268
Views
3
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Identification and Analysis of Neutrophil Extracellular Trap-Related Genes in Osteoarthritis by Bioinformatics and Experimental Verification

, ORCID Icon, , , ORCID Icon, , , & show all
Pages 3837-3852 | Received 19 Apr 2023, Accepted 11 Aug 2023, Published online: 31 Aug 2023

References

  • Battistelli M, Favero M, Burini D, et al. Morphological and ultrastructural analysis of normal, injured and osteoarthritic human knee menisci. Eur J Histochem. 2019;63:2998. doi:10.4081/ejh.2019.2998
  • Donell S. Subchondral bone remodelling in osteoarthritis. EFORT Open Rev. 2019;4:221–229. doi:10.1302/2058-5241.4.180102
  • Favero M, El-Hadi H, Belluzzi E, et al. Infrapatellar fat pad features in osteoarthritis: a histopathological and molecular study. Rheumatology. 2017;56:1784–1793. doi:10.1093/rheumatology/kex287
  • Poole AR. Osteoarthritis as a whole joint disease. HSS J. 2012;8:4–6. doi:10.1007/s11420-011-9248-6
  • Martel-Pelletier J, Barr AJ, Cicuttini FM, et al. Osteoarthritis. Nat Rev Dis Primers. 2016;2:16072. doi:10.1038/nrdp.2016.72
  • Wang T, He C. Pro-inflammatory cytokines: the link between obesity and osteoarthritis. Cytokine Growth Factor Rev. 2018;44:38–50. doi:10.1016/j.cytogfr.2018.10.002
  • Barnett R. Osteoarthritis. Lancet. 2018;391:1985. doi:10.1016/S0140-6736(18)31064-X
  • Yao Q, Wu X, Tao C, et al. Osteoarthritis: pathogenic signaling pathways and therapeutic targets. Signal Transduct Target Ther. 2023;8:56. doi:10.1038/s41392-023-01330-w
  • Tore NG, Oskay D, Haznedaroglu S. The quality of physiotherapy and rehabilitation program and the effect of telerehabilitation on patients with knee osteoarthritis. Clin Rheumatol. 2023;42:903–915. doi:10.1007/s10067-022-06417-3
  • Liu X, Arfman T, Wichapong K, Reutelingsperger CPM, Voorberg J, Nicolaes GAF. PAD4 takes charge during neutrophil activation: impact of PAD4 mediated NET formation on immune-mediated disease. J Thromb Haemost. 2021;19:1607–1617. doi:10.1111/jth.15313
  • Song YH, Wang ZJ, Kang L, et al. PADs and NETs in digestive system: from physiology to pathology. Front Immunol. 2023;14:1077041. doi:10.3389/fimmu.2023.1077041
  • Lazar S, Kahlenberg JM. Systemic lupus erythematosus: new diagnostic and therapeutic approaches. Annu Rev Med. 2023;74:339–352. doi:10.1146/annurev-med-043021-032611
  • Liu X, Huo Y, Zhao J, et al. Endothelial cell protein C receptor regulates neutrophil extracellular trap-mediated rheumatoid arthritis disease progression. Int Immunopharmacol. 2022;112:109249. doi:10.1016/j.intimp.2022.109249
  • Spengler J, Lugonja B, Ytterberg AJ, et al. Release of active peptidyl arginine deiminases by neutrophils can explain production of extracellular citrullinated autoantigens in rheumatoid arthritis synovial fluid. Arth Rheumatol. 2015;67:3135–3145. doi:10.1002/art.39313
  • Zhang Y, Guo L, Dai Q, et al. A signature for pan-cancer prognosis based on neutrophil extracellular traps. J Immunother Cancer. 2022;10:e004210. doi:10.1136/jitc-2021-004210
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47. doi:10.1093/nar/gkv007
  • Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12:77. doi:10.1186/1471-2105-12-77
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12:453–457. doi:10.1038/nmeth.3337
  • Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013;14:7. doi:10.1186/1471-2105-14-7
  • Li Y, Qi D, Zhu B, Ye X. Analysis of m6A RNA methylation-related genes in liver hepatocellular carcinoma and their correlation with survival. Int J Mol Sci. 2021;22:1474. doi:10.3390/ijms22031474
