Pathways Activated during Human Asthma Exacerbation as Revealed by Gene Expression Patterns in Blood

Background Asthma exacerbations remain a major unmet clinical need. The difficulty in obtaining airway tissue and bronchoalveolar lavage samples during exacerbations has greatly hampered study of naturally occurring exacerbations. This study was conducted to determine if mRNA profiling of peripheral blood mononuclear cells (PBMCs) could provide information on the systemic molecular pathways involved during asthma exacerbations. Methodology/Principal Findings Over the course of one year, gene expression levels during stable asthma, exacerbation, and two weeks after an exacerbation were compared using oligonucleotide arrays. For each of 118 subjects who experienced at least one asthma exacerbation, the gene expression patterns in a sample of peripheral blood mononuclear cells collected during an exacerbation episode were compared to patterns observed in multiple samples from the same subject collected during quiescent asthma. Analysis of covariance identified genes whose levels of expression changed during exacerbations and returned to quiescent levels by two weeks. Heterogeneity among visits in expression profiles was examined using K-means clustering. Three distinct exacerbation-associated gene expression signatures were identified. One signature indicated that, even among patients without symptoms of respiratory infection, genes of innate immunity were activated. Antigen-independent T cell activation mediated by IL15 was also indicated by this signature. A second signature revealed strong evidence of lymphocyte activation through antigen receptors and subsequent downstream events of adaptive immunity. The number of genes identified in the third signature was too few to draw conclusions on the mechanisms driving those exacerbations. Conclusions/Significance This study has shown that analysis of PBMCs reveals systemic changes accompanying asthma exacerbation and has laid the foundation for future comparative studies using PBMCs.

[1]  F. Finkelman,et al.  Advances in mechanisms of asthma, allergy, and immunology in 2010. , 2011, The Journal of allergy and clinical immunology.

[2]  S. Wenzel.  Eosinophils in asthma--closing the loop or opening the door? , 2009, The New England journal of medicine.

[3]  P. N. Souëf.  Gene-environmental interaction in the development of atopic asthma: new developments. , 2009 .

[4]  H. Hammad,et al.  House dust mite allergen induces asthma via Toll-like receptor 4 triggering of airway structural cells , 2009, Nature Medicine.

[5]  D. Broide,et al.  Advances in mechanisms of asthma, allergy, and immunology in 2008. , 2009, The Journal of allergy and clinical immunology.

[6]  Florence Demenais,et al.  CD14 and toll-like receptor gene polymorphisms, country living, and asthma in adults. , 2009, American journal of respiratory and critical care medicine.

[7]  U. Bjornsdottir,et al.  Biological Mechanism Associated with Asthma Exacerbation Attack as Revealed By Gene Expression Patterns of Peripheral Blood Mononuclear Cells , 2009 .

[8]  T. Arinami,et al.  Expression profiling of genes related to asthma exacerbations 1 2 Condensed title : Asthma exacerbation and Microarray 3 4 , 2010 .

[9]  Gordon K. Smyth,et al.  Testing significance relative to a fold-change threshold is a TREAT , 2009, Bioinform..

[10]  R. Hegde,et al.  Allergenicity resulting from functional mimicry of a Toll-like receptor complex protein , 2008, Nature.

[11]  Yusuke Nakamura,et al.  Host molecular defense mechanisms against Chlamydophila pneumoniae and genetic studies of immune-response-related genes in asthma. , 2009, Recent patents on inflammation & allergy drug discovery.

[12]  Jodie L Simpson,et al.  Innate immunity in asthma. , 2008, Paediatric respiratory reviews.

[13]  S. Johnston,et al.  Etiology of asthma exacerbations. , 2008, The Journal of allergy and clinical immunology.

[14]  P. Burgel,et al.  Epidermal growth factor receptor-mediated innate immune responses and their roles in airway diseases , 2008, European Respiratory Journal.

[15]  J. D. Clark,et al.  In vitro allergen challenge of peripheral blood induces differential gene expression in mononuclear cells of asthmatic patients: inhibition of cytosolic phospholipase A2α overcomes the asthma-associated response , 2008, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[16]  T. Seemungal,et al.  Recent advances in exacerbations of asthma , 2008, Thorax.

[17]  Mike Thomas,et al.  Cluster analysis and clinical asthma phenotypes. , 2008, American journal of respiratory and critical care medicine.

