Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus

PLoS ONE

Volumn 4, Issue 7, 2009, Pages

  Abbas, Alexander R ^a   Wolslegel, Kristen ^a   Seshasayee, Dhaya ^a   Modrusan, Zora ^a   Clark, Hilary F ^a  

^a GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AZATHIOPRINE; B7 ANTIGEN; CD69 ANTIGEN; COMPLEMENT COMPONENT C3; COMPLEMENT COMPONENT C4; CORTICOSTEROID; INTERFERON; MYCOPHENOLIC ACID; PADGEM PROTEIN;

ACCURACY; ADULT; ARTICLE; AUTOIMMUNE DISEASE; B LYMPHOCYTE ACTIVATION; BLOOD ANALYSIS; CELL ACTIVATION; CELL KINETICS; CELL MATURATION; CELL POPULATION; CELL TYPE; CONTROLLED STUDY; DISEASE SEVERITY; FEMALE; GRANULOCYTE; HELPER CELL; HUMAN; HUMAN CELL; IMMUNE SYSTEM; IMMUNOCOMPETENT CELL; IMMUNOSUPPRESSIVE TREATMENT; LABORATORY DIAGNOSIS; LEUKOCYTE; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; MONOCYTE; NATURAL KILLER CELL; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PROTEIN DENATURATION; SYSTEMIC LUPUS ERYTHEMATOSUS; T LYMPHOCYTE ACTIVATION; VALIDATION PROCESS; B LYMPHOCYTE; BLOOD; CASE CONTROL STUDY; IMMUNOLOGY; LYMPHOCYTE ACTIVATION; T LYMPHOCYTE;

B-LYMPHOCYTES; CASE-CONTROL STUDIES; HUMANS; LUPUS ERYTHEMATOSUS, SYSTEMIC; LYMPHOCYTE ACTIVATION; T-LYMPHOCYTES;

EID: 67749112023     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006098     Document Type: Article

References (35)

