Global methylation patterns in idiopathic pulmonary fibrosis

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Rabinovich, Einat I ^a   Kapetanaki, Maria G ^a   Steinfeld, Israel ^b   Gibson, Kevin F ^a   Pandit, Kusum V ^a   Yu, Guoying ^a   Yakhini, Zohar ^b,c   Kaminski, Naftali ^a  

^a UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^c Agilent Laboratories   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

APOPTOSIS; ARTICLE; CELL METABOLISM; CONTROLLED STUDY; CