Does gene expression analysis inform us in rheumatoid arthritis?

Annals of the Rheumatic Diseases

Volumn 69, Issue SUPPL. 1, 2010, Pages

  Haupl T ^a   Stuhlmuller B ^a   Grutzkau A ^b   Radbruch, A ^b   Burmester, G R ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b German Arthritis Research Center   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADALIMUMAB; ANTIRHEUMATIC AGENT; DISEASE MODIFYING ANTIRHEUMATIC DRUG; INFLIXIMAB; METHOTREXATE; NONSTEROID ANTIINFLAMMATORY AGENT; BIOLOGICAL MARKER; GLUCOCORTICOID; TUMOR NECROSIS FACTOR INHIBITOR;

CARTILAGE CELL; CELL INFILTRATION; CELL ISOLATION; DRUG EFFECT; FIBROBLAST; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; HUMAN; MICROARRAY ANALYSIS; PERIPHERAL BLOOD MONONUCLEAR CELL; PRIORITY JOURNAL; REVIEW; RHEUMATOID ARTHRITIS; SYNOVIUM; TREATMENT RESPONSE; BLOOD ANALYSIS; CARTILAGE; CELL ACTIVATION; CELL DIFFERENTIATION; GENE ACTIVITY; GENE EXPRESSION REGULATION; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC DATABASE; PATIENT SELECTION; PREDICTION; SIGNAL TRANSDUCTION; TREATMENT INDICATION;

ARTHRITIS, RHEUMATOID; BIOLOGICAL MARKERS; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; SPECIMEN HANDLING; SYNOVIAL MEMBRANE;

EID: 75749109331     PISSN: 00034967     EISSN: 14682060     Source Type: Journal    
DOI: 10.1136/ard.2009.119487     Document Type: Review

References (61)

