dsRNA-induced changes in gene expression profiles of primary nasal and bronchial epithelial cells from patients with asthma, rhinitis and controls

Respiratory Research

Cornelis M van Drunen²  Peter J Sterk³  Elisabeth H Bel³  Wytske J Fokkens²  Silvia Luiten²  Aeilko H Zwinderman¹  Ariane H Wagener³ 

[1] Department of Clinical Epidemiology, Biostatistics & Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands;Department of Otorhinolaryngology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands;Department of Respiratory Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands

关键词: dsRNA;    Gene expression;    Epithelium;    Rhinitis;    Asthma;   

Others  :  790747
DOI  :  10.1186/1465-9921-15-9

 received in 2013-10-10, accepted in 2014-01-17,  发布年份 2014

【 摘 要 】

Background

Rhinovirus infections are the most common cause of asthma exacerbations. The complex responses by airway epithelium to rhinovirus can be captured by gene expression profiling. We hypothesized that: a) upper and lower airway epithelium exhibit differential responses to double-stranded RNA (dsRNA), and b) that this is modulated by the presence of asthma and allergic rhinitis.

Objectives

Identification of dsRNA-induced gene expression profiles of primary nasal and bronchial epithelial cells from the same individuals and examining the impact of allergic rhinitis with and without concomitant allergic asthma on expression profiles.

Methods

This study had a cross-sectional design including 18 subjects: 6 patients with allergic asthma with concomitant rhinitis, 6 patients with allergic rhinitis, and 6 healthy controls. Comparing 6 subjects per group, the estimated false discovery rate was approximately 5%. RNA was extracted from isolated and cultured primary epithelial cells from nasal biopsies and bronchial brushings stimulated with dsRNA (poly(I:C)), and analyzed by microarray (Affymetrix U133+ PM Genechip Array). Data were analysed using R and the Bioconductor Limma package. Overrepresentation of gene ontology groups were captured by GeneSpring GX12.

Results

In total, 17 subjects completed the study successfully (6 allergic asthma with rhinitis, 5 allergic rhinitis, 6 healthy controls). dsRNA-stimulated upper and lower airway epithelium from asthma patients demonstrated significantly fewer induced genes, exhibiting reduced down-regulation of mitochondrial genes. The majority of genes related to viral responses appeared to be similarly induced in upper and lower airways in all groups. However, the induction of several interferon-related genes (IRF3, IFNAR1, IFNB1, IFNGR1, IL28B) was impaired in patients with asthma.

Conclusions

dsRNA differentially changes transcriptional profiles of primary nasal and bronchial epithelial cells from patients with allergic rhinitis with or without asthma and controls. Our data suggest that respiratory viruses affect mitochondrial genes, and we identified disease-specific genes that provide potential targets for drug development.

