Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
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Abstract
Analyzing host cells' transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will help delineate biological processes underlying viral pathogenesis. First, analysis of expression profiles of lung cell lines A549 and Calu3 revealed upregulation of antiviral interferon signaling genes in response to all three SARS-CoV-2, MERS-CoV, or influenza A virus (IAV) infections. However, perturbations in expression of genes involved in inflammatory, mitochondrial, and autophagy processes were specifically observed in SARS-CoV-2-infected cells. Next, a validation study in infected human nasopharyngeal samples also revealed perturbations in autophagy and mitochondrial processes. Specifically, mTOR expression, mitochondrial ribosomal, mitochondrial complex I, lysosome acidification, and mitochondrial fission promoting genes were concurrently downregulated in both infected cell lines and human samples. SARS-CoV-2 infection impeded autophagic flux either by upregulating GSK3B in lung cell lines or by downregulating autophagy genes, SNAP29, and lysosome acidification genes in human samples, contributing to increased viral replication. Therefore, drugs targeting lysosome acidification or autophagic flux could be tested as intervention strategies. Finally, age-stratified SARS-CoV-2-positive human data revealed impaired upregulation of chemokines, interferon-stimulated genes, and tripartite motif genes that are critical for antiviral signaling. Together, this analysis has revealed specific aspects of autophagic and mitochondrial function that are uniquely perturbed in SARS-CoV-2-infected host cells.
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SciScore for 10.1101/2020.05.13.092536: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources In this dataset, the A549 treatment conditions included mock, infection with influenza A virus (IAV) (N=2 per group), and infection with SARS-CoV-2 at 2 (high titer, N=3 per group) and 0.2 (low titer, N=3 per group) multiplicity of infection (MOI), after transduction with a vector expressing human ACE2 (hACE2) (N=3 per group). A549suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)From this dataset the raw gene count matrix for 2 healthy … SciScore for 10.1101/2020.05.13.092536: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources In this dataset, the A549 treatment conditions included mock, infection with influenza A virus (IAV) (N=2 per group), and infection with SARS-CoV-2 at 2 (high titer, N=3 per group) and 0.2 (low titer, N=3 per group) multiplicity of infection (MOI), after transduction with a vector expressing human ACE2 (hACE2) (N=3 per group). A549suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)From this dataset the raw gene count matrix for 2 healthy human lung biopsy and one COVID-19 samples (2 technical replicates), and Calu3 cells infected with SARS-CoV-2 at 2 MOI (N=3 per group) were also analyzed. Calu3suggested: KCLB Cat# 30055, RRID:CVCL_0609)Software and Algorithms Sentences Resources Human lung single-cell RNA-seq (scRNA-seq) data with 57 annotated cell types was downloaded from Synapse (accession syn21041850) (101). Synapsesuggested: (Synapse, RRID:SCR_006307)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04322773 Terminated Anti-il6 Treatment of Serious COVID-19 Disease With Threaten… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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