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.

Nimotuzumab Increases the Recovery Rate of Severe and Critical COVID-19 Patients: Evaluation in the Real-World Scenario

“…Martinez et al, found higher levels of EGFR in COVID-19 individuals vs. community associated pneumonia subjects (19) and osimertinib, a well-known EGFR antagonist, showed in vitro anti-SARS-CoV-2 action (22) and prevented the virus cytopathic effect (23). In addition, several phosphoproteomic studies of SARS-CoV-2-infected cells disclosed that the virus activates EGFR (24). According Camara and Brandao, EGFR is the main influential receptor involved in COVID-19 (25).…”

MALDI MS-Based Investigations for SARS-CoV-2 Detection

“…From the perspective of a high-throughput, routine, diagnostic clinical setting, a viral infection diagnostic tool should consist of an integrated analytical platform, which needs to be fast, sensitive, highly specific, reproducible, and cost-effective. MS techniques have rapidly complemented or replaced conventional methods in clinical diagnostic laboratories and have been successfully implemented in the investigation of viruses and their pathogenesis [17,[21][22][23][24][25][26][27][97][98][99]. In particular, MALDI-MS has become an indispensable and versatile method for biochemical and clinical investigations [100,101].…”

Use of MALDI-TOF mass spectrometry for virus identification: a review

“…In the last decade or even in recent years, numerous reviews focusing on the use of various MS-based methods in clinical microbiology for the detection of different types of pathogens have been published; most of these reviews concentrated on bacterial pathogens and only marginally covered viral pathogens. 29–33 However, with the advent of the COVID-19 pandemic crisis, the literature has been expanded with reviews on the use of MS-based methods for the study and detection of SARS-CoV-2. Recently, reviews on various MS-based strategies for determining the impacts of COVID-19-infection on host cells have been reported.…”