Measuring proteomic changes associated with viral infections and neurodegenerative diseases using mass spectrometry

Abstract

Viral infection and the resultant cellular stress can trigger significant changes to the cellular host proteome. Viral proteases essential to viral replication have been shown to cleave human host protein substrates as a mechanism of immune response evasion. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19 and the resulting COVID-19 pandemic. The widespread impact of this virus illustrates the need to better understand its biology and the role of its viral proteases. We used mass spectrometry to characterize the host protein substrates of the SARS-CoV-2 viral proteases that play a role in its evasion of the immune response. We show that bromodomain-containing protein 2 (BRD2) and splicing factor proline- and glutamine-rich (SFPQ) are potential substrates of the SARS-CoV-2 main (Mpro) and papain-like viral proteases (PLpro), respectively. The identification of these human host protein substrates aids in our understanding of the biology of viral infection and how the SARS-CoV-2 virus may evade the host's immune response. Our results may also provide a foundation of knowledge that can be used to guide studies of potential future coronaviruses, similar to how SARS-CoV-1 studies have guided SARS-CoV-2 studies. Additionally, we highlight the use of mass spectrometry as a powerful tool to study proteomic changes in neurodegenerative diseases, viral infections in the cells of the central nervous system, and protein mistranslation. Our investigation into the role of gasdermin-D in multiple sclerosis, using a cuprizone mouse model, demonstrates changes in protein abundance with disease suggesting increased astrocyte and microglia activity. Furthermore, infection of human astrocytes with monkeypox virus (MPXV) and vaccinia virus (VACV) demonstrates the greater impact of MPXV infection on mitochondrial protein functions, compared to VACV infection. Lastly, we present alternative approaches for the identification of protein mistranslation due to oxidative stress and the disrupted function of the methionyl-tRNA synthetase (MARS). These results highlight the need for bioinformatic and database-driven analysis, in addition to traditional mass spectrometry, for the identification of low abundance mistranslational events.