Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells

References

• Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020 Feb 19;20(5):533–534.
   PubMed Web of Science ®Google Scholar
• Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar;579(7798):270–273.
   PubMed Web of Science ®Google Scholar
• Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020 Mar;579(7798):265–269.
   PubMed Web of Science ®Google Scholar
• Rohde C, Becker S, Krahling V. Marburg virus regulates the IRE1/XBP1-dependent unfolded protein response to ensure efficient viral replication. Emerg Microbes Infect. 2019;8(1):1300–1313.
   PubMed Web of Science ®Google Scholar
• Monteil V, Kwon H, Prado P, et al. Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell. 2020 May 14;181(4):905–913.e7.
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139–140.
   PubMed Web of Science ®Google Scholar
• Willforss J, Chawade A, Levander F. NormalyzerDE: online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis. J Proteome Res. 2019 Feb 1;18(2):732–740.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015 Apr 20;43(7):e47.
   PubMed Web of Science ®Google Scholar
• Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016 Jul 8;44(W1):W90–W97.
   PubMed Web of Science ®Google Scholar
• Csardi G, Nepusz T. The igraph software package for complex network research. Inter J Complex Syst. 2006;1695(5):1–9.
   Google Scholar
• Erdős P, Rényi A. On the strength of connectedness of a random graph. Acta Mathematica Hungarica. 1961;12(1-2):261–267.
   Google Scholar
• Traag VA, Waltman L, van Eck NJ. From Louvain to Leiden: guaranteeing well-connected communities. Sci Rep. 2019 Mar 26;9(1):5233.
   PubMed Web of Science ®Google Scholar
• Brysbaert G, Mauri T, Lensink MF. (2018). Cytoscape [version 1; referees: 3 approved].
   Google Scholar
• Riehmann P, Hanfler M, Froehlich B, editors. (2005). Interactive sankey diagrams. IEEE Symposium on Information Visualization, INFOVIS 2005: IEEE.
   Google Scholar
• Zhang W, Svensson Akusjarvi S, Sonnerborg A, et al. Characterization of inducible transcription and translation-competent HIV-1 using the RNAscope ISH technology at a single-cell resolution. Front Microbiol. 2018;9:2358.
   PubMed Web of Science ®Google Scholar
• Luo Q, Zhang L, Wei F, et al. mTORC1 negatively regulates the replication of classical swine fever virus through autophagy and IRES-dependent translation. iScience. 2018 May 25;3:87–101.
   PubMed Web of Science ®Google Scholar
• Bojkova D, Klann K, Koch B, et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature. 2020 May 14;583(7816):469–472.
   PubMed Web of Science ®Google Scholar
• Cimmino F, Avitabile M, Lasorsa VA, et al. HIF-1 transcription activity: HIF1A driven response in normoxia and in hypoxia. BMC Med Genet. 2019;20(1):37.
   PubMed Web of Science ®Google Scholar
• Gordon DE, Jang GM, Bouhaddou M, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30;583(7816):459–468.
   PubMed Web of Science ®Google Scholar
• Weinlich R, Green DR. The two faces of receptor interacting protein kinase-1. Mol Cell. 2014 Nov 20;56(4):469–480.
   PubMed Web of Science ®Google Scholar
• Kawamata N, Chen J, Koeffler HP. Suberoylanilide hydroxamic acid (SAHA; vorinostat) suppresses translation of cyclin D1 in mantle cell lymphoma cells. Blood. 2007 Oct 1;110(7):2667–2673.
   PubMed Web of Science ®Google Scholar
• Ranadheera C, Coombs KM, Kobasa D. Comprehending a killer: the Akt/mTOR signaling pathways are temporally high-jacked by the highly pathogenic 1918 influenza virus. EBioMedicine. 2018 Jun;32:142–163.
   PubMed Web of Science ®Google Scholar
• Ehrhardt C, Ludwig S. A new player in a deadly game: influenza viruses and the PI3K/Akt signalling pathway. Cell Microbiol. 2009 Jun;11(6):863–871.
   PubMed Web of Science ®Google Scholar
• Mizutani T, Fukushi S, Saijo M, et al. JNK and PI3k/Akt signaling pathways are required for establishing persistent SARS-CoV infection in Vero E6 cells. Biochim Biophys Acta. 2005 Jun 30;1741(1-2):4–10.
   PubMed Web of Science ®Google Scholar
• Kindrachuk J, Ork B, Hart BJ, et al. Antiviral potential of ERK/MAPK and PI3K/AKT/mTOR signaling modulation for Middle East respiratory syndrome coronavirus infection as identified by temporal kinome analysis. Antimicrob Agents Chemother. 2015 Feb;59(2):1088–1099.
   PubMed Web of Science ®Google Scholar
• Zhou J, Callapina M, Goodall GJ, et al. Functional integrity of nuclear factor kappaB, phosphatidylinositol 3'-kinase, and mitogen-activated protein kinase signaling allows tumor necrosis factor alpha-evoked Bcl-2 expression to provoke internal ribosome entry site-dependent translation of hypoxia-inducible factor 1alpha. Cancer Res. 2004 Dec 15;64(24):9041–9048.
