Perspectives and limitations of gene expression profiling in rheumatology: New molecular strategies

Arthritis Research and Therapy

Volumn 6, Issue 4, 2004, Pages 140-146

  Häupl, Thomas ^a   Krenn, Veit ^a   Stuhlmüller, Bruno ^a   Radbruch, Andreas ^b   Burmester, Gerd R ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b DEUTSCHES RHEUMA FORSCHUNGSZENTRUM   (Germany)

Author keywords

Expression profiling; Genomics; Molecular strategies; Pathway models; Signatures

Indexed keywords

ARTICLE; BIOCHEMISTRY; BIOINFORMATICS; CLINICAL PRACTICE; DIAGNOSTIC PROCEDURE; DRUG EFFICACY; DRUG TARGETING; EXPERIMENTATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC DISORDER; GENETIC SCREENING; GENOMICS; HUMAN; HUMAN GENOME; INFLAMMATION; LONG TERM CARE; NONHUMAN; PATHOGENESIS; PATHOLOGY; PATIENT MONITORING; PHYSIOLOGY; PROGNOSIS; PROTEIN FUNCTION; PROTEOMICS; RHEUMATOLOGY; TREATMENT PLANNING;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENETIC TECHNIQUES; HUMANS; RHEUMATOLOGY;

EID: 4444329582     PISSN: 14786354     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (44)