【 授权许可】

   
2014 Wagener et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Busse WW, Lemanske RF Jr, Gern JE: Role of viral respiratory infections in asthma and asthma exacerbations. Lancet 2010, 376:826-834.
• [2]Corne JM, Marshall C, Smith S, Schreiber J, Sanderson G, Holgate ST, Johnston SL: Frequency, severity, and duration of rhinovirus infections in asthmatic and non-asthmatic individuals: a longitudinal cohort study. Lancet 2002, 359:831-834.
• [3]Sulakvelidze I, Inman MD, Rerecich T, O’Byrne PM: Increases in airway eosinophils and interleukin-5 with minimal bronchoconstriction during repeated low-dose allergen challenge in atopic asthmatics. Eur Respir J 1998, 11:821-827.
• [4]Green RM, Custovic A, Sanderson G, Hunter J, Johnston SL, Woodcock A: Synergism between allergens and viruses and risk of hospital admission with asthma: case–control study. BMJ 2002, 324:763.
• [5]Cruz AA, Popov T, Pawankar R, Annesi-Maesano I, Fokkens W, Kemp J, Ohta K, Price D, Bousquet J: Common characteristics of upper and lower airways in rhinitis and asthma: ARIA update, in collaboration with GA(2)LEN. Allergy 2007, 62(Suppl 84):1-41.
• [6]Lopez-Souza N, Favoreto S, Wong H, Ward T, Yagi S, Schnurr D, Finkbeiner WE, Dolganov GM, Widdicombe JH, Boushey HA, Avila PC: In vitro susceptibility to rhinovirus infection is greater for bronchial than for nasal airway epithelial cells in human subjects. J Allergy Clin Immunol 2009, 123:1384-1390.
• [7]Bochkov YA, Hanson KM, Keles S, Brockman-Schneider RA, Jarjour NN, Gern JE: Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma. Mucosal Immunol 2010, 3:69-80.
• [8]Contoli M, Message SD, Laza-Stanca V, Edwards MR, Wark PA, Bartlett NW, Kebadze T, Mallia P, Stanciu LA, Parker HL, Slater L, Lewis-Antes A, Kon OM, Holgate ST, Davies DE, Kotenko SV, Papi A, Johnston SL: Role of deficient type III interferon-lambda production in asthma exacerbations. Nat Med 2006, 12:1023-1026.
• [9]Wark PA, Johnston SL, Bucchieri F, Powell R, Puddicombe S, Laza-Stanca V, Holgate ST, Davies DE: Asthmatic bronchial epithelial cells have a deficient innate immune response to infection with rhinovirus. J Exp Med 2005, 201:937-947.
• [10]Wang Q, Nagarkar DR, Bowman ER, Schneider D, Gosangi B, Lei J, Zhao Y, McHenry CL, Burgens RV, Miller DJ, Sajjan U, Hershenson MB: Role of double-stranded RNA pattern recognition receptors in rhinovirus-induced airway epithelial cell responses. J Immunol 2009, 183:6989-6997.
• [11]Wagener AH, Zwinderman AH, Luiten S, Fokkens WJ, Bel EH, Sterk PJ, van Drunen CM: The impact of allergic rhinitis and asthma on human nasal and bronchial epithelial gene expression. PLoS One 2013, 8:e80257.
• [12]From the Global Strategy for Asthma Management and Prevention, Global Initiative for Asthma (GINA). 2012. http://www.ginasthma.org webcite
• [13]Crapo RO, Casaburi R, Coates AL, Enright PL, Hankinson JL, Irvin CG, MacIntyre NR, McKay RT, Wanger JS, Anderson SD, Cockcroft DW, Fish JE, Sterk PJ: Guidelines for methacholine and exercise challenge testing-1999. This official statement of the American Thoracic Society was adopted by the ATS Board of Directors, July 1999. Am J Respir Crit Care Med 2000, 161:309-329.
• [14]Bousquet J, Khaltaev N, Cruz AA, Denburg J, Fokkens WJ, Togias A, Zuberbier T, Baena-Cagnani CE, Canonica GW, van Weel C, et al.: Allergic Rhinitis and its Impact on Asthma (ARIA) 2008 update (in collaboration with the World Health Organization, GA(2)LEN and AllerGen). Allergy 2008, 63(Suppl 86):8-160.
• [15]Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:3.
• [16]Hochberg Y, Benjamini Y: More powerful procedures for multiple significance testing. Stat Med 1990, 9:811-818.
• [17]Benjamini Y, Yekutieli D: The control of the false discovery rate in multiple testing under dependency. Ann Statist 2001, 29:1165-1188.
• [18]Ferreira JA, Zwinderman A: Approximate sample size calculations with microarray data: an illustration. Stat Appl Genet Mol Biol 2006, 5:Article 25.
• [19]Vroling AB, Jonker MJ, Luiten S, Breit TM, Fokkens WJ, van Drunen CM: Primary nasal epithelium exposed to house dust mite extract shows activated expression in allergic individuals. Am J Respir Cell Mol Biol 2008, 38:293-299.
• [20]Woodruff PG, Boushey HA, Dolganov GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu SS, Dao-Pick TP, Pantoja C, Erle DJ, Yamamoto KR, Fahy JV: Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc Natl Acad Sci U S A 2007, 104:15858-15863.
• [21]Baines KJ, Hsu AC, Tooze M, Gunawardhana LP, Gibson PG, Wark PA: Novel immune genes associated with excessive inflammatory and antiviral responses to rhinovirus in COPD. Respir Res 2013, 14:15. BioMed Central Full Text
• [22]Khaitov MR, Laza-Stanca V, Edwards MR, Walton RP, Rohde G, Contoli M, Papi A, Stanciu LA, Kotenko SV, Johnston SL: Respiratory virus induction of alpha-, beta- and lambda-interferons in bronchial epithelial cells and peripheral blood mononuclear cells. Allergy 2009, 64:375-388.