  • Cao X, He J, Chen A, et al. Comprehensive analysis of necroptosis landscape in skin cutaneous melanoma for appealing its implications in prognosis estimation and microenvironment status. J Pers Med. 2023;13:245. doi:10.3390/jpm13020245
  • Xia J, Sun L, Xu S, et al. A model using support vector machines recursive feature elimination (SVM-RFE) Algorithm to Classify Whether COPD patients have been continuously managed according to GOLD guidelines. Int J Chron Obstruct Pulmon Dis. 2020;15:2779–2786. doi:10.2147/COPD.S271237
  • Franz M, Rodriguez H, Lopes C, et al. GeneMANIA update 2018. Nucleic Acids Res. 2018;46:W60–w64. doi:10.1093/nar/gky311
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102:15545–15550. doi:10.1073/pnas.0506580102
  • Tang J, Su N, Zhou S, et al. Fibroblast growth factor receptor 3 inhibits osteoarthritis progression in the knee joints of adult mice. Arthritis Rheumatol. 2016;68:2432–2443. doi:10.1002/art.39739
  • Hu J, Du H, Yuan Y, et al. MFG-E8 knockout aggravated nonalcoholic steatohepatitis by promoting the activation of TLR4/NF-κB signaling in mice. Mediators Inflamm. 2022;2022:1–13. doi:10.1155/2022/5188895
  • Sun X, Zhen X, Hu X, et al. Osteoarthritis in the middle-aged and elderly in china: prevalence and influencing factors. Int J Environ Res Public Health. 2019;16:4701. doi:10.3390/ijerph16234701
  • Yang J, Hu S, Bian Y, et al. Targeting cell death: pyroptosis, ferroptosis, apoptosis and necroptosis in osteoarthritis. Front Cell Dev Biol. 2021;9:789948. doi:10.3389/fcell.2021.789948
  • Fousert E, Toes R, Desai J. Neutrophil extracellular traps (NETs) take the central stage in driving autoimmune responses. Cells. 2020;9:915. doi:10.3390/cells9040915
  • Papayannopoulos V, Metzler KD, Hakkim A, Zychlinsky A. Neutrophil elastase and myeloperoxidase regulate the formation of neutrophil extracellular traps. J Cell Biol. 2010;191:677–691. doi:10.1083/jcb.201006052
  • Ferreira MR, Santos GA, Biagi CA, Silva Junior WA, Zambuzzi WF. GSVA score reveals molecular signatures from transcriptomes for biomaterials comparison. J Biomed Mater Res A. 2021;109:1004–1014. doi:10.1002/jbm.a.37090
  • Handelman GS, Kok HK, Chandra RV, Razavi AH, Lee MJ, Asadi H. eDoctor: machine learning and the future of medicine. J Intern Med. 2018;284:603–619. doi:10.1111/joim.12822
  • Abdelwahab A, Palosaari S, Abdelwahab SA, et al. Differential synovial tissue expression of TLRs in seropositive and seronegative rheumatoid arthritis: a preliminary report. Autoimmunity. 2021;54:23–34. doi:10.1080/08916934.2020.1864729
  • Huo YX, Huang L, Zhang DF, et al. Identification of SLC25A37 as a major depressive disorder risk gene. J Psychiatr Res. 2016;83:168–175. doi:10.1016/j.jpsychires.2016.09.011
  • Zou J, Li Y, Liao N, et al. Identification of key genes associated with polycystic ovary syndrome (PCOS) and ovarian cancer using an integrated bioinformatics analysis. J Ovarian Res. 2022;15:30. doi:10.1186/s13048-022-00962-w
  • Slovacek H, Khanna R, Poredos P, et al. Interrelationship of MMP-9, Proteoglycan-4, and inflammation in osteoarthritis patients undergoing total hip arthroplasty. Clin Appl Thromb Hemost. 2021;27:1076029621995569. doi:10.1177/1076029621995569
  • Malemud CJ. Negative Regulators of JAK/STAT signaling in rheumatoid arthritis and osteoarthritis. Int J Mol Sci. 2017;18:484. doi:10.3390/ijms18030484
  • Wei J, Gao C, Hu K, et al. Knockdown of DAPK1 attenuates IL-1β-induced extracellular matrix degradation and inflammatory response in osteoarthritis chondrocytes via regulating the p38 MAPK-signaling pathway. Allergol Immunopathol. 2022;50:169–175. doi:10.15586/aei.v50i6.744