Capturing the heterogeneity in systemic sclerosis with genome-wide expression profiling

Expert Review of Clinical Immunology

Volumn 7, Issue 4, 2011, Pages 463-473

  Sargent, Jennifer L ^a   Whitfield, Michael L ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

animal models; gene expression profiling; intrinsic subsets; scleroderma; signaling; systemic sclerosis; TGF

Indexed keywords

ALPHA1 INTERFERON; AUTOANTIBODY; CD44V ANTIGEN; COLLAGEN; GAMMA INTERFERON; METALLOTHIONEIN; TRANSFORMING GROWTH FACTOR BETA; WNT PROTEIN;

B LYMPHOCYTE; BLOOD CELL; CD4+ T LYMPHOCYTE; COLLAGEN METABOLISM; DIZYGOTIC TWINS; DNA MICROARRAY; ENDOTHELIUM CELL; EPITHELIUM CELL; EXTRACELLULAR MATRIX; FIBROBLAST CULTURE; FIBROSING ALVEOLITIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HIGH RISK PATIENT; HUMAN; LUNG FIBROSIS; LUNG LAVAGE; LUNG PARENCHYMA; MICROARRAY ANALYSIS; NONHUMAN; PATIENT CODING; PATIENT IDENTIFICATION; PROTEIN EXPRESSION; REVIEW; SCLERODERMA; SKIN; SKIN BIOPSY; SKIN FIBROBLAST; SMOOTH MUSCLE FIBER; SYSTEMIC SCLEROSIS; T LYMPHOCYTE; UPREGULATION;

ANIMALS; DISEASE MODELS, ANIMAL; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LEUKOCYTES, MONONUCLEAR; LUNG; SCLERODERMA, SYSTEMIC; SIGNAL TRANSDUCTION; SKIN; TRANSFORMING GROWTH FACTOR BETA;

EID: 79960908376     PISSN: 1744666X     EISSN: 17448409     Source Type: Journal    
DOI: 10.1586/eci.11.41     Document Type: Review

References (82)

