SARS-CoV-2 infection remodels the host protein thermal stability landscape

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS-CoV-2 hijacks host cellular machineries on a systems-wide scale so that potential host-directed therapy can be developed. In situ proteome-wide abundance and thermal stability measurements using thermal proteome profiling (TPP), can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS-CoV-2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and regulation of RNA splicing. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS-CoV-2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS-CoV-2 infection.

Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing

“…Taken together our data reveal alterations in abundance for many host proteins with the majority showing higher abundance upon infection. Other proteomics studies recently published also report on a large number of significantly altered proteins upon SARS-CoV-2 infection, however with varying fraction of upregulated versus downregulated proteins depending on time point of measurement (6,14).…”

“…Upon infection, viruses commonly hijack host cell machinery to enable replication. This leads to re-organization of the cellular proteome composition (2,3) such as up-or downregulation of signaling pathways (4)(5)(6) which can be quantified by large-scale omics methods. Additionally, host cells may alter abundance of proteins related to cellular defense and homeostasis.…”

Recent advances in isobaric labeling and applications in quantitative proteomics

“…Since TPP's inception, there have been several new methods developed to improve and expand its applicability [ 131 ]. TPP has been expanded to monitor membrane proteins, phosphorylated proteins and peptides via phosphoproteomics combined with TPP (phospho‐TPP), bacteria, plants, plasmodium, yeast, viruses, tissue samples, and plasma membrane proteins [ 132 , 133 , 134 , 135 , 136 , 137 , 138 , 139 , 140 , 141 , 142 , 143 , 144 , 145 ]. Other protocol‐based methods include a two‐dimensional approach that studies protein abundance and regulation changes simultaneously, a proteome integral solubility alteration (PISA) to increase throughput and reduction in data analysis, and utilization of a vacuum manifold to increase throughput [ 146 , 147 ].…”

Individual COVID‐19 disease trajectories revealed by plasma proteomics

“…Mass spectrometry (MS)‐based proteomics is an ideal technology to detect and measure the changes in proteins occurring due to the infection. In the context of cell‐based models, this technology has been applied to study how SARS‐CoV‐2 takes control of its target cell in order to identify potential host targeting drugs that could inhibit viral replication (Bouhaddou et al , 2020; Gordon et al , 2020; Selkrig et al , 2021). However, to understand the process of infection and its impact on human physiology, direct measurements of patient material are needed.…”