Exploration of effective biomarkers and infiltrating Immune cells in Osteoarthritis based on bioinformatics analysis

References

• Katz JN, Arant KR, Loeser RF. Diagnosis and treatment of hip and knee osteoarthritis: a review. Jama. 2021;325(6):568–578.
   PubMed Web of Science ®Google Scholar
• Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990–2017: a systematic analysis for the global burden of disease study 2017. Lancet. 2018;392(10159):1789–1858.
   PubMed Web of Science ®Google Scholar
• Vincent TL. Targeting mechanotransduction pathways in osteoarthritis: a focus on the pericellular matrix. Curr Opin Pharmacol. 2013;13(3):449–454.
   PubMed Web of Science ®Google Scholar
• Scanzello CR, Goldring SR. The role of synovitis in osteoarthritis pathogenesis. Bone. 2012;51(2):249–257.
   PubMed Web of Science ®Google Scholar
• Woodell-May JE, Sommerfeld SD. Role of inflammation and the immune system in the progression of osteoarthritis. J Orthop Res. 2020;38(2):253–257.
   PubMed Web of Science ®Google Scholar
• Zhang H, Cai D, Bai X. Macrophages regulate the progression of osteoarthritis. Osteoarthritis Cartilage. 2020;28(5):555–561.
   PubMed Web of Science ®Google Scholar
• Li M, Yin H, Yan Z, et al. The immune microenvironment in cartilage injury and repair. Acta Biomater. 2022;140:23–42.
   PubMed Web of Science ®Google Scholar
• Nedunchezhiyan U, Varughese I, Sun AR, et al. Obesity, inflammation, and immune system in osteoarthritis. Front Immunol. 2022;13:907750.
   PubMed Web of Science ®Google Scholar
• Molnar V, Matišić V, Kodvanj I, et al. Cytokines and chemokines involved in osteoarthritis pathogenesis. Int J Mol Sci. 2021;22(17):9208.
   PubMed Web of Science ®Google Scholar
• Wu ZY, Du G, Lin YC. Identifying hub genes and immune infiltration of osteoarthritis using comprehensive bioinformatics analysis. J Orthop Surg Res. 2021;16(1):630.
   PubMed Web of Science ®Google Scholar
• Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 2017;18(1):220.
   PubMed Web of Science ®Google Scholar
• Attur M, Duan X, Cai L, et al. Periostin loss-of-function protects mice from post-traumatic and age-related osteoarthritis. Arthritis Res Ther. 2021;23(1):104.
   PubMed Web of Science ®Google Scholar
• Woetzel D, Huber R, Kupfer P, et al. Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation. Arthritis Res Ther. 2014;16(2):R84.
   PubMed Web of Science ®Google Scholar
• Bhattacharya S, Dunn P, Thomas CG, et al. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data. 2018;5(1):180015.
   PubMed Web of Science ®Google Scholar
• Davis S, Meltzer PS. GEOquery: a bridge between the gene expression omnibus (GEO) and BioConductor. Bioinformatics. 2007;23(14):1846–1847.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47–e47.
   PubMed Web of Science ®Google Scholar
• Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.
   PubMed Web of Science ®Google Scholar
• Shen W, Song Z, Zhong X, et al. Sangerbox: a comprehensive, interaction-friendly clinical bioinformatics analysis platform. iMeta. 2022;1(3):e36.
   Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Lex A, Gehlenborg N, Strobelt H, et al. UpSet: visualization of intersecting sets. IEEE Trans Visual Comput Graphics. 2014;20(12):1983–1992.
   PubMed Web of Science ®Google Scholar
• Ito K, Murphy D. Application of ggplot2 to pharmacometric graphics. CPT Pharmacometrics Syst Pharmacol. 2013;2(10):e79.
   PubMedGoogle Scholar
• Kulkarni P, Martson A, Vidya R, et al. Pathophysiological landscape of osteoarthritis. Adv Clin Chem. 2021;100:37–90.
   PubMed Web of Science ®Google Scholar
• Lin R, Deng C, Li X, et al. Copper-incorporated bioactive glass-ceramics inducing anti-inflammatory phenotype and regeneration of cartilage/bone interface. Theranostics. 2019;9(21):6300–6313.
   PubMed Web of Science ®Google Scholar
• Mahon OR, Kelly DJ, McCarthy GM, et al. Osteoarthritis-associated basic calcium phosphate crystals alter immune cell metabolism and promote M1 macrophage polarization. Osteoarthritis Cartilage. 2020;28(5):603–612.
   PubMed Web of Science ®Google Scholar
• Deng Z, Zhang Q, Zhao Z, et al. Crosstalk between immune cells and bone cells or chondrocytes. Int Immunopharmacol. 2021;101(Pt A):108179.
   PubMedGoogle Scholar
• Culemann S, Grüneboom A, Nicolás-Ávila J, et al. Locally renewing resident synovial macrophages provide a protective barrier for the joint. Nature. 2019;572(7771):670–675.
   PubMed Web of Science ®Google Scholar
• Manferdini C, Paolella F, Gabusi E, et al. From osteoarthritic synovium to synovial-derived cells characterization: synovial macrophages are key effector cells. Arthritis Res Ther. 2016;18(1):83.
