Using bioinformatics and systems biology methods to identify the mechanism of interaction between COVID-19 and nonalcoholic fatty liver disease.

Wenbo Dong, Yan Jin, Hongshuo Shi, Xuecheng Zhang, Jinshu Chen, Hongling Jia, Yongchen Zhang
Author Information
  1. Wenbo Dong: Shandong Traditional Chinese Medicine University, Jinan, China.
  2. Yan Jin: Shandong Traditional Chinese Medicine University, Jinan, China.
  3. Hongshuo Shi: Shandong Traditional Chinese Medicine University, Jinan, China.
  4. Xuecheng Zhang: Beijing University of Chinese Medicine, Beijing, China.
  5. Jinshu Chen: Shandong Traditional Chinese Medicine University, Jinan, China.
  6. Hongling Jia: The Second Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China. ORCID
  7. Yongchen Zhang: Shandong Traditional Chinese Medicine University, Jinan, China.

Abstract

Nonalcoholic fatty liver disease (NAFLD) is considered a risk factor for severe COVID-19, but the mechanism remains unknown. This study used bioinformatics to help define the relationship between these diseases. The GSE147507 (COVID-19), GSE126848 (NAFLD), and GSE63067 (NAFLD-2) datasets were screened using the Gene Expression Omnibus. Common differentially expressed genes were then identified using a Venn diagram. Gene ontology analysis and KEGG pathway enrichment were performed on the differentially expressed genes. A protein-protein interaction network was also constructed using the STRING platform, and key genes were identified using the Cytoscape plugin. GES63067 was selected for validation of the results. Analysis of ferroptosis gene expression during the development of the 2 diseases and prediction of their upstream miRNAs and lncRNAs. In addition, transcription factors (TFs) and miRNAs related to key genes were identified. Effective drugs that act on target genes were found in the DSigDB. The GSE147507 and GSE126848 datasets were crossed to obtain 28 co-regulated genes, 22 gene ontology terms, 3 KEGG pathways, and 10 key genes. NAFLD may affect COVID-19 progression through immune function and inflammatory signaling pathways. CYBB was predicted to be a differential ferroptosis gene associated with 2 diseases, and the CYBB-hsa-miR-196a/b-5p-TUG1 regulatory axis was identified. TF-gene interactions and TF-miRNA coregulatory network were constructed successfully. A total of 10 drugs, (such as Eckol, sulfinpyrazone, and phenylbutazone) were considered as target drugs for Patients with COVID-19 and NAFLD. This study identified key gene and defined molecular mechanisms associated with the progression of COVID-19 and NAFLD. COVID-19 and NAFLD progression may regulate ferroptosis through the CYBB-hsa-miR-196a/b-5p-TUG1 axis. This study provides additional drug options for the treatment of COVID-19 combined with NAFLD disease.