1. Guenther R, Krenn V, Häupl T. [Expression analyses for rheumatoid arthritis]. Z Rheumatol 2008;67:4, 17-22.
2. Grútzkau A, Grun J, Häupl T, et al. [Gene expression in inflammatory rheumatic diseases]. Dtsch Med Wochenschr 2007;132:1888-91.
3. Maglott D, Ostell J, Pruitt KD, et al. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007;35:D26- 31.
4. Rebhan M, Chalifa-Caspi V, Prilusky J, et al. GeneCards: integrating information about genes, proteins and diseases. Trends Genet 1997;13:163.
5. Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008;36:D480-4.
6. Hamosh A, Scott AF, Amberger JS, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33:D514-7.
7. Nikitin A, Egorov S, Daraselia N, et al. Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 2003;19:2155-7.
8. Jenssen TK, Laegreid A, Komorowski J, et al. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001;28:21-8.
9. The Gene Ontology Consortium. The Gene Ontology project in 2008. Nucleic Acids Res 2008;36:D440-4.
10. Delorme B, Ringe J, Pontikoglou C, et al. Specific lineage-priming of bone marrow mesenchymal stem cells provides the molecular framework for their plasticity. Stem Cells 2009;27:1142-51.
11. Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res 2007;35:D760-5.
12. Parkinson H, Kapushesky M, Shojatalab M, et al. ArrayExpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 2007;35:D747-50.
13. Day A, Carlson MR, Dong J, et al. Celsius: a community resource for Affymetrix microarray data. Genome Biol 2007;8:R112.
14. Saal LH, Troein C, Vallon-Christersson J, et al. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol 2002;3:SOFTWARE0003.
15. Maurer M, Molidor R, Sturn A, et al. MARS: microarray analysis, retrieval, and storage system. BMC Bioinformatics 2005;6:101.
16. Menssen A, Edinger G, Grun JR, et al. SiPaGene: a new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. BMC Genomics 2009;10:98.
17. van der Pouw Kraan TC, van Gaalen FA, Huizinga TW, et al. 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;4:187-96.
18. van der Pouw Kraan TC, van Gaalen FA, Kasperkovitz PV, 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;48:2132-45.
19. Lindberg J, af Klint E, Ulfgren AK, et al. Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology. Arthritis Res Ther 2006;8:R47.
20. Tsubaki T, Arita N, Kawakami T, et al. Characterization of histopathology and geneexpression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens. Arthritis Res Ther 2005;7:R825-36.
21. Lequerre T, Bansard C, Vittecoq O, et al. Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia. Arthritis Res Ther 2009;11:R99.
22. Tripmacher R, Gaber T, Dziurla R, et al. Human CD4(+) T cells maintain specific functions even under conditions of extremely restricted ATP production. Eur J Immunol 2008;38:1631-42.
23. Huber R, Hummert C, Gausmann U, et al. Identification of intra-group, interindividual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane. Arthritis Res Ther 2008;10:R98.
24. Bramlage CP, Häupl T, Kaps C, et al. Decrease in expression of bone morphogenetic proteins 4 and 5 in synovial tissue of patients with osteoarthritis and rheumatoid arthritis. Arthritis Res Ther 2006;8:R58.
25. Bramlage CP, Kaps C, Ungethum U, et al. Modulatory effects of inflammation and therapy on GDF-5 expression in rheumatoid arthritis synovium. Scand J Rheumatol 2008;37:401-9.
26. Pierer M, Rethage J, Seibl R, et al. Chemokine secretion of rheumatoid arthritis synovial fibroblasts stimulated by Toll-like receptor 2 ligands. J Immunol 2004;172:1256-65.
27. Kasperkovitz PV, Timmer TC, Smeets TJ, 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 myofibroblast-like phenotype and high-inflammation synovitis. Arthritis Rheum 2005;52:430-41.
28. Pohlers D, Beyer A, Koczan D, et al. Constitutive upregulation of the transforming growth factor-beta pathway in rheumatoid arthritis synovial fibroblasts. Arthritis Res Ther 2007;9:R59.
29. Galligan CL, Baig E, Bykerk V, et al. Distinctive gene expression signatures in rheumatoid arthritis synovial tissue fibroblast cells: correlates with disease activity. Genes Immun 2007;8:480-91.
30. Timmer TC, Baltus B, Vondenhoff M, et al. Inflammation and ectopic lymphoid structures in rheumatoid arthritis synovial tissues dissected by genomics technology: identification of the interleukin-7 signaling pathway in tissues with lymphoid neogenesis. Arthritis Rheum 2007;56:2492- 502.
31. Auer J, Blass M, Schulze-Koops H, et al. Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis. Arthritis Res Ther 2007;9:R94.
32. Elliott SF, Coon CI, Hays E, et al. Bcl-3 is an interleukin-1-responsive gene in chondrocytes and synovial fibroblasts that activates transcription of the matrix metalloproteinase 1 gene. Arthritis Rheum 2002;46:3230-9.
33. Vincenti MP, Brinckerhoff CE. Early response genes induced in chondrocytes stimulated with the inflammatory cytokine interleukin-1beta. Arthritis Res 2001;3:381-8.
34. Gebauer M, Saas J, Sohler F, et al. Comparison of the chondrosarcoma cell line SW1353 with primary human adult articular chondrocytes with regard to their gene expression profile and reactivity to IL-1beta. Osteoarthritis Cartilage 2005;13:697-708.
