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Research Articles

Identification of cuproptosis-related asthma diagnostic genes by WGCNA analysis and machine learning

, PhD, , MM & , PhD
Pages 2052-2063 | Received 26 Mar 2023, Accepted 08 May 2023, Published online: 14 Jun 2023

References

  • 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. Science. 2022;375(6586):1254–1261. doi:10.1126/science.abf0529.
  • Wang Y, Zhang L, Zhou F. Cuproptosis: a new form of programmed cell death. Cell Mol Immunol. 2022;19(8):867–868. doi:10.1038/s41423-022-00866-1.
  • Cobine PA, Brady DC. Cuproptosis: cellular and molecular mechanisms underlying copper-induced cell death. Mol Cell. 2022;82(10):1786–1787. doi:10.1016/j.molcel.2022.05.001.
  • Duan W-J, He R-R. Cuproptosis: copper-induced regulated cell death. Sci China Life Sci. 2022;65(8):1680–1682. doi:10.1007/s11427-022-2106-6.
  • Li S-R, Bu L-L, Cai L. Cuproptosis: lipoylated TCA cycle proteins-mediated novel cell death pathway. Sig Transduct Target Ther. 2022;7(1):158. doi:10.1038/s41392-022-01014-x.
  • Miller RL, Grayson MH, Strothman K. Advances in asthma: new understandings of asthma’s natural history, risk factors, underlying mechanisms, and clinical management. J Allergy Clin Immunol. 2021;148(6):1430–1441. doi:10.1016/j.jaci.2021.10.001.
  • Del Giacco S, Couto M, Firinu D, Garcia-Larsen V. Management of intermittent and persistent asthma in adolescent and high school athletes. J Allergy Clin Immunol Pract. 2020;8(7):2166–2181. doi:10.1016/j.jaip.2020.05.003.
  • Humbert M, Holgate S, Boulet LP, Bousquet J. Asthma control or severity: that is the question. Allergy. 2007;62(2): 95–101. doi:10.1111/j.1398-9995.2006.01308.x.
  • Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007.
  • Aubert L, Nandagopal N, Steinhart Z, Lavoie G, Nourreddine S, Berman J, Saba-El-Leil MK, Papadopoli D, Lin S, Hart T, et al. Copper bioavailability is a KRAS-specific vulnerability in colorectal cancer. Nat Commun. 2020;11(1):3701. doi:10.1038/s41467-020-17549-y.
  • Dong J, Wang X, Xu C, Gao M, Wang S, Zhang J, Tong H, Wang L, Han Y, Cheng N, et al. Inhibiting NLRP3 inflammasome activation prevents copper-induced neuropathology in a murine model of Wilson’s disease. Cell Death Dis. 2021;12(1):87. doi:10.1038/s41419-021-03397-1.
  • Polishchuk EV, Merolla A, Lichtmannegger J, Romano A, Indrieri A, Ilyechova EY, Concilli M, De Cegli R, Crispino R, Mariniello M, et al. Activation of autophagy, observed in liver tissues from patients with wilson disease and from ATP7B-deficient animals, protects hepatocytes from copper-induced apoptosis. Gastroenterology. 2019;156(4):1173–1189.e5. doi:10.1053/j.gastro.2018.11.032.
  • Ren X, Li Y, Zhou Y, Hu W, Yang C, Jing Q, Zhou C, Wang X, Hu J, Wang L, et al. Overcoming the compensatory elevation of NRF2 renders hepatocellular carcinoma cells more vulnerable to disulfiram/copper-induced ferroptosis. Redox Biol. 2021;46:102122. doi:10.1016/j.redox.2021.102122.
  • Serang S, Jacobucci R, Brimhall KC, Grimm KJ. Exploratory mediation analysis via regularization. Struct Equ Modeling. 2017;24(5):733–744. doi:10.1080/10705511.2017.1311775.
  • Xue G, Hua L, Zhou N, Li J. Characteristics of immune cell infiltration and associated diagnostic biomarkers in ulcerative colitis: results from bioinformatics analysis. Bioengineered. 2021;12(1):252–265. doi:10.1080/21655979.2020.1863016.
