Comparative evaluation of miRNA expression between in vitro and in vivo airway epithelium demonstrates widespread differences

American Journal of Pathology

Volumn 183, Issue 5, 2013, Pages 1405-1410

  Chen, Peter ^a   Edelman, Jeffrey D ^a   Gharib, Sina A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ADULT; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; EPITHELIUM CELL; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; IN VIVO STUDY; INJURY; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RESPIRATORY EPITHELIUM; TISSUE REPAIR;

ADULT; CELLS, CULTURED; EPITHELIAL CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; MIDDLE AGED; RESPIRATORY MUCOSA; SIGNAL TRANSDUCTION; WOUND HEALING;

EID: 84886681643     PISSN: 00029440     EISSN: 15252191     Source Type: Journal    
DOI: 10.1016/j.ajpath.2013.07.007     Document Type: Article

References (37)

1. B.N. Lambrecht, and H. Hammad The airway epithelium in asthma Nat Med 18 2012 684 692
2. D. Parker, and A. Prince Innate immunity in the respiratory epithelium Am J Respir Cell Mol Biol 45 2011 189 201
3. D. Proud, and R. Leigh Epithelial cells and airway diseases Immunol Rev 242 2011 186 204
4. T.A. Wynn Integrating mechanisms of pulmonary fibrosis J Exp Med 208 2011 1339 1350
5. J.L. Sporty, L. Horálková, and C. Ehrhardt In vitro cell culture models for the assessment of pulmonary drug disposition Expert Opin Drug Metab Toxicol 4 2008 333 345
6. R. Wu, G.H. Sato, and M.J. Whitcutt Developing differentiated epithelial cell cultures: airway epithelial cells Fundam Appl Toxicol 6 1986 580 590
7. S.H. Randell, M.L. Fulcher, W. O'Neal, and J.C. Olsen Primary epithelial cell models for cystic fibrosis research Methods Mol Biol 742 2011 285 310
8. A.J. Ross, L.A. Dailey, L.E. Brighton, and R.B. Devlin Transcriptional profiling of mucociliary differentiation in human airway epithelial cells Am J Respir Cell Mol Biol 37 2007 169 185
9. C. Mathis, C. Poussin, D. Weisensee, S. Gebel, A. Hengstermann, A. Sewer, V. Belcastro, Y. Xiang, S. Ansari, S. Wagner, J. Hoeng, and M. Peitsch Human bronchial epithelial cells exposed in vitro to cigarette smoke at the air-liquid interface resemble bronchial epithelium from human smokers Am J Physiol Lung Cell Mol Physiol 304 2013 L489 L503
10. A. Martinez-Anton, M. Sokolowska, S. Kern, A.S. Davis, S. Alsaaty, J.K. Taubenberger, J. Sun, R. Cai, R.L. Danner, M. Eberlein, C. Logun, and J.H. Shelhamer Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells Am J Respir Cell Mol Biol 49 2013 384 395
11. M. Kesimer, S. Kirkham, R.J. Pickles, A.G. Henderson, N.E. Alexis, G. DeMaria, D. Knight, D.J. Thornton, and J.K. Sheehan Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways? Am J Physiol Lung Cell Mol Physiol 296 2009 L92 L100
12. A.S. Shah, Y. Ben-Shahar, T.O. Moninger, J.N. Kline, and M.J. Welsh Motile cilia of human airway epithelia are chemosensory Science 325 2009 1131 1134
13. A. Dvorak, A.E. Tilley, R. Shaykhiev, R. Wang, and R.G. Crystal Do airway epithelium air-liquid cultures represent the in vivo airway epithelium transcriptome? Am J Respir Cell Mol Biol 44 2011 465 473
14. A.A. Pezzulo, T.D. Starner, T.E. Scheetz, G.L. Traver, A.E. Tilley, B.G. Harvey, R.G. Crystal, P.B. McCray Jr., and J. Zabner The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia Am J Physiol Lung Cell Mol Physiol 300 2011 L25 L31
15. D.P. Bartel MicroRNAs: target recognition and regulatory functions Cell 136 2009 215 233