   PubMedGoogle Scholar
• Wood MJ, Leckenby A, Reynolds G, et al. Macrophage proliferation distinguishes 2 subgroups of knee osteoarthritis patients. JCI Insight. 2019;4(2):125325.
   Web of Science ®Google Scholar
• Lv Z, Xu X, Sun Z, et al. TRPV1 alleviates osteoarthritis by inhibiting M1 macrophage polarization via Ca(2+)/CaMKII/Nrf2 signaling pathway. Cell Death Dis. 2021;12(6):504.
   PubMed Web of Science ®Google Scholar
• Lu Y, Liu L, Pan J, et al. MFG-E8 regulated by miR-99b-5p protects against osteoarthritis by targeting chondrocyte senescence and macrophage reprogramming via the NF-κB pathway. Cell Death Dis. 2021;12(6):533.
   PubMed Web of Science ®Google Scholar
• Lu J, Zhang H, Pan J, et al. Fargesin ameliorates osteoarthritis via macrophage reprogramming by downregulating MAPK and NF-κB pathways. Arthritis Res Ther. 2021;23(1):142.
   PubMed Web of Science ®Google Scholar
• Hsueh MF, Zhang X, Wellman SS, et al. Synergistic roles of macrophages and neutrophils in osteoarthritis progression. Arthritis Rheumatol. 2021;73(1):89–99.
   PubMed Web of Science ®Google Scholar
• Rosshirt N, Trauth R, Platzer H, et al. Proinflammatory T cell polarization is already present in patients with early knee osteoarthritis. Arthritis Res Ther. 2021;23(1):37.
   PubMed Web of Science ®Google Scholar
• Li YS, Luo W, Zhu SA, et al. T cells in osteoarthritis: alterations and Beyond. Front Immunol. 2017;8:356.
   PubMed Web of Science ®Google Scholar
• Eltit F, Mohammad N, Medina I, et al. Perivascular lymphocytic aggregates in hip prosthesis-associated adverse local tissue reactions demonstrate Th1 and Th2 activity and exhausted CD8(+) cell responses. Journal Orthopaedic Research. 2021;39(12):2581–2594.
   PubMed Web of Science ®Google Scholar
• Alahdal M, Zhang H, Huang R, et al. Potential efficacy of dendritic cell immunomodulation in the treatment of osteoarthritis. Rheumatology. 2021;60(2):507–517.
   PubMed Web of Science ®Google Scholar
• Tardif G, Hum D, Pelletier JP, et al. Differential gene expression and regulation of the bone morphogenetic protein antagonists follistatin and gremlin in normal and osteoarthritic human chondrocytes and synovial fibroblasts. Arthritis Rheum. 2004;50(8):2521–2530.
   PubMedGoogle Scholar
• Tardif G, Pelletier JP, Boileau C, et al. The BMP antagonists follistatin and gremlin in normal and early osteoarthritic cartilage: an immunohistochemical study. Osteoarthr Cartil. 2009;17(2):263–270.
   PubMed Web of Science ®Google Scholar
• Huang X, Zhong L, van Helvoort E, et al. The expressions of Dickkopf-related protein 1 and Frizzled-related protein are negatively correlated to local inflammation and osteoarthritis severity. Cartilage. 2021;12(4):496–504.
   PubMed Web of Science ®Google Scholar
• Yi J, Jin Q, Zhang B, et al. Gremlin-1 concentrations are correlated with the severity of knee osteoarthritis. Med Sci Monit. 2016;22:4062–4065.
   PubMed Web of Science ®Google Scholar
• Ouyang X, Ding Y, Yu L, et al. Circ_SPG11 plays contributing effects on IL-1β-induced chondrocyte apoptosis and ECM degradation via miR-665 inhibition-mediated GREM1 upregulation. Clin Immunol. 2021;233:108889.
   PubMed Web of Science ®Google Scholar
• Lepelletier Y, Moura IC, Hadj-Slimane R, et al. Immunosuppressive role of semaphorin-3A on T cell proliferation is mediated by inhibition of actin cytoskeleton reorganization. Eur J Immunol. 2006;36(7):1782–1793.
   PubMed Web of Science ®Google Scholar
• Okubo M, Kimura T, Fujita Y, et al. Semaphorin 3A is expressed in human osteoarthritic cartilage and antagonizes vascular endothelial growth factor 165-promoted chondrocyte migration: an implication for chondrocyte cloning. Arthritis Rheum. 2011;63(10):3000–3009.
   PubMed Web of Science ®Google Scholar
• Sumi C, Hirose N, Yanoshita M, et al. Semaphorin 3A inhibits inflammation in chondrocytes under excessive mechanical stress. Mediators Inflamm. 2018;2018:1–9.
   Web of Science ®Google Scholar
• Sun J, Wei X, Wang Z, et al. Inflammatory milieu cultivated Sema3A signaling promotes chondrocyte apoptosis in knee osteoarthritis. J Cell Biochem. 2018;119(3):2891–2899.
