Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis

Thorax

Volumn 68, Issue 12, 2013, Pages 1114-1121

  Yang, Ivana V ^a,b,c   Coldren, Christopher D ^a   Leach, Sonia M ^b   Seibold, Max A ^b   Murphy, Elissa ^a   Lin, Jia ^b   Rosen, Rachel ^a   Neidermyer, Amanda J ^a   McKean, David F ^a   Groshong, Steve D ^a,b   Cool, Carlyne ^a,b   Cosgrove, Gregory P ^a,b   Lynch, David A ^a,b   Brown, Kevin K ^a,b   Schwarz, Marvin I ^a,b   Fingerlin, Tasha E ^c   Schwartz, David A ^a,b  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b DEPARTMENT OF MEDICINE   (United States)

^c Global Health and Health Disparities   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

KERATIN; MATRILYSIN; MATRIX METALLOPROTEINASE; MUCIN 5B; OSTEOPONTIN;

ADULT; ARTICLE; CONTROLLED STUDY; DNAH6 GENE; DNAH7 GENE; DNAI1 GENE; FEMALE; FIBROSING ALVEOLITIS; GENE; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; HISTOLOGY; HUMAN; HUMAN TISSUE; INTERSTITIAL PNEUMONIA; MAJOR CLINICAL STUDY; MALE; MICROSCOPIC HONEYCOMBING; MMP7 GENE; MUC5B GENE; PRIORITY JOURNAL; RPGRIP1L GENE; TRANSCRIPTOMICS; UNUSUAL INTERSTITIAL PNEUMONIA;

INTERSTITIAL FIBROSIS;

ADULT; AGED; CASE-CONTROL STUDIES; CILIA; GENE EXPRESSION PROFILING; HUMANS; IDIOPATHIC PULMONARY FIBROSIS; MALE; MATRIX METALLOPROTEINASE 7; MIDDLE AGED; MUCIN-5B; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; RNA; TRANSCRIPTOME;

EID: 84887454672     PISSN: 00406376     EISSN: 14683296     Source Type: Journal    
DOI: 10.1136/thoraxjnl-2012-202943     Document Type: Article

References (30)

1. King T, Costabel U, Cordier J-F, et al. American Thoracic Society. Idiopathic pulmonary fibrosis: diagnosis and treatment. International consensus statement. American Thoracic Society (ATS), and the European Respiratory Society (ERS). Am J Respir Crit Care Med 2000;161(2 Pt 1):646-64
2. Konishi K, Gibson KF, Lindell KO, et al. Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2009;180:167-75
3. Selman M, Pardo A, Barrera L, et al. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Am J Respir Crit Care Med 2006;173:188-98 (Pubitemid 43187891)
4. Zuo F, Kaminski N, Eugui E, et al. Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Proc Natl Acad Sci USA 2002;99:6292-7 (Pubitemid 34493305)
5. Yang IV, Burch LH, Steele MP, et al. Gene expression profiling of familial and sporadic interstitial pneumonia. Am J Respir Crit Care Med 2007;175: 45-54 (Pubitemid 46105308)
6. Travis WD, King TE, Bateman ED, et al. American Thoracic Society/European Respiratory Society International Multidisciplinary Consensus Classification of the Idiopathic Interstitial Pneumonias. This joint statement of the American Thoracic Society (ATS), and the European Respiratory Society (ERS) was adopted by the ATS board of directors, June 2001 and by the ERS Executive Committee, June 2001. Am J Respir Crit Care Med. 2002;165:277-304
7. Tumor Analysis Best Practices Working Group. Expression profiling-best practices for data generation and interpretation in clinical trials. Nat Rev Genet 2004;5:229-37
8. Irizarry RA, Bolstad BM, Collin F, et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003;31:e15
9. Hunter L, Taylor RC, Leach SM, et al. GEST: a gene expression search tool based on a novel Bayesian similarity metric. Bioinformatics 2001;17(Suppl 1): S115-22 (Pubitemid 33793501)
10. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 2008;3:1101-8 (Pubitemid 351818697)
11. Pillai SG, Kong X, Edwards LD, et al. Loci identified by genome-wide association studies influence different disease-related phenotypes in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2010;182:1498-505
12. Zhou X, Baron RM, Hardin M, et al. Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP. Hum Mol Genet 2012;21:1325-35
13. El Zein L, Ait-Lounis A, Morle L, et al. RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies. J Cell Sci 2009;122(Pt 17):3180-9
14. Cigna N, Moshai E Farrokhi, Brayer S, et al. The hedgehog system machinery controls transforming growth factor-beta-dependent myofibroblastic differentiation in humans: involvement in idiopathic pulmonary fibrosis. Am J Pathol 2012;181:2126-37
15. Ramos C, Becerril C, Montano M, et al. FGF-1 reverts epithelial- mesenchymal transition induced by TGF-?1 through MAPK/ERK kinase pathway. Am J Physiol Lung Cell Mol Physiol 2010;299:L222-31
16. Khalil N, Xu YD, O?Connor R, et al. Proliferation of pulmonary interstitial fibroblasts is mediated by transforming growth factor-beta1-induced release of extracellular fibroblast growth factor-2 and phosphorylation of p38 MAPK and JNK. J Biol Chem 2005;280:43000-9 (Pubitemid 43049264)
17. Antoniades HN, Bravo MA, Avila RE, et al. Platelet-derived growth factor in idiopathic pulmonary fibrosis. J Clin Invest 1990;86:1055-64 (Pubitemid 20370408)
18. Nagaoka I, Trapnell BC, Crystal RG. Upregulation of platelet-derived growth factor-A and -B gene expression in alveolar macrophages of individuals with idiopathic pulmonary fibrosis. J Clin Invest 1990;85:2023-7 (Pubitemid 20192983)
19. Konigshoff M, Kramer M, Balsara N, et al. WNT1-inducible signaling protein-1 mediates pulmonary fibrosis in mice and is upregulated in humans with idiopathic pulmonary fibrosis. J Clin Invest 2009;119:772-87
20. Henderson WR Jr, Chi EY, Ye X, et al. Inhibition of Wnt/beta-catenin/CREB binding protein (CBP) signaling reverses pulmonary fibrosis. Proc Natl Acad Sci USA 2010;107:14309-14
21. Gross TJ, Hunninghake GW. Idiopathic pulmonary fibrosis. N Engl J Med 2001;345:517-25 (Pubitemid 32758505)
22. Rock JR, Barkauskas CE, Cronce MJ, et al. Multiple stromal populations contribute to pulmonary fibrosis without evidence for epithelial to mesenchymal transition. Proc Natl Acad Sci USA 2011;108:E1475-83
23. Seibold MA, Wise AL, Speer MC, et al. A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med 2011;364:1503-12
24. Gharib SA, Altemeier WA, Van Winkle LS, et al. Matrix metalloproteinase-7 coordinates airway epithelial injury response and differentiation of ciliated cells. Am J Respir Cell Mol Biol 2013;48:390-6
25. Alizadeh A, Eisen M, Davis R, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-11 (Pubitemid 30082188)
26. Rosenwald A, Wright G, Leroy K, et al. Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J Exp Med 2003;198:851-62 (Pubitemid 37152922)
27. Hedenfalk I, Duggan D, Chen Y, et al. Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001;344:539-48 (Pubitemid 32167867)
28. vant Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530-6 (Pubitemid 34130608)
29. Spira A, Beane JE, Shah V, et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 2007;13:361-6 (Pubitemid 46376687)
30. Chen HY, Yu SL, Chen CH, et al. A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med 2007;356:11-20.