Background The characterization of miRNAs and their target mRNAs involved in regulation of the immune process is an area of intense research and relatively little is known governing these processes in allergic inflammation. Here we present novel findings defining the miRNA and mRNA transcriptome in eosinophilic esophagitis (EoE), an increasing recognized allergic disorder. Methods Esophageal epithelial miRNA and mRNA from five paired biopsies pre- and post-treatment with glucocorticosteroids were profiled using Taqman and Affymetrix arrays. Validation was performed on additional paired biopsies, untreated EoE specimens and normal controls. Differentially regulated miRNAs and mRNAs were generated, within which miRNA-mRNA target pairs with high predicted confidence were identified. Results Compared to the post-glucocorticoid treated esophageal mucosa, of all the 377 miRNA sequences examined, 32 miRNAs were significantly upregulated and four downregulated in the pre-treated biopsies. MiR-214 was the most upregulated (150 fold) and miR-146b-5b, 146a, 145, 142-3p and 21 were upregulated by at least 10 fold. Out of 12 miRNAs chosen for validation by qRT-PCR, five (miR-214, 146b-5p, 146a, 142-3p and 21) were confirmed and 11 shared the same trend. When the expression of the 12 miRNAs in the EoE mucosa was compared to unrelated normal mucosa, six (miR-214, 146b-5p, 146a, 21, 203, and 489) showed similar significant changes as in the paired samples and 10 of them shared the same trend. In the same five pairs of samples used to profile miRNA, 311 mRNAs were down-regulated and 35 were up-regulated in pre-treated EoE mucosa. Among them, 164 mRNAs were identified as potential targets of differentially regulated miRNAs. Further analysis revealed that immune-related genes, targeted and non-targeted by miRNAs, were among the most important genes involved in the pathogenesis of EoE. Conclusions Our findings add to the accumulating body of data defining a regulatory role for miRNA in immune and allergic processes.
References
[1]
Liacouras CA, Furuta GT, Hirano I, Atkins D, Attwood SE, et al. (2011) Eosinophilic esophagitis: updated consensus recommendations for children and adults. J Allergy Clin Immunol 128: 3–20.
[2]
Abonia JP, Rothenberg ME (2012) Eosinophilic esophagitis: rapidly advancing insights. Annu Rev Med 63: 421–434.
[3]
Blanchard C, Wang N, Stringer KF, Mishra A, Fulkerson PC, et al. (2006) Eotaxin-3 and a uniquely conserved gene-expression profile in eosinophilic esophagitis. J Clin Invest 116: 536–547.
[4]
Blanchard C, Mingler MK, Vicario M, Abonia JP, Wu YY, et al. (2007) IL-13 involvement in eosinophilic esophagitis: transcriptome analysis and reversibility with glucosteroids. J Allergy Clin Immunol 120: 1292–1300.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for micrRNA genomics. Nucleic Acids Res 36: D154–158.
[7]
O’Connell RM, Rao DS, Baltimore D (2012) MicroRNA regulation of inflammatory responses. Annu Rev Immunol 30: 295–312.
[8]
Mattes J, Collison A, Plank M, Phipps S, Foster PS (2009) Antagonism of microRNA-126 suppresses the effector function of TH2 cells and the development of allergic airways disease. Proc Natl Acad Sci USA 106: 18704–18709.
[9]
Lu TX, Munitz A, Rothenberg ME (2009) MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression. J Immunol 182: 4994–5002.
[10]
Collison A, Herbert C, Siegle JS, Mattes J, Foster PS, et al. (2011) Altered expression of microRNA in the airway wall in chronic asthma: miR-126 as a potential therapeutic target. BMC Pulm Med 11: 29.
[11]
Collison A, Mattes J, Plank M, Foster PS (2011) Inhibition of house dust mite-induced allergic airways disease by antagonism of microRNA-145 is comparable to glucocorticoid treatment. J Allergy Clin Immunol 128: 160–167.
[12]
Garbacki N, Di Valentin E, Huynh-Thu VA, Geurts P, Irrthum A, et al. (2011) MicroRNAs profiling in murine models of acute and chronic asthma: A relationship with mRNAs targets. PloS ONE 6: e16509.
[13]
Lu TX, Sherrill JD, Wen T, Plassard AJ, Besse JA, et al. (2012) MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids and assessment as disease markers. J Allergy Clin Immunol 129: 1064–1075.
[14]
Resnick MB, Sabo E, Meitner PA, Kim SS, Cho Y, et al. (2006) Global analysis of the human gastric epithelial transcriptome altered by Helicobacter pylori eradication in vitro. Gut 55: 1717–1724.
[15]
Allantaz F, Cheng DT, Bergauer T, Ravindran P, Rossier MF, et al. (2012) Expression profiling of human immune cell subsets identifies miRNA-mRNA regulatory relationships correlated with cell type specific expression. PLoS ONE 7: 29979.
[16]
Mathé EA, Nguyen GH, Bowman ED, Zhao Y, Budhu A, et al. (2009) MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clin Cancer Res 15: 6192–6200.
