“Multiomics” Approaches to Understand and Treat COVID-19: Mass Spectrometry and Next-Generation Sequencing

Abstract

In the race against COVID-19 for timely therapeutic developments, mass spectrometry-based high-throughput methods have been valuable. COVID-19 manifests an extremely diverse spectrum of phenotypes from asymptomatic to life-threatening, drastic elevations in immune response or cytokine storm, multiple organ failure and death. These observations warrant a detailed understanding of associated molecular mechanisms to develop therapies. In this direction, high-throughput methods that generate large datasets focusing on changes in protein interactions, lipid metabolism, transcription, and epigenetic regulation of gene expression are extremely beneficial sources of information. Hence, mass spectrometry-based methods have been employed in several studies to detect changes in interactions among host proteins, and between host and viral proteins in COVID-19 patients. The methods have also been used to characterize host and viral proteins, and analyze lipid metabolism in COVID-19 patients. Information obtained using the above methods are complemented by high-throughput analysis of transcriptomic and epigenomic changes associated with COVID-19, coupled with next-generation sequencing. Hence, this review discusses the most recent studies focusing on the methods described above. The results establish the importance of mass spectrometry-based studies towards understanding the infection process, immune imbalance, disease mechanism, and indicate the potential of the methods’ therapeutic developments and biomarker screening against COVID-19 and future outbreaks.

Developmental Impacts of Epigenetics and Metabolism in COVID-19

“…Collectively, the available information establishes a strong foundation for further research in epigenetics and metabolism associated with viral infections, involving large cohorts of patients and utilizing cutting-edge multiomcs coupled with next-generation sequencing and advanced bioinformatics analysis [7,9,50,[142][143][144]. These studies will contribute to targeted therapeutic development and precision medicine (Figure 3).…”

How Is Mass Spectrometry Tackling the COVID-19 Pandemic?

“…Still and despite this progress, the full potential of MS applications against the COVID-19 pandemic remains to be seen. While previous MS-based reviews have zoomed in primarily on how MS approaches complement other types of diagnostics (Mahmud and Garrett, 2020;SoRelle et al, 2020;Appiasie et al, 2021;Yuan and Hu, 2021;Zhong et al, 2021;Amiri-Dashatan et al, 2022;Lima et al, 2022;Spick et al, 2022), in the following paragraphs, we will also showcase examples of MS-based strategies focused on improving our understanding of the SARS-CoV-2 virus' pathophysiology.…”

Editorial: The application of OMICS technologies to interrogate host-virus interactions

“…More recently, network analysis has been progressively used to identify promising targets for therapeutic interventions and drug repurposing, and is now playing a role in vaccine development studies ( Hagan et al., 2015 ; Pulendran et al., 2021 ). At the same time, reduced sequencing costs and evolving hardware capabilities now allow for massive projects involving multi-omics data integration ( Sammut et al., 2022 ) and reviewed in ( Wang et al 2019 ; Appiasie et al., 2021 ). Therefore, this Research Topic discloses the state-of-the-art omics technology applied to virus-host interactions.…”