Identification of differentially expressed and methylated genes associated with rheumatoid arthritis based on network

References

• Singh JA , Saag KG , Bridges SL , et al. 2015 american college of rheumatology guideline for the treatment of rheumatoid arthritis. Arthritis Care & Research. 2016;68:1–25.
   PubMed Web of Science ®Google Scholar
• Betts KA , Griffith J , Ganguli A , et al. Economic burden and treatment patterns of cycling between conventional synthetic disease-modifying antirheumatic drugs among biologic-treated patients with rheumatoid arthritis. Clin Ther. 2016;38:1205–1216.
   PubMed Web of Science ®Google Scholar
• Drosos AA , Pelechas E , Voulgari PV. Radiological findings of the cervical spine in rheumatoid arthritis: what a rheumatologist should know. Curr Rheumatol Rep. 2020;22:19.
   PubMed Web of Science ®Google Scholar
• Lo J , Chan L , Flynn S. A systematic review of the incidence, prevalence, costs, and activity/work limitations of amputation, osteoarthritis, rheumatoid arthritis, back pain, multiple sclerosis, spinal cord injury, stroke, and traumatic brain injury in the United States: a 2019 update. Arch Phys Med Rehabil. 2020. Forthcoming.
   PubMedGoogle Scholar
• Li Z. A new look at rheumatology in China-opportunities and challenges. Nat Rev Rheumatol. 2015;11:313–317.
   PubMed Web of Science ®Google Scholar
• Croia C , Bursi R , Sutera D , et al. One year in review 2019: pathogenesis of rheumatoid arthritis. Clin Exp Rheumatol. 2019;37:347–357.
   PubMed Web of Science ®Google Scholar
• Giannini D , Antonucci M , Petrelli F , et al. One year in review 2020: pathogenesis of rheumatoid arthritis. Clin Exp Rheumatol. 2020;38:387–397.
   PubMed Web of Science ®Google Scholar
• Viatte S , Barton A. Genetics of rheumatoid arthritis susceptibility, severity, and treatment response. Semin Immunopathol. 2017;39:395–408.
   PubMed Web of Science ®Google Scholar
• Balandraud N , Roudier J. Epstein-Barr virus and rheumatoid arthritis. Joint Bone Spine. 2018;85:165–170.
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of dna methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–492.
   PubMed Web of Science ®Google Scholar
• Li WC , Bai DL , Xu Y , et al. Identification of differentially expressed genes in synovial tissue of rheumatoid arthritis and osteoarthritis in patients. J Cell Biochem. 2019;120:4533–4544.
   PubMed Web of Science ®Google Scholar
• Nemtsova MV , Zaletaev DV , Bure IV , et al. Epigenetic changes in the pathogenesis of rheumatoid arthritis. Front Genet. 2019;10:570.
   PubMed Web of Science ®Google Scholar
• Ciechomska M , Roszkowski L , Maslinski W. DNA methylation as a future therapeutic and diagnostic target in rheumatoid arthritis. Cells. 2019;8:953.
   Web of Science ®Google Scholar
• Brandt B , Rashidiani S , Bán Á , et al. DNA methylation-governed gene expression in autoimmune arthritis. IJMS. 2019;20:5646.
   Google Scholar
• Fang G , Zhang Q H , Tang Q , et al. Comprehensive analysis of gene expression and DNA methylation datasets identify valuable biomarkers for rheumatoid arthritis progression. Oncotarget. 2018;9(3):2977–2983.
   PubMedGoogle Scholar
• Zhang L , Ma S , Wang H , et al. Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of dna methylation and gene expression profiling. Gene. 2017;634:62–67.
   PubMed Web of Science ®Google Scholar
• Huang Y , Zheng S , Wang R , et al. Ccl5 and related genes might be the potential diagnostic biomarkers for the therapeutic strategies of rheumatoid arthritis. Clin Rheumatol. 2019;38:2629–2635.
   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:R84.
   PubMed Web of Science ®Google Scholar
• Wang Q , Rozelle AL , Lepus CM , et al. Identification of a central role for complement in osteoarthritis. Nat Med. 2011;17:1674–1679.
   PubMed Web of Science ®Google Scholar
• Zhu H , Wu LF , Mo XB , et al. Rheumatoid arthritis-associated DNA methylation sites in peripheral blood mononuclear cells. Ann Rheum Dis. 2019;78:36–42.
   PubMed Web of Science ®Google Scholar
• Morris TJ , Butcher LM , Feber A , et al. Champ: 450k chip analysis methylation pipeline. Bioinformatics. 2014;30:428–430.