[17]
Kan T, Meltzer SJ (2009) MicroRNAs in Barrett’s esophagus and esophageal adenocarcinoma. Curr Opin Pharmacol 9: 727–732.
[18]
Godwin JG, Ge X, Stephen K, Jurisch A, Tullius SG, et al. (2010) Identification of a microRNA signature of renal ischemia perfusion injury. Proc Natl Acad Sci USA 107: 14339–14344.
[19]
Denby L, Ramdas V, McBride MW, Wang J, Robinson H, et al. (2011) miR-21 and miR-214 are consistently modulated during renal injury in rodent models. Am J Pathol 179: 661–672.
[20]
Hackett TL, Warner SM, Stefanowicz D, Shaheen F, Pechkovsky DV, et al. (2009) Induction of epithelial-mesenchymal transition in primary airway epithelial cells from patients with asthma by transforming growth factor beta. Am J Respir Crit Care Med 180: 122–133.
[21]
Johnson JR, Roos A, Berg t, Nord M, Fuxe J (2011) Chronic respiratory aeroallergen exposure to mice induces epithelial-mesenchymal transition in the larger airways. PLoS One 6: e16175.
[22]
Straumann A, Spichtin HP, Grize L (2003) Natural history of primary eosinophilic esophagitis: a follow-up of 30 adult patients for up to 11.5 years. Gastroenterology 125: 1660–1669.
Chehade M, Sampson HA, Morotti RA, Magid MS (2007) Esophageal subepithelial fibrosis in children with eosinophilic esophagitis. J Pediatr Gastroenterol Nutr 45: 319–328.
[25]
Kagalwalla AF, Akhtar N, Woodruff SA, Rea B, Masterson JC, et al. (2012) Eosinophilic Esophagitis: Epithelial Mesenchymal Transition Contributes to Esophageal Remodeling and Reverses With Treatment. Journal of Allergy and Clinical Immunology 129: 1387–1396.
[26]
Hua Z, Chun W, Fang-Yuan C (2011) MicroRNA-146a and hemopoietic disorders. Int J Hematol 94: 224–229.
[27]
Li N, Xu X, Xiao B, Zhu ED, Li BS, et al. (2011) H. pylori related proinflammatory cytokines contribute to the induction of miR-146a in human gastric epithelial cells. Mol Biol Rep 39: 4655–4661.
[28]
Taganov KD, Boldin MP, Chang KJ, Baltimore D (2006) NF-kappa-B-dependent induction of microRNA miR-146, an inhibitor targeted to signalling proteins of innate immune responses. Proc Natl Acad Sci USA 103: 12481–12486.
[29]
Persad R, Huynh HQ, Hao L, Ha JR, Sergi C, et al. (2012) Angiogenic remodeling in pediatric eosinophilic esophagitis is associated with increased levels of VEGFA, angiogenin, IL-8 and activation of the TNF-a-NFkB pathway. J Pediatr Gastroenterol Nutr Feb 10 EPUB.
[30]
Gavett Sh, O’Hearn DJ, Huang SK, Finkelman FD, Wills-Karp M (1995) Interleukin 12 inhibits antigen induced airway hyperresponsiveness, inflammation, and Th2 cytokine expression in mice. J Exp Med 182: 1527–1536.
[31]
Liu G, Friggeri A, Yang Y, Milosevic J, Ding Q, et al. (2010) miR-21 mediated fibrogenic activation of pulmonary fibroblasts and lung fibrosis. J Exp Med 207: 1589–1597.
[32]
Zarjou A, Yang S, Abraham E, Agarwal A, Liu G (2011) Identification of a microRNA signature in renal fibrosis: role of miR-21. Am J Physiol Renal Physiol 301: 793–801.
[33]
Pieztsch J, Hoppmann S (2009) Human S100A12: a novel key player in inflammation? Amino Acids 36: 381–389.
[34]
Sato N, Hitomi J (2002) S100P expression in human esophageal epithelial cells: Human esophageal epithelial cells sequentially produce different S100 proteins in the process of differentiation. Anat Rec 267: 60–69.
[35]
Chu HW, Balzar S, Westcott JY, Trudeau JB, Sun Y, et al. (2002) Expression and activation of 15-lipoxygenase pathway in severe asthma: relationship to eosinophilic phenotype and collagen deposition. Clin Exp Allergy 32: 1558–1565.
[36]
Sigal E, Grunberger D, Cashman JR, Craik CS, Caughey GH, et al. (1988) Arachidonate 15-lipoxygenase from human eosinophil-enriched leukocytes: partial purification and properties. Biochem Biophys Res Commun 150: 376–383.
[37]
Nadel JA, Conrad DJ, Ueki IF, Schuster A, Sigal E (1991) Immunocytochemical localization of arachidonate 15-lipoxygenase in erythrocytes, leukocytes, and airway cells. J Clin Invest 87: 1139–1145.
[38]
Macmillan DK, Hill E, Sala A, Sigal E, Shuman T, et al. (1994) Eosinophil 15-lipoxygenase is a leukotriene A4 synthase. J Biol Chem 269: 26663–26668.