• [23]Calven J, Yudina Y, Uller L: Rhinovirus and dsRNA induce RIG-I-Like receptors and expression of Interferon beta and lambda1 in human bronchial smooth muscle cells. PLoS One 2013, 8:e62718.
• [24]Aguilera-Aguirre L, Bacsi A, Saavedra-Molina A, Kurosky A, Sur S, Boldogh I: Mitochondrial dysfunction increases allergic airway inflammation. J Immunol 2009, 183:5379-5387.
• [25]Bowler RP: Oxidative stress in the pathogenesis of asthma. Curr Allergy Asthma Rep 2004, 4:116-122.
• [26]Jamaluddin M, Tian B, Boldogh I, Garofalo RP, Brasier AR: Respiratory syncytial virus infection induces a reactive oxygen species-MSK1-phospho-Ser-276 RelA pathway required for cytokine expression. J Virol 2009, 83:10605-10615.
• [27]El-Bacha T, Da Poian AT: Virus-induced Changes in mitochondrial bioenergetics as potential targets for therapy. Int J Biochem Cell Biol 2013, 45:41-46.
• [28]Kaarbø M, Ager-Wick E, Osenbroch PØ, Kilander A, Skinnes R, Müller F, Eide L: Human Cytomegalovirus infection increases mitochondrial biogenesis. Mitochondrion 2011, 11:935-945.
• [29]Firat E, Saveanu L, Aichele P, Staeheli P, Huai J, Gaedicke S, Nil A, Besin G, Kanzler B, van Endert P, Niedermann G: The role of endoplasmic reticulum-associated aminopeptidase 1 in immunity to infection and in cross-presentation. J Immunol 2007, 178:2241-2248.
• [30]Zhou D, Li P, Lin Y, Lott JM, Hislop AD, Canaday DH, Brutkiewicz RR, Blum JS: Lamp-2a facilitates MHC class II presentation of cytoplasmic antigens. Immunity 2005, 22:571-581.
• [31]Lieden A, Ekelund E, Kuo IC, Kockum I, Huang CH, Mallbris L, Lee SP, Seng LK, Chin GY, Wahlgren CF, Palmer CN, Bjorksten B, Stahle M, Nordenskjold M, Bradley M, Chua KY, D’Amato M: Cornulin, a marker of late epidermal differentiation, is down-regulated in eczema. Allergy 2009, 64:304-311.
• [32]Molfetta R, Belleudi F, Peruzzi G, Morrone S, Leone L, Dikic I, Piccoli M, Frati L, Torrisi MR, Santoni A, Paolini R: CIN85 regulates the ligand-dependent endocytosis of the IgE receptor: a new molecular mechanism to dampen mast cell function. J Immunol 2005, 175:4208-4216.
• [33]Sandilands A, Smith FJ, Irvine AD, McLean WH: Filaggrin’s fuller figure: a glimpse into the genetic architecture of atopic dermatitis. J Invest Dermatol 2007, 127:1282-1284.
• [34]Wolf R, Lewerenz V, Buchau AS, Walz M, Ruzicka T: Human S100A15 splice variants are differentially expressed in inflammatory skin diseases and regulated through Th1 cytokines and calcium. Exp Dermatol 2007, 16:685-691.
• [35]Jiang H, Rao K, Halayko AJ, Liu X, Stephens NL: Ragweed sensitization-induced increase of myosin light chain kinase content in canine airway smooth muscle. Am J Respir Cell Mol Biol 1992, 7:567-573.
• [36]Rosendahl A, Pardali E, Speletas M, Ten DP, Heldin CH, Sideras P: Activation of bone morphogenetic protein/Smad signaling in bronchial epithelial cells during airway inflammation. Am J Respir Cell Mol Biol 2002, 27:160-169.
• [37]Taube C, Thurman JM, Takeda K, Joetham A, Miyahara N, Carroll MC, Dakhama A, Giclas PC, Holers VM, Gelfand EW: Factor B of the alternative complement pathway regulates development of airway hyperresponsiveness and inflammation. Proc Natl Acad Sci U S A 2006, 103:8084-8089.
• [38]Ungvari I, Hullam G, Antal P, Kiszel PS, Gezsi A, Hadadi E, Virag V, Hajos G, Millinghoffer A, Nagy A, Kiss A, Semsei AF, Temesi G, Melegh B, Kisfali P, Szell M, Bikov A, Galffy G, Tamasi L, Falus A, Szalai C: Evaluation of a partial genome screening of two asthma susceptibility regions using bayesian network based bayesian multilevel analysis of relevance. PLoS One 2012, 7:e33573.
• [39]Chhin B, Pham JT, El ZL, Kaiser K, Merrot O, Bouvagnet P: Identification of transcripts overexpressed during airway epithelium differentiation. Eur Respir J 2008, 32:121-128.
• [40]Inglis PN, Boroevich KA, Leroux MR: Piecing together a ciliome. Trends Genet 2006, 22:491-500.
• [41]Lai CK, Gupta N, Wen X, Rangell L, Chih B, Peterson AS, Bazan JF, Li L, Scales SJ: Functional characterization of putative cilia genes by high-content analysis. Mol Biol Cell 2011, 22:1104-1119.
• [42]Knowles MR, Boucher RC: Mucus clearance as a primary innate defense mechanism for mammalian airways. J Clin Invest 2002, 109:571-577.
• [43]Thomas B, Rutman A, Hirst RA, Haldar P, Wardlaw AJ, Bankart J, Brightling CE, O’Callaghan C: Ciliary dysfunction and ultrastructural abnormalities are features of severe asthma. J Allergy Clin Immunol 2010, 126:722-729.
• [44]Kawai T, Akira S: Innate immune recognition of viral infection. Nat Immunol 2006, 7:131-137.
• [45]Sha Q, Truong-Tran AQ, Plitt JR, Beck LA, Schleimer RP: Activation of airway epithelial cells by toll-like receptor agonists. Am J Respir Cell Mol Biol 2004, 31:358-364.
• [46]Bousquet J, Schunemann HJ, Samolinski B, Demoly P, Baena-Cagnani CE, Bachert C, Bonini S, Boulet LP, Bousquet PJ, Brozek JL, et al.: Allergic Rhinitis and its Impact on Asthma (ARIA): achievements in 10 years and future needs. J Allergy Clin Immunol 2012, 130:1049-1062.