2,083
Views
1
CrossRef citations to date
0
Altmetric
Technology

Unraveling the copper-death connection: Decoding COVID-19‘s immune landscape through advanced bioinformatics and machine learning approaches

, , , &
Article: 2310359 | Received 01 Sep 2023, Accepted 23 Jan 2024, Published online: 11 Mar 2024

References

  • Diagne ML, Rwezaura H, Tchoumi SY, Tchuenche JM. A mathematical model of COVID-19 with vaccination and treatment. Comput Math Method M. 2021 Sep 4;2021:1–17. doi:10.1155/2021/1250129.
  • Jiang Y, Huo Z, Qi X, Zuo T, Wu Z. Copper-induced tumor cell death mechanisms and antitumor theragnostic applications of copper complexes. Nanomedicine (Lond). 2022;17(5):303–324. doi:10.2217/nnm-2021-0374.
  • Cui X, Wang Y, Liu H, Shi M, Wang J, Wang Y. The molecular mechanisms of defective copper metabolism in diabetic cardiomyopathy. Oxid Med Cell Longev. 2022 Oct 4;2022:5418376. doi:10.1155/2022/5418376.
  • Shribman S, Poujois A, Bandmann O, Czlonkowska A, Warner TT. Wilson’s disease: update on pathogenesis, biomarkers and treatments. J Neurol Neurosurg Psychiatry. 2021;92(10):1053–1061. doi:10.1136/jnnp-2021-326123.
  • Ginès P, Krag A, Abraldes JG, Solà E, Fabrellas N, Kamath PS. Liver cirrhosis. Lancet. 2021;398(10308):1359–1376. doi:10.1016/S0140-6736(21)01374-X.
  • Varanasi SK, Kaech SM, Bui JD. SnapShot: cancer immunoediting. Cell. 2022;185(21):4038–4038.e1. doi:10.1016/j.cell.2022.09.027.
  • Zavros Y, Merchant JL. The immune microenvironment in gastric adenocarcinoma. Nat Rev Gastroenterol Hepatol. 2022;19(7):451–467. doi:10.1038/s41575-022-00591-0.
  • Lv B, Wang Y, Ma D, Cheng W, Liu J, Yong T, Chen H, Wang C. Immunotherapy: reshape the tumor immune microenvironment. Front Immunol. 2022 Jul 6;13:844142. doi:10.3389/fimmu.2022.844142.
  • Singh SK, Kumar D, Rathore AS. Understanding oxidation propensity in GCSF and assessment of its safety and efficacy. Pharm Res. 2020 Sep 29;37(10):207. doi:10.1007/s11095-020-02928-3.
  • Gusev E, Sarapultsev A, Solomatina L, Chereshnev V. SARS-CoV-2-specific immune response and the pathogenesis of COVID-19. Int J Mol Sci. 2022 Feb 2;23(3):1716. doi:10.3390/ijms23031716.
  • Wang Z, Mo S, Han P, Liu L, Liu Z, Fu X, Tian Y. The role of UXT in tumors and prospects for its application in hepatocellular carcinoma. Future Oncol. 2022;18(29):3335–48. doi:10.2217/fon-2022-0582.
  • Clough E, Barrett T. The gene expression omnibus database. Methods Mol Biol. 2016;1418:93–110. doi:10.1007/978-1-4939-3578-9_5.
  • Tsvetkov P, Coy S, Petrova B, Dreishpoon M, Verma A, Abdusamad M, Rossen J, Joesch-Cohen L, Humeidi R, Spangler RD. et al. Copper induces cell death by targeting lipoylated TCA cycle proteins [published correction appears in Science. 2022 Apr 22;376(6591): eabq4855]. Science. 2022;375(6586):1254–61. doi:10.1126/science.abf0529.
  • Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–7. doi:10.1038/nmeth.3337.
  • Ali HR, Chlon L, Pharoah PD, Markowetz F, Caldas C, Ladanyi M. Patterns of immune infiltration in breast cancer and their clinical implications: a gene-expression-based retrospective study. PLoS Med. 2016 Dec 13;13(12):e1002194. doi:10.1371/journal.pmed.1002194.
  • Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573. doi:10.1093/bioinformatics/btq170.
  • Du Y, Miao W, Jiang X, Cao J, Wang B, Wang Y, Yu J, Wang X, Liu H. The epithelial to mesenchymal transition related gene calumenin is an adverse prognostic factor of bladder cancer correlated with tumor microenvironment remodeling, gene mutation, and ferroptosis [published correction appears in Front Oncol. 2023 May 11;13: 1185029]. Front Oncol. 2021 Jun 3;(11):683951. doi:10.3389/fonc.2021.683951.
  • Rezaei Z, Ranjbaran J, Safarpour H, Nomiri S, Salmani F, Chamani E, Larki P, Brunetti O, Silvestris N, Tavakoli T. et al. Identification of early diagnostic biomarkers via WGCNA in gastric cancer. Biomed Pharmacother. 2022;145:112477. doi:10.1016/j.biopha.2021.112477.