1. Rivero SJ, Diaz-Jouanen E, Alarcon-Segovia D (1978) Lymphopenia in systemic lupus erythematosus. Clinical, diagnostic, and prognostic significance. Arthritis Rheum 21: 295-305.
2. Blanco P, Palucka AK, Gill M, Pascual V, Banchereau J (2001) Induction of dendritic cell differentiation by IFN-alpha in systemic lupus erythematosus. Science 294: 1540-1543.
3. Gaipl US, Voll RE, Sheriff A, Franz S, Kalden JR, et al. (2005) Impaired clearance of dying cells in systemic lupus erythematosus. Autoimmun Rev 4: 189-194.
4. Lub-de Hooge MN, de Vries EG, de Jong S, Bijl M (2005) Soluble TRAIL concentrations are raised in patients with systemic lupus erythematosus. Ann Rheum Dis 64: 854-858.
5. Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, et al. (2003) Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci U S A 100: 2610-2615.
6. Bennett L, Palucka AK, Arce E, Cantrell V, Borvak J, et al. (2003) Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med 197: 711-723.
7. Sigurdsson S, Nordmark G, Goring HH, Lindroos K, Wiman AC, et al. (2005) Polymorphisms in the tyrosine kinase 2 and interferon regulatory factor 5 genes are associated with systemic lupus erythematosus. Am J Hum Genet 76: 528-537.
8. Graham RR, Kozyrev SV, Baechler EC, Reddy MV, Plenge RM, et al. (2006) A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 38: 550-555.
9. Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, et al. (2007) STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med 357: 977-986.
10. Speed T (2003) Statistical Analysis of Gene Expression Microarray Data: Chapman & Hall/CRC.
11. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
12. Abbas AR, Baldwin D, Ma Y, Ouyang W, Gurney A, et al. (2005) Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun 6: 319-331.
13. Lu P, Nakorchevskiy A, Marcotte EM (2003) Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A 100: 10370-10375.
14. Wang M, Master SR, Chodosh LA (2006) Computational expression deconvolution in a complex mammalian organ. BMC Bioinformatics 7: 328.
15. Maas K, Chan S, Parker J, Slater A, Moore J, et al. (2002) Cutting edge: molecular portrait of human autoimmune disease. J Immunol 169: 5-9.
16. Green MR, Kennell AS, Larche MJ, Seifert MH, Isenberg DA, et al. (2007) Natural killer T cells in families of patients with systemic lupus erythematosus: their possible role in regulation of IGG production. Arthritis Rheum 56: 303-310.
17. Papadimitraki ED, Choulaki C, Koutala E, Bertsias G, Tsatsanis C, et al. (2006) Expansion of toll-like receptor 9-expressing B cells in active systemic lupus erythematosus: implications for the induction and maintenance of the autoimmune process. Arthritis Rheum 54: 3601-3611.
18. Santini SM, Lapenta C, Logozzi M, Parlato S, Spada M, et al. (2000) Type I interferon as a powerful adjuvant for monocyte-derived dendritic cell development and activity in vitro and in Hu-PBL-SCID mice. J Exp Med 19: 1777-1788.
19. Richez C, Yasuda K, Watkins AA, Akira S, Lafyatis R, et al. (2009) TLR4 ligands induce IFN-alpha production by mouse conventional dendritic cells and human monocytes after IFN-beta priming. J Immunol 182: 820-828.
20. Helbig KJ, Lau DT, Semendric L, Harley HA, Beard MR (2005) Analysis of ISG expression in chronic hepatitis C identifies viperin as a potential antiviral effector. Hepatology 42: 702-710.
21. Crow MK (2007) Type I interferon in systemic lupus erythematosus. Curr Top Microbiol Immunol 316: 359-386.
22. Green MR, Kennell AS, Larche MJ, Seifert MH, Isenberg DA, et al. (2005) Natural killer cell activity in families of patients with systemic lupus erythematosus: demonstration of a killing defect in patients. Clin Exp Immunol 141: 165-173.
23. Xu L, Zhang L, Yi Y, Kang HK, Datta SK (2004) Human lupus T cells resist inactivation and escape death by upregulating COX-2. Nat Med 10: 411-415.
24. Hahn BH, Ebling F, Singh RR, Singh RP, Karpouzas G, et al. (2005) Cellular and molecular mechanisms of regulation of autoantibody production in lupus. Ann N Y Acad Sci 1051: 433-441.
25. Chan RW, Lai FM, Li EK, Tam LS, Chow KM, et al. (2006) Imbalance of Th1/ Th2 transcription factors in patients with lupus nephritis. Rheumatology (Oxford) 45: 951-957.
26. Lit LC, Wong CK, Li EK, Tam LS, Lam CW, et al. (2007) Elevated gene expression of Th1/Th2 associated transcription factors is correlated with disease activity in patients with systemic lupus erythematosus. J Rheumatol 34: 89-96.
27. Davis P, Percy JS, Russell AS (1977) Correlation between levels of DNA antibodies and clinical disease activity in SLE. Ann Rheum Dis 36: 157-159.
28. Rastin M, Hatef MR, Tabasi N, Sheikh A, Morad Abbasi J, et al. (2007) Sex hormones and peripheral white blood cell subsets in systemic lupus erythematosus patients. Iran J Immunol 4: 110-115.
29. Bonelli M, Savitskaya A, Steiner CW, Rath E, Smolen JS, et al. (2009) Phenotypic and functional analysis of CD4+CD252Foxp3+ T cells in patients with systemic lupus erythematosus. J Immunol 182: 1689-1695.
30. Zimmer J, Andres E, Hentges F (2008) NK cells and Treg cells: a fascinating dance cheek to cheek. Eur J Immunol 38: 2942-2945.
31. Pisetsky DS (2008) The role of innate immunity in the induction of autoimmunity. Autoimmun Rev 8: 69-72.
32. Lahdesmaki H, Shmulevich L, Dunmire V, Yli-Harja O, Zhang W (2005) In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics 6: 54.
33. Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R (2004) Deconvolving cell cycle expression data with complementary information. Bioinformatics 20 Suppl 1: I23-I30.
34. Buess M, Nuyten DS, Hastie T, Nielsen T, Pesich R, et al. (2007) Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. Genome Biol 8: R191.
35. Team RDC (2008) R: A Language and Environment for Statistical Computing.