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

• Published in: PROTEOMICS Vol. 21; no. 10; pp. e2000279 - n/a
• Main Authors: Ahsan, Nagib, Rao, R. Shyama Prasad, Wilson, Rashaun S., Punyamurtula, Ujwal, Salvato, Fernanda, Petersen, Max, Ahmed, Mohammad Kabir, Abid, M. Ruhul, Verburgt, Jacob C., Kihara, Daisuke, Yang, Zhibo, Fornelli, Luca, Foster, Steven B., Ramratnam, Bharat
• Format: Journal Article Web Resource
• Language: English
• Published: Germany John Wiley & Sons, Inc 01.05.2021; Wiley Subscription Services, Inc; John Wiley and Sons Inc
• Subjects: 1-Phosphatidylinositol 3-kinase; AKT protein; biomarkers; Comparative analysis; comparative proteomics; COVID‐19; EphA2 protein; Epidermal growth factor receptors; Infections; Kinases; kinase‐substrate signaling; MAP kinase; Mass spectrometry; Mass spectroscopy; Molecular modelling; Pathogenesis; Platforms; post‐translational modifications; Proteins; Proteomes; Proteomics; Rap1 protein; Review; Scientific imaging; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spectroscopy; targeted proteomics; Tissues; top‐down proteomics; Viral diseases; Viral infections; COVID-19; comparative proteomics; kinase-substrate signaling; top-down proteomics; biomarkers; targeted proteomics; post-translational modifications
• DOI: 10.1002/pmic.202000279
• ISSN: 1615-9853

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.