Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis

International Journal of Rheumatic Diseases

Volumn 20, Issue 8, 2017, Pages 971-979

  Ma, Chunhui ^a   Lv, Qi ^b   Teng, Songsong ^a   Yu, Yinxian ^a   Niu, Kerun ^a   Yi, Chengqin ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b TONGJI UNIVERSITY   (China)

Author keywords

differentially expressed genes; functional annotation; rheumatoid arthritis; small molecule drugs; weighted gene co expression network analysis

Indexed keywords

PAPAVERINE; SANGUINARINE; ANTIRHEUMATIC AGENT; BENZOPHENANTHRIDINE DERIVATIVE; ISOQUINOLINE DERIVATIVE; TRANSCRIPTOME;

ARTICLE; C3AR1 GENE; CASE CONTROL STUDY; CCL19 GENE; CCR1 GENE; CD97 GENE; CLINICAL ARTICLE; CONTROLLED STUDY; CXCL1 GENE; FYB GENE; GENE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MAPPING; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC SCREENING; HOMEOSTASIS; HUMAN; IKBKE GENE; IMMUNE RESPONSE; INFLAMMATION; LYZ GENE; MICROARRAY ANALYSIS; PATHOGENESIS; PLN GENE; PPT1 GENE; PREDICTIVE VALUE; PRIORITY JOURNAL; RHEUMATOID ARTHRITIS; WEIGHTED GENE COEXPRESSION NETWORK ANALYSIS; BIOLOGY; CLUSTER ANALYSIS; DNA MICROARRAY; DRUG EFFECT; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; PROCEDURES; SIGNAL TRANSDUCTION;

ANTIRHEUMATIC AGENTS; ARTHRITIS, RHEUMATOID; BENZOPHENANTHRIDINES; CASE-CONTROL STUDIES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; ISOQUINOLINES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PAPAVERINE; SIGNAL TRANSDUCTION; TRANSCRIPTOME;

EID: 85018816413     PISSN: 17561841     EISSN: 1756185X     Source Type: Journal    
DOI: 10.1111/1756-185X.13063     Document Type: Article

References (48)