1. Suzuki A, Yamada R, Chang X, Tokuhiro S, Sawada T, Suzuki M, Nagasaki M, Nakayama-Hamada M, Kawaida R, Ono M, et al.: Functional haplotypes of PAD14, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat Genet 2003, 34:395-402.
2. Visser H, le Cessie S, Vos K, Breedveld FC, Hazes JM: How to diagnose rheumatoid arthritis early: a prediction model for persistent (erosive) arthritis. Arthritis Rheum 2002, 46:357-365.
3. Furst DE, Breedveld FC, Kalden JR, Smolen JS, Burmester GR, Dougados M, Emery P, Gibofsky A, Kavanaugh AF, Keystone EC, et al.: Updated consensus statement on biological agents for the treatment of rheumatoid arthritis and other immune mediated inflammatory diseases (May 2003). Ann Rheum Dis 2003, 62 (Suppl 2):ii2-ii9.
4. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW: Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 1997, 94:2150-2155.
5. 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.
6. Crow MK, Wohlgemuth J: Microarray analysis of gene expression in lupus. Arthritis Res Ther 2003, 5:279-287.
7. Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, Espe KJ, Shark KB, Grande WJ, Hughes KM, Kapur V, et al.: Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci USA 2003, 100:2610-2615.
8. Bennett L, Palucka AK, Arce E, Cantrell V, Borvak J, Banchereau J, Pascual V: Interferon and granulopolesis signatures in systemic lupus erythrematosus blood. J Exp Med 2003, 197:711-723.
9. Han GM, Chen SL, Shen N, Ye S, Bao CD, Gu YY: Analysis of gene expression profiles in human systemic lupus erythematosus using oligonucleotide microarray. Genes Immun 2003, 4:177-186.
10. Gu J, Marker-Hermann E, Baeten D, Tsai WC, Gladman D, Xiong M, Deister H, Kuipers JG, Huang F, Song YW, et al.: A 588-gene microarray analysis of the peripheral blood mononuclear cells of spondyloarthropathy patients. Rheumatology (Oxford) 2002, 41:759-766.
11. 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.
12. 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.
13. Krenn V, Morawietz L, Häupl T, Neidel J, König A: Grading of chronic synovitis - a histopathological grading system for molecular and diagnostic pathology. Path Res Pract 2002, 198:317-325.
14. Häupl T, Stuhlmuller B, Janitz M, Kiesslich O, Rohrlach T, Kaps C, Tandon N, Morawietz L, Girnus A, Wachtel A, et al.: Gene expression profiling in rheumatoid arthritis. Z Rheumatol 2003, 62 (Suppl 1):PDo-50.
15. Häupl T, Kaps C, Kiesslich O, Rohrlach T, Morawietz L, Neidel J, Pruss A, Krenn V, Gursche A, Zacher J, et al.: Synovial gene expression profiles in chronic joint diseases. Osteoarthritis Cartilage 2003, 11 (Suppl 1):S101.
16. Morawietz L, Gehrke T, Frommelt L, Gratze P, Bosio A, Moller J, Gerstmayer B, Krenn V: Differential gene expression in the periprosthetic membrane: lubricin as a new possible pathogenetic factor in prosthesis loosening. Virchows Arch 2003, 443:57-66.
17. Judex M, Neumann E, Lechner S, Dietmaier W, Ballhorn W, Grifka J, Gay S, Scholmerich J, Kullmann F, Muller-Ladner U: Laser-mediated microdissection facilitates analysis of area-specific gene expression in rheumatoid synovium. Arthritis Rheum 2003, 48:97-102.
18. Pierer M, Rethage J, Seibl R, Lauener R, Brentano F, Wagner U, Hantzschel H, Michel BA, Gay RE, Gay S, et al.: Chemokine secretion of rheumatoid arthritis synovial fibroblasts stimulated by Toll-like receptor 2 ligands. J Immunol 2004, 172:1256-1265.
19. Wester L, Koczan D, Holmberg J, Olofsson P, Thiesen HJ, Holmdahl R, Ibrahim S: Differential gene expression in pristane-induced arthritis susceptible DA versus resistant E3 rats. Arthritis Res Ther 2003, 5:R361-R372.
20. Alexander JJ, Saxena AK, Bao L, Jacob A, Haas M, Quigg RJ: Prominent renal expression of a murine leukemia retrovirus in experimental systemic lupus erythematosus. J Am Soc Nephrol 2002, 13:2869-2877.
21. Azuma T, Takei M, Yoshikawa T, Nagasugi Y, Kato M, Otsuka M, Shiraiwa H, Sugano S, Mitamura K, Sawada S, et al.: Identification of candidate genes for Sjogren's syndrome using MRL/lpr mouse model of Sjogren's syndrome and cDNA micro-array analysis. Immunol Lett 2002, 81:171-176.
22. Firneisz G, Zehavi I, Vermes C, Hanyecz A, Frieman JA, Glant TT: Identification and quantification of disease-related gene clusters. Bioinformatics 2003,19:1781-1786.
23. Courtenay JS, Dallman MJ, Dayan AD, Martin A, Mosedale B: Immunisation against heterologous type II collagen induces arthritis in mice. Nature 1980, 283:666-668.
24. Glant TT, Mikecz K, Arzoumanian A, Poole AR: Proteoglycan-induced arthritis in BALB/c mice. Clinical features and histopathology. Arthritis Rheum 1987, 30:201-212.
25. Aidinis V, Plows D, Haralambous S, Armaka M, Papadopoulos P, Kanaki MZ, Koczan D, Thiesen HJ, Kollias G: Functional analysis of an arthritogenic synovial fibroblast. Arthritis Res Ther 2003, 5:R140-R157.
26. Grant EP, Pickard MD, Briskin MJ, Gutierrez-Ramos JC: Gene expression profiles: creating new perspectives in arthritis research. Arthritis Rheum 2002, 46:874-884.
27. Haque KA, Pfeiffer RM, Beerman MB, Struewing JP, Chanock SJ, Bergen AW: Performance of high-throughput DNA quantification methods. BMC Biotechnol 2003, 3:20.
28. Dunbar SA, Vander Zee CA, Oliver KG, Karem KL, Jacobson JW: Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J Microbiol Methods 2003, 53:245-252.
29. Bernacki SH, Farkas DH, Shi W, Chan V, Liu Y, Beck JC, Bailey KS, Pratt VM, Monaghan KG, Matteson KJ, et al.: Bioelectronic sensor technology for detection of cystic fibrosis and hereditary hemochromatosis mutations. Arch Pathol Lab Med 2003, 127:1565-1572.
30. Lenigk R, Liu RH, Athavale M, Chen Z, Ganser D, Yang J, Rauch C, Liu Y, Chan B, Yu H, et al.: Plastic biochannel hybridization devices: a new concept for microfluidic DNA arrays. Anal Biochem 2002, 311:40-49.
31. Vernon SID, Farkas DH, Unger ER, Chan V, Miller DL, Chen YP, Blackburn GF, Reeves WC: Bioelectronic DNA detection of human papillomaviruses using eSensor trade mark: a model system for detection of multiple pathogens. BMC Infect Dis 2003, 3:12.
32. Ramakrishnan R, Dorris D, Lublinsky A, Nguyen A, Domanus M, Prokhorova A, Gieser L, Touma E, Lockner R, Tata. M, et al.: An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res 2002, 30:e3O.
33. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS: BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 2002, Suppl 56-58: 60-61.
34. Cook EB, Stahl JL, Lowe L, Chen R, Morgan E, Wilson J, Varro R, Chan A, Graziano FM, Barney NP: Simultaneous measurement of six cytokines in a single sample of human tears using microparticle-based flow cytometry: allergics vs. non-allergics. J Immunol Methods 2001, 254:109-118.
35. Herzel H, Beule D, Kielbasa S, Korbel J, Sers C, Malik A, Eickhoff H, Lehrach H, Schuchhardt J: Extracting information from cDNA arrays. Chaos 2001, 11:98-107.
36. 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.
37. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, et al.: Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci USA 2001, 98:10787-10792.
38. Ringner M, Peterson C: Microarray-based cancer diagnosis with artificial neural networks. Biotechniques 2003, Suppl:30-35.
39. Voit EO, Radivoyevitch T: Biochemical systems analysis of genome-wide expression data. Bioinformatics 2000, 16:1023- 1037.
40. Somogyi R, Greller LD: The dynamics of molecular networks: applications to therapeutic discovery. Drug Discov Today 2001, 6:1267-1277.
41. Firestein GS, Pisetsky DS: DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology. Arthritis Rheum 2002, 46:859-861.
42. Krenn V, Petersen I, Morawietz L, Häupl T, Köpenick A, Dietel M, Konthur Z, Skriner K: Tissue arrays in proteomics. Path Res Pract 2004, 200:95-103.
43. Grützkau A, Grün J, Rudwaleit M, Goldschmidt L, Janitz M, Burmester GR, Radbruch A, Häupl T: Gene expression profiling of monocytes in rheumatoid arthritis. Z Rheumatol 2003, 62 (Suppl 1):FE1-FE4.
44. Geschwind DH: Sharing gene expression date: an array of options. Nat Rev Neurosci 2001, 2:435-438.