16. M. Selbach, B. Schwanhäusser, N. Thierfelder, Z. Fang, R. Khanin, and N. Rajewsky Widespread changes in protein synthesis induced by microRNAs Nature 455 2008 58 63
17. B.P. Lewis, C.B. Burge, and D.P. Bartel Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 2005 15 20
18. A. Kozomara, and S. Griffiths-Jones miRBase: integrating microRNA annotation and deep-sequencing data Nucleic Acids Res 39 2011 D152 D157
19. S.P. Nana-Sinkam, M.G. Hunter, G.J. Nuovo, T.D. Schmittgen, R. Gelinas, D. Galas, and C.B. Marsh Integrating the microRNome into the study of lung disease Am J Respir Crit Care Med 179 2009 4 10
20. P. Mestdagh, P. Van Vlierberghe, A. De Weer, D. Muth, F. Westermann, F. Speleman, and J. Vandesompele A novel and universal method for microRNA RT-qPCR data normalization Genome Biol 10 2009 R64
21. V.G. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to the ionizing radiation response [Erratum appeared in Proc Natl Acad Sci USA 2001, 98:10515] Proc Natl Acad Sci USA 98 2001 5116 5121
22. B.P. Lewis, I.-H. Shih, M.W. Jones-Rhoades, D.P. Bartel, and C.B. Burge Prediction of mammalian microRNA targets Cell 115 2003 787 798
23. R.A. Irizarry, B.M. Bolstad, F. Collin, L.M. Cope, B. Hobbs, and T.P. Speed Summaries of Affymetrix GeneChip probe level data Nucleic Acids Res 31 2003 e15
24. J. Wang, D. Duncan, Z. Shi, and B. Zhang WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 Nucleic Acids Res 41 2013 W77 W83
25. B. Zhang, S. Kirov, and J. Snoddy WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Res 33 2005 W741 W748
26. H. Guo, N.T. Ingolia, J.S. Weissman, and D.P. Bartel Mammalian microRNAs predominantly act to decrease target mRNA levels Nature 466 2010 835 840
27. D. Baek, J. Villén, C. Shin, F.D. Camargo, S.P. Gygi, and D.P. Bartel The impact of microRNAs on protein output Nature 455 2008 64 71
28. L.P. Lim, N.C. Lau, P. Garrett-Engele, A. Grimson, J.M. Schelter, J. Castle, D.P. Bartel, P.S. Linsley, and J.M. Johnson Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs Nature 433 2005 769 773
29. S. Bagga, J. Bracht, S. Hunter, K. Massirer, J. Holtz, R. Eachus, and A.E. Pasquinelli Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation Cell 122 2005 553 563
30. T.M. Witkos, E. Koscianska, and W.J. Krzyzosiak Practical aspects of microRNA target prediction Curr Mol Med 11 2011 93 109
31. P. Alexiou, M. Maragkakis, G.L. Papadopoulos, M. Reczko, and A.G. Hatzigeorgiou Lost in translation: an assessment and perspective for computational microRNA target identification Bioinformatics 25 2009 3049 3055
32. R.G. Crystal, S.H. Randell, J.F. Engelhardt, J. Voynow, and M.E. Sunday Airway epithelial cells: current concepts and challenges Proc Am Thorac Soc 5 2008 772 777
33. P.C. Baer, and J. Bereiter-Hahn Epithelial cells in culture: injured or differentiated cells? Cell Biol Int 36 2012 771 777
34. A.J. Engler, S. Sen, H.L. Sweeney, and D.E. Discher Matrix elasticity directs stem cell lineage specification Cell 126 2006 677 689
35. D.C. Gruenert, W.E. Finkbeiner, and J.H. Widdicombe Culture and transformation of human airway epithelial cells Am J Physiol 268 1995 L347 L360
36. C.J. Sherr, and R.A. DePinho Cellular senescence: minireview mitotic clock or culture shock Cell 102 2000 407 410
37. K.V. Pandit, J. Milosevic, and N. Kaminski MicroRNAs in idiopathic pulmonary fibrosis Transl Res 157 2011 191 199