1. Firestein GS (2003) Evolving concepts of rheumatoid arthritis. Nature 423(6937), 356–61.
2. Janossy G, Duke O, Poulter L, Panayi G, Bofill M, Goldstein G (1981) Rheumatoid arthritis: a disease of T-lymphocyte/macrophage immunoregulation. Lancet 318(8251), 839–42.
3. Haringman JJ, Ludikhuize J, Tak PP (2004) Chemokines in joint disease: the key to inflammation? Ann Rheum Dis 63(10), 1186–94.
4. Katschke KJ, Rottman JB, Ruth JH et al. (2001) Differential expression of chemokine receptors on peripheral blood, synovial fluid, and synovial tissue monocytes/macrophages in rheumatoid arthritis. Arthritis Rheum 44(5), 1022–32.
5. Epstein FH, Harris ED Jr (1990) Rheumatoid arthritis: pathophysiology and implications for therapy. N Engl J Med 322(18), 1277–89.
6. Devauchelle V, Marion S, Cagnard N et al. (2004) DNA microarray allows molecular profiling of rheumatoid arthritis and identification of pathophysiological targets. Genes Immun 5(8), 597–608.
7. Fulci V, Scappucci G, Sebastiani GD et al. (2010) miR-223 is overexpressed in T-lymphocytes of patients affected by rheumatoid arthritis. Hum Immunol 71 (2), 206–11.
8. Chen G, Lu C, Zha Q et al. (2012) A network-based analysis of traditional Chinese medicine cold and hot patterns in rheumatoid arthritis. Complement Ther Med 20 (1), 23–30.
9. Presson AP, Sobel EM, Papp JC et al. (2008) Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Syst Biol 2 (1), 1.
10. Woetzel D (2014) Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation. Arthritis Res Ther 16 (2), 1–22.
11. Broeren MG, De VM, Bennink MB et al. (2015) Disease-regulated gene therapy with anti-inflammatory interleukin-10 under control of the CXCL10 promoter for the treatment of rheumatoid arthritis. Hum Gene 27(3), 244–54.
12. Carvalho B, Bengtsson H, Speed TP, Irizarry RA (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8 (2), 485–99.
13. Warnes GR, Bolker B, Bonebakker L et al. (2009) gplots: various R programming tools for plotting data. R package version 2 (4).
14. Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet mMolec Biol 4 (1), 118.
15. Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9 (1), 1.
16. Lamb J (2007) The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer 7 (1), 54–60.
17. Lamb J, Crawford ED, Peck D et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313(5795), 1929–35.
18. Da Wei Huang BTS, Lempicki RA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4 (1), 44–57.
19. Zlotnik A, Yoshie O (2000) Chemokines: a new classification system and their role in immunity. Immunity 12 (2), 121–7.
20. Koch AE, Kunkel SL, Shah MR et al. (1995) Growth-related gene product alpha. A chemotactic cytokine for neutrophils in rheumatoid arthritis. J Immunol 155(7), 3660–6.
21. Golds EE, Mason P, Nyirkos P (1989) Inflammatory cytokines induce synthesis and secretion of gro protein and a neutrophil chemotactic factor but not β2-microglobulin in human synovial cells and fibroblasts. Biochem J 259 (2), 585–8.
22. Mayilyan KR (2012) Complement genetics, deficiencies, and disease associations. Protein Cell 3(7), 487–96.
23. Fujikado N, Saijo S, Iwakura Y (2006) Identification of arthritis-related gene clusters by microarray analysis of two independent mouse models for rheumatoid arthritis. Arthritis Res Ther 8 (4), R100.
24. Lebre MC, Vergunst CE, Choi IYK et al. (2011) Why CCR2 and CCR5 blockade failed and why CCR1 blockade might still be effective in the treatment of rheumatoid arthritis. PLoS ONE 6, e21772.
25. Tak PP (2013) Chemokine receptor CCR1 antagonist CCX354-C treatment for rheumatoid arthritis: CARAT-2, a randomised, placebo controlled clinical trial. Ann Rheum Dis 72(3), 337–44.
26. Pickens SR, Chamberlain ND, Volin MV, Pope RM, Mandelin AM, Shiva S (2011) Characterization of CCL19 and CCL21 in rheumatoid arthritis. Arthritis Rheum 63(4), 914–22.
27. Brühl H, Mack M, Niedermeier M, Lochbaum D, Schölmerich J, Straub R (2008) Functional expression of the chemokine receptor CCR7 on fibroblast-like synoviocytes. Rheumatology 47(12), 1771–4.
