Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease

Arthritis and Rheumatism

Volumn 52, Issue 3, 2005, Pages 865-876

  Tan, Filemon K ^a   Hildebrand, Bernard August ^a   Lester, Malisa S ^a   Stivers, David N ^b   Pounds, Stanley ^c   Zhou, Xiaodong ^a   Wallis, Debra D ^a   Milewicz, Dianna M ^a   Reveille, John D ^a   Mayes, Maureen D ^a   Jin, Li ^d   Arnett Jr , Frank C ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^d UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARTILAGE OLIGOMERIC MATRIX PROTEIN; COLLAGEN; COLLAGEN FIBRIL; COLLAGEN TYPE 7; DECAY ACCELERATING FACTOR; ENDOSTATIN; RNA; TRANSCRIPTOME; VASCULOTROPIN B;

ANGIOGENESIS; ARTICLE; CELL CULTURE; CLINICAL ARTICLE; COMPLEMENT ACTIVATION; CONTROLLED STUDY; DNA MICROARRAY; EXTRACELLULAR MATRIX; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENETIC ANALYSIS; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA ISOLATION; SKIN BIOPSY; SKIN FIBROBLAST; SYSTEMIC SCLEROSIS; UNINDEXED SEQUENCE;

DERMIS; FIBROBLASTS; GENE EXPRESSION REGULATION; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SCLERODERMA, SYSTEMIC; TRANS-ACTIVATION (GENETICS);

EID: 20144366026     PISSN: 00043591     EISSN: None     Source Type: Journal    
DOI: 10.1002/art.20871     Document Type: Article

References (55)