[18]  W. Busse,et al.  The presence of rhinovirus in lower airways of patients with bronchial asthma. , 2008, American journal of respiratory and critical care medicine.

[19]  T. Nakayama,et al.  Toll-like receptors in the respiratory system: Their roles in inflammation , 2008, Current allergy and asthma reports.

[20]  P. Casán,et al.  Anti-inflammatory effects of high-dose inhaled fluticasone versus oral prednisone in asthma exacerbations , 2007, European Respiratory Journal.

[21]  E. R. Sutherland,et al.  Asthma and atypical bacterial infection. , 2007, Chest.

[22]  I. Adcock,et al.  Role of TLR2, TLR4, and MyD88 in murine ozone-induced airway hyperresponsiveness and neutrophilia. , 2007, Journal of applied physiology.

[23]  Neil W Johnston,et al.  Understanding the September asthma epidemic , 2007, Journal of Allergy and Clinical Immunology.

[24]  P. Barnes,et al.  Scientific rationale for using a single inhaler for asthma control , 2007, European Respiratory Journal.

[25]  K. Marquette,et al.  Efficacy of IL-13 neutralization in a sheep model of experimental asthma. , 2007, American journal of respiratory cell and molecular biology.

[26]  Jie Zhu,et al.  Bronchial mucosal inflammation and upregulation of CXC chemoattractants and receptors in severe exacerbations of asthma , 2007, Thorax.

[27]  J. Sprent,et al.  Cytokines and T-cell homeostasis. , 2003, Current opinion in immunology.

[28]  Y. Ko,et al.  Association of interferon‐γ and interferon regulatory factor 1 polymorphisms with asthma in a family‐based association study in Taiwan , 2006, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[29]  K. Deichmann,et al.  Confirmation of association of IL‐15 with pediatric asthma and comparison of different controls , 2006, Allergy.

[30]  S. Holgate,et al.  The role of Toll-like receptors and related receptors of the innate immune system in asthma , 2006, Current opinion in allergy and clinical immunology.

[31]  S. Bowler,et al.  Doubling daily inhaled corticosteroid dose is ineffective in mild to moderately severe attacks of asthma in adults , 2005, Internal medicine journal.

[32]  N. Papadopoulos,et al.  Rhinovirus viremia in children with respiratory infections. , 2005, American journal of respiratory and critical care medicine.

[33]  Gordon K Smyth,et al.  Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  R. Devlin,et al.  TLR-2 is involved in airway epithelial cell response to air pollution particles. , 2005, Toxicology and applied pharmacology.

[35]  S. Akira,et al.  Tamm-Horsfall glycoprotein links innate immune cell activation with adaptive immunity via a Toll-like receptor-4-dependent mechanism. , 2005, The Journal of clinical investigation.

[36]  M. Wills-Karp,et al.  Interleukin‐13 in asthma pathogenesis , 2004, Immunological reviews.

[37]  Jyotsna Batra,et al.  Suggestive evidence of association of C-159T functional polymorphism of the CD14 gene with atopic asthma in northern and northwestern Indian populations , 2004, Immunogenetics.

[38]  E. Silverman,et al.  TOLL-like receptor 10 genetic variation is associated with asthma in two independent samples. , 2004, American journal of respiratory and critical care medicine.

[39]  P. Söderkvist,et al.  A TLR4 polymorphism is associated with asthma and reduced lipopolysaccharide-induced interleukin-12(p70) responses in Swedish children. , 2004, The Journal of allergy and clinical immunology.

[40]  K. Strauch,et al.  Multilocus haplotype analyses reveal association between 5 novel IL-15 polymorphisms and asthma. , 2004, The Journal of allergy and clinical immunology.

[41]  Marsha Wills Karp.  Interleukin-13 in asthma pathogenesis , 2004 .

[42]  D. Nowak,et al.  Toll-like receptor 2 as a major gene for asthma in children of European farmers. , 2004, The Journal of allergy and clinical immunology.

[43]  A. Tattersfield,et al.  Doubling the dose of inhaled corticosteroid to prevent asthma exacerbations: randomised controlled trial , 2004, The Lancet.

[44]  T. Wynn.  IL-13 effector functions. , 2003, Annual review of immunology.

