| Literature DB >> 32595654 |
Mahmood Yaseen Hachim1,2, Saba Al Heialy2,3, Ibrahim Yaseen Hachim1, Rabih Halwani1, Abiola C Senok2, Azzam A Maghazachi1, Qutayba Hamid1,3.
Abstract
Current guidelines for COVID-19 management recommend the utilization of various repurposed drugs. Despite ongoing research toward the development of a vaccine against SARS-CoV-2, such a vaccine will not be available in time to contribute to the containment of the ongoing pandemic. Therefore, there is an urgent need to develop a framework for the rapid identification of novel targets for diagnostic and therapeutic interventions. We analyzed publicly available transcriptomic datasets of SARS-CoV infected humans and mammals to identify consistent differentially expressed genes then validated in SARS-CoV-2 infected epithelial cells transcriptomic datasets. Comprehensive toxicogenomic analysis of the identified genes to identify possible interactions with clinically proven drugs was carried out. We identified IFITM3 as an early upregulated gene, and valproic acid was found to enhance its mRNA expression as well as induce its antiviral action. These findings indicate that analysis of publicly available transcriptomic and toxicogenomic data represents a rapid approach for the identification of novel targets and molecules that can modify the action of such targets during the early phases of emerging infections like COVID-19.Entities:
Keywords: COVID-19; SARS-CoV-2; antiviral immunity; interferon-induced transmembrane proteins; valproic acid
Mesh:
Substances:
Year: 2020 PMID: 32595654 PMCID: PMC7301886 DOI: 10.3389/fimmu.2020.01372
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
List of publicly available transcriptomics datasets retrieved from Gene Expression Omnibus (GEO) and used in the study.
| 1. | Absence of host innate immune responses in SARS-CoV-infected ferrets upon subsequent challenge | Ferret | SARS-CoV (TOR2) | GSE11704 | ( |
| 2. | Dynamic innate immune responses of human bronchial epithelial cells against SARS-CoV and DOHV infection | 2B4 cells, a clonal derivative of Calu-3 cells | Urbani strain of SARS-CoV | GSE17400 | ( |
| 3. | Comparative pathogenesis of three human and zoonotic SARS-CoV strains in cynomolgus macaques | Cynomolgus macaques | Recombinant SARS-CoV bearing variant S glycoproteins (Urbani, GZ02 and HC/SZ/6103) | GSE23955 | ( |
| 4. | SM001: SARS CoV MA15 infection of C57Bl/6 mouse model – data from 4 viral doses at 1, 2, 4 and 7 days post infection. | C57BL/6 mice | SARS CoV MA15 | GSE33266 | ( |
| 5. | SCL005: icSARS CoV Urbani or icSARS deltaORF6 infections of the 2B4 clonal derivative of Calu-3 cells - Time course | Calu-3 cells | icSARS CoV or the icSARS deltaORF6 mutant | GSE33267 | ( |
| 6. | SCL006,icSARS CoV urbani or icSARS Bat SRBD (spike receptor binding domain from the wild type strain urbani to allow for infection of human and non-human primate cells) infections of the 2B4 clonal derivative of calu-3 cells - Time course | Calu-3 cells | icSARS CoV or the cSARS Bat SRBD strain | GSE37827 | ( |
| 7. | SHAE002: SARS-CoV, SARS-dORF6 and SARS-BatSRBD infection of HAE cultures. | HAE cultures | SARS-CoV, SARS-dORF6 or SARS-BatSRBD | GSE47960 | ( |
| 8. | SCL008: icSARS CoV, icSARS-deltaNSP16 or icSARS ExoNI infections of the 2B4 clonal derivative of Calu-3 cells - Time course | 2B-4 cells (clonal derivatives of Calu-3 cells) | icSARS CoV, icSARS deltaNSP16 or icSARS ExoNI | GSE48142 | ( |
| 9. | SM003 - icSARS CoV, SARS MA15 wild type and SARS BatSRBD mutant virus infections of C57BL6 mice - A time course | C57BL6 | icSARS CoV, Wild Type SARS MA15 or SARS BatSRBD mutant viruses | GSE50000 | ( |
| 10. | The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis | BALB/c Ola Hsd mice | MA15 | GSE52920 | ( |
| 11. | Genome wide identification of SARS-CoV susceptibility loci using the collaborative cross | C57BL/6J | MA15 | GSE64660 | |
| 12. | Mouse lung tissue transcriptome response to a mouse-adapted strain of SARS-CoV in wild type C57BL6/NJ mice and TLR3-/- mice | C57BL6/NJ | MA15 | GSE68820 | ( |
Genes symbols and description for the common DEGs in 9 out of the 12 transcriptomics datasets due to SARS-CoV infection of the lung in the first 48 h post-infection.