   PubMed Web of Science ®Google Scholar
• Huang YH , Khor SS , Zheng X , et al. A high-resolution HLA imputation system for the Taiwanese population: a study of the Taiwan Biobank. Pharmacogenomics J. 2020. Forthcoming. HLA & KIR imputation network (HKimp.net).
   Web of Science ®Google Scholar
• Kampstra ASB , Toes REM. Hla class ii and rheumatoid arthritis: the bumpy road of revelation. Immunogenetics. 2017;69:597–603.
   PubMed Web of Science ®Google Scholar
• Stuhlmüller B , Mans K , Tandon N , et al. Genomic stratification by expression of hla-drb4 alleles identifies differential innate and adaptive immune transcriptional patterns - a strategy to detect predictors of methotrexate response in early rheumatoid arthritis. Clin Immunol. 2016;171:50–61.
   PubMed Web of Science ®Google Scholar
• Sumbul A , Jeevan G , Sandeep V , et al. A comprehensive gene expression meta-analysis identifies novel immune signatures in rheumatoid arthritis patients. Front Immunol. 2017;8:74.
   PubMed Web of Science ®Google Scholar
• Krista K , Antti K , Riitta K , et al. Stat6 and stat1 pathway activation in circulating lymphocytes and monocytes as predictor of treatment response in rheumatoid arthritis. PLoS One. 2016;11:e0167975.
   PubMed Web of Science ®Google Scholar
• Kotrych D , Dziedziejko V , Safranow K , et al. Cxcl9 and cxcl10 gene polymorphisms in patients with rheumatoid arthritis. Rheumatol Int. 2015;35:1319–1323.
   PubMedGoogle Scholar
• Alam J , Jantan I , Bukhari SNA. Rheumatoid arthritis: recent advances on its etiology, role of cytokines and pharmacotherapy. Biomed Pharmacother. 2017;92:615–633.
   PubMed Web of Science ®Google Scholar
• Kliebenstein DJ. Using networks to identify and interpret natural variation. Curr Opin Plant Biol. 2020;54:122–126.
   PubMed Web of Science ®Google Scholar
• Kotni MK , Zhao M , Wei DQ. Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation. Orphanet J Rare Dis. 2016;11:148.
   PubMed Web of Science ®Google Scholar
• Selvaraj G , Kaliamurthi S , Kaushik AC , et al. Identification of target gene and prognostic evaluation for lung adenocarcinoma using gene expression meta-analysis, network analysis and neural network algorithms. J Biomed Inform. 2018;86:120–134..
   PubMed Web of Science ®Google Scholar
• Bondt A , Hafkenscheid L , Falck D, et al . ACPA IgG galactosylation associates with disease activity inpregnant patients with rheumatoid arthritis. Ann Rheum Dis. 2018;77(8):1130–1136.
   PubMed Web of Science ®Google Scholar
• Mcinnes IB , Buckley CD , Isaacs JD. Cytokines in rheumatoid arthritis – shaping the immunological landscape. Nat Rev Rheumatol. 2016;12:63–68.
   PubMed Web of Science ®Google Scholar
• Fu H , Hu D , Zhang L , et al. Role of extracellular vesicles in rheumatoid arthritis. Mol Immunol. 2018;93:125–132.
   PubMed Web of Science ®Google Scholar
• Shimizu Y , Kohyama M , Yorifuji H , et al. FcγRIIIA-mediated activation of NK cells by IgG heavy chain complexed with MHC class II molecules. Int Immunol. 2019;31:303–314.
   PubMed Web of Science ®Google Scholar
• An Q , Yan W , Zhao Y , et al. Enhanced neutrophil autophagy and increased concentrations of il-6, il-8, il-10 and mcp-1 in rheumatoid arthritis. Int Immunopharmacol. 2018;65:119–128.
   PubMed Web of Science ®Google Scholar
• Lin Z , Min Y , Jiayin D , et al. Chemokine signaling pathway involved in ccl2 expression in patients with rheumatoid arthritis. Yonsei Med J. 2015;56:1134–1142.
   PubMed Web of Science ®Google Scholar
• Kikuta J , Ishii M. Osteoclast migration, differentiation and function: novel therapeutic targets for rheumatic diseases. Rheumatology (Oxford). 2013;52:226–234.
   PubMed Web of Science ®Google Scholar
• Rump L , Mattey DL , Kehoe O , et al. An initial investigation into endothelial cc chemokine expression in the human rheumatoid synovium. Cytokine. 2017;97:133–140.