  • Huang M-L, Hung Y-H, Lee WM, Li RK, Jiang B-R. SVM-RFE based feature selection and Taguchi parameters optimization for multiclass SVM classifier. Sci World J. 2014;2014:795624. doi:10.1155/2014/795624.
  • Pathan M, Keerthikumar S, Ang C-S, Gangoda L, Quek CYJ, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, et al. FunRich: an open access standalone functional enrichment and interaction network analysis tool. Proteomics. 2015;15(15):2597–2601. doi:10.1002/pmic.201400515.
  • Yang S, Cheng Y, Wang X, Wei P, Wang H, Tan S. Identification of the immune cell infiltration landscape in hepatocellular carcinoma to predict prognosis and guide immunotherapy. Front Genet. 2021;12:777931. doi:10.3389/fgene.2021.777931.
  • Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4(1):17. doi:10.2202/1544-6115.1128.
  • Chen C, Liu YQ, Qiu SX, Li Y, Yu NJ, Liu K, Zhong LM. Five metastasis-related mRNAs signature predicting the survival of patients with liver hepatocellular carcinoma. BMC Cancer. 2021;21(1):693. doi:10.1186/s12885-021-08431-1.
  • Wang F, Lin H, Su Q, Li C. Cuproptosis-related lncRNA predict prognosis and immune response of lung adenocarcinoma. World J Surg Onc. 2022;20(1):275. doi:10.1186/s12957-022-02727-7.
  • Sockrider M, Fussner L. What is asthma? Am J Respir Crit Care Med. 2020;202(9):P25–P26. doi:10.1164/rccm.2029P25.
  • Wu X, Wang P, Zhang Y, Gao L, Zheng B, Xu Y, Mo J. Toll-like receptor characterization correlates with asthma and is predictive of diagnosis. DNA Cell Biol. 2020;39(7):1313–1321. doi:10.1089/dna.2020.5543.
  • Berthon BS, Gibson PG, Wood LG, MacDonald-Wicks LK, Baines KJ. A sputum gene expression signature predicts oral corticosteroid response in asthma. Eur Respir J. 2017;49(6):1700180. doi:10.1183/13993003.00180-2017.
  • Milger K, Götschke J, Krause L, Nathan P, Alessandrini F, Tufman A, Fischer R, Bartel S, Theis FJ, Behr J, et al. Identification of a plasma miRNA biomarker signature for allergic asthma: a translational approach. Allergy. 2017;72(12):1962–1971. doi:10.1111/all.13205.
  • Peng L, Wen L, Shi QF, Gao F, Huang B, Meng J, Hu CP, Wang CM. Scutellarin ameliorates pulmonary fibrosis through inhibiting NF-κB/NLRP3-mediated epithelial-mesenchymal transition and inflammation. Cell Death Dis. 2020;11(11):978. doi:10.1038/s41419-020-03178-2.
  • Tsang T, Posimo JM, Gudiel AA, Cicchini M, Feldser DM, Brady DC. Copper is an essential regulator of the autophagic kinases ULK1/2 to drive lung adenocarcinoma. Nat Cell Biol. 2020;22(4):412–424. doi:10.1038/s41556-020-0481-4.
  • Wang L, Sun C, Li X, Mao C, Qian J, Wang J, Wu J, Li Q, Bai C, Han B, et al. A pharmacogenetics study of platinum-based chemotherapy in lung cancer: ABCG2 polymorphism and its genetic interaction with SLC31A1 are associated with response and survival. J Cancer. 2021;12(5):1270–1283. doi:10.7150/jca.51621.
  • Zhang Z, Wang J, Chen O. Identification of biomarkers and pathogenesis in severe asthma by coexpression network analysis. BMC Med Genomics. 2021;14(1):51. doi:10.1186/s12920-021-00892-4.
  • Zheng P, Huang C, Leng D, Sun B, Zhang XD. Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma. BMC Med Genomics. 2020;13(1):136. doi:10.1186/s12920-020-00785-y.
  • Nchioua R, Kmiec D, Müller JA, Conzelmann C, Groß R, Swanson CM, Neil SJD, Stenger S, Sauter D, Münch J, et al. SARS-CoV-2 is restricted by zinc finger antiviral protein despite preadaptation to the low-CpG environment in humans. mBio. 2020;11(5):e01930-20. doi:10.1128/mBio.01930-20.
