Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches.

Abstract

While protein-protein interaction is the first step of the SARS-CoV-2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and rationalize the results obtained by various mass spectrometry (MS)-based proteomic approaches applied to the functional characterization of proteins and pathways associated with SARS-CoV-2-mediated infections in humans. Comparative analysis of cell-lines versus tissue samples indicates that our knowledge in proteome profile alternation in response to SARS-CoV-2 infection is still incomplete and the tissue-specific response to SARS-CoV-2 infection can probably not be recapitulated efficiently by in vitro experiments. However, regardless of the viral infection period, sample types, and experimental strategies, a thorough cross-comparison of the recently published proteome, phosphoproteome, and interactome datasets led to the identification of a common set of proteins and kinases associated with PI3K-Akt, EGFR, MAPK, Rap1, and AMPK signaling pathways. Ephrin receptor A2 (EPHA2) was identified by 11 studies including all proteomic platforms, suggesting it as a potential future target for SARS-CoV-2 infection mechanisms and the development of new therapeutic strategies. We further discuss the potentials of future proteomics strategies for identifying prognostic SARS-CoV-2 responsive age-, gender-dependent, tissue-specific protein targets.

• Authors: Nagib Ahsan, R Shyama Prasad Rao, Rashaun S Wilson, Ujwal Punyamurtula, Fernanda Salvato, Max Petersen, Mohammad Kabir Ahmed, M Ruhul Abid, Jacob C Verburgt, Daisuke Kihara, Zhibo Yang, Luca Fornelli, Steven B Foster, Bharat Ramratnam
• Journal: Proteomics (Proteomics) Vol. 21 Issue 10 Pg. e2000279 (05 2021) ISSN: 1615-9861 [Electronic] Germany
• PMID: 33860983 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, U.S. Gov't, Non-P.H.S., Review)
• Copyright: © 2021 Wiley-VCH GmbH.

Chemical References

• Proteome
• Protein Kinases
• Receptor, EphA2

Topics

• Animals
• COVID-19 (diagnosis, metabolism, pathology)
• Host-Pathogen Interactions
• Humans
• Mass Spectrometry (methods)
• Protein Interaction Mapping (methods)
• Protein Interaction Maps
• Protein Kinases (analysis, metabolism)
• Protein Processing, Post-Translational
• Proteome (analysis, metabolism)
• Proteomics (methods)
• Receptor, EphA2 (analysis, metabolism)
• SARS-CoV-2 (physiology)
• Signal Transduction