Identification of key biomolecules in rheumatoid arthritis through the reconstruction of comprehensive disease-specific biological networks

References

• Catrina AI, Svensson CI, Malmström V, et al. Mechanisms leading from systemic autoimmunity to joint-specific disease in rheumatoid arthritis. Nat Rev Rheumatol. 2017;13 (2):79–86.
   PubMed Web of Science ®Google Scholar
• Gibofsky A. Epidemiology, pathophysiology, and diagnosis of rheumatoid arthritis: a synopsis. Am J Manag Care. 2014;20(Suppl:7):S128–S135.
   Google Scholar
• Song X, Lin Q. Genomics, transcriptomics and proteomics to elucidate the pathogenesis of rheumatoid arthritis. Rheumatol Int. 2017;37(8):1257–1265.
   PubMed Web of Science ®Google Scholar
• Kori M, Gov E, Arga KY. Molecular signatures of ovarian diseases: insights from network medicine perspective. Syst Biol Reprod Med. 2016;62(4):266–282.
   PubMed Web of Science ®Google Scholar
• Gov E, Kori M, Arga KY. Multiomics analysis of tumor microenvironment reveals Gata2 and miRNA-124-3p as potential novel biomarkers in ovarian cancer. OMICS. 2017;21(10):603–615.
   PubMed Web of Science ®Google Scholar
• Calimlioglu B, Karagoz K, Sevimoglu T, et al. Tissue-specific molecular biomarker signatures of type 2 diabetes: an integrative analysis of transcriptomics and protein–protein interaction data. OMICS. 2015;19(9):563–573.
   PubMed Web of Science ®Google Scholar
• Kori M, Arga KY. Potential biomarkers and therapeutic targets in cervical cancer: insights from the meta-analysis of transcriptomics data within network biomedicine perspective. PloS One. 2018;13(7):e0200717.
   PubMed Web of Science ®Google Scholar
• Islam T, Rahman R, Gov E, et al. Drug targeting and biomarkers in head and neck cancers: insights from systems biology analyses. OMICS. 2018;22(6):422–436.
   PubMed Web of Science ®Google Scholar
• Khan A, Ali A, Junaid M, et al. Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. BMC Syst Biol. 2018;2(S4):39.
   Google Scholar
• Noori E, Kazemi B, Bandehpour M, et al. Deciphering crucial genes in coeliac disease by bioinformatics analysis. Autoimmunity. 2019;1–12.
   PubMed Web of Science ®Google Scholar
• Ye H, Zhang J, Wang J, et al. CD4 T-cell transcriptome analysis reveals aberrant regulation of STAT3 and Wnt signaling pathways in rheumatoid arthritis: evidence from a case–control study. Arthritis Res Ther. 2015;17(1):76.
   PubMed Web of Science ®Google Scholar
• Ekwall AKH, Whitaker JW, Hammaker D, et al. The rheumatoid arthritis risk gene LBH regulates growth in fibroblast‐like synoviocytes. Arthritis Rheum. 2015;67(5):1193–1202.
   Web of Science ®Google Scholar
• Ouyang Q, Wu J, Jiang Z, et al. Microarray expression profile of circular RNAs in peripheral blood mononuclear cells from rheumatoid arthritis patients. Cell Physiol Biochem. 2017;42(2):651–659.
   PubMed Web of Science ®Google Scholar
• Choi S, You S, Kim D, et al. Transcription factor NFAT5 promotes macrophage survival in rheumatoid arthritis. J Clin Invest. 2017;127(3):954–969.
   PubMed Web of Science ®Google Scholar
• Lin J, He Y, Chen J, et al. A critical role of transcription factor YY1 in rheumatoid arthritis by regulation of interleukin-6. J. Autoimmun. 2017;77:67–75.
   PubMed Web of Science ®Google Scholar
• Ambros V. The functions of animal microRNAs. Nature. 2004;431(7006):350–355.
   PubMed Web of Science ®Google Scholar
• Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281–297.
   PubMed Web of Science ®Google Scholar
• Huang Y, Shen XJ, Zou Q, et al. Biological functions of microRNAs: a review. J Physiol Biochem. 2011;67(1):129–139.
   PubMed Web of Science ®Google Scholar
• Hao F, Lee RJ, Zhong L, et al. Hybrid micelles containing methotrexate-conjugated polymer and co-loaded with microRNA-124 for rheumatoid arthritis therapy. Theranostics. 2019;9(18):5282–5297.
   PubMed Web of Science ®Google Scholar
• Hong BK, You S, Yoo SA, et al. MicroRNA-143 and-145 modulate the phenotype of synovial fibroblasts in rheumatoid arthritis. Exp Mol Med. 2017;49(8):e363–e363.