  • Han Q, Cheng P, Yang H, Liang H, Lin F. Altered expression of microRNA-365 is related to the occurrence and development of non-small-cell lung cancer by inhibiting TRIM25 expression. J Cell Physiol. 2019;234(12):22321–22330. doi:10.1002/jcp.28798.
  • Yin J, Zhang Y, Zhang Y, Peng F, Lu Y. Reporting on two novel fusions, DYSF-ALK and ITGAV-ALK, coexisting in one patient with adenocarcinoma of lung, sensitive to crizotinib. J Thorac Oncol. 2018;13(3):e43–e45. doi:10.1016/j.jtho.2017.10.025.
  • Tian P, Liu Y, Zeng H, Tang Y, Lizaso A, Ye J, Shao L, Li Y. Unique molecular features and clinical outcomes in young patients with non-small cell lung cancer harboring ALK fusion genes. J Cancer Res Clin Oncol. 2020;146(4):935–944. doi:10.1007/s00432-019-03116-6.
  • Qureshi N, Chi J, Qian Y, Huang Q, Duan S. Looking for the genes related to lung cancer from nasal epithelial cells by network and pathway analysis. Front Genet. 2022;13:942864. doi:10.3389/fgene.2022.942864.
  • Zhang X, Cui Y, Ding X, Liu S, Han B, Duan X, Zhang H, Sun T. Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis. Bioengineered. 2021;12(1):1457–1470. doi:10.1080/21655979.2021.1908029.
  • Ryan BM, Zanetti KA, Robles AI, Schetter AJ, Goodman J, Hayes RB, Huang W-Y, Gunter MJ, Yeager M, Burdette L, et al. Germline variation in NCF4, an innate immunity gene, is associated with an increased risk of colorectal cancer. Int J Cancer. 2014;134(6):1399–1407. doi:10.1002/ijc.28457.
  • Martner A, Aydin E, Hellstrand K. NOX2 in autoimmunity, tumor growth and metastasis. J Pathol. 2019; 247(2):151–154. doi:10.1002/path.5175.
  • Huang L, Zhang Y, Li Z, Zhao X, Xi Z, Chen H, Shi H, Xin T, Shen R, Wang T. MiR-4319 suppresses colorectal cancer progression by targeting ABTB1. United Eur Gastroenterol J. 2019;7(4):517–528. doi:10.1177/2050640619837440.
  • Wan Q, Tang J, Han Y, Wang D. Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma. Exp Eye Res. 2018;166:13–20. doi:10.1016/j.exer.2017.10.007.
  • Bousquet M, Nguyen D, Chen C, Shields L, Lodish HF. MicroRNA-125b transforms myeloid cell lines by repressing multiple mRNA. Haematologica. 2012;97(11):1713–1721. doi:10.3324/haematol.2011.061515.
  • Yang F, Zhang S, Meng Q, Zhou F, Pan B, Liu F, Yu Y. CXCR1 correlates to poor outcomes of EGFR-TKI against advanced non-small cell lung cancer by activating chemokine and JAK/STAT pathway. Pulm Pharmacol Ther. 2021;67:102001. doi:10.1016/j.pupt.2021.102001.
  • Tang KH, Li S, Khodadadi-Jamayran A, Jen J, Han H, Guidry K, Chen T, Hao Y, Fedele C, Zebala JA, et al. Combined inhibition of SHP2 and CXCR1/2 promotes antitumor T-cell response in NSCLC. Cancer Discov. 2022;12(1):47–61. doi:10.1158/2159-8290.CD-21-0369.
  • Kormann MSD, Hector A, Marcos V, Mays LE, Kappler M, Illig T, Klopp N, Zeilinger S, Carevic M, Rieber N, et al. CXCR1 and CXCR2 haplotypes synergistically modulate cystic fibrosis lung disease. Eur Respir J. 2012;39(6):1385–1390. doi:10.1183/09031936.00130011.
  • Cui F, Yue Y, Zhang Y, Zhang Z, Zhou HS. Advancing biosensors with machine learning. ACS Sens. 2020;5(11):3346–3364. doi:10.1021/acssensors.0c01424.
  • Deo RC. Machine learning in medicine. Circulation. 2015;132(20):1920–1930. doi:10.1161/CIRCULATIONAHA.115.001593.
  • Greener JG, Kandathil SM, Moffat L, Jones DT. A guide to machine learning for biologists. Nat Rev Mol Cell Biol. 2022;23(1):40–55. doi:10.1038/s41580-021-00407-0.

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