Home Systems biology Study identifies enzyme with significant impact on SARS-CoV-2 replication

Study identifies enzyme with significant impact on SARS-CoV-2 replication

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By applying a systems biology approach, a recent bioRxiv* preprinted research paper by scientists at Icahn’s Mount Sinai School of Medicine in New York Unveils Interactions between the Mitogen Activated Protein Kinase (MAPK) Pathway Responsible for Regulating the Expression of Critical Inflammatory Mediators in human lung epithelial cells.

Severe cases of coronavirus disease (COVID-19), which are caused by SARS-CoV-2, are associated with extreme inflammatory processes in the lungs that can lead to acute respiratory distress syndrome, lung failure or multiple organ failure – and even death.

Previous studies have shown that the p38 / MAPK pathway is activated during infection with the aforementioned virus and that inhibition of p38 can slow down inflammatory cytokine expression and viral replication, implying that inhibition of p38 may in fact target several mechanisms related to the pathogenesis of SARS-CoV-2.

However, while the exact mechanisms by which our body’s p38 / MAPK pathway is able to modulate inflammatory cytokine gene expression and RNA stability are described in detail, how inhibition of p38 / MAPK can reduce SARS-CoV remains a mystery. 2 replication.

In addition, there are four different isoforms of p38 kinase (i.e. proteins similar to each other that perform analogous roles in cells) and different effector kinases downstream, so we still don’t know which ones. kinases at which levels of the p38 / MAPK pathway can impact SARS-CoV-2 replication.

Therefore, it sparked the interest of a group of scientists led by Dr Christina A. Higgins and Dr Jeffrey R. Johnson of the Icahn School of Medicine at Mount Sinai in New York (USA). They have used a plethora of cutting edge methods to answer these insightful questions.

A comprehensive research approach

In this study, researchers combined small interfering RNA (siRNA) screening, quantitative proteomics, as well as chemical and genetic disturbances to elucidate the interactions between the p38 / MAPK pathway and SARS-CoV-2 in infected cells.

Specifically, four isoforms of the p38 kinase (p38α, p38β, p38γ, p38δ) were evaluated in depth and putative substrates of p38β were impartially identified, with substantial relevance beyond the biology of SARS-CoV -2. In addition, gene ontology enrichment and kinase activity analyzes were also continued.

In short, their overall research approach covered a wide range of classical virology techniques (such as plaque assays for direct counting of infectious particles) and relatively modern approaches such as genetic sequencing and mass spectrometry.

A key player in the replication of SARS-CoV-2

This study found that several components of the p38 / MAPK pathway can positively and negatively impact SARS-CoV-2 infection. Overall, the activity of this pathway increases dramatically during SARS-CoV-2 infection in human lung cells.

Meta-analysis of SARS-CoV-2 proteomics studies reveals systematically regulated pathways across species and cell types.  A) Schematic of experimental design.  B) Average of protein groups and phosphorylation site groups quantified under each condition.  Error bars correspond to the standard deviation.  C) The number of differentially expressed protein clusters and phosphorylation site clusters for SARS-CoV-2 infected cells folds over simulated infected cells E) Analysis of kinase activity based on profiles of log2fold change from this study and published studies indicated.  The absolute value of the Normalized Enrichment Score (NES) is indicated by the size of the nodes and the -Log10 (p-value) is indicated by the color scale.  Decreases in kinase activity are indicated by negative values ​​of -LogP.  F) The log2-fold change profiles transformed by the Z-score of p38 / MAPK kinases p38α and MK2 in this study and published studies indicated.  Each row represents a protein substrate of the respective kinase with the log2-fold maximum change of all phosphorylation sites, each substrate being indicated by the color scale.

Meta-analysis of proteomics studies on SARS-CoV-2 reveals systematically regulated pathways across species and cell types. A) Schematic of experimental design. B) Average of protein groups and phosphorylation site groups quantified under each condition. Error bars correspond to the standard deviation. C) The number of differentially expressed protein clusters and phosphorylation site clusters for SARS-CoV-2 infected cells folds over simulated infected cells E) Analysis of kinase activity based on profiles of log2fold change from this study and published studies indicated. The absolute value of the Normalized Enrichment Score (NES) is indicated by the size of the nodes and the -Log10 (p-value) is indicated by the color scale. Decreases in kinase activity are indicated by negative -LogP values. F) The log2-fold change profiles transformed by the Z-score of p38 / MAPK kinases p38α and MK2 in this study and published studies indicated. Each row represents a protein substrate of the respective kinase with the log2-fold maximum change of all phosphorylation sites, each substrate being indicated by the color scale.

From the kinase isoforms that have been tested, p38β has been shown to be an essential host factor for the replication of SARS-CoV-2 in human lung epithelial cells, but also for the translation of viral proteins without innate immune detection. The researchers also found that inhibiting p38 can reduce viral protein levels but does not impact viral messenger RNA (mRNA) levels.

Finally, inhibition of p38 has been shown to decrease phosphorylation levels at several sites of the core (or N) protein of SARS-CoV-2, which is a multifunctional structure that binds to the genome of the Viral RNA and packs it into a long helical structure.

Implications for the treatment of COVID-19

These results not only improve our understanding of the basic biology of SARS-CoV-2, but can also be used to identify new drug targets for the treatment of COVID-19 and to pave the way for the identification of kinase substrates that can be widely applied in different research. areas.

“These data, in addition to other research focused on p38ß, underscore the need for specific inhibitors and reagents of p38ß to help better characterize this isoform,” say the study authors in this report. bioRxiv preprint paper.

“p38β does not appear to be essential, and it has a significantly smaller active site than p38α which may allow the development of specific inhibitors, so we believe that p38β may be an attractive target,” they add.

In any case, further studies are needed to solve the enigma of p38ß promoting the translation of viral proteins, as well as to evaluate its role in the replication of other coronaviruses, but also of other families of viral agents. potentially emerging.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be considered conclusive, guide clinical practice / health-related behavior, or treated as established information.


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