| DDX58 | DExD/H-box helicase 58 | 11 |
| IFI44 | interferon induced protein 44 | 11 |
| IFIT1 | interferon induced protein with tetratricopeptide repeats 1 | 11 |
| IFIT2 | interferon induced protein with tetratricopeptide repeats 2 | 11 |
| IFIT3 | interferon induced protein with tetratricopeptide repeats 3 | 11 |
| ISG15 | ISG15 ubiquitin like modifier | 11 |
| MX1 | MX dynamin like GTPase 1 | 11 |
| MX2 | MX dynamin like GTPase 2 | 11 |
| OAS3 | 2′-5′-oligoadenylate synthetase 3 | 11 |
| XAF1 | XIAP associated factor 1 | 11 |
| BST2 | bone marrow stromal cell antigen 2 | 10 |
| CXCL10 | C-X-C motif chemokine ligand 10 | 10 |
| DHX58 | DExH-box helicase 58 | 10 |
| IFIH1 | interferon induced with helicase C domain 1 | 10 |
| IL6 | interleukin 6 | 10 |
| IRF7 | interferon regulatory factor 7 | 10 |
| OAS2 | 2′-5′-oligoadenylate synthetase 2 | 10 |
| PARP14 | poly(ADP-ribose) polymerase family member 14 | 10 |
| RSAD2 | radical S-adenosyl methionine domain containing 2 | 10 |
| SP100 | SP100 nuclear antigen | 10 |
| STAT1 | signal transducer and activator of transcription 1 | 10 |
| USP18 | ubiquitin specific peptidase 18 | 10 |
| BATF2 | basic leucine zipper ATF-like transcription factor 2 | 9 |
| CXCL11 | C-X-C motif chemokine ligand 11 | 9 |
| EPSTI1 | epithelial stromal interaction 1 | 9 |
| HERC6 | HECT and RLD domain containing E3 ubiquitin protein ligase family member 6 | 9 |
| IFI35 | interferon induced protein 35 | 9 |
| IFITM3 | interferon induced transmembrane protein 3 | 9 |
| ISG20 | interferon stimulated exonuclease gene 20 | 9 |
| PARP9 | poly(ADP-ribose) polymerase family member 9 | 9 |
| PLAC8 | placenta associated 8 | 9 |
| RTP4 | receptor transporter protein 4 | 9 |
| SAMD9L | sterile alpha motif domain containing 9 like | 9 |
| SP110 | SP110 nuclear body protein | 9 |
| TRAFD1 | TRAF-type zinc finger domain containing 1 | 9 |
| TRIM21 | tripartite motif containing 21 | 9 |
| ZBP1 | Z-DNA binding protein 1 | 9 |
| ZC3HAV1 | zinc finger CCCH-type containing, antiviral 1 | 9 |
Figure 1Common DEGs among mammals and human cells infected with SARS-CoV virus extracted from publicly available transcriptomics datasets.
Number of shared DEGs in different models infected with SARS-CoV extracted from publicly available transcriptomics datasets.
| [COVID-19] | 271 |
| [COVID-19] and [Cynomolgus maca] | 16 |
| [COVID-19] and [Ferret] | 28 |
| [COVID-19] and [Ferret] and [Cynomolgus maca] | 1 |
| [COVID-19] and [Human lung cell] | 1 |
| [COVID-19] and [Human lung cell] and [Cynomolgus maca] | 3 |
| [COVID-19] and [Human lung cell] and [Mice] | 1 |
| [COVID-19] and [Human lung cell] and [Mice] and [Cynomolgus maca] | 9 |
| [COVID-19] and [Mice] | 2 |
| [COVID-19] and [Mice] and [Cynomolgus maca] | 3 |
| [COVID-19] and [Mice] and [Ferret] | 1 |
| [Cynomolgus maca] | 688 |
| [Ferret] | 1,522 |
| [Ferret] and [Cynomolgus maca] | 61 |
| [Human lung cell] | 2 |
| [Human lung cell] and [Cynomolgus maca] | 4 |
| [Human lung cell] and [Mice] | 4 |
| [Human lung cell] and [Mice] and [Cynomolgus maca] | 4 |
| [Mice] | 49 |
| [Mice] and [Cynomolgus maca] | 8 |
| [Mice] and [Ferret] | 2 |
Figure 2Enriched Ontology Clustering for the 38 identified DEGs.
