughout the SARS-CoV-2 infection is unknown. In this work, we developed a high-density antibody microarray and performed an in-depth proteomics analysis of serum samples collected from early COVID-19 (n = 15) and influenza (n = 13) patients. We identified a large set of differentially expressed proteins (n = 132) that participate in a landscape of inflammation and immune signaling related to the SARS-CoV-2 infection. Furthermore, the significant correlations of neutrophil and lymphocyte with the CCL2 and CXCL10 mediated cytokine signaling pathways was identified. These information are valuable for the understanding of COVID-19 pathogenesis, identification of biomarkers and development of the optimal anti-inflammation therapy.
Subject(s)
Blood Proteins/immunology , Coronavirus Infections/immunology , Cough/immunology , Cytokine Release Syndrome/immunology , Fever/immunology , Headache/immunology , Influenza, Human/immunology , Myalgia/immunology , Pneumonia, Viral/immunology , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus/pathogenicity , Blood Proteins/genetics , COVID-19 , Child , Coronavirus Infections/genetics , Coronavirus Infections/physiopathology , Coronavirus Infections/virology , Cough/genetics , Cough/physiopathology , Cough/virology , Cytokine Release Syndrome/genetics , Cytokine Release Syndrome/physiopathology , Cytokine Release Syndrome/virology , Cytokines/genetics , Cytokines/immunology , Female , Fever/genetics , Fever/physiopathology , Fever/virology , Gene Expression Profiling , Gene Expression Regulation , Headache/genetics , Headache/physiopathology , Headache/virology , Humans , Influenza, Human/genetics , Influenza, Human/physiopathology , Influenza, Human/virology , Male , Middle Aged , Myalgia/genetics , Myalgia/physiopathology , Myalgia/virology , Orthomyxoviridae/pathogenicity , Pandemics , Pneumonia, Viral/genetics , Pneumonia, Viral/physiopathology , Pneumonia, Viral/virology , Protein Array Analysis , Proteome/genetics , Proteome/immunology , Receptors, Cytokine/genetics , Receptors, Cytokine/immunology , SARS-CoV-2 , Signal Transduction/immunologyABSTRACT
As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their protein expression profiles including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the breast cancer oncogene BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein-coding regions of the African green monkey and the Vero cell line genomes. Monitoring changes of the proteome on viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors, and proteins involved in innate immunity. Based on a library of 98 stable-isotope labeled synthetic peptides representing 11 SARS-CoV-2 proteins, we developed PRM (parallel reaction monitoring) assays for nano-flow and micro-flow LC-MS/MS. We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of MS-based proteomics for SARS-CoV-2 research and testing.