1. Kissin EY, Korn JH. Fibrosis in scleroderma. Rheum Dis Clin North Am 2003;29:351-69.
2. Claman HN, Giorno RC, Seibold JR. Endothelial and fibroblastic activation in scleroderma: the myth of the "uninvolved skin." Arthritis Rheum 1991;34:1495-501.
3. Varga J. Scleroderma and Smads: dysfunctional Smad family dynamics culminating in fibrosis [review]. Arthritis Rheum 2002; 46:1703-13.
4. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, et al. The transcriptional program in the response of human fibroblasts to serum. Science 1999;283:83-7.
5. Vuorio T, Makela JK, Vuorio E. Activation of type I collagen genes in cultured scleroderma fibroblasts. J Cell Biochem 1985; 28:105-13.
6. Subcommittee for Scleroderma Criteria of the American Rheumatism Association Diagnostic and Therapeutic Criteria Committee. Preliminary criteria for the classification of systemic sclerosis (scleroderma). Arthritis Rheum 1980;23:581-90.
7. Leroy EC, Black C, Fleischmajer R, Jablonska S, Krieg T, Medsger TA Jr, et al. Scleroderma (systemic sclerosis): classification, subsets and pathogenesis. J Rheumatol 1988;15:202-5.
8. Clements PJ, Lachenbruch PA, Seibold JR, Zee B, Steen VD, Brennan P, et al. Skin thickness score in systemic sclerosis: an assessment of interobserver variability in 3 independent studies. J Rheumatol 1993;20:1892-6.
9. Wallis DD, Tan FK, Kielty CM, Kimball MD, Arnett FC, Milewicz DM. Abnormalities in fibrillin 1-containing microfibrils in dermal fibroblast cultures from patients with systemic sclerosis (scleroderma). Arthritis Rheum 2001;44:1855-64.
10. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat Biotechnol 2002;20:940-3.
11. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 2002;30:e51.
12. Simon RM, Dobbin K. Experimental design of DNA microarray experiments. Biotechniques 2003;34:S16-21.
13. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002;30:e15.
14. Wright GW, Simon RM. A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 2003;19:2448-55.
15. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001;98:5116-21.
16. Pounds S, Cheng C. Improving false discovery rate estimation. Bioinformatics 2004;20:1737-45.
17. Radmacher MD, McShane LM, Simon R. A paradigm for class prediction using gene expression profiles. J Comput Biol 2002;9: 505-11.
18. Dudoit S, Fridlyand F, Speed TP. Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc 2002;97:77-87.
19. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A 2001;98: 15149-54.
20. Simon R, Radmacher MD, Dobbin K, McShane LM. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003;95:14-8.
21. Simon R, Korn E, McShane LM, Radmacher MD, Wright GW, Zhao Y. Design and analysis of DNA microarray investigations. New York: Springer-Verlag; 2003.
22. Simon R, Lam A. BRB ArrayTools user guide, version 3.2. Biometric Research Branch, National Cancer Institute; 2004.
23. Bryan C, Knight C, Black CM, Silman AJ. Prediction of five-year survival following presentation with scleroderma: development of a simple model using three disease factors at first visit. Arthritis Rheum 1999;42:2660-5.
24. Clements PJ, Hurwitz EL, Wong WK, Seibold JR, Mayes M, White B, et al. Skin thickness score as a predictor and correlate of outcome in systemic sclerosis: high-dose versus low-dose penicillamine trial. Arthritis Rheum 2000;43:2445-54.
25. Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A 2003;100:4702-5.
26. Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, et al. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A 2003;100:12319-24.
27. Krieg T, Perlish JS, Fleischmajer R, Braun-Falco O. Collagen synthesis in scleroderma: selection of fibroblast populations during subcultures. Arch Dermatol Res 1985;277:373-6.
28. Jelaska A, Arakawa M, Broketa G, Korn JH. Heterogeneity of collagen synthesis in normal and systemic sclerosis skin fibroblasts: increased proportion of high collagen-producing cells in systemic sclerosis fibroblasts. Arthritis Rheum 1996;39:1338-46.
29. Fichard A, Kleman JP, Ruggiero F. Another look at collagen V and XI molecules. Matrix Biol 1995;14:515-31.
30. Tan FK. Systemic sclerosis: the susceptible host (genetics and environment). Rheum Dis Clin North Am 2003;29:211-37.
31. Neptune ER, Frischmeyer PA, Arking DE, Myers L, Bunton TE, Gayraud B, et al. Dysregulation of TGF-β activation contributes to pathogenesis in Marfan syndrome. Nat Genet 2003;33:407-11.
32. Venneker GT, van den Hoogen FH, Boerbooms AM, Bos JD, Asghar SS. Aberrant expression of membrane cofactor protein and decay-accelerating factor in the endothelium of patients with systemic sclerosis: a possible mechanism of vascular damage. Lab Invest 1994;70:830-5.
33. Ponta H, Sherman L, Herrlich PA. CD44: from adhesion molecules to signalling regulators. Nat Rev Mol Cell Biol 2003;4:33-45.
34. Chiu RK, Carpenito C, Dougherty ST, Hayes GM, Dougherty GJ. Identification and characterization of CD44RC, a novel alternatively spliced soluble CD44 isoform that can potentiate the hyaluronan binding activity of cell surface CD44. Neoplasia 1999;1:446-52.
35. Koch AE, Kronfeld-Harrington LB, Szekanecz Z, Cho MM, Haines GK, Harlow LA, et al. In situ expression of cytokines and cellular adhesion molecules in the skin of patients with systemic sclerosis: their role in early and late disease. Pathobiology 1993; 61:239-46.
36. Brunet A, Park J, Tran H, Hu LS, Hemmings BA, Greenberg ME. Protein kinase SGK mediates survival signals by phosphorylating the forkhead transcription factor FKHRL1 (FOXO3a). Mol Cell Biol 2001;21:952-65.
37. Mikosz CA, Brickley DR, Sharkey MS, Moran TW, Conzen SD. Glucocorticoid receptor-mediated protection from apoptosis is associated with induction of the serine/threonine survival kinase gene, sgk-1. J Biol Chem 2001;276:16649-54.
38. Ryynanen J, Sollberg S, Parente MG, Chung LC, Christiano AM, Uitto J. Type VII collagen gene expression by cultured human cells and in fetal skin: abundant mRNA and protein levels in epidermal keratinocytes. J Clin Invest 1992;89:163-8.
39. Keene DR, Sakai LY, Lunstrum GP, Morris NP, Burgeson RE. Type VII collagen forms an extended network of anchoring fibrils. J Cell Biol 1987;104:611-21.
40. Rudnicka L, Varga J, Christiano AM, Iozzo RV, Jimenez SA, Uitto J. Elevated expression of type VII collagen in the skin of patients with systemic sclerosis: regulation by transforming growth factor-β. J Clin Invest 1994;93:1709-15.
41. Miosge N, Sasaki T, Timpl R. Angiogenesis inhibitor endostatin is a distinct component of elastic fibers in vessel walls. FASEB J 1999;13:1743-50.
42. O'Reilly MS, Boehm T, Shing Y, Fukai N, Vasios G, Lane WS, et al. Endostatin: an endogenous inhibitor of angiogenesis and tumor growth. Cell 1997;88:277-85.
43. Dhanabal M, Ramchandran R, Waterman MJ, Lu H, Knebelmann B, Segal M, et al. Endostatin induces endothelial cell apoptosis. J Biol Chem 1999;274:11721-6.
44. Rehn M, Pihlajaniemi T. α 1(XVIII), a collagen chain with frequent interruptions in the collagenous sequence, a distinct tissue distribution, and homology with type XV collagen. Proc Natl Acad Sci U S A 1994;91:4234-8.
45. Sasaki T, Larsson H, Tisi D, Claesson-Welsh L, Hohenester E, Timpl R. Endostatins derived from collagens XV and XVIII differ in structural and binding properties, tissue distribution and antiangiogenic activity. J Mol Biol 2000;301:1179-90.
46. Hebbar M, Peyrat JP, Hornez L, Hatron PY, Hachulla E, Devulder B. Increased concentrations of the circulating angiogenesis inhibitor endostatin in patients with systemic sclerosis. Arthritis Rheum 2000;43:889-93.
47. Jia JD, Bauer M, Sedlaczek N, Herbst H, Ruehl M, Hahn EG, et al. Modulation of collagen XVIII/endostatin expression in lobular and biliary rat liver fibrogenesis. J Hepatol 2001;35:386-91.
48. Olofsson B, Pajusola K, Kaipainen A, von Euler G, Joukov V, Saksela O, et al. Vascular endothelial growth factor B, a novel growth factor for endothelial cells. Proc Natl Acad Sci U S A 1996;93:2576-81.
49. Murphy BJ, Andrews GK, Bittel D, Discher DJ, McCue J, Green CJ, et al. Activation of metallothionein gene expression by hypoxia involves metal response elements and metal transcription factor-1. Cancer Res 1999;59:1315-22.
50. Li X, Chen H, Epstein PN. Metallothionein protects islets from hypoxia and extends islet graft survival by scavenging most kinds of reactive oxygen species. J Biol Chem 2004;279:765-71.
51. Butcher HL, Kennette WA, Collins O, Zalups RK, Koropatnick J. Metallothionein mediates the level and activity of nuclear factor κB in murine fibroblasts. J Pharmacol Exp Ther 2004; 310:589-98.
52. Karin M, Yamamoto Y, Wang QM. The IKK NF-κ B system: a treasure trove for drug development. Nat Rev Drug Discov 2004;3:17-26.
53. Van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999-2009.
54. Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, et al. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med 2004;350:1828-37.
55. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002;8:816-24.