   PubMedGoogle Scholar
• Rajasekhar M, Olsson AM, Steel KJ, et al. MicroRNA-155 contributes to enhanced resistance to apoptosis in monocytes from patients with rheumatoid arthritis. J. Autoimmun. 2017;79:53–62.
   PubMed Web of Science ®Google Scholar
• Ayeldeen G, Nassar Y, Ahmed H, et al. Possible use of miRNAs-146a and-499 expression and their polymorphisms as diagnostic markers for rheumatoid arthritis. Mol Cell Biochem. 2018;449(1-2):145–156.
   PubMed Web of Science ®Google Scholar
• Pauley KM, Satoh M, Chan AL, et al. Upregulated miR-146a expression in peripheral blood mononuclear cells from rheumatoid arthritis patients. Arthritis Res Ther. 2008;10(4):R101.
   PubMed Web of Science ®Google Scholar
• Barabási AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011;12(1):56–68.
   PubMed Web of Science ®Google Scholar
• Hayashi J, Kihara M, Kato H, et al. A proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritis. Clin Proteom. 2015;12(1):20.
   PubMed Web of Science ®Google Scholar
• Whitaker JW, Boyle DL, Bartok B, et al. Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets. PloS One. 2015;10(4):e0124254.
   PubMed Web of Science ®Google Scholar
• Ungethuem U, Haeupl T, Witt H, et al. Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis. Physiol Genomics. 2010;42(4):267–282.
   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
• Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 2012;41(D1):D991–D995.
   PubMed Web of Science ®Google Scholar
• Yarilina A, Park-Min KH, Antoniv T, et al. TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon–response genes. Nat Immunol. 2008;9(4):378–387.
   PubMed Web of Science ®Google Scholar
• Kang K, Park SH, Chen J, et al. Interferon-γ represses M2 gene expression in human macrophages by disassembling enhancers bound by the transcription factor MAF. Immunity. 2017;47(2):235–250. e234.
   PubMed Web of Science ®Google Scholar
• Gautier L, Cope L, Bolstad BM, et al. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20(3):307–315.
   PubMed Web of Science ®Google Scholar
• Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.
   PubMed Web of Science ®Google Scholar
• Bolstad BM, Irizarry RA, Åstrand M, et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2):185–193.
   PubMed Web of Science ®Google Scholar
• Smyth GK, Ritchie M, Thorne N, et al. LIMMA: linear models for microarray data. In Bioinformatics and computational biology solutions using r and bioconductor. Statistics for biology and health. New York (NY): Springer; 2003.
   Google Scholar
• Kamburov A, Stelzl U, Lehrach H, et al. The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res. 2013;41(D1):D793–D800.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40(D1):D109–D114.
   PubMed Web of Science ®Google Scholar
• Croft D, O'Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011;39(Database):D691–D697.
   PubMedGoogle Scholar
• Karagoz K, Sevimoglu T, Arga KY. Integration of multiple biological features yields high confidence human protein interactome. J Theor Biol. 2016;403:85–96.
   PubMed Web of Science ®Google Scholar
• Smoot ME, Ono K, Ruscheinski J, et al. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432.
   PubMed Web of Science ®Google Scholar
• Gov E, Arga KY. Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network. IET Syst Biol. 2016;10(6):219–228.
   PubMed Web of Science ®Google Scholar
• Bovolenta LA, Acencio ML, Lemke N. HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. BMC Genomics. 2012;13(1):405.
   PubMedGoogle Scholar
• Chou CH, Chang NW, Shrestha S, et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016;44(D1):D239–D247.
   PubMed Web of Science ®Google Scholar
• Huang DW, Sherman BT, Tan Q, et al. The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007;8(9):R183.
   PubMed Web of Science ®Google Scholar
• Thomas PD, Kejariwal A, Campbell MJ, et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003;31(1):334–341.
   PubMed Web of Science ®Google Scholar
• Carmona-Saez P, Chagoyen M, Tirado F, et al. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol. 2007;8(1):R3.
   PubMed Web of Science ®Google Scholar
• Turanli B, Gulfidan G, Arga KY. Transcriptomic-guided drug repositioning supported by a new bioinformatics search tool: geneXpharma. OMICS. 2017;21(10):584–591.
   PubMed Web of Science ®Google Scholar
• Broeren MG, de Vries M, Bennink MB, et al. Disease-regulated gene therapy with anti-inflammatory interleukin-10 under the control of the CXCL10 promoter for the treatment of rheumatoid arthritis. Hum Gene Ther. 2016;27(3):244–254.
