Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology

Arthritis Research and Therapy

Volumn 8, Issue 2, 2006, Pages

  Lindberg, Johan ^a   af Klint, Erik ^b   Ulfgren, Ann Kristin ^b   Stark, André ^b   Andersson, Tove ^a   Nilsson, Peter ^a   Klareskog, Lars ^b   Lundeberg, Joakim ^a  

^a ALBANOVA UNIVERSITY CENTER   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AGED; ARTHROSCOPY; BIOPSY; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPLICATION; DNA MICROARRAY; FEMALE; GENE EXPRESSION; GENETICS; HUMAN; IMMUNOHISTOCHEMISTRY; MALE; METABOLISM; MIDDLE AGED; ORTHOPEDIC SURGERY; PATHOLOGY; PROCEDURES; RHEUMATOID ARTHRITIS; SYNOVITIS; SYNOVIUM;

AGED; ARTHRITIS, RHEUMATOID; ARTHROSCOPY; BIOPSY; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION; HUMANS; IMMUNOHISTOCHEMISTRY; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORTHOPEDIC PROCEDURES; SYNOVIAL MEMBRANE; SYNOVITIS;

EID: 70350540689     PISSN: 14786354     EISSN: 14786362     Source Type: Journal    
DOI: 10.1186/ar1903     Document Type: Article

References (48)

