55
Views
4
CrossRef citations to date
0
Altmetric
Original Article

Detection of gene expression signatures related to underlying disease and treatment in rheumatoid arthritis patients

, , , , , , & show all
Pages 729-740 | Received 29 Mar 2012, Accepted 02 Jul 2012, Published online: 02 Jan 2014

REFERENCES

  • Lequerre T, Coulouarn C, Derambure C, Lefebvre G, Vittecoq 0, Daveau M, et al. A new tool for rheumatology: large-scale analysis of gene expression. Joint Bone Spine. 2003;70(4): 248–56.
  • van Baarsen LG, Bos CL, van der Pouw Kraan TC, Verweij CL. Transcription profiling of rheumatic diseases. Arthr Res Ther 2009;11(1):207.
  • Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, Espe KJ, et al. Interferon-inducible gene expression signa-ture in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci USA. 2003;100(5):2610–5.
  • Crow MK, Kirou KA, Wohlgemuth J. Microanay analysis of interferon-regulated genes in SLE. Autoimmunity. 2003;36(8): 481–90.
  • Lequerre T, Bansard C, Vittecoq 0, Derambure C, Hiron M, Daveau M, et al. Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression pro-filing in synovia. Arthr Res Ther. 2009;11(3):R99.
  • Reynier F, Pachot A, Paye M, Xu Q, Tunel-Davin F, Petit F, et al. Specific gene expression signature associated with devel-opment of autoimmune type-I diabetes using whole-blood microanay analysis. Genes Immun. 2010;11(3):269–78.
  • Bennett CN, Green JE. Genomic analyses as a guide to target identification and preclinical testing of mouse models of breast cancer. Toxicol Pathol. 2010;38(1):88–95.
  • Fayad W, Fryknas M, Brnjic S, Olofsson MH, Larsson R, Linder S. Identification of a novel topoisomerase inhibitor effective in cells overexpressing drug efflux transporters. PLoS One. 2009; 4(10):e7238.
  • Yao Y, Richman L, Higgs BW, Morehouse CA, de los Reyes M, Brohawn P, et al. Neutralization of interferon-alpha/beta-inducible genes and downstream effect in a phase I trial of an anti-interferon-alpha monoclonal antibody in systemic lupus erythematosus. Arthr Rheum. 2009;60(6):1785–96.
  • Kunz G. Use of a genomic test (MammaPrintTm) in daily clinical practice to assist in risk stratification of young breast cancer patients. Arch Gynecol Obstet. 2011;283(3):597–602.
  • Bansard C, Lequerre T, Daveau M, Boyer 0, Tron F, Salier JP, et al. Can rheumatoid arthritis responsiveness to methotrexate and biolo-gics be predicted? Rheumatology (Oxford). 2009;48(9):1021–8.
  • Koczan D, Drynda S, Hecker M, Drynda A, Guthke R, Kekow J, et al. Molecular discrimination of responders and nonresponders to anti-TNF alpha therapy in rheumatoid arthritis by etanercept. Arthr Res Ther. 2008;10(3):R50.
  • Lequerre T, Gauthier-Jauneau AC, Bansard C, Derambure C, Hiron M, Vittecoq 0, et al. Gene profiling in white blood cells predicts infliximab responsiveness in rheumatoid arthritis. Arthr Res Ther. 2006;8(4):R105.
  • Sekiguchi N, Kawauchi S, Furuya T, Inaba N, Matsuda K, Ando S, et al. Messenger ribonucleic acid expression profile in peripheral blood cells from RA patients following treatment with an anti-TNF-alpha monoclonal antibody, infliximab. Rheuma-tology (Oxford). 2008;47(6):780–8.
  • van Baarsen LG, Wijbrandts CA, Rustenburg F, Cantaert T, van der Pouw Kraan TC, Baeten DL, et al. Regulation of IFN response gene activity during infliximab treatment in rheumatoid arthritis is associated with clinical response to treatment. Arthr Res Ther. 2010;12(1):R11.
  • van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, Voskuyl AE, Rustenburg F, Baggen JM, et al. Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis. 2007;66(8):1008–14.
  • Arnett FC, Edworthy SM, Bloch DA, McShane DJ, Fries JF, Cooper NS, et al. The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. Arthr Rheum. 1988;31(3):315–24.
  • Prevoo ML, van't Hof MA, Kuper HH, van Leeuwen MA, van de Putte LB, van Riel PL. Modified disease activity scores that include twenty-eight-joint counts. Development and validation in a prospective longitudinal study of patients with rheumatoid arthritis. Arthr Rheum. 1995;38(1):44–8.
  • Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162(1):156–9.
  • Saeed AT, Sharov V, White J, Li J, Liang W, Bhagabati N, et al. TM4: a free, open-source system for microanay data manage-ment and analysis. Biotechniques. 2003;34(2):374–8.
  • Saeed AT, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. TM4 microarray software suite. Methods Enzymol. 2006;411:134–93.
  • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.
