Quantitative Temporal Viromics

Abstract

The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry–based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Virus-host protein co-expression networks reveal temporal organization and strategies of viral infection

“…We gathered experimental protein abundances from time resolved proteome experiments employing tandem mass tags (TMM) and triple-stage mass spectrometry (MS3), which considerably reduce experimental noise and allow precise quantitation of thousands of viral and host proteins 1 . In particular, we analysed protein abundance data from four large double-stranded DNA viruses.…”

“…The fourth virus analysed, Vaccinia virus (VACV) 3 is an archetype of the pox viral family and genetically related to variola virus, responsible for smallpox. Although up to 19 different viruses have been studied with temporal proteomic techniques 1 , we selected those viruses with a relatively large genome and a sizable number of quantified viral proteins, and at least five experimental time points. Details on the viruses and data sets are provided in Supplemental Table S1.…”

“…We found that only ∼12-18% of all quantified host proteins were differentially expressed (FDR < 0.05) with respect to the non-infected case at least at one time point, but nearly all quantified viral proteins over-expressed with respect to the control (Table S1). We note that the experimental protein quantification protocol is the same for all viruses analysed 1 , and all time-point samples per virus are analysed in the same LC-MS/MS run, which reduces experimental variability and allows for reliable comparisons across conditions (post-infection time). Nevertheless, to take into account possible effects of composition bias between samples, we used trimmed mean of M-values (TMM) normalization 72 of data for further analyses, as has been done in other quantitative temporal viromics studies 2 .…”

“…Throughout an infection, viruses hijack different cellular processes of the host cell, dynamically remodelling the abundance, modifications and interactions of many proteins. Recent improvements in proteomic techniques have enabled precise quantification of thousands of host and viral proteins at different times post-infection 1 . By simultaneously measuring the abundance of host and viral proteins in a reference (non-infected) situation, these experiments open the possibility to examine which proteins are significantly altered during the infection and when, thus highlighting biologically relevant pathways and potential therapeutic targets 1–3 .…”

“…Currently, most analyses of time-resolved proteome abundances have focused on clustering proteins by similarity in expression profiles, followed by functional analysis such as pathway or gene set enrichment analysis (GSEA) 1,4 . These studies have revealed host signalling and metabolic pathways affected by the viral infection 2,5,6 and unveiled viral strategies to evade the immune response of the host cell 3,7–9 .…”