35. Aigner T, Haag J, Zimmer R. Functional genomics, evo-devo and systems biology: a chance to overcome complexity? Curr Opin Rheumatol 2007;19:463-70.
36. Andreas K, Lübke C, Häupl T, et al. Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study. Arthritis Res Ther 2008;10:R9.
37. Häupl T, Yahyawi M, Lübke C, et al. Gene expression profiling of rheumatoid arthritis synovial cells treated with antirheumatic drugs. J Biomol Screen 2007;12:328-40.
38. Maas K, Chan S, Parker J, et al. Cutting edge: molecular portrait of human autoimmune disease. J Immunol 2002;169:5-9.
39. Olsen N, Sokka T, Seehorn CL, et al. A gene expression signature for recent onset rheumatoid arthritis in peripheral blood mononuclear cells. Ann Rheum Dis 2004;63:1387-92.
40. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, et al. Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 2007;66:1008-14.
41. Bennett L, Palucka AK, Arce E, et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med 2003;197:711-23.
42. Baechler EC, Batliwalla FM, Karypis G, et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci U S A 2003;100: 2610-15.
43. van der Pouw Kraan TC, van Baarsen LG, Wijbrandts CA, et al. Expression of a pathogen-response program in peripheral blood cells defines a subgroup of rheumatoid arthritis patients. Genes Immun 2008;9:16-22.
44. Junta CM, Sandrin-Garcia P, Fachin-Saltoratto AL, et al. Differential gene expression of peripheral blood mononuclear cells from rheumatoid arthritis patients may discriminate immunogenetic, pathogenic and treatment features. Immunology 2009;127:365-72.
45. Häupl T, Ostensen M, Grützkau A, et al. Reactivation of rheumatoid arthritis after pregnancy: increased phagocyte and recurring lymphocyte gene activity. Arthritis Rheum 2008;58:2981- 92.
46. Häupl T, Ostensen M, Grützkau A, et al. Interaction between rheumatoid arthritis and pregnancy: correlation of molecular data with clinical disease activity measures. Rheumatology (Oxford) 2008;47(Suppl 3):iii19-22.
47. Haas CS, Creighton CJ, Pi X, et al. Identification of genes modulated in rheumatoid arthritis using complementary DNA microarray analysis of lymphoblastoid B cell lines from disease-discordant monozygotic twins. Arthritis Rheum 2006;54:2047-60.
48. Szodoray P, Alex P, Frank MB, et al. A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis. Rheumatology (Oxford) 2006;45:1466-76.
49. Turrel-Davin F, Tournadre A, Pachot A, et al. FoxO3a involved in neutrophil and T cell survival is overexpressed in rheumatoid blood and synovial tissue. Ann Rheum Dis 2010; In press.
50. Nakamura N, Shimaoka Y, Tougan T, et al. Isolation and expression profiling of genes upregulated in bone marrow-derived mononuclear cells of rheumatoid arthritis patients. DNA Res 2006;13:169-83.
51. Kastrinaki MC, Sidiropoulos P, Roche S, et al. Functional, molecular and proteomic characterisation of bone marrow mesenchymal stem cells in rheumatoid arthritis. Ann Rheum Dis 2008;67:741-9.
52. Bridges SL Jr. The genetics of rheumatoid arthritis: influences on susceptibility, severity, and treatment response. Curr Rheumatol Rep 1999;1:164-71.
53. Hyrich KL, Lunt M, Dixon WG, et al. Effects of switching between anti-TNF therapies on HAQ response in patients who do not respond to their first anti-TNF drug. Rheumatology (Oxford) 2008;47:1000-5.
54. Lindberg J, af Klint E, Catrina AI, et al. Effect of infliximab on mRNA expression profiles in synovial tissue of rheumatoid arthritis patients. Arthritis Res Ther 2006;8:R179.
55. Reunanen N, Li SP, Ahonen M, et al. Activation of p38 alpha MAPK enhances collagenase-1 (matrix metalloproteinase (MMP)-1) and stromelysin-1 (MMP-3) expression by mRNA stabilization. J Biol Chem 2002;277:32360-8.
56. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, et al. Responsiveness to anti-tumour necrosis factor alpha therapy is related to pre-treatment tissue inflammation levels in rheumatoid arthritis patients. Ann Rheum Dis 2008;67:563-6.
57. Koczan D, Drynda S, Hecker M, et al. Molecular discrimination of responders and nonresponders to anti-TNF alpha therapy in rheumatoid arthritis by etanercept. Arthritis Res Ther 2008;10:R50.
58. Lequerre T, Gauthier-Jauneau AC, Bansard C, et al. Gene profiling in white blood cells predicts infliximab responsiveness in rheumatoid arthritis. Arthritis Res Ther 2006;8:R105.
59. Sekiguchi N, Kawauchi S, Furuya T, et al. Messenger ribonucleic acid expression profile in peripheral blood cells from RA patients following treatment with an anti-TNF-alpha monoclonal antibody, infliximab. Rheumatology (Oxford) 2008;47:780-8.
60. Stuhlmüller B, Häupl T, Tandon N, et al. Micrarray analysis for molecular characterization of disease activity and measuring outcomes of anti-tumour necrosis factor therapy in rheumatoid arthritis. Arthritis Res Ther 2005;7(Suppl 1):P159.
61. Andreas K, Häupl T, Lübke C, et al. Antirheumatic drug response signatures in human chondrocytes: potential molecular targets to stimulate cartilage regeneration. Arthritis Res Ther 2009;11:R15.