Identification of Novel Predictor Classifiers for Inflammatory Bowel Disease by Gene Expression Profiling

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Montero Meléndez, Trinidad ^a   Llor, Xavier ^b   García Planella, Esther ^c   Perretti, Mauro ^a   Suárez, Antonio ^d  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d UNIVERSITY OF GRANADA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AZATHIOPRINE; BIOLOGICAL MARKER; GLUCOCORTICOID; GLUCOCORTICOID RECEPTOR; INFLIXIMAB; MERCAPTOPURINE; PREDNISONE;

ALGORITHM; ARTICLE; AUTOPHAGY; CLASS PREDICTION; CLASSIFIER; CLINICAL ARTICLE; COLON BIOPSY; COMPUTER PROGRAM; CONTROLLED STUDY; CROHN DISEASE; DIFFERENTIAL DIAGNOSIS; DISEASE SEVERITY; DRUG RESPONSE; ENDOCYTOSIS; ENTERITIS; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SCREENING; HUMAN; IMMUNE RESPONSE; INFLAMMATION; MACHINE LEARNING; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PATIENT CODING; PATIENT SATISFACTION; PERSONALIZED MEDICINE; PREDICTOR CLASSIFIER; PROGNOSIS; PROTEIN DEGRADATION; REAL TIME POLYMERASE CHAIN REACTION; ULCERATIVE COLITIS;

COLITIS, ULCERATIVE; CROHN DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; INFLAMMATION; INFLAMMATORY BOWEL DISEASES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS;

EID: 84885405400     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0076235     Document Type: Article

References (24)

1. Maloy KJ, Powrie F, (2011) Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature 474: 298-306.
2. Beaugerie L, Sokol H, (2012) Clinical, serological and genetic predictors of inflammatory bowel disease course. World J Gastroenterol 18: 3806-3813.
3. Lichtenstein GR, Hanauer SB, Sandborn WJ, (2009) Practice Parameters Committee of American College of Gastroenterology. Management of Crohn's disease in adults. Am J Gastroenterol 104: 465-483.
4. D'Haens G, Baert F, van Assche G, Caenepeel P, Vergauwe P, et al. (2008) Early combined immunosuppression or conventional management in patients with newly diagnosed Crohn's disease: an open randomised trial. Lancet 371: 660-667.
5. Lewis JD, (2011) The utility of biomarkers in the diagnosis and therapy of inflammatory bowel disease. Gastroenterology 140: 1817-1826.
6. Van Limbergen J, Philpott D, Griffiths AM, (2011) Genetic profiling in inflammatory bowel disease: from association to bedside. Gastroenterology 141: 1566-1571.
7. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009.
8. Bonome T, Levine DA, Shih J, Randonovich M, Pise-Masison CA, et al. (2008) A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer. Cancer Res 68: 5478-5486.
9. McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, et al. (2010) A CD8+ T cell transcription signature predicts prognosis in autoimmune disease. Nat Med 16: 586-591.
10. Medina I, Montaner D, Tarraga J, Dopazo J, (2007) Prophet, a web-based tool for class prediction using microarray data. Bioinformatics 23: 390-391.
11. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, et al. (2003) PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids ReS 31: 334-341.
12. Ford LT, Berg JD, (2010) Thiopurine S-methyltransferase (TPMT) assessment prior to starting thiopurine drug treatment; a pharmacogenomic test whose time has come. J Clin Pathol 63: 288-295.
13. Simon R, Radmacher MD, Dobbin K, McShane LM, (2003) Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 95: 14-18.
14. Lee JC, Lyons PA, McKinney EF, Sowerby JM, Carr EJ, et al. (2011) Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis. J Clin Invest 121: 4170-4179.
15. Bonapace L, Bornhauser BC, Schmitz M, Cario G, Ziegler U, et al. (2010) Induction of autophagy-dependent necroptosis is required for childhood acute lymphoblastic leukemia cells to overcome glucocorticoid resistance. J Clin Invest 120: 1310-1323.
16. Sengupta S, Wasylyk B, (2001) Ligand-dependent interaction of the glucocorticoid receptor with p53 enhances their degradation by Hdm2. Genes Dev 15: 2367-2380.
17. Oz HS, Zhong J, de Villiers WJ, (2009) Pattern recognition scavenger receptors, SR-A and CD36, have an additive role in the development of colitis in mice. Dig Dis Sci 54: 2561-2567.
18. Lu HK, Mitchell A, Endoh Y, Hampartzoumian T, Huynh O, et al. (2012) LILRA2 Selectively Modulates LPS-Mediated Cytokine Production and Inhibits Phagocytosis by Monocytes PLoS One. 7: e33478.
19. Tedla N, An H, Borges L, Vollmer-Conna U, Bryant K, Geczy C, et al. (2011) Expression of activating and inhibitory leukocyte immunoglobulin-like receptors in rheumatoid synovium: correlations to disease activity. Tissue Antigens 77: 305-316.
20. Srivastava MD, Kulaylat MN, (2004) Gene expression profiles of late colonic Crohn's disease. J Med 35: 233-255.
21. Svensson SL, Pasupuleti M, Walse B, Malmsten M, Mörgelin M, et al. (2010) Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution. J Biol Chem 285: 16105-16115.
22. Gersemann M, Becker S, Nuding S, Antoni L, Ott G, et al. (2012) Olfactomedin-4 is a glycoprotein secreted into mucus in active IBD. J Crohns Colitis 6: 425-434.
23. Liu W, Yan M, Liu Y, Wang R, Li C, et al. (2010) Olfactomedin 4 down-regulates innate immunity against Helicobacter pylori infection. Proc Natl Acad Sci USA 107: 11056-11061.
24. Hakonarson H, Bjornsdottir US, Halapi E, Bradfield J, Zink F, et al. (2005) Profiling of genes expressed in peripheral blood mononuclear cells predicts glucocorticoid sensitivity in asthma patients. Proc Natl Acad Sci USA 102: 14789-14794.