[45]  J. Bernstein,et al.  The -159 C-->T polymorphism of CD14 is associated with nonatopic asthma and food allergy. , 2003, The Journal of allergy and clinical immunology.

[46]  M. Watson,et al.  Expression , 2019, The Oxford Handbook of Western Music and Philosophy.

[47]  L. Kwak,et al.  Toll-Like Receptor 4-Dependent Activation of Dendritic Cells by β-Defensin 2 , 2002, Science.

[48]  Richard M. Simon,et al.  Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data , 2002, Bioinform..

[49]  D. Golenbock,et al.  Cutting Edge: The Immunostimulatory Activity of the Lung Surfactant Protein-A Involves Toll-Like Receptor 41 , 2002, The Journal of Immunology.

[50]  G. Freeman,et al.  Critical role of CD81 in cognate T-B cell interactions leading to Th2 responses. , 2002, International immunology.

[51]  Michael Rehli,et al.  Novel Signal Transduction Pathway Utilized by Extracellular HSP70 , 2002, The Journal of Biological Chemistry.

[52]  Y. Li,et al.  IL-15 mimics T cell receptor crosslinking in the induction of cellular proliferation, gene expression, and cytotoxicity in CD8+ memory T cells , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[53]  L. Kwak,et al.  Toll-like receptor 4-dependent activation of dendritic cells by beta-defensin 2. , 2002, Science.

[54]  C. Janeway,et al.  Innate immune recognition. , 2002, Annual review of immunology.

[55]  W. Hancock,et al.  Fibrinogen Stimulates Macrophage Chemokine Secretion Through Toll-Like Receptor 41 , 2001, The Journal of Immunology.

[56]  D. Milton,et al.  Endotoxin-stimulated innate immunity: A contributing factor for asthma. , 2001, The Journal of allergy and clinical immunology.

[57]  Pierre Baldi,et al.  A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes , 2001, Bioinform..

[58]  Jerome F. Strauss,et al.  The Extra Domain A of Fibronectin Activates Toll-like Receptor 4* , 2001, The Journal of Biological Chemistry.

[59]  K. Ihara,et al.  Association of IFN-γ and IFN regulatory factor 1 polymorphisms with childhood atopic asthma , 2001 .

[60]  D. Postma,et al.  Association of a promoter polymorphism of the CD14 gene and atopy. , 2001, American journal of respiratory and critical care medicine.

[61]  K. Ihara,et al.  Association of IFN-gamma and IFN regulatory factor 1 polymorphisms with childhood atopic asthma. , 2001, The Journal of allergy and clinical immunology.

[62]  D. Kasprowicz,et al.  Stimulation of the B Cell Receptor, CD86 (B7-2), and the β2-Adrenergic Receptor Intrinsically Modulates the Level of IgG1 and IgE Produced per B Cell1 , 2000, The Journal of Immunology.

[63]  Lack of Induction by Rhinoviruses of Systemic Type I Interferon Production or Enhanced MxA Protein Expression During the Common Cold , 1999, European Journal of Clinical Microbiology and Infectious Diseases.

[64]  D D Donaldson,et al.  Interleukin-13: central mediator of allergic asthma , 1998 .

[65]  J. Sprent,et al.  Potent and selective stimulation of memory-phenotype CD8+ T cells in vivo by IL-15. , 1998, Immunity.

[66]  T. Mak,et al.  The Transcription Factor Interferon Regulatory Factor 1 (IRF-1) Is Important during the Maturation of Natural Killer 1.1+ T Cell Receptor–α/β+ (NK1+ T) Cells, Natural Killer Cells, and Intestinal Intraepithelial T Cells , 1998, The Journal of experimental medicine.

[67]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[68]  Alfred O. Berg,et al.  Clinical Guidelines And Primary Care Guidelines For The Diagnosis And Management Of Asthma , 2012 .

[69]  M. Lara,et al.  Guidelines For The Diagnosis And Management Of Asthma , 1992, The Journal of the American Board of Family Medicine.

[70]  P. Rousseeuw.  Silhouettes: a graphical aid to the interpretation and validation of cluster analysis , 1987 .

[71]  J. A. Hartigan,et al.  A k-means clustering algorithm , 1979 .

[72]  Maurice K. Wong,et al.  Algorithm AS136: A k-means clustering algorithm. , 1979 .