Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

• Published in: Molecular & cellular proteomics Vol. 19; no. 9; pp. 1503 - 1522
• Main Authors: Zecha, Jana, Lee, Chien-Yun, Bayer, Florian P., Meng, Chen, Grass, Vincent, Zerweck, Johannes, Schnatbaum, Karsten, Michler, Thomas, Pichlmair, Andreas, Ludwig, Christina, Kuster, Bernhard
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2020; American Society for Biochemistry and Molecular Biology
• Subjects: A549 Cells; ACE2; Amino Acid Sequence; Angiotensin-Converting Enzyme 2; Animals; Betacoronavirus - genetics; Betacoronavirus - pathogenicity; BRCA1 Protein - genetics; BRCA1 Protein - metabolism; Caco-2 Cells; Case-Control Studies; Chlorocebus aethiops; clinical proteomics; Coronavirus Infections - genetics; Coronavirus Infections - pathology; Coronavirus Infections - virology; COVID-19; Gene Expression Regulation; Gene Ontology; Host-Pathogen Interactions - genetics; Humans; Indicators and Reagents; label-free quantification; mass spectrometry; Molecular Sequence Annotation; Open Reading Frames; Pandemics; parallel reaction monitoring; Peptidyl-Dipeptidase A - genetics; Peptidyl-Dipeptidase A - metabolism; Pneumonia, Viral - genetics; Pneumonia, Viral - pathology; Pneumonia, Viral - virology; Proteomics - instrumentation; Proteomics - methods; SARS-CoV-2; Serine Endopeptidases - genetics; Serine Endopeptidases - metabolism; Signal Recognition Particle - genetics; Signal Recognition Particle - metabolism; Signal Transduction; stable-isotope labeling; targeted mass spectrometry; Vero Cells; Vero E6; Viral Proteins - classification; Viral Proteins - genetics; Viral Proteins - metabolism; Virus Internalization; COVID-19; ACE2; SARS-CoV-2; parallel reaction monitoring; label-free quantification; clinical proteomics; mass spectrometry; targeted mass spectrometry; stable-isotope labeling; Vero E6
• ISSN: 1535-9476; 1535-9484
• DOI: 10.1074/mcp.RA120.002164

As the COVID-19 pandemic continues to spread, research on SARS-CoV-2 is also rapidly evolving and the number of associated manuscripts on preprint servers is soaring. To facilitate proteomic research, Zecha et al. present protein expression profiles of four model cell lines and investigate the response of Vero E6 cells to viral infection. Further, they evaluate the feasibility of proteomic analysis for SARS-CoV-2 diagnostics and critically discuss the merits of proteomic approaches in the context of the COVID-19 research. [Display omitted] Highlights •In-depth proteomes of 4 SARS-CoV-2 cell line models (Vero E6, Calu-3, Caco-2, A549).•Proteomic evidence for thousands of Chlorocebus sabaeus proteins.•Proteomic response of Vero E6 cells to SARS-CoV-2 infection.•Synthetic peptides, spectral libraries, and targeted assays for SARS-CoV-2 proteins. 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.