   PubMed Web of Science ®Google Scholar
• Klimiuk PA , Sierakowski S , Domyslawska I , et al. Serum chemokines in patients with rheumatoid arthritis treated with etanercept. Rheumatol Int. 2011;31:457–461.
   PubMed Web of Science ®Google Scholar
• Shah D , Wanchu A , Bhatnagar A. Interaction between oxidative stress and chemokines: possible pathogenic role in systemic lupus erythematosus and rheumatoid arthritis. Immunobiology. 2011;216:1010–1017.
   PubMed Web of Science ®Google Scholar
• Devito A. Interferon γ-induced chemokines in psoriatic arthritis. Clin Ter. 2014;165:e442–e446.
   PubMedGoogle Scholar
• Lurati A , Laria A , Gatti A , et al. Different T cells’ distribution and activation degree of th17 cd4+ cells in peripheral blood in patients with osteoarthritis, rheumatoid arthritis, and healthy donors: preliminary results of the magenta clicao study. Open Access Rheumatol. 2015;7:63–68.
   PubMedGoogle Scholar
• Perdriger A , Guggenbuhl P , Chalés G , et al. The role of hla-dr-dr and hla-dr-dp interactions in genetic susceptibility to rheumatoid arthritis. Human Immunology. 1996;46:42–48.
   PubMed Web of Science ®Google Scholar
• Feng X , Hao X , Shi R , et al. Detection and comparative analysis of methylomic biomarkers of rheumatoid arthritis. Front Genet. 2020;11:238.
   PubMed Web of Science ®Google Scholar
• Karami J , Aslani S , Tahmasebi MN , et al. Epigenetics in rheumatoid arthritis; fibroblast-like synoviocytes as an emerging paradigm in the pathogenesis of the disease. Immunol Cell Biol. 2020;98:171–186.
   PubMed Web of Science ®Google Scholar
• Nair N , Wilson AG , Barton A. DNA methylation as a marker of response in rheumatoid arthritis. Pharmacogenomics. 2017;18:1323–1332..
   PubMed Web of Science ®Google Scholar
• Viatte S , Plant D , Raychaudhuri S. Genetics and epigenetics of rheumatoid arthritis. Nat Rev Rheumatol. 2013;9:141–153.
   PubMed Web of Science ®Google Scholar
• Koch A , Joosten SC , Feng Z , et al. Author correction: analysis of dna methylation in cancer: location revisited. Nat Rev Clin Oncol. 2018;15:467.
   PubMed Web of Science ®Google Scholar
• Karouzakis E , Gay RE , Gay S , et al. Increased recycling of polyamines is associated with global DNA hypomethylation in rheumatoid arthritis synovial fibroblasts. Arthritis Rheum. 2012;64:1809–1817. 
   PubMed Web of Science ®Google Scholar
• Liu CT , Min L , Wang YJ , et al. shRNA-mediated knockdown of KNTC1 suppresses cell viability and induces apoptosis in esophageal squamous cell carcinoma. Int J Oncol. 2019;54:1053–1060.
   PubMed Web of Science ®Google Scholar
• Srivastava S , Chen L. Comparison between the stochastic search variable selection and the least absolute shrinkage and selection operator for genome-wide association studies of rheumatoid arthritis. BMC Proc. 2009;3:S21.
   PubMedGoogle Scholar
• Stuhlmann T , Planells-Cases R , Jentsch TJ. Lrrc8/vrac anion channels enhance β-cell glucose sensing and insulin secretion. Nat Commun. 2018;9:1974.
   PubMed Web of Science ®Google Scholar
• Riquelme P , Amodio G , Macedo C , et al. Dhrs9 is a stable marker of human regulatory macrophages. Transplantation. 2017;101:2731–2738.
   PubMed Web of Science ®Google Scholar
• Bauman DR , Steckelbroeck S , Williams MV , et al. Identification of the major oxidative 3alpha-hydroxysteroid dehydrogenase in human prostate that converts 5alpha-androstane-3alpha,17beta-diol to 5alpha-dihydrotestosterone: a potential therapeutic target for androgen-dependent disease. Mol Endocrinol. 2006;20:444–458.
   PubMed Web of Science ®Google Scholar
• Cutolo M , Capellino S , Montagna P , et al. New roles for estrogens in rheumatoid arthritis. Clin Exp Rheumatol. 2003;21:687–690.
   PubMed Web of Science ®Google Scholar
• Wieczorek S , Franke A , Yin H , et al. Association of UCP2-866 G/A polymorphism with chronic inflammatory diseases. Genes Immun. 2009;10:601–605.
   PubMed Web of Science ®Google Scholar