Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis

Arthritis Research and Therapy

Volumn 17, Issue 1, 2015, Pages

  Chakravarty, Eliza F ^a   Martyanov, Viktor ^b   Fiorentino, David ^c   Wood, Tammara A ^b   Haddon, David James ^c   Jarrell, Justin Ansel ^c   Utz, Paul J ^c   Genovese, Mark C ^c   Whitfield, Michael L ^b   Chung, Lorinda ^c,d  

^a OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^b DARTMOUTH MEDICAL SCHOOL   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d VA PALO ALTO HEALTH CARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABATACEPT; CD28 ANTIGEN; PLACEBO; IMMUNOSUPPRESSIVE AGENT; TMIGD2 PROTEIN, HUMAN;

ADULT; ADVERSE OUTCOME; ARTICLE; CONTROLLED STUDY; CUTANEOUS SYSTEMIC SCLEROSIS; DERMATITIS; DISEASE DURATION; DOUBLE BLIND PROCEDURE; DRUG EFFICACY; DRUG SAFETY; FEMALE; FEVER; GENE EXPRESSION; HEADACHE; HUMAN; HUMAN TISSUE; IMMUNE RESPONSE; INFECTION; MAJOR CLINICAL STUDY; MALE; PRURITUS; RANDOMIZED CONTROLLED TRIAL; SKIN BIOPSY; SYSTEMIC SCLEROSIS; TREATMENT OUTCOME; BIOSYNTHESIS; DNA MICROARRAY; DRUG EFFECTS; MIDDLE AGED; SCLERODERMA, DIFFUSE;

ABATACEPT; ADULT; ANTIGENS, CD28; DOUBLE-BLIND METHOD; FEMALE; GENE EXPRESSION; HUMANS; IMMUNOSUPPRESSIVE AGENTS; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SCLERODERMA, DIFFUSE;

EID: 84933518561     PISSN: 14786354     EISSN: 14786362     Source Type: Journal    
DOI: 10.1186/s13075-015-0669-3     Document Type: Article

References (27)

1. Medsger Jr TA. Natural history of systemic sclerosis and the assessment of disease activity, severity, functional status, and psychologic well-being. Rheum Dis Clin North Am. 2003;29:255-73.
2. Roumm AD, Whiteside TL, Medsger Jr TA, Rodnan GP. Lymphocytes in the skin of patients with progressive systemic sclerosis. Quantification, subtyping, and clinical correlations. Arthritis Rheum. 1984;27:645-53.
3. Prescott RJ, Freemont AJ, Jones CJ, Hoyland J, Fielding P. Sequential dermal microvascular and perivascular changes in the development of scleroderma. J Pathol. 1992;166:255-63.
4. Freundlich B, Jimenez SA. Phenotype of peripheral blood lymphocytes in patients with progressive systemic sclerosis: activated T lymphocytes and the effect of D-penicillamine therapy. Clin Exp Immunol. 1987;69:375-84.
5. Needleman BW, Wigley FM, Stair RW. Interleukin-1, interleukin-2, interleukin-4, interleukin-6, tumor necrosis factor-aα, and interferon-γ levels in sera from patients with scleroderma. Arthritis Rheum. 1992;35:67-72.
6. Hasegawa M, Fujimoto M, Kikuchi K, Takehara K. Elevated serum levels of interleukin 4 (IL-4), IL-10, IL-13 in patients with systemic sclerosis. J Rheumatol. 1997;24:328-32.
7. Sakkas LI, Tourtellotte C, Berney S, Myers AR, Platsoucas CD. Increased levels of alternatively spliced interleukin 4 (IL-4d2) transcripts in peripheral blood mononuclear cells from patients with systemic sclerosis. Clin Diagn Lab Immunol. 1999;6:660-4.
8. Kurasawa K, Hirose K, Sano H, Endo H, Shinkai H, Nawata Y, et al. Increased interleukin-17 production in patients with systemic sclerosis. Arthritis Rheum. 2000;43:2455-63.
9. Clements P, Lachenbruch P, Siebold J, White B, Weiner S, Martin R, et al. Inter and intraobserver variability of total skin thickness score (modified Rodnan TSS) in systemic sclerosis. J Rheumatol. 1995;22:1281-5.
10. Hinchcliff M, Huang CC, Wood TA, Matthew Mahoney J, Martyanov V, Bhattacharyya S, et al. Molecular signatures in skin associated with clinical improvement during mycophenolate treatment in systemic sclerosis. J Invest Dermatol. 2013;133:1979-89.
11. Milano A, Pendergrass SA, Sargent JL, George LK, McCalmont TH, Connolly MK, et al. Molecular subsets in the gene expression signatures of scleroderma skin. PLoS One. 2008;3:e2696.
12. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet. 2006;38:500-1.
13. Gould J, Getz G, Monti S, Reich M, Mesirov JP. Comparative gene marker selection suite. Bioinformatics. 2006;22:1924-5.
14. de Hoon MJ, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics. 2004;20:1453-4.
15. Saldanha AJ. Java Treeview-extensible visualization of microarray data. Bioinformatics. 2004;20:3246-8.
16. Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007;35:W193-200.
17. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545-50.
18. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267-73.
19. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999;27:29-34.
20. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2011;39:D691-7.
21. Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462:108-12.
22. Pendergrass SA, Lemaire R, Francis IP, Mahoney JM, Lafyatis R, Whitfield ML. Intrinsic gene expression subsets of diffuse cutaneous systemic sclerosis are stable in serial skin biopsies. J Invest Dermatol. 2012;132:1363-73.
23. Khanna D, Furst DE, Hays RD, Park GS, Wong WK, Seibold JR, et al. Minimally important difference in diffuse systemic sclerosis: results from the D-penicillamine study. Ann Rheum Dis. 2006;65:1325-9.
24. Elhai M, Meunier M, Matucci-Cerinic M, Maurer B, Riemekasten G, Leturcq T, et al. Outcomes of patients with systemic sclerosis-associated polyarthritis and myopathy treated with tocilizumab or abatacept: a EUSTAR observational study. Ann Rheum Dis. 2013;72:1217-20.
25. Chung L, Denton CP, Distler O, Furst DE, Khanna D, Merkel PA, et al. Clinical trial design in scleroderma: where are we and where do we go next? Clin Exp Rheumatol. 2012;30:S97-102.
26. Merkel PA, Silliman NP, Clements PJ, Denton CP, Furst DE, Mayes MD, et al. Patterns and predictors of change in outcome measures in clinical trials in scleroderma: an individual patient meta-analysis of 629 subjects with diffuse cutaneous systemic sclerosis. Arthritis Rheum. 2012;64:3420-9.
27. Oliveros JC. Venny. An interactive tool for comparing lists with Venn's diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html (2007-2015). Accessed 9 Mar 2015.