References

  1. J Hepatol. 2020 Aug;73(2):451-453 [PMID: 32278005]
  2. Allergy Asthma Clin Immunol. 2006 Sep 15;2(3):98-108 [PMID: 20525154]
  3. J Reprod Immunol. 2010 May;85(1):40-6 [PMID: 20356631]
  4. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W169-75 [PMID: 17576678]
  5. Biomed J. 2019 Feb;42(1):19-26 [PMID: 30987701]
  6. Curr Obes Rep. 2021 Jun;10(2):134-161 [PMID: 33751456]
  7. Nat Biotechnol. 2020 Aug;38(8):970-979 [PMID: 32591762]
  8. J Hepatol. 2022 Apr;76(4):910-920 [PMID: 34902531]
  9. Cell. 2012 May 25;149(5):1060-72 [PMID: 22632970]
  10. J Virol. 2006 Aug;80(16):8151-7 [PMID: 16873271]
  11. Asian J Psychiatr. 2022 Mar;69:102981 [PMID: 34973636]
  12. World J Gastroenterol. 2016 Nov 21;22(43):9488-9505 [PMID: 27920470]
  13. Eur J Histochem. 2022 Jun 21;66(3): [PMID: 35726536]
  14. J Comput Chem. 2016 Jun 30;37(17):1559-64 [PMID: 27010673]
  15. Bioinformatics. 2015 Sep 15;31(18):3069-71 [PMID: 25990557]
  16. Protein Sci. 2022 Jan;31(1):47-53 [PMID: 34423492]
  17. Expert Rev Gastroenterol Hepatol. 2021 Jul;15(7):783-796 [PMID: 33557653]
  18. Comput Biol Med. 2021 Jul;134:104459 [PMID: 34020127]
  19. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61 [PMID: 14681407]
  20. mSphere. 2020 May 13;5(3): [PMID: 32404512]
  21. J Hematol Oncol. 2019 Mar 29;12(1):34 [PMID: 30925886]
  22. Hepatobiliary Pancreat Dis Int. 2017 Feb;16(1):65-79 [PMID: 28119261]
  23. Nat Biotechnol. 2021 Jul;39(7):846-854 [PMID: 33767396]
  24. Endocrinol Metab (Seoul). 2013 Mar;28(1):41-5 [PMID: 24396649]
  25. Dev Cell. 2021 Dec 6;56(23):3250-3263.e5 [PMID: 34706264]
  26. EBioMedicine. 2021 Aug;70:103500 [PMID: 34311326]
  27. Hepatol Int. 2021 Feb;15(1):21-35 [PMID: 33548031]
  28. Database (Oxford). 2015 Sep 30;2015: [PMID: 26424082]
  29. Autoimmun Rev. 2020 Jul;19(7):102573 [PMID: 32387470]
  30. Liver Int. 2019 May;39(5):788-801 [PMID: 30843314]
  31. J Gastroenterol Hepatol. 2021 Oct;36(10):2903-2910 [PMID: 33973273]
  32. Int J Mol Sci. 2020 Feb 28;21(5): [PMID: 32121273]
  33. Am J Respir Crit Care Med. 2020 Dec 1;202(11):1509-1519 [PMID: 32866033]
  34. Am J Pathol. 2021 Dec;191(12):2064-2071 [PMID: 34506752]
  35. Cell Death Discov. 2020 Nov 25;6:130 [PMID: 33251029]
  36. J Int Med Res. 2021 Nov;49(11):3000605211059681 [PMID: 34816740]
  37. Genome Biol. 2019 Sep 2;20(1):185 [PMID: 31477170]
  38. J Immunol. 2015 Mar 15;194(6):2587-95 [PMID: 25662996]
  39. PLoS Comput Biol. 2014 Apr 24;10(4):e1003516 [PMID: 24763310]
  40. J Korean Med Sci. 2021 Oct 25;36(41):e291 [PMID: 34697932]
  41. Molecules. 2021 Jun 21;26(12): [PMID: 34205704]
  42. Medicina (Kaunas). 2021 Oct 03;57(10): [PMID: 34684094]
  43. J Inflamm Res. 2022 Apr 05;15:2181-2198 [PMID: 35411172]
  44. Mymensingh Med J. 2020 Jul;29(3):589-595 [PMID: 32844798]
  45. J Inflamm Res. 2021 Jun 29;14:2851-2863 [PMID: 34234510]
  46. Nat Commun. 2016 Mar 21;7:11037 [PMID: 26996437]
  47. World J Gastroenterol. 2017 May 21;23(19):3407-3417 [PMID: 28596677]
  48. Hum Genomics. 2021 Mar 16;15(1):18 [PMID: 33726831]
  49. Science. 2010 Oct 15;330(6002):362-6 [PMID: 20947763]
  50. Cell Mol Gastroenterol Hepatol. 2022;13(1):257-274 [PMID: 34506952]
  51. Nat Rev Microbiol. 2016 Aug;14(8):523-34 [PMID: 27344959]
  52. Cancer Immunol Immunother. 2017 Aug;66(8):1079-1087 [PMID: 28638976]
  53. Comp Med. 2021 Oct 1;71(5):411-432 [PMID: 34548126]
  54. Lancet. 2020 Feb 15;395(10223):497-506 [PMID: 31986264]
  55. iScience. 2022 Jul 15;25(8):104750 [PMID: 35942097]
  56. Eur J Clin Invest. 2020 Oct;50(10):e13338 [PMID: 32589264]
  57. J Cell Biochem. 2014 Aug;115(8):1403-11 [PMID: 24700636]
  58. Isr Med Assoc J. 2020 Aug;22(8):494-500 [PMID: 33236582]
  59. Mol Psychiatry. 2008 Oct;13(10):930-8 [PMID: 17667962]
  60. Mol Med. 2021 Dec 20;27(1):161 [PMID: 34930105]
  61. Lupus. 2022 Jul;31(8):985-997 [PMID: 35588147]
  62. Nucleic Acids Res. 2019 Jan 8;47(D1):D330-D338 [PMID: 30395331]
  63. Nutrients. 2021 Apr 24;13(5): [PMID: 33923255]
  64. Int J Mol Sci. 2022 Mar 22;23(7): [PMID: 35408790]
  65. Lancet. 2020 Mar 28;395(10229):1033-1034 [PMID: 32192578]
  66. Med Sci (Paris). 2003 Jan;19(1):63-9 [PMID: 12836193]
  67. Cell Death Dis. 2020 Feb 3;11(2):88 [PMID: 32015325]
  68. Biochim Biophys Acta Gen Subj. 2019 Sep;1863(9):1398-1409 [PMID: 31229492]
  69. BMC Syst Biol. 2010 Nov 08;4:150 [PMID: 21059252]

MeSH Term

Humans
Non-alcoholic Fatty Liver Disease
Systems Biology
Gene Expression Profiling
COVID-19
MicroRNAs
Computational Biology
Gene Regulatory Networks

Chemicals

MicroRNAs

Word Cloud

Created with Highcharts 10.0.0COVID-19NAFLDgenesidentifiedusingkeygenediseasestudydiseasesferroptosisdrugsprogressionfattyliverconsideredmechanismbioinformaticsGSE147507GSE126848datasetsGenedifferentiallyexpressedontologyKEGGinteractionnetworkconstructed2miRNAstargetpathways10mayassociatedCYBB-hsa-miR-196a/b-5p-TUG1axisNonalcoholicriskfactorsevereremainsunknownusedhelpdefinerelationshipGSE63067NAFLD-2screenedExpressionOmnibusCommonVenndiagramanalysispathwayenrichmentperformedprotein-proteinalsoSTRINGplatformCytoscapepluginGES63067selectedvalidationresultsAnalysisexpressiondevelopmentpredictionupstreamlncRNAsadditiontranscriptionfactorsTFsrelatedEffectiveactfoundDSigDBcrossedobtain28co-regulated22terms3affectimmunefunctioninflammatorysignalingCYBBpredicteddifferentialregulatoryTF-geneinteractionsTF-miRNAcoregulatorysuccessfullytotalEckolsulfinpyrazonephenylbutazonePatientsdefinedmolecularmechanismsregulateprovidesadditionaldrugoptionstreatmentcombinedUsingsystemsbiologymethodsidentifynonalcoholic

Similar Articles

Cited By (2)