1. Barnett AJ, Miller MH, Littlejohn GO. A survival study of patients with scleroderma diagnosed over 30 years (1953-1983): the value of a simple cutaneous classification in the early stages of the disease. J Rheumatol. 15(2), 276-283 (1988) (Pubitemid 18073752)
2. LeRoy EC, Black C, Fleischmajer R et al. Scleroderma (systemic sclerosis): classification, subsets and pathogenesis. J Rheumatol. 15(2), 202-205 (1988) (Pubitemid 18073738)
3. Bolster MB, Silver RM. Lung disease in systemic sclerosis (scleroderma). Baillieres Clin. Rheumatol. 7(1), 79-97 (1993) (Pubitemid 23071215)
4. Black CM, Welsh KI, Maddison PJ, Jayson MI, Bernstein RM. HLA antigens, autoantibodies and clinical subsets in scleroderma. Br J. Rheumatol. 23(4), 267-271 (1984) (Pubitemid 14015863)
5. Akesson A, Wollheim FA. Organ manifestations in 100 patients with progressive systemic sclerosis: a comparison between the CREST syndrome and diffuse scleroderma. Br J. Rheumatol. 28(4), 281-286 (1989) (Pubitemid 19205920)
6. Merkel PA, Silliman NP, Denton CP et al. Validity, reliability, and feasibility of durometer measurements of scleroderma skin disease in a multicenter treatment trial. Arthritis Rheum. 59(5), 699-705 (2008) (Pubitemid 351679546)
7. Rodnan GP, Lipinski E, Luksick J. Skin thickness and collagen content in progressive systemic sclerosis and localized scleroderma. Arthritis Rheum. 22(2), 130-140 (1979) (Pubitemid 9156666)
8. Clements P, Lachenbruch P, Siebold J et al. Inter and intraobserver variability of total skin thickness score (modified Rodnan TSS) in systemic sclerosis. J Rheumatol. 22(7), 1281-1285 (1995)
9. Furst DE, Clements PJ, Steen VD et al. The modified Rodnan skin score is an accurate reflection of skin biopsy thickness in systemic sclerosis. J Rheumatol. 25(1), 84-88 (1998) (Pubitemid 28060123)
10. Clements PJ, Hurwitz EL, Wong WK et al. Skin thickness score as a predictor and correlate of outcome in systemic sclerosis: high-dose versus low-dose penicillamine trial. Arthritis Rheum. 43(11), 2445-2454 (2000)
11. Steen VD, Medsger TA Jr. Improvement in skin thickening in systemic sclerosis associated with improved survival. Arthritis Rheum. 44(12), 2828-2835 (2001) (Pubitemid 34016202)
12. Verrecchia F, Laboureau J, Verola O et al. Skin involvement in scleroderma-where histological and clinical scores meet. Rheumatology (Oxford) 46(5), 833-841 (2007) (Pubitemid 47061718)
13. Steen VD. Autoantibodies in systemic sclerosis. Semin Arthritis Rheum. 35(1), 35-42 (2005) (Pubitemid 41111469)
14. Herrick A, Rooney B, Finn J, Silman A. Lack of relationship between functional ability and skin score in patients with systemic sclerosis. J Rheumatol. 28(2), 292-295 (2001) (Pubitemid 32165135)
15. Hanitsch LG, Burmester GR, Witt C et al. Skin sclerosis is only of limited value to identify SSc patients with severe manifestations-an analysis of a distinct patient subgroup of the German Systemic Sclerosis Network (DNSS) Register. Rheumatology (Oxford) 48(1), 70-73 (2009)
16. Medsger TA, Steen VD. Classification, prognosis. In: Systemic Sclerosis. Clements, PJ, Furst, DE (Eds). Williams & Wilkins, Baltimore, MD, USA, 51-64 (1996)
17. Siebold JR. Chapter 79: Scleroderma. In: Kelleys Textbook of Rheumatology. Harris ED Jr, Budd RC, Firestein GS, Genovese MC, Sergent JS, Ruddy S, Sledge CB. (Eds). Elsevier & Saunders, Amsterdam, The Netherlands, 1279-1308 (2005)
18. Hildebrandt S, Jackh G, Weber S, Peter HH. A long-term longitudinal isotypic study of anti-topoisomerase I autoantibodies. Rheumatol. Int. 12(6), 231-234 (1993) (Pubitemid 23089737)
19. Dick T, Mierau R, Bartz-Bazzanella P et al. Coexistence of antitopoisomerase I and anticentromere antibodies in patients with systemic sclerosis. Ann Rheum. Dis. 61(2), 121-127 (2002) (Pubitemid 34098426)
20. Grassegger A, Pohla-Gubo G, Frauscher M, Hintner H. Autoantibodies in systemic sclerosis (scleroderma): clues for clinical evaluation, prognosis and pathogenesis. Wien Med. Wochenschr 158(1-2), 19-28 (2008) (Pubitemid 351268498)