  • Lleonart R, Naf D, Browning H, Weissmann C. A novel, quan-titative bioassay for type I interferon using a recombinant indi-cator cell line. Biotechnology (N Y). 1990;8(12):1263–7.
  • Yao Y, Higgs BW, Richman L, White B, Jallal B. Use of type I interferon-inducible mRNAs as pharmacodynamic markers and potential diagnostic markers in trials with sifalimumab, an anti-IFNalpha antibody, in systemic lupus erythematosus. Arthr Res 'Ther. 2010;12[Suppl 1]:S6.
  • Bauer JW, Baechler EC, Petri M, Batliwalla FM, Crawford D, Ortmann WA, et al. Elevated serum levels of interferon-regulated chemokines are biomarkers for active human systemic lupus erythematosus. PLoS Med. 2006;3(12):e491.
  • Bennett L, Palucka AK, Arce E, Cantrell V, Borvak J, Banche-reau J, et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 2003;197(6):711–23.
  • Crow MK. Type I. Interferon and autoimmune disease. Auto-immunity. 2003;36(8):445–6.
  • Lyons PA, McKinney EF, Rayner TF, Hatton A, Woffendin HB, Koukoulaki M, et al. Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis. Ann Rheum Dis. 2010;69(6): 1208–13.
  • Nikpour M, Dempsey AA, Urowitz MB, Gladman DD, Barnes DA. Association of a gene expression profile from whole blood with disease activity in systemic lupus erythaematosus. Ann Rheum Dis. 2008;67(8):1069–75.
  • Banchereau J, Pascual V. Type I interferon in systemic lupus erythematosus and other autoimmune diseases. Immunity. 2006; 25(3):383–92.
  • Bave U, Magnusson M, Eloranta ML, Perers A, Alm GV, Ron-nblom L. Fc gamma Rila is expressed on natural IFN-alpha-producing cells (plasmacytoid dendritic cells) and is required for the IFN-alpha production induced by apoptotic cells combined with lupus IgG. J Immunol. 2003;171(6):3296–302.
  • Bave U, Nordmark G, Lovgren T, Ronnelid J, Cajander S, Elo-ranta ML, et al. Activation of the type I interferon system in primary Sjogren's syndrome: a possible etiopathogenic mecha-nism. Arthr Rheum. 2005;52(4):1185–95.
  • Eloranta ML, Barbasso HS, Ulfgren AK, Ronnblom L, Alm GV, Lundberg IE. A possible mechanism for endogenous activation of the type I interferon system in myositis patients with anti-Jo-1 or anti-Ro 52/anti-Ro 60 autoantibodies. Arthr Rheum. 2007;56(9): 3112–24.
  • Lovgren T, Eloranta ML, Bave U, Alm GV, Ronnblom L. Induction of interferon-alpha production in plasmacytoid den-dritic cells by immune complexes containing nucleic acid released by necrotic or late apoptotic cells and lupus IgG. Arthr Rheum. 2004;50(6):1861–72.
  • van Holten J, Smeets TJ, Blankert P, Tak PP. Expression of interferon beta in synovial tissue from patients with rheumatoid arthritis: comparison with patients with osteoarthritis and reactive arthritis. Ann Rheum Dis. 2005;64(12):1780–2.
  • Thurlings RM, Boumans M, Tekstra J, van Roon JA, Vos K, van Westing DM, et al. Relationship between the type I interferon signature and the response to rituximab in rheumatoid arthritis patients. Arthritis Rheum 2010;62(12):3607–14.
  • Palucka AK, Blanck JP, Bennett L, Pascual V, Banchereau J. Cross-regulation of TNF and IFN-alpha in autoimmune diseases. Proc Natl Acad Sci USA. 2005;102(9):3372–7.
  • Reynier F, Petit F, Paye M, Turrel-Davin F, Imbert PE, Hot A, et al. Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis. PLoS One. 2011;6(10):e24828.
  • Bienkowska JR, Dalgin GS, Batliwalla F, Allaire N, Roubenoff R, Gregersen PK, et al. Convergent random forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response. Genomics. 2009;94(6): 423–32.
  • Julia A, Erra A, Palacio C, Tomas C, Sans X, Barcelo P, et al. An eight-gene blood expression profile predicts the response to inf-fiximab in rheumatoid arthritis. PLoS One. 2009;4(10):e7556.
  • Feske S, Picard C, Fischer A. Immunodeficiency due to mutations in ORAI1 and STIM1. Clin Immunol. 2010;135(2):169–82.
  • Khanna R, Chang MC, Joiner WJ, Kaczmarek LK, Schlichter LC. hSK4/hIK1, a calmodulin-binding KCa channel in human T lymphocytes. Roles in proliferation and volume regulation. J Biol Chem. 1999;274(21):14838–49.
  • Tang X, Pan F, Xia G, Liao F, Ge R, Mei Y, et al. A single-nucleotide polymorphism marker within the FCRL5 gene and HLA-B27 positive Han Chinese ankylosing spondylitis patients. Tissue Antigens. 2009;74(4):314–6.
  • Campbell JA, Davis RS, Lilly LM, Fremont DH, French AR, Carayannopoulos LN. Cutting edge: FcR-like 5 on innate B cells is targeted by a poxvirus MHC class I-like immunoevasin. J Immunol. 2010;185(1):28–32.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.