28. Yamashita M, Iwama N, Date F et al. (2009) Macrophages participate in lymphangiogenesis in idiopathic diffuse alveolar damage through CCL19-CCR7 signal. Hum Pathol 40(11), 1553–63.
29. Kuscher K, Danelon G, Paoletti S et al. (2009) Synergy-inducing chemokines enhance CCR2 ligand activities on monocytes. Eur J Immunol 39(4), 1118–28.
30. Dieu MC, Vanbervliet B, Vicari A et al. (1998) Selective recruitment of immature and mature dendritic cells by distinct chemokines expressed in different anatomic sites. J Exp Med 188 (2), 373–86.
31. Page G, Lebecque S, Miossec P (2002) Anatomic localization of immature and mature dendritic cells in an ectopic lymphoid organ: correlation with selective chemokine expression in rheumatoid synovium. J Immunol 168(10), 5333–41.
32. Andreas K, Lübke C, Häupl T et al. (2008) Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study. Arthritis Res Ther 10 (1), R9.
33. Lu J-Y, Hofmann SL (2006) Thematic review series: lipid posttranslational modifications. Lysosomal metabolism of lipid-modified proteins. J Lipid Res 47(7), 1352–7.
34. Shafeeq S, Yesilkaya H, Kloosterman TG et al. (2011) The cop operon is required for copper homeostasis and contributes to virulence in Streptococcus pneumoniae. Mol Microbiol 81(5), 1255–70.
35. MacLennan DH, Kranias EG (2003) Phospholamban: a crucial regulator of cardiac contractility. Nat Rev Mol Cell Biol 4(7), 566–77.
36. Ellingsen T, Hansen I, Thorsen J et al. (2014) Upregulated baseline plasma CCL19 and CCR7 cell-surface expression on monocytes in early rheumatoid arthritis normalized during treatment and CCL19 correlated with radiographic progression. Scand J Rheumatol 43 (2), 91–100.
37. Nanki T (2016) Treatment for rheumatoid arthritis by chemokine blockade. Nihon Rinshō Men'eki Gakkai kaishi 39(3), 172.
38. Banda NK, Hyatt S, Antonioli AH et al. (2012) Role of C3a receptors, C5a receptors, and complement protein C6 deficiency in collagen antibody-induced arthritis in mice. J Immunol 188(3), 1469–78.
39. Vrba J, Dolezel P, Vicar J, et al. (2009) Cytotoxic activity of sanguinanrine and dihydrosanguinarine in human promyolocytic leukemia HL-60 cells. Toxicology in vitro 23 (4), 580–8.
40. Lenfeld J, Kroutil M, Maršálek E, Slavik J, Preininger V, Šimánek V (1981) Antiinflammatory activity of quaternary benzophenanthridine alkaloids from Chelidonoum majus. Planta Med 43 (10), 161–5.
41. Niu X, Fan T, Li W, Xing W, Huang H (2012) The anti-inflammatory effects of sanguinarine and its modulation of inflammatory mediators from peritoneal macrophages. Eur J Pharmacol 689 (1), 262–9.
42. Hong C, Chen S, Ding H et al. (2015) An involvement of SR-B1 mediated p38 MAPK signaling pathway in serum amyloid A-induced angiogenesis in rheumatoid arthritis. Mol Immunol 66 (2), 340–5.
43. Zou S, Wang C, Cui Z et al. (2015) β-Elemene induces apoptosis of human rheumatoid arthritis fibroblast-like synoviocytes via reactive oxygen species-dependent activation of p38 mitogen-activated protein kinase. Pharmacol Rep Pr 68 (1), 7–11.
44. Li J, Yang PA, Wu Q et al. (2013) Death receptor 5–targeted depletion of interleukin-23–producing macrophages, th17, and th1/17 associated with defective tyrosine phosphatase in mice and patients with rheumatoid arthritis. Arthritis Rheum 65(10), 2594–605.
45. Vordenbäumen S, Braukmann A, Petermann K et al. (2011) Casein α s1 is expressed by human monocytes and upregulates the production of GM-CSF via p38 MAPK. J Immunol 186(1), 592–601.
46. Hamann J, Wishaupt JO, Van Lier RA, Smeets TJ, Breedveld FC, Tak PP (1999) Expression of the activation antigen CD 97 and its ligand CD 55 in rheumatoid synovial tissue. Arthritis Rheum 42(4), 650–8.
47. van der Pouw Kraan TC, van Gaalen FA, Kasperkovitz PV et al. (2003) Rheumatoid arthritis is a heterogeneous disease: evidence for differences in the activation of the STAT-1 pathway between rheumatoid tissues. Arthritis Rheum 48(8), 2132–45.
48. Chandra R, Aneja R, Rewal C, Konduri R, Dass SK, Agarwal S (2000) An opium alkaloid-Papaverine ameliorates ethanol-induced hepatotoxicity: diminution of oxidative stress. Indian J Clin Biochem 15 (2), 155–60.