  • Wang Z, Liu J, Wang Y, Guo H, Li F, Cao Y, Zhao L, Chen H. Identification of key biomarkers associated with immunogenic cell death and their regulatory mechanisms in severe acute pancreatitis based on WGCNA and machine learning. Int J Mol Sci. 2023 Feb 3;24(3):3033. doi:10.3390/ijms24033033.
  • Gao XM, Zhou XH, Jia MW, Wang XZ, Liu D. Identification of key genes in sepsis by WGCNA. Prev Med. 2023;172:107540. doi:10.1016/j.ypmed.2023.107540.
  • Rigatti SJ. Random Forest. J Insur Med. 2017;47(1):31–39. doi:10.17849/insm-47-01-31-39.1.
  • Anand D, Pandey B, Pandey DK. A novel hybrid feature selection model for classification of neuromuscular dystrophies using Bhattacharyya coefficient, genetic algorithm and radial basis function based support vector machine. Interdiscip Sci Comput Life Sci. 2018;10(2):244–250. doi:10.1007/s12539-016-0183-6.
  • Ma C, Li F, Wang Z, Luo H. A novel immune-related gene signature predicts prognosis of Lung Adenocarcinoma. Biomed Res Int. 2022 Apr 9;2022:4995874. doi:10.1155/2022/4995874.
  • Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC. GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics. 2018;34(13):i555–i564. doi:10.1093/bioinformatics/bty271.
  • Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013 Jan 16;14:7. doi:10.1186/1471-2105-14-7.
  • Shah K, Al-Haidari A, Sun J, Kazi JU. T cell receptor (TCR) signaling in health and disease. Signal Transduct Target Ther. 2021 Dec 13;6(1):412. doi:10.1038/s41392-021-00823-w.
  • Park JJ, Lee KAV, Lam SZ, Moon KS, Fang Z, Chen S. Machine learning identifies T cell receptor repertoire signatures associated with COVID-19 severity. Commun Biol. 2023 Jan 20;6(1):76. doi:10.1038/s42003-023-04447-4.
  • Wang G, Wang Y, Jiang S, Fan W, Mo C, Gong W, Chen H, He D, Huang J, Ou M. et al. Comprehensive analysis of TCR repertoire of COVID-19 patients in different infected stage. Genes Genomics. 2022;44(7):813–822. doi:10.1007/s13258-022-01261-w.
  • Prager I, Watzl C. Mechanisms of natural killer cell-mediated cellular cytotoxicity. J Leukoc Biol. 2019;105(6):1319–1329. doi:10.1002/JLB.MR0718-269R.
  • Christofides A, Konstantinidou E, Jani C, Boussiotis VA. The role of peroxisome proliferator-activated receptors (PPAR) in immune responses. Metabolism. 2021;114:154338. doi:10.1016/j.metabol.2020.154338.
  • Read SA, Obeid S, Ahlenstiel C, Ahlenstiel G. The role of zinc in antiviral immunity. Adv Nutr. 2019;10(4):696–710. doi:10.1093/advances/nmz013.
  • de Jesus JR, Galazzi RM, Lopes Júnior CA, Arruda MAZ. Trace element homeostasis in the neurological system after SARS-CoV-2 infection: insight into potential biochemical mechanisms [published online ahead of print, 2022 Feb 26]. J Trace Elements Med Biol. 2022;71:126964. doi:10.1016/j.jtemb.2022.126964.
  • Gong T, Liu Y, Tian Z, Zhang M, Gao H, Peng Z, Yin S, Cheung CW, Liu Y. Identification of immune-related endoplasmic reticulum stress genes in sepsis using bioinformatics and machine learning. Front Immunol. 2022 Sep 20;13:995974. doi:10.3389/fimmu.2022.995974.
  • Lai Y, Lin P, Lin F, Chen M, Lin C, Lin X, Wu L, Zheng M, Chen J. Identification of immune microenvironment subtypes and signature genes for Alzheimer’s disease diagnosis and risk prediction based on explainable machine learning. Front Immunol. 2022 Dec 8;13:1046410. doi:10.3389/fimmu.2022.1046410.
  • Ko S, Choi J, Ahn J. GVES: machine learning model for identification of prognostic genes with a small dataset. Sci Rep. 2021 Jan 11;11(1):439. doi:10.1038/s41598-020-79889-5.
  • Shrock E, Fujimura E, Kula T, Timms RT, Lee I-H, Leng Y, Robinson ML, Sie BM, Li MZ, Chen Y. et al. Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science. 2020;370(6520):eabd4250. doi:10.1126/science.abd4250.