   PubMed Web of Science ®Google Scholar
• MacDonald IJ, Liu SC, Su CM, et al. Implications of angiogenesis involvement in arthritis. Int J Mol Sci. 2018;19(7):2012.
   PubMed Web of Science ®Google Scholar
• Maes C, Carmeliet P, Moermans K, et al. Impaired angiogenesis and endochondral bone formation in mice lacking the vascular endothelial growth factor isoforms VEGF164 and VEGF188. Mech Dev. 2002;111(1–2):61–73.
   PubMed Web of Science ®Google Scholar
• Midy V, Plouët J. Vasculotropin/vascular endothelial growth factor induces differentiation in cultured osteoblasts. Biochem Biophys Res Commun. 1994;199(1):380–386.
   PubMed Web of Science ®Google Scholar
• Zelzer E, Mamluk R, Ferrara N, et al. VEGFA is necessary for chondrocyte survival during bone development. Development. 2004;131(9):2161–2171.
   PubMed Web of Science ®Google Scholar
• Xiao P, Zhu X, Sun J, et al. Cartilage tissue miR-214-3p regulates the TrkB/ShcB pathway paracrine VEGF to promote endothelial cell migration and angiogenesis. Bone. 2021;151:116034.
   PubMed Web of Science ®Google Scholar
• Cao F, Chen Y, Wang X, et al. Therapeutic effect and potential mechanisms of intra-articular injections of miR-140-5p on early-stage osteoarthritis in rats. Int Immunopharmacol. 2021;96:107786.
   PubMed Web of Science ®Google Scholar
• Ferrao Blanco MN, Domenech Garcia H, Legeai-Mallet L, et al. Tyrosine kinases regulate chondrocyte hypertrophy: promising drug targets for osteoarthritis. Osteoarth Cartil. 2021;29(10):1389–1398.
   PubMed Web of Science ®Google Scholar
• Li K, Zhang Y, Zhang Y, et al. Tyrosine kinase fyn promotes osteoarthritis by activating the β-catenin pathway. Ann Rheum Dis. 2018;77(6):935–943.
   PubMed Web of Science ®Google Scholar
• Sui C, Zhang L, Hu Y. MicroRNA‑let‑7a inhibition inhibits LPS‑induced inflammatory injury of chondrocytes by targeting IL6R. Mol Med Rep. 2019;20(3):2633–2640.
   PubMed Web of Science ®Google Scholar
• Zheng LW, Lan CN, Kong Y, et al. Exosomal miR-150 derived from BMSCs inhibits TNF-α-mediated osteoblast apoptosis in osteonecrosis of the femoral head by GREM1/NF-κB signaling. Regen Med. 2022;17(10):739–753.
   PubMed Web of Science ®Google Scholar
• Song Y, Zeng S, Zheng G, et al. FOXO3a-driven miRNA signatures suppresses VEGF-A/NRP1 signaling and breast cancer metastasis. Oncogene. 2021;40(4):777–790.
   PubMed Web of Science ®Google Scholar
• Xuan Y, Wang J, Zhang X, et al. Resveratrol attenuates high Glucose-Induced osteoblast dysfunction via AKT/GSK3β/FYN-Mediated NRF2 activation. Front Pharmacol. 2022;13:862618.
   PubMed Web of Science ®Google Scholar
• Liu Y, Yuan J, Zhang Q, et al. Circ_0016347 modulates proliferation, migration, invasion, cell cycle, and apoptosis of osteosarcoma cells via the miR-661/IL6R axis. Autoimmunity. 2022;55(4):264–274.
   PubMed Web of Science ®Google Scholar
• Ganta VC, Choi M, Farber CR, et al. Antiangiogenic VEGF(165)b regulates macrophage polarization via S100A8/S100A9 in peripheral artery disease. Circulation. 2019;139(2):226–242.
   PubMed Web of Science ®Google Scholar
• Dong D, Zhang Y, He H, et al. Alpinetin inhibits macrophage infiltration and atherosclerosis by improving the thiol redox state: requirement of GSk3β/Fyn-dependent Nrf2 activation. Faseb j. 2022;36(4):e22261.
   PubMed Web of Science ®Google Scholar
• Weng YS, Tseng HY, Chen YA, et al. MCT-1/miR-34a/IL-6/IL-6R signaling axis promotes EMT progression, cancer stemness and M2 macrophage polarization in triple-negative breast cancer. Mol Cancer. 2019;18(1):42.
   PubMed Web of Science ®Google Scholar
• Oussa NA, Dahmani A, Gomis M, et al. VEGF requires the receptor NRP-1 to inhibit lipopolysaccharide-dependent dendritic cell maturation. J Immunol. 2016;197(10):3927–3935.
   PubMed Web of Science ®Google Scholar
• Sarris M, Andersen KG, Randow F, et al. Neuropilin-1 expression on regulatory T cells enhances their interactions with dendritic cells during antigen recognition. Immunity. 2008;28(3):402–413.
   PubMed Web of Science ®Google Scholar
• Stradner MH, Cheung KP, Lasorella A, et al. Id2 regulates hyporesponsive invariant natural killer T cells. Immunol Cell Biol. 2016;94(7):640–645.
   PubMed Web of Science ®Google Scholar