Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing (original) (raw)
Sherrill JD, Rothenberg ME . Genetic dissection of eosinophilic esophagitis provides insight into disease pathogenesis and treatment strategies. J Allergy Clin Immunol 2011; 128: 23–32. ArticleCAS Google Scholar
Noel RJ, Putnam PE, Rothenberg ME . Eosinophilic esophagitis. N Engl J Med 2004; 351: 940–941. ArticleCAS Google Scholar
Noel RJ, Rothenberg ME . Eosinophilic esophagitis. Curr Opin Pediatr 2005; 17: 690–694. Article Google Scholar
Ronkainen J, Talley NJ, Aro P, Storskrubb T, Johansson SE, Lind T et al. Prevalence of oesophageal eosinophils and eosinophilic oesophagitis in adults: the population-based Kalixanda study. Gut 2007; 56: 615–620. Article Google Scholar
Blanchard C, Wang N, Stringer KF, Mishra A, Fulkerson PC, Abonia JP et al. Eotaxin-3 and a uniquely conserved gene-expression profile in eosinophilic esophagitis. J Clin Invest 2006; 116: 536–547. ArticleCAS Google Scholar
Blanchard C, Mingler MK, Vicario M, Abonia JP, Wu YY, Lu TX et al. IL-13 involvement in eosinophilic esophagitis: transcriptome analysis and reversibility with glucocorticoids. J Allergy Clin Immunol 2007; 120: 1292–1300. ArticleCAS Google Scholar
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y . RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008; 18: 1509–1517. ArticleCAS Google Scholar
Schultheis PJ, Clarke LL, Meneton P, Miller ML, Soleimani M, Gawenis LR et al. Renal and intestinal absorptive defects in mice lacking the NHE3 Na+/H+ exchanger. Nat Genet 1998; 19: 282–285. ArticleCAS Google Scholar
Guttman M, Rinn JL . Modular regulatory principles of large non-coding RNAs. Nature 2012; 482: 339–346. ArticleCAS Google Scholar
Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M et al. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res 2012; 22: 1006–1014. ArticleCAS Google Scholar
Lu TX, Sherrill JD, Wen T, Plassard AJ, Besse JA, Abonia JP et al. MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers. J Allergy Clin Immunol 2012; 129: 1064–75 e9. ArticleCAS Google Scholar
Lu TX, Lim EJ, Wen T, Plassard AJ, Hogan SP, Martin LJ et al. MiR-375 is downregulated in epithelial cells after IL-13 stimulation and regulates an IL-13-induced epithelial transcriptome. Mucosal Immunol 2012; 5: 388–396. ArticleCAS Google Scholar
Lu S, Mukkada VA, Mangray S, Cleveland K, Shillingford N, Schorl C et al. MicroRNA profiling in mucosal biopsies of eosinophilic esophagitis patients pre and post treatment with steroids and relationship with mRNA targets. PLoS ONE 2012; 7: e40676. ArticleCAS Google Scholar
Bhattacharya B, Carlsten J, Sabo E, Kethu S, Meitner P, Tavares R et al. Increased expression of eotaxin-3 distinguishes between eosinophilic esophagitis and gastroesophageal reflux disease. Hum Pathol 2007; 38: 1744–1753. ArticleCAS Google Scholar
Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science 2013; 341: 789–792. ArticleCAS Google Scholar
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012; 22: 1775–1789. ArticleCAS Google Scholar
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2012; 22: 1760–1774. ArticleCAS Google Scholar
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009; 106: 11667–11672. ArticleCAS Google Scholar
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458: 223–227. ArticleCAS Google Scholar
Mercer TR, Dinger ME, Mattick JS . Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10: 155–159. ArticleCAS Google Scholar
Wang KC, Chang HY . Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43: 904–914. ArticleCAS Google Scholar
Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 2013; 493: 231–235. ArticleCAS Google Scholar
Blanchard C, Stucke EM, Burwinkel K, Caldwell JM, Collins MH, Ahrens A et al. Coordinate interaction between IL-13 and epithelial differentiation cluster genes in eosinophilic esophagitis. J Immunol 2010; 184: 4033–4041. ArticleCAS Google Scholar
Sherrill JD, Kc K, Wu D, Djukic Z, Caldwell JM, Stucke EM et al. Desmoglein-1 regulates esophageal epithelial barrier function and immune responses in eosinophilic esophagitis. Mucosal Immunol 2013; 7: 718–729. Article Google Scholar
Andl CD, Mizushima T, Nakagawa H, Oyama K, Harada H, Chruma K et al. Epidermal growth factor receptor mediates increased cell proliferation, migration, and aggregation in esophageal keratinocytes in vitro and in vivo. J Biol Chem 2003; 278: 1824–1830. ArticleCAS Google Scholar
Harada H, Nakagawa H, Oyama K, Takaoka M, Andl CD, Jacobmeier B et al. Telomerase induces immortalization of human esophageal keratinocytes without p16INK4a inactivation. Mol Cancer Res 2003; 1: 729–738. CASPubMed Google Scholar
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7: 562–578. ArticleCAS Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25. Article Google Scholar
Garber M, Grabherr MG, Guttman M, Trapnell C . Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011; 8: 469–477. ArticleCAS Google Scholar
Sherrill JD, Gao PS, Stucke EM, Blanchard C, Collins MH, Putnam PE et al. Variants of thymic stromal lymphopoietin and its receptor associate with eosinophilic esophagitis. J Allergy Clin Immunol 2010; 126: 160–5 e3. ArticleCAS Google Scholar
Chen J, Bardes EE, Aronow BJ, Jegga AG . ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 2009; 37 (Web Server issue): W305–W311. ArticleCAS Google Scholar