Modular Transcriptional Repertoire Analyses of Adults With Systemic Lupus Erythematosus Reveal Distinct Type I and Type II Interferon Signatures

The role of interferon‐α (IFNα) in the pathogenesis of systemic lupus erythematosus (SLE) is strongly supported by gene expression studies. The aim of this study was to improve characterization of the blood IFN signature in adult SLE patients.

[1]  Milton W. Taylor,et al.  Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment , 2008, Journal of Translational Medicine.

[2]  Virginia Pascual,et al.  An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis , 2010, Nature.

[3]  Virginia Pascual,et al.  Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood , 2003, The Journal of experimental medicine.

[4]  M. Petri,et al.  Longitudinal expression of type I interferon responsive genes in systemic lupus erythematosus , 2009, Lupus.

[5]  M. Ward,et al.  Validity of clinical associations of biomarkers in translational research studies: the case of systemic autoimmune diseases , 2010, Arthritis research & therapy.

[6]  V. Pascual,et al.  A genomic approach to human autoimmune diseases. , 2010, Annual review of immunology.

[7]  Ramil N. Nurtdinov,et al.  Search for Specific Biomarkers of IFNβ Bioactivity in Patients with Multiple Sclerosis , 2011, PloS one.

[8]  K. Kirou,et al.  Anti-interferon alpha treatment in SLE. , 2013, Clinical immunology.

[9]  L. Wodicka,et al.  Genomic analysis of the host response to hepatitis C virus infection , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[10]  V. Pascual,et al.  TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus , 2010, Nature.

[11]  D. Furst,et al.  Association of increased interferon-inducible gene expression with disease activity and lupus nephritis in patients with systemic lupus erythematosus. , 2006, Arthritis and rheumatism.

[12]  K. Honda,et al.  A critical link between Toll-like receptor 3 and type II interferon signaling pathways in antiviral innate immunity , 2008, Proceedings of the National Academy of Sciences.

[13]  P. Kiener,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. , 2009, Arthritis and rheumatism.

[14]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[15]  M. Petri,et al.  Baseline predictors of systemic lupus erythematosus flares: data from the combined placebo groups in the phase III belimumab trials. , 2013, Arthritis and rheumatism.

[16]  D. Gladman,et al.  Association of a gene expression profile from whole blood with disease activity in systemic lupus erythaematosus , 2007, Annals of the rheumatic diseases.

[17]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[18]  M. Crow,et al.  Microarray Analysis of Interferon-regulated Genes in SLE , 2003, Autoimmunity.

[19]  D. Gladman,et al.  Lack of association between the interferon-α signature and longitudinal changes in disease activity in systemic lupus erythematosus , 2008, Annals of the rheumatic diseases.

[20]  D. Isenberg,et al.  Fifty years of anti-ds DNA antibodies: are we approaching journey's end? , 2007, Rheumatology.

[21]  P. Brown,et al.  Interferon and Biologic Signatures in Dermatomyositis Skin: Specificity and Heterogeneity across Diseases , 2012, PloS one.

[22]  M. Peterson,et al.  Coordinate overexpression of interferon‐α–induced genes in systemic lupus erythematosus , 2004 .

[23]  J F Fries,et al.  The 1982 revised criteria for the classification of systemic lupus erythematosus. , 1982, Arthritis and rheumatism.

[24]  M. Aringer,et al.  Activation of the interferon-gamma signaling pathway in systemic lupus erythematosus peripheral blood mononuclear cells. , 2009, Arthritis and rheumatism.

[25]  Kelly Domico,et al.  Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines. , 2013, Immunity.

[26]  Mimi Y. Kim,et al.  Classification and definition of major flares in SLE clinical trials , 1999, Lupus.

[27]  C. Cheadle,et al.  Precise probes of type II interferon activity define the origin of interferon signatures in target tissues in rheumatic diseases , 2012, Proceedings of the National Academy of Sciences.

[28]  S. Greenberg,et al.  Patients with systemic lupus erythematosus, myositis, rheumatoid arthritis and scleroderma share activation of a common type I interferon pathway , 2011, Annals of the rheumatic diseases.

