title: Combining gene expression microarray- and cluster analysis with sequence-based predictions to identify regulators of IL-13 in allergy.
abstract: The Th2 cytokine IL-13 plays a key role in allergy, by regulating IgE, airway hyper secretion, eosinophils and mast cells. In this study, we aimed to identify novel transcription factors (TFs) that potentially regulated IL-13. We analyzed Th2 polarized naïve T cells from four different blood donors with gene expression microarrays to find clusters of genes that were correlated or anti-correlated with IL13. These clusters were further filtered, by selecting genes that were functionally related. In these clusters, we identified three transcription factors (TFs) that were predicted to regulate the expression of IL13, namely CEBPB, E2F6 and AHR. siRNA mediated knockdowns of these TFs in naïve polarized T cells showed significant increases of IL13, following knockdown of CEBPB and E2F6, but not AHR. This suggested an inhibitory role of CEBPB and E2F6 in the regulation of IL13 and allergy. This was supported by analysis of E2F6, but not CEBPB, in allergen-challenged CD4+ T cells from six allergic patients and six healthy controls, which showed decreased expression of E2F6 in patients. In summary, our findings indicate an inhibitory role of E2F6 in the regulation of IL-13 and allergy. The analytical approach may be generally applicable to elucidate the complex regulatory patterns in Th2 cell polarization and allergy.
authors.affiliation: The Center for Individualized Medication, Linköping University, Linköping, Sweden.
authors.forename: Sören
authors.initials: S
authors.lastname: Bruhn
authors.forename: Mark
authors.initials: M
authors.lastname: Katzenellenbogen
authors.forename: Mika
authors.initials: M
authors.lastname: Gustafsson
authors.forename: Andrea
authors.initials: A
authors.lastname: Krönke
authors.forename: Birte
authors.initials: B
authors.lastname: Sönnichsen
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
authors.forename: Mikael
authors.initials: M
authors.lastname: Benson
mesh_terms: D000328:Adult; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D022782:CCAAT-Enhancer-Binding Protein-beta / Q000235:genetics; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology* / Q000378:metabolism; D016000:Cluster Analysis; D050701:E2F6 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D018793:Interleukin-13 / Q000378:metabolism*; D015848:Interleukin-5 / Q000032:analysis; D008213:Lymphocyte Activation; D008297:Male; D034622:RNA Interference; D034741:RNA, Small Interfering; D018336:Receptors, Aryl Hydrocarbon / Q000235:genetics; D006255:Rhinitis, Allergic, Seasonal / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D022782:CCAAT-Enhancer-Binding Protein-beta; D050701:E2F6 Transcription Factor; D018793:Interleukin-13; D015848:Interleukin-5; D034741:RNA, Small Interfering; D018336:Receptors, Aryl Hydrocarbon; D014157:Transcription Factors; C111235:AHR protein, human; C545012:CEBPB protein, human; C491744:E2F6 protein, human