   PubMed Web of Science ®Google Scholar
• Safran M, Dalah I, Alexander J, et al. GeneCards Version 3: the human gene integrator. Database. 2010;2010(0):baq020–baq020.
   PubMedGoogle Scholar
• Udalova IA, Mantovani A, Feldmann M. Macrophage heterogeneity in the context of rheumatoid arthritis. Nat Rev Rheumatol. 2016;12(8):472–485.
   PubMed Web of Science ®Google Scholar
• Kolodziej L. An exploratory study of the interplay between decreased concentration of tryptophan, accumulation of kynurenines, and inflammatory arthritis. Iubmb Life. 2012;64(12):983–987.
   PubMed Web of Science ®Google Scholar
• Patel S, Leal AD, Gorski DH. The homeobox gene Gax inhibits angiogenesis through inhibition of nuclear factor-κb-dependent endothelial cell gene expression. Cancer Res. 2005;65(4):1414–1424.
   PubMed Web of Science ®Google Scholar
• Choi S, Lee K, Jung H, et al. Kruppel-like factor 4 positively regulates autoimmune arthritis in mouse models and rheumatoid arthritis in patients via modulating cell survival and inflammation factors of fibroblast-like synoviocyte. Front Immunol. 2018;9:1339.
   PubMed Web of Science ®Google Scholar
• Bonelli M, Dalwigk K, Platzer A, et al. IRF1 is critical for the TNF-driven interferon response in rheumatoid fibroblast-like synoviocytes. Exp Mol Med. 2019;51(7):75.
   PubMedGoogle Scholar
• Bartok B, Firestein GS. Fibroblast‐like synoviocytes: key effector cells in rheumatoid arthritis. Immunol Rev. 2010;233(1):233–255.
   PubMed Web of Science ®Google Scholar
• Padgett KA, Lan RY, Leung PC, et al. Primary biliary cirrhosis is associated with altered hepatic microRNA expression. J. Autoimmun. 2009;32(3-4):246–253.
   PubMed Web of Science ®Google Scholar
• Firestein GS, McInnes IB. Immunopathogenesis of rheumatoid arthritis. Immunity. 2017;46(2):183–196.
   PubMed Web of Science ®Google Scholar
• Orr C, Vieira-Sousa E, Boyle DL, et al. Synovial tissue research: a state-of-the-art review. Nat Rev Rheumatol. 2017;13(8):463–475.
   PubMed Web of Science ®Google Scholar
• Kasperkovitz P, Verbeet N, Smeets T, et al. Activation of the STAT1 pathway in rheumatoid arthritis. Ann Rheum Dis. 2004;63(3):233–239.
   PubMed Web of Science ®Google Scholar
• Scheinman RI, Trivedi R, Vermillion S, et al. Functionalized STAT1 siRNA nanoparticles regress rheumatoid arthritis in a mouse model. Nanomedicine. 2011;6(10):1669–1682.
   PubMed Web of Science ®Google Scholar
• Kuuliala K, Kuuliala A, Koivuniemi R, et al. STAT6 and STAT1 pathway activation in circulating lymphocytes and monocytes as predictor of treatment response in rheumatoid arthritis. PloS One. 2016;11(12):e0167975.
   PubMed Web of Science ®Google Scholar
• Wang S, Wang L, Wu C, et al. E2F2 directly regulates the STAT1 and PI3K/AKT/NF-κB pathways to exacerbate the inflammatory phenotype in rheumatoid arthritis synovial fibroblasts and mouse embryonic fibroblasts. Arthritis Res Ther. 2018;20(1):225.
   PubMedGoogle Scholar
• Croker BA, Handman E, Hayball JD, et al. Rac2‐deficient mice display perturbed T‐cell distribution and chemotaxis, but only minor abnormalities in TH1 responses. Immunol Cell Biol. 2002;80(3):231–240.
   PubMed Web of Science ®Google Scholar
• Klar A, Navon-Elkan P, Rubinow A, et al. Prolidase deficiency: it looks like systemic lupus erythematosus but it is not. Eur J Pediatr. 2010;169(6):727–732.
   PubMed Web of Science ®Google Scholar
• Shi X, Ye H, Yao X, et al. The involvement and possible mechanism of NR4A1 in chondrocyte apoptosis during osteoarthritis. Am J Transl Res. 2017;9(2):746–754.
   PubMed Web of Science ®Google Scholar
• Nakasa T, Shibuya H, Nagata Y, et al. The inhibitory effect of microRNA‐146a expression on bone destruction in collagen‐induced arthritis. Arthritis Rheumatol. 2011;63(6):1582–1590.
   PubMed Web of Science ®Google Scholar