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

References

• 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).
   PubMed Web of Science ®Google Scholar
• LeRoy EC, Black C, Fleischmajer R et al. Scleroderma (systemic sclerosis): classification, subsets and pathogenesis. J. Rheumatol.15(2), 202–205 (1988).
   PubMed Web of Science ®Google Scholar
• Bolster MB, Silver RM. Lung disease in systemic sclerosis (scleroderma). Baillieres Clin. Rheumatol.7(1), 79–97 (1993).
   PubMedGoogle Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Steen VD, Medsger TA Jr. Improvement in skin thickening in systemic sclerosis associated with improved survival. Arthritis Rheum.44(12), 2828–2835 (2001).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Steen VD. Autoantibodies in systemic sclerosis. Semin. Arthritis Rheum.35(1), 35–42 (2005).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• Medsger TA, Steen VD. Classification, prognosis. In: Systemic Sclerosis. Clements, PJ, Furst, DE (Eds). Williams & Wilkins, Baltimore, MD, USA, 51–64 (1996).
   Google Scholar
• Siebold JR. Chapter 79: Scleroderma. In: Kelley’s 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).
   Google Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Grassegger A, Pohla-Gubo G, Frauscher M, Hintner H. Autoantibodies in systemic sclerosis (scleroderma): clues for clinical evaluation, prognosis and pathogenesis. Wien Med. Wochenschr158(1–2), 19–28 (2008).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Barnett AJ, Miller M, Littlejohn GO. The diagnosis and classification of scleroderma (systemic sclerosis). Postgrad. Med. J.64(748), 121–125 (1988).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Steen VD, Medsger TA Jr. Severe organ involvement in systemic sclerosis with diffuse scleroderma. Arthritis Rheum.43(11), 2437–2444 (2000).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Perou CM, Sorlie T, Eisen MB et al. Molecular portraits of human breast tumours. Nature406(6797), 747–752 (2000).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Whitfield ML, Finlay DR, Murray JI et al. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc. Natl Acad. Sci. USA100(21), 12319–12324 (2003).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Milano A, Pendergrass SA, Sargent JL et al. Molecular subsets in the gene expression signatures of scleroderma skin. PLoS ONE3(7), e2696 (2008).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Vuorio T, Makela JK, Vuorio E. Activation of type I collagen genes in cultured scleroderma fibroblasts. J. Cell Biochem.28(2), 105–113 (1985).
   PubMedGoogle Scholar
• Kim D, Peck A, Santer D et al. Induction of interferon-α by scleroderma sera containing autoantibodies to topoisomerase I: association of higher interferon-α activity with lung fibrosis. Arthritis Rheum.58(7), 2163–2173 (2008).
   PubMedGoogle Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMedGoogle Scholar
• Pendergrass SA, Hayes E, Farina G et al. Limited systemic sclerosis patients with pulmonary arterial hypertension show biomarkers of inflammation and vascular injury. PLoS ONE5(8), e12106 (2010).
   PubMed Web of Science ®Google Scholar
• Liu ET. Mechanism-derived gene expression signatures and predictive biomarkers in clinical oncology. Proc. Natl Acad. Sci. USA102(10), 3531–3532 (2005).
   PubMed Web of Science ®Google Scholar
• Wong DJ, Chang HY. Learning more from microarrays: insights from modules and networks. J. Invest. Dermatol.125(2), 175–182 (2005).
   PubMedGoogle Scholar
• Sorlie T, Perou CM, Tibshirani R et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA98(19), 10869–10874 (2001).
   PubMed Web of Science ®Google Scholar
• 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. Cancer98(8), 1327–1335 (2008).
   PubMed Web of Science ®Google Scholar
• Sargent JL, Milano A, Connolly MK, Whitfield ML. Scleroderma gene expression and pathway signatures. Curr. Rheumatol. Rep.10(3), 205–211 (2008).
   PubMedGoogle Scholar
• 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. USA102(43), 15545–15550 (2005).
   PubMed Web of Science ®Google Scholar
• Sargent JL, Milano A, Bhattacharyya S et al. A TGFβ-responsive gene signature is associated with a subset of diffuse scleroderma with increased disease severity. J. Invest. Dermatol.130(3), 694–705 (2010).
   PubMed Web of Science ®Google Scholar
• Chambers RC, Leoni P, Kaminski N, Laurent GJ, Heller RA. Global expression profiling of fibroblast responses to transforming growth factor-β1 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• Barisic-Dujmovic T, Boban I, Clark SH. Regulation of collagen gene expression in the Tsk2 mouse. J. Cell Physiol.215(2), 464–471 (2008).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Sonnylal S, Denton CP, Zheng B et al. Postnatal induction of transforming growth factor β signaling in fibroblasts of mice recapitulates clinical, histologic, and biochemical features of scleroderma. Arthritis Rheum.56(1), 334–344 (2007).
   PubMed Web of Science ®Google Scholar
• Denton CP, Zheng B, Evans LA et al. Fibroblast-specific expression of a kinase-deficient type II transforming growth factor β (TGFβ) receptor leads to paradoxical activation of TGFβ signaling pathways with fibrosis in transgenic mice. J. Biol. Chem.278(27), 25109–25119 (2003).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• Ellwood-Yen K, Graeber TG, Wongvipat J et al. Myc-driven murine prostate cancer shares molecular features with human prostate tumors. Cancer Cell4(3), 223–238 (2003).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMedGoogle Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar
• 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).
   PubMed Web of Science ®Google Scholar