   PubMed Web of Science ®Google Scholar
• Chen H, Ning X, Jiang Z. Caspases control antiviral innate immunity. Cell Mol Immunol. 2017 Sep;14(9):736–747.
   PubMed Web of Science ®Google Scholar
• Zwergal A, Quirling M, Saugel B, et al. C/EBP beta blocks p65 phosphorylation and thereby NF-kappa B-mediated transcription in TNF-tolerant cells. J Immunol. 2006 Jul 1;177(1):665–672.
   PubMed Web of Science ®Google Scholar
• Hensley LE, Fritz LE, Jahrling PB, et al. Interferon-beta 1a and SARS coronavirus replication. Emerg Infect Dis. 2004 Feb;10(2):317–319.
   PubMed Web of Science ®Google Scholar
• Spiegel M, Pichlmair A, Martinez-Sobrido L, et al. Inhibition of beta interferon induction by severe acute respiratory syndrome coronavirus suggests a two-step model for activation of interferon regulatory factor 3. J Virol. 2005 Feb;79(4):2079–2086.
   PubMed Web of Science ®Google Scholar
• Le Sage V, Cinti A, Amorim R, et al. Adapting the stress response: viral subversion of the mTOR signaling pathway. Viruses. 2016;8(6):152.
   PubMed Web of Science ®Google Scholar
• Zhao C, Chen J, Cheng L, et al. Deficiency of HIF-1alpha enhances influenza A virus replication by promoting autophagy in alveolar type II epithelial cells. Emerg Microbes Infect. 2020 Dec;9(1):691–706.
   PubMed Web of Science ®Google Scholar
• Zecha J, Lee CY, Bayer FP, et al. Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing. Mol Cell Proteomics. 2020 Jun 26;mcp.RA120.002164. doi:10.1074/mcp.RA120.002164. Online ahead of print.
   PubMed Web of Science ®Google Scholar
• Chu H, Chan JF-W, Yuen TT-T, et al. Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study. The Lancet Microbe. 2020 May;1(1):E14–E23.
   PubMedGoogle Scholar
• Zhou Y, Hou Y, Shen J, et al. Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. 2020;6:14.
   PubMed Web of Science ®Google Scholar
• Murray JL, McDonald NJ, Sheng J, et al. Inhibition of influenza A virus replication by antagonism of a PI3K-AKT-mTOR pathway member identified by gene-trap insertional mutagenesis. Antivir Chem Chemother. 2012 May 14;22(5):205–215.
   PubMedGoogle Scholar
• Alsuwaidi AR, George JA, Almarzooqi S, et al. Sirolimus alters lung pathology and viral load following influenza A virus infection. Respir Res. 2017 Jul 11;18(1):136.
   PubMed Web of Science ®Google Scholar
• Wang CH, Chung FT, Lin SM, et al. Adjuvant treatment with a mammalian target of rapamycin inhibitor, sirolimus, and steroids improves outcomes in patients with severe H1N1 pneumonia and acute respiratory failure. Crit Care Med. 2014 Feb;42(2):313–321.
   PubMed Web of Science ®Google Scholar
• Shi G, Ozog S, Torbett BE, et al. mTOR inhibitors lower an intrinsic barrier to virus infection mediated by IFITM3. Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):E10069–e10078.
   PubMed Web of Science ®Google Scholar
• Gassen NC, Papies J, Bajaj T, et al. Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics. bioRxiv. 2020:2020.04.15.997254.
   Google Scholar
• Denisova OV, Söderholm S, Virtanen S, et al. Akt inhibitor MK2206 prevents influenza pH1N1 virus infection in vitro. Antimicrob Agents Chemother. 2014 Jul;58(7):3689–3696.
   PubMed Web of Science ®Google Scholar
• Zhao M. Cytokine storm and immunomodulatory therapy in COVID-19: role of chloroquine and anti-IL-6 monoclonal antibodies. Int J Antimicrob Agents. 2020 Jun;55(6):105982.
   PubMed Web of Science ®Google Scholar
• Pinno J, Bongartz H, Klepsch O, et al. Interleukin-6 influences stress-signalling by reducing the expression of the mTOR-inhibitor REDD1 in a STAT3-dependent manner. Cell Signal. 2016 Aug;28(8):907–916.
   PubMed Web of Science ®Google Scholar
• Harcourt J, Tamin A, Lu X, et al. Severe acute respiratory syndrome coronavirus 2 from patient with 2019 Novel coronavirus disease, United States. Emerg Infect Dis. 2020 Jun;26(6):1266–1273.
   PubMed Web of Science ®Google Scholar
• Tang BS, Chan KH, Cheng VC, et al. Comparative host gene transcription by microarray analysis early after infection of the Huh7 cell line by severe acute respiratory syndrome coronavirus and human coronavirus 229E. J Virol. 2005 May;79(10):6180–6193.
   PubMed Web of Science ®Google Scholar