Enriched Ontology Clustering for the 38 DEGs identified with Genes symbols in each category.
| GO biological processes | GO:0060337 | Type I interferon signaling pathway | −36.0121 | −31.994 | 19/95 | BST2, IFI35, IFIT2, IFIT1, IFIT3, IRF7, ISG20, MX1, MX2, OAS2, OAS3, SP100, STAT1, ISG15, IFITM3, USP18, XAF1, ZBP1, RSAD2, TRIM21, DDX58, IL6, CXCL10, CXCL11, PARP14, PARP9, ZC3HAV1, DHX58 |
| GO biological processes | GO:0051607 | Defense response to virus | −33.8766 | −30.160 | 22/248 | BST2, IFIT2, IFIT1, IFIT3, IL6, CXCL10, IRF7, ISG20, MX1, MX2, OAS2, OAS3, STAT1, ISG15, IFITM3, DDX58, ZC3HAV1, RTP4, IFIH1, DHX58, PARP9, RSAD2, IFI44, PLAC8, BATF2 |
| Reactome gene sets | R-HSA-1169410 | Antiviral mechanism by IFN-stimulated genes | −14.292 | −11.274 | 9/81 | IFIT1, MX1, MX2, OAS2, OAS3, STAT1, ISG15, USP18, DDX58 |
| KEGG pathway | hsa05164 | Influenza A | −12.9643 | −9.967 | 10/173 | IL6, CXCL10, IRF7, MX1, OAS2, OAS3, STAT1, DDX58, IFIH1, RSAD2, BST2, SP100, TRIM21, IFITM3, PARP14, PARP9, IFIT1 |
| GO biological processes | GO:0060759 | Regulation of response to cytokine stimulus | −10.9357 | −8.032 | 9/188 | IL6, IRF7, STAT1, USP18, DDX58, PARP14, IFIH1, ZBP1, PARP9, ZC3HAV1 |
| GO biological processes | GO:0032479 | Regulation of type I interferon production | −10.6988 | −7.826 | 8/127 | IRF7, TRIM21, STAT1, ISG15, DDX58, IFIH1, DHX58, ZBP1, TRAFD1, USP18, PARP14, PARP9, RSAD2, CXCL10, BST2, IL6, IFIT1, SP100, BATF2 |
| GO biological processes | GO:0035455 | Response to interferon-alpha | −9.83448 | −7.021 | 5/21 | BST2, IFIT2, IFIT3, MX2, IFITM3, STAT1, XAF1 |
| KEGG pathway | hsa04623 | Cytosolic DNA-sensing pathway | −7.31693 | –.600 | 5/63 | IL6, CXCL10, IRF7, DDX58, ZBP1, USP18, TRIM21 |
| GO biological processes | GO:0050688 | Regulation of defense response to virus | −6.93272 | −4.247 | 5/75 | IFIT1, STAT1, DDX58, DHX58, PARP9, BST2, IL6, RSAD2 |
| KEGG pathway | hsa04620 | Toll-like receptor signaling pathway | −6.22049 | −3.626 | 5/104 | IL6, CXCL10, IRF7, CXCL11, STAT1, OAS2, ISG15, IFI44, PLAC8, HERC6, DHX58, SP100 |
| GO biological processes | GO:0050777 | negative regulation of immune response | −3.98249 | −1.608 | 4/156 | BST2, TRAFD1, PARP14, DHX58 |
| GO biological processes | GO:0002262 | Myeloid cell homeostasis | −2.78923 | −0.508 | 3/148 | IL6, STAT1, ISG15, IRF7, BATF2 |
| GO biological processes | GO:0051100 | Negative regulation of binding | −2.61062 | −0.352 | 3/171 | IFIT2, IFIT1, SP100, PARP9 |
| GO biological processes | GO:0043902 | Positive regulation of multi-organism process | −2.50748 | −0.264 | 3/186 | IFIT1, TRIM21, DHX58, IFITM3 |
Figure 3Gene expression of the shortlisted genes in healthy epithelium infected with SARS-CoV-2 compared to mock-infected cells from the transcriptomics dataset (GSE147507).
Chemicals shown to upregulate or downregulate IFITM3 mRNA expression in at least two studies as shown in the Comparative Toxicogenomics Database (http://ctdbase.org/).
| Valproic acid | D014635 | 99-66-1 | Valproic acid results in increased expression of IFITM3 mRNA | increases | 3 | 2 |
| Nanotubes, carbon | D037742 | Nanotubes, carbon analog results in increased expression of IFITM3 mRNA | increases | 2 | 1 | |
| Nickel | D009532 | 7440-02-0 | Nickel results in increased expression of IFITM3 mRNA | increases | 2 | 1 |
| Tert-butylhydroperoxide | D020122 | 75-91-2 | tert-Butylhydroperoxide results in increased expression of IFITM3 mRNA | increases | 2 | 1 |
| Pirinixic acid | C006253 | 50892-23-4 | Pirinixic acid results in decreased expression of IFITM3 mRNA | decreases | 3 | 2 |
| Acetaminophen | D000082 | 103-90-2 | Acetaminophen results in decreased expression of IFITM3 mRNA | decreases | 2 | 1 |
| Ethinyl estradiol | D004997 | 57-63-6 | Ethinyl Estradiol results in decreased expression of IFITM3 mRNA | decreases | 2 | 2 |
Figure 4Normalized gene expression of IFITM3 in the blood of patients on responder valproic acid monotherapy (VA R) and non-response (VA NR) compared to healthy controls (H) extracted from the transcriptomic dataset (GSE143272).