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Authors: Appelberg et al

Link to paper: https://www.biorxiv.org/content/10.1101/2020.04.30.070383v1

Journal/ Pre-Print: BioRxiv

Tags: Autophagy/Lysosome, Biochemistry, Bioinformatics, Cell Biology, Drug discovery/Drug repurpose, Proteomics

Research Highlights

1. SARS-CoV-2 infection results in changes in the TNF, mTOR, HIF-1α and ERbB pathways

2. mTORC1 signalling was enhanced at initial infection times, but reduced at 72 hours post-infection

3. HIF1-α signalling was inhibited at all infection timepoints

Summary

This study investigates the regulation of host cell biology by SARS-CoV-2 in Huh7 (hepatocarcinoma) cells. The authors performed a time course of infection at 24, 48 and 72 hours using RNA-seq and proteomics and constructed a network of altered pathways. The study identified that TNF, mTOR, HIF-1α and ERbB were dysregulated during infection with interesting temporal dynamics. Specifically, mTORC1 signalling (pS6K1 and p4EBP1) was initially enhanced, but diminished at 72 hours, while HIF1-α was reduced during all infection time points. This study opens up a range of questions, such as the potential therapeutic effect of rapalogs for SARS-CoV-2.

Impact for SARS-CoV2/COVID19 research efforts

Understand the virology and/or cell biology of SARS-CoV2/COVID19: this study identifies a dysregulation in cellular pathways following infection.

Study Type

· In vitro study

Strengths and limitations of the paper

Novelty: The study is novel in that it shows a dysregulation in host pathways, which are important for proliferation, survival and cell death. The authors suggest that rapamycin can be re-purposed for therapeutic use.

Standing in the field: There is evidence for the mTOR pathway being used in MERS-CoV infection and rapamycin can alleviate the infection rate (Kindrachuk, Antimicrob Agents Chemother, 2015). Additionally, a SARS-CoV-2-human protein interaction network identified rapamycin in a range of compounds that could be considered clinically (Gordon et al, Nature, 2020).

Appropriate statistics: Figure 1b/d statistical test not described anywhere

Viral model used: SARS-CoV-2 from Swedish patient; HuH7 cell line

Translatability: Authors suggest that rapamycin treatment might be considered clinically.

Main limitations:

1. How and why mTOR and other pathways change during infection not discussed. The authors could create knockouts/overexpression systems to investigate this.

2. Network of changing proteins could be a lot more informative – what genes are in the clusters of up- or down-regulated genes?

3. The authors explore S6K1 and 4EBP1 but not ULK1, which could be very important for viral evasion strategies.

4. Greater clarity needed for how genes with high centrality presented in S1 and S2 fall into the TNF, mTOR, HIF-1α and ERbB pathways as claimed. Similarly, not clear how Sankey plot proteins were selected.

5. The study utilised a single cell line as the model to understand the cell biology of SARS-CoV-2 infection, which may provide a biased result.

6. The research does not fully validate the results obtained from the bioinformatic analysis.

7. Since most of the signalling pathway relies on the phosphorylation rather than the change of abundance, it is necessary to include the phosphorylation modification during the proteomics analysis.