21. Koenig M, Dieude M, Senecal JL. Predictive value of antinuclear autoantibodies: the lessons of the systemic sclerosis autoantibodies. Autoimmun Rev. 7(8), 588-593 (2008)
22. Scussel-Lonzetti L, Joyal F, Raynauld JP et al. Predicting mortality in systemic sclerosis: analysis of a cohort of 309 French Canadian patients with emphasis on features at diagnosis as predictive factors for survival. Medicine (Baltimore) 81(2), 154-167 (2002) (Pubitemid 34218570)
23. Maricq HR, Valter I. A working classification of scleroderma spectrum disorders: a proposal and the results of testing on a sample of patients. Clin Exp. Rheumatol. 22(3 Suppl. 33), S5-S13 (2004) (Pubitemid 39162028)
24. Ferri C, Valentini G, Cozzi F et al. Systemic sclerosis: demographic, clinical, and serologic features and survival in 1,012 Italian patients. Medicine (Baltimore) 81(2), 139-153 (2002) (Pubitemid 34218569)
25. Barnett AJ, Miller M, Littlejohn GO. The diagnosis and classification of scleroderma (systemic sclerosis). Postgrad. Med J. 64(748), 121-125 (1988) (Pubitemid 18068758)
26. Medsger TA Jr, Silman AJ, Steen VD et al. A disease severity scale for systemic sclerosis: development and testing. J Rheumatol. 26(10), 2159-2167 (1999) (Pubitemid 29487010)
27. Steen VD, Medsger TA Jr. Severe organ involvement in systemic sclerosis with diffuse scleroderma. Arthritis Rheum. 43(11), 2437-2444 (2000)
28. Shand L, Lunt M, Nihtyanova S et al. Relationship between change in skin score and disease outcome in diffuse cutaneous systemic sclerosis: application of a latent linear trajectory model. Arthritis Rheum. 56(7), 2422-2431 (2007) (Pubitemid 47173590)
29. Perera A, Fertig N, Lucas M et al. Clinical subsets, skin thickness progression rate, and serum antibody levels in systemic sclerosis patients with anti-topoisomerase I antibody. Arthritis Rheum. 56(8), 2740-2746 (2007) (Pubitemid 47237293)
30. Perou CM, Sorlie T, Eisen MB et al. Molecular portraits of human breast tumours. Nature 406(6797), 747-752 (2000)
31. Ross DT, Scherf U, Eisen MB et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 24(3), 227-235 (2000) (Pubitemid 30132189)
32. Whitfield ML, Finlay DR, Murray JI et al. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc. Natl Acad. Sci. USA 100(21), 12319-12324 (2003) (Pubitemid 37271558)
33. Gardner H, Shearstone JR, Bandaru R et al. Gene profiling of scleroderma skin reveals robust signatures of disease that are imperfectly reflected in the transcript profiles of explanted fibroblasts. Arthritis Rheum. 54(6), 1961-1973 (2006) (Pubitemid 43877946)
34. Milano A, Pendergrass SA, Sargent JL et al. Molecular subsets in the gene expression signatures of scleroderma skin. PLoS ONE 3(7), e2696 (2008)
35. Tan FK, Zhou X, Mayes MD et al. Signatures of differentially regulated interferon gene expression and vasculotrophism in the peripheral blood cells of systemic sclerosis patients. Rheumatology (Oxford) 45(6), 694-702 (2006) (Pubitemid 43985337)
36. Duan H, Fleming J, Pritchard DK et al. Combined analysis of monocyte and lymphocyte messenger RNA expression with serum protein profiles in patients with scleroderma. Arthritis Rheum. 58(5), 1465-1474 (2008) (Pubitemid 351705936)
37. Grigoryev DN, Mathai SC, Fisher MR et al. Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res. 151(4), 197-207 (2008)
38. Luzina IG, Atamas SP, Wise R, Wigley FM, Xiao HQ, White B. Gene expression in bronchoalveolar lavage cells from scleroderma patients. Am J Respir. Cell Mol. Biol. 26(5), 549-557 (2002) (Pubitemid 34315862)
39. Luzina IG, Atamas SP, Wise R et al. Occurrence of an activated, profibrotic pattern of gene expression in lung CD8+ T cells from scleroderma patients. Arthritis Rheum. 48(8), 2262-2274 (2003) (Pubitemid 36959208)
40. Hsu E, Shi H, Jordan RM, Lyons-Weiler J, Pilewski JM, Feghali-Bostwick CA. Lung tissues in patients with systemic sclerosis have gene expression patterns unique to pulmonary fibrosis and pulmonary hypertension. Arthritis Rheum. 63(3), 783-794 (2011)
41. Zhou X, Tan FK, Xiong M et al. Systemic sclerosis (scleroderma): specific autoantigen genes are selectively overexpressed in scleroderma fibroblasts. J Immunol., 167(12), 7126-7133 (2001) (Pubitemid 33144210)