[29]  B. Ryffel,et al.  IFN-γ Receptor Deletion Prevents Autoantibody Production and Glomerulonephritis in Lupus-Prone (NZB × NZW)F1 Mice , 1998, The Journal of Immunology.

[30]  G. Dougan,et al.  Host Responses to Melioidosis and Tuberculosis Are Both Dominated by Interferon-Mediated Signaling , 2013, PloS one.

[31]  V. Pascual,et al.  Transcriptional Blood Signatures Distinguish Pulmonary Tuberculosis, Pulmonary Sarcoidosis, Pneumonias and Lung Cancers , 2013, PloS one.

[32]  M. Crow.  Type I interferon and autoimmune disease. , 2003, Autoimmunity.

[33]  W. White,et al.  A randomized, double-blind, placebo-controlled, phase I study of MEDI-545, an anti-interferon-alfa monoclonal antibody, in subjects with chronic psoriasis. , 2010, Journal of the American Academy of Dermatology.

[34]  Kenneth G. C. Smith,et al.  Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis , 2009, Annals of the rheumatic diseases.

[35]  M. Hochberg,et al.  Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. , 1997, Arthritis and rheumatism.

[36]  Virginia Pascual,et al.  A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. , 2008, Immunity.

[37]  M. Crow.  IntroductionType I Interferon and Autoimmune Disease , 2003 .

[38]  M. David,et al.  Immunomodulatory functions of type I interferons , 2012, Nature Reviews Immunology.

[39]  Mimi Y. Kim,et al.  Combined oral contraceptives in women with systemic lupus erythematosus. , 2005, The New England journal of medicine.

[40]  P. Gregersen,et al.  Interferon-regulated chemokines as biomarkers of systemic lupus erythematosus disease activity: a validation study. , 2009, Arthritis and rheumatism.

[41]  V. Pascual,et al.  Current perspectives on systems immunology approaches to rheumatic diseases. , 2013, Arthritis and rheumatism.

[42]  L. Rönnblom,et al.  The interferon signature in autoimmune diseases , 2013, Current opinion in rheumatology.

[43]  M. Peterson,et al.  Activation of the interferon-alpha pathway identifies a subgroup of systemic lupus erythematosus patients with distinct serologic features and active disease. , 2005, Arthritis and rheumatism.

[44]  Simon Yu,et al.  INTERFEROME v2.0: an updated database of annotated interferon-regulated genes , 2012, Nucleic Acids Res..

[45]  K. Kalunian,et al.  Sifalimumab, a Human Anti–Interferon-α Monoclonal Antibody, in Systemic Lupus Erythematosus: A Phase I Randomized, Controlled, Dose-Escalation Study , 2013, Arthritis and rheumatism.

[46]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[47]  D. Levy,et al.  Functional Crosstalk between Type I and II Interferon through the Regulated Expression of STAT1 , 2010, PLoS biology.

[48]  N. Kamatani,et al.  Excessive Production of IFN-γ in Patients with Systemic Lupus Erythematosus and Its Contribution to Induction of B Lymphocyte Stimulator/B Cell-Activating Factor/TNF Ligand Superfamily-13B1 , 2008, The Journal of Immunology.

[49]  G. Cheng,et al.  Systematic identification of type I and type II interferon-induced antiviral factors , 2012, Proceedings of the National Academy of Sciences.

[50]  J. Moslehi,et al.  Roles of interferon-gamma and interleukin-4 in murine lupus. , 1997, The Journal of clinical investigation.

[51]  J. Moslehi,et al.  Roles of Interferon-g and Interleukin-4 in Murine Lupus , 2013 .

[52]  B. Jallal,et al.  Biomarkers for systemic lupus erythematosus , 2012, International journal of rheumatic diseases.

[53]  G. Karypis,et al.  Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Kevin A. Robertson,et al.  Reversible Inhibition of Murine Cytomegalovirus Replication by Gamma Interferon (IFN-γ) in Primary Macrophages Involves a Primed Type I IFN-Signaling Subnetwork for Full Establishment of an Immediate-Early Antiviral State , 2011, Journal of Virology.

[55]  Weida Tong,et al.  Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells , 2011, BMC medicine.