1. Arnett FC: Revised criteria for the classification of rheumatoid arthritis. Bull Rheum Dis 1989, 38:1-6.
2. Dolhain RJ, Ter Haar NT, De Kuiper R, Nieuwenhuis IG, Zwinderman AH, Breedveld FC, Miltenburg AM: Distribution of T cells and signs of T-cell activation in the rheumatoid joint: Implications for semiquantitative comparative histology. Br J Rheumatol 1998, 37:324-330.
3. Lindblad S, Hedfors E: Intraarticular variation in synovitis. Local macroscopic and microscopic signs of inflammatory activity are significantly correlated. Arthritis Rheum 1985, 28 977-986.
4. Hutton CW, Hinton C, Dieppe PA: Intra-articular variation of synovial changes in knee arthritis: Biopsy study comparing changes in patellofemoral synovium and the medial tibiofemoral synovium. Br J Rheumatol 1987, 26:5-8.
5. Kennedy TD, Plater-Zyberk C, Partridge TA, Woodrow DF, Maini RN: Representative sample of rheumatoid synovium: A morphometric study. J Clin Pathol 1988, 41:841-846.
6. Kirkham B, Portek I, Lee CS, Stavros B, Lenarczyk A, Lassere M, Edmonds J: Intraarticular variability of synovial membrane histology, immunohistology, and cytokine mRNA expression in patients with rheumatoid arthritis. J Rheumatol 1999, 26:777-784.
7. Ulfgren AK, Grondal L, Lindblad S, Khademi M, Johnell O, Klareskog L, Andersson U: Interindividual and intra-articular variation of proinflammatory cytokines in patients with rheumatoid arthritis: potential implications for treatment. Ann Rheum Dis 2000, 59 439-447.
8. Boyle DL, Rosengren S, Bugbee W, Kavanaugh A, Firestein GS: Quantitative biomarker analysis of synovial gene expression by real-time PCR. Arthritis Res Ther 2003, 5:R352-R360.
9. Chung CH, Parker JS, Karaca G, Wu J, Funkhouser WK, Moore D, Butterfoss D, Xiang D, Zanation A, Yin X, et al.: Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell 2004, 5:489-500.
10. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
11. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, et al.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
12. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, et al.: Molecular portraits of human breast tumours. Nature 2000, 406 747-752.
13. Valk PJ, Verhaak RG, Beijen MA, Erpelinck CA, Barjesteh van Waalwijk van Doorn-Khosrovani S, Boer JM, Beverloo HB, Moorhouse MJ, van der Spek PJ, Lowenberg B, et al.: Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med 2004, 350 1617-1628.
14. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
15. Jarvis JN: Diagnostic and prognostic potential of gene microarrays in rheumatoid arthritis. Expert Rev Mol Diagn 2005, 5 655-659.
16. Jarvis JN, Dozmorov I, Jiang K, Frank MB, Szodoray P, Alex P, Centola M: Novel approaches to gene expression analysis of active polyarticular juvenile rheumatoid arthritis. Arthritis Res Ther 2004, 6 R15-R32.
17. Batliwalla FM, Baechler EC, Xiao X, Li W, Balasubramanian S, Khalili H, Damle A, Ortmann WA, Perrone A, Kantor AB, et al.: Peripheral blood gene expression profiling in rheumatoid arthritis. Genes Immun 2005, 6:388-397.
18. Maas K, Chan S, Parker J, Slater A, Moore J, Olsen N, Aune TM: Cutting edge: Molecular portrait of human autoimmune disease. J Immunol 2002, 169:5-9.
19. Olsen N, Sokka T, Seehorn CL, Kraft B, Maas K, Moore J, Aune TM: A gene expression signature for recent onset rheumatoid arthritis in peripheral blood mononuclear cells. Ann Rheum Dis 2004, 63 1387-1392.
20. Jeong JG, Kim JM, Cho H, Hahn W, Yu SS, Kim S: Effects of IL-1beta on gene expression in human rheumatoid synovial fibroblasts. Biochem Biophys Res Commun 2004, 324:3-7.
21. Zhang HG, Hyde K, Page GP, Brand JP, Zhou J, Yu S, Allison DB, Hsu HC, Mountz JD: Novel tumor necrosis factor alpha-regulated genes in rheumatoid arthritis. Arthritis Rheum 2004, 50:420-431.
22. Gallagher J, Howlin J, McCarthy C, Murphy EP, Bresnihan B, FitzGerald O, Godson C, Brady HR, Martin F: Identification of Naf1/ABIN-1 among TNF-alpha-induced expressed genes in human synoviocytes using oligonucleotide microarrays. FEBS Lett 2003, 551:8-12.
23. Tsubaki T, Arita N, Kawakami T, Shiratsuchi T, Yamamoto H, Takubo N, Yamada K, Nakata S, Yamamoto S, Nose M: Characterization of histopathology and gene-expression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens. Arthritis Res Ther 2005, 7:R825-R836.
24. Schmutz C, Hulme A, Burman A, Salmon M, Ashton B, Buckley C, Middleton J: Chemokine receptors in the rheumatoid sUnovium: upregulation of CXCR5. Arthritis Res Ther 2005, 7:R217-R229.
25. van der Pouw Kraan TC, van Gaalen FA, Huizinga TW, Pieterman E, Breedveld FC, Verweij CL: Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair. Genes Immun 2003, 4:187-196.
26. Devauchelle V, Marion S, Cagnard N, Mistou S, Falgarone G, Breban M, Letourneur F, Pitaval A, Alibert O, Lucchesi C, et al.: DNA microarray allows molecular profiling of rheumatoid arthritis and identification of pathophysiological targets. Genes Immun 2004, 5:597-608.
27. Kasperkovitz PV, Timmer TC, Smeets TJ, Verbeet NL, Tak PP, van Baarsen LG, Baltus B, Huizinga TW, Pieterman E, Fero M, et al.: Fibroblast-like synoviocytes derived from patients with rheumatoid arthritis show the imprint of synovial tissue heterogeneity: Evidence of a link between an increased myofibroblastlike phenotype and high-inflammation synovitis. Arthritis Rheum 2005, 52 430-441.
28. Lorenz P, Ruschpler P, Koczan D, Stiehl P, Thiesen HJ: From transcriptome to proteome: Differentially expressed proteins identified in synovial tissue of patients suffering from rheumatoid arthritis and osteoarthritis by an initial screen with a panel of 791 antibodies. Proteomics 2003, 3:991-1002.
29. Huh SJ, Paik DJ, Chung HS, Youn J: Regulation of GRB2 and FLICE2 expression by TNF-alpha in rheumatoid synovium. Immunol Lett 2003, 90:93-96.
30. van der Pouw Kraan TC, van Gaalen FA, Kasperkovitz PV, Verbeet NL, Smeets TJ, Kraan MC, Fero M, Tak PP, Huizinga TW, Pieterman E, et al. Rheumatoid arthritis is a heterogeneous disease: Evidence for differences in the activation of the STAT-1 pathway between rheumatoid tissues. Arthritis Rheum 2003, 48:2132-2145.
31. Baeten D, Van den Bosch F, Elewaut D, Stuer A, Veys EM, De Keyser F: Needle arthroscopy of the knee with synovial biopsy sampling: Technical experience in 150 patients. Clin Rheumatol 1999, 18 434-441.
32. KTH microarray core facility homepage [http://www.ktharray.se/]
33. Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, Mueller O, Schroeder A, Auffray C: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis tracesb. Nucleic Acids Res 2005, 33:e56.
34. Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, et al.: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2005:D553-D555.
35. Team RDC: A Language and Environment for Statistical Computing Vienna: R Foundation for Statistical Computing; 2004.
36. Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70.
37. Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, KlApa M, Currier T, Thiagarajan M, et al.: TM4: a free, opensource system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
38. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
39. Fleiss JL: Statistical Methods for Rates and Proportions New York: John Wiley; 1981.
40. Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:ARticle 3.
41. Bengtsson H: aroma - An R Object-oriented Microarray Analysis Environment. [Preprints in Mathematical Sciences, no. 18.] Lund: Centre for Mathematical Sciences, Lund Institute of Technology; 2004.
42. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier O, Ge Y, Gentry J, et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80.
43. Smyth GK, Speed TP: Normalization of cDNA microarray data. Methods 2003, 31:265-273.
44. Lonnstedt I, Speed TP: Replicated microarray data. Stat Sin 2002, 12:31-46.
45. Reiner A, Yekutieli D, Benjamini Y: Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003, 19:368-375.
46. Smyth GK, Michaud J, Scott H: The use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21:2067-2075.
47. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
48. Sneath PHA, Sokal RR: Numerical Taxonomy; The Principles and Practice of Numerical Classification San Francisco: WH Freeman; 1973.