42. Tan FK, Hildebrand BA, Lester MS et al. Classification analysis of the transcriptosome of nonlesional cultured dermal fibroblasts from systemic sclerosis patients with early disease. Arthritis Rheum. 52(3), 865-876 (2005) (Pubitemid 40365110)
43. Zhou X, Tan FK, Xiong M, Arnett FC, Feghali-Bostwick CA. Monozygotic twins clinically discordant for scleroderma show concordance for fibroblast gene expression profiles. Arthritis Rheum. 52(10), 3305-3314 (2005) (Pubitemid 41447114)
44. Fuzii HT, Yoshikawa GT, Junta CM et al. Affected and non-affected skin fibroblasts from systemic sclerosis patients share a gene expression profile deviated from the one observed in healthy individuals. Clin Exp. Rheumatol. 26(5), 866-874 (2008)
45. Vuorio T, Makela JK, Vuorio E. Activation of type I collagen genes in cultured scleroderma fibroblasts. J Cell Biochem. 28(2), 105-113 (1985) (Pubitemid 15057434)
46. Kim D, Peck A, Santer D et al. Induction of interferon-a by scleroderma sera containing autoantibodies to topoisomerase I: association of higher interferon-a activity with lung fibrosis. Arthritis Rheum. 58(7), 2163-2173 (2008) (Pubitemid 351988110)
47. Bos CL, van Baarsen LG, Timmer TC et al. Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers. Genes Immun. 10(3), 210-218 (2009)
48. Assassi S, Mayes MD, Arnett FC et al. Systemic sclerosis and lupus: points in an interferon-mediated continuum. Arthritis Rheum. 62(2), 589-598 (2010)
49. Pendergrass SA, Hayes E, Farina G et al. Limited systemic sclerosis patients with pulmonary arterial hypertension show biomarkers of inflammation and vascular injury. PLoS ONE 5(8), e12106 (2010)
50. Liu ET. Mechanism-derived gene expression signatures and predictive biomarkers in clinical oncology. Proc. Natl Acad. Sci. USA 102(10), 3531-3532 (2005) (Pubitemid 40354646)
51. Wong DJ, Chang HY. Learning more from microarrays: insights from modules and networks. J Invest. Dermatol. 125(2), 175-182 (2005) (Pubitemid 41648148)
52. Sorlie T, Perou CM, Tibshirani R et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98(19), 10869-10874 (2001) (Pubitemid 32878711)
53. Julka PK, Chacko RT, Nag S et al. A Phase II study of sequential neoadjuvant gemcitabine plus doxorubicin followed by gemcitabine plus cisplatin in patients with operable breast cancer: prediction of response using molecular profiling. Br J. Cancer 98(8), 1327-1335 (2008) (Pubitemid 351543585)
54. Sargent JL, Milano A, Connolly MK, Whitfield ML. Scleroderma gene expression and pathway signatures. Curr Rheumatol. Rep. 10(3), 205-211 (2008)
55. Subramanian A, Tamayo P, Mootha VK et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102(43), 15545-15550 (2005) (Pubitemid 41528093)
56. Sargent JL, Milano A, Bhattacharyya S et al. A TGFb-responsive gene signature is associated with a subset of diffuse scleroderma with increased disease severity. J Invest. Dermatol. 130(3), 694-705 (2010)
57. Chambers RC, Leoni P, Kaminski N, Laurent GJ, Heller RA. Global expression profiling of fibroblast responses to transforming growth factor-b1 reveals the induction of inhibitor of differentiation-1 and provides evidence of smooth muscle cell phenotypic switching. Am J Pathol. 162(2), 533-546 (2003) (Pubitemid 36267860)
58. Chung L, Fiorentino DF, Benbarak MJ et al. Molecular framework for response to imatinib mesylate in systemic sclerosis. Arthritis Rheum. 60(2), 584-591 (2009)
59. Zhang Y, McCormick LL, Desai SR, Wu C, Gilliam AC. Murine sclerodermatous graft-versus-host disease, a model for human scleroderma: cutaneous cytokines, chemokines, and immune cell activation. J Immunol. 168(6), 3088-3098 (2002) (Pubitemid 34211692)
60. Ruzek MC, Jha S, Ledbetter S, Richards SM, Garman RD. A modified model of graft-versus-host-induced systemic sclerosis (scleroderma) exhibits all major aspects of the human disease. Arthritis Rheum. 50(4), 1319-1331 (2004) (Pubitemid 38480843)
61. Green MC, Sweet HO, Bunker LE. Tight-skin, a new mutation of the mouse causing excessive growth of connective tissue and skeleton. Am J Pathol. 82(3), 493-512 (1976)
62. Asano N, Fujimoto M, Yazawa N et al. B Lymphocyte signaling established by the CD19/CD22 loop regulates autoimmunity in the tight-skin mouse. Am J Pathol. 165(2), 641-650 (2004) (Pubitemid 38971393)
63. Hasegawa M, Hamaguchi Y, Yanaba K et al. B-lymphocyte depletion reduces skin fibrosis and autoimmunity in the tight-skin mouse model for systemic sclerosis. Am J Pathol. 169(3), 954-966 (2006) (Pubitemid 44411958)
64. Christner PJ, Peters J, Hawkins D, Siracusa LD, Jimenez SA. The tight skin 2 mouse. An animal model of scleroderma displaying cutaneous fibrosis and mononuclear cell infiltration. Arthritis Rheum. 38(12), 1791-1798 (1995) (Pubitemid 26010280)
65. Gentiletti J, McCloskey LJ, Artlett CM, Peters J, Jimenez SA, Christner PJ. Demonstration of autoimmunity in the tight skin-2 mouse: a model for scleroderma. J Immunol. 175(4), 2418-2426 (2005) (Pubitemid 41113852)
66. Barisic-Dujmovic T, Boban I, Clark SH. Regulation of collagen gene expression in the Tsk2 mouse. J Cell Physiol. 215(2), 464-471 (2008) (Pubitemid 351468958)
67. Yamamoto T, Takagawa S, Katayama I et al. Animal model of sclerotic skin. I: Local injections of bleomycin induce sclerotic skin mimicking scleroderma. J Invest. Dermatol. 112(4), 456-462 (1999) (Pubitemid 29171935)
68. Sonnylal S, Denton CP, Zheng B et al. Postnatal induction of transforming growth factor b signaling in fibroblasts of mice recapitulates clinical, histologic, and biochemical features of scleroderma. Arthritis Rheum. 56(1), 334-344 (2007) (Pubitemid 46106207)
69. Denton CP, Zheng B, Evans LA et al. Fibroblast-specific expression of a kinase-deficient type II transforming growth factor b (TGFb) receptor leads to paradoxical activation of TGFb signaling pathways with fibrosis in transgenic mice. J Biol. Chem. 278(27), 25109-25119 (2003) (Pubitemid 37548675)
70. Sato N, Sanjuan IM, Heke M, Uchida M, Naef F, Brivanlou AH. Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev Biol. 260(2), 404-413 (2003) (Pubitemid 36960088)
71. Ellwood-Yen K, Graeber TG, Wongvipat J et al. Myc-driven murine prostate cancer shares molecular features with human prostate tumors. Cancer Cell 4(3), 223-238 (2003) (Pubitemid 37163836)
72. Herschkowitz JI, Simin K, Weigman VJ et al. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol. 8(5), R76 (2007)
73. Sweet-Cordero A, Mukherjee S, Subramanian A et al. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet. 37(1), 48-55 (2005) (Pubitemid 40070939)
74. Lee JS, Chu IS, Mikaelyan A et al. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat Genet. 36(12), 1306-1311 (2004) (Pubitemid 39577940)
75. Bennett CN, Green JE. Unlocking the power of cross-species genomic analyses: identification of evolutionarily conserved breast cancer networks and validation of preclinical models. Breast Cancer Res. 10(5), 213 (2008)
76. Radstake TR, Gorlova O, Rueda B et al. Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus. Nat Genet. 42(5), 426-429 (2010)
77. Zhou X, Lee JE, Arnett FC et al. HLA-DPB1 and DPB2 are genetic loci for systemic sclerosis: a genome-wide association study in Koreans with replication in North Americans. Arthritis Rheum. 60(12), 3807-3814 (2009)
78. Gilchrist FC, Bunn C, Foley PJ et al. Class II HLA associations with autoantibodies in scleroderma: a highly significant role for HLA-DP. Genes Immun. 2(2), 76-81 (2001) (Pubitemid 33674232)
79. Ito I, Kawaguchi Y, Kawasaki A et al. Association of a functional polymorphism in the IRF5 region with systemic sclerosis in a Japanese population. Arthritis Rheum. 60(6), 1845-1850 (2009)
80. Rueda B, Broen J, Simeon C et al. The STAT4 gene influences the genetic predisposition to systemic sclerosis phenotype. Hum Mol. Genet. 18(11), 2071-2077 (2009)
81. Tsuchiya N, Kawasaki A, Hasegawa M et al. Association of STAT4 polymorphism with systemic sclerosis in a Japanese population. Ann Rheum. Dis. 68(8), 1375-1376 (2009)
82. Diaz-Gallo LM, Gourh P, Broen J et al. Analysis of the influence of PTPN22 gene polymorphisms in systemic sclerosis. Ann Rheum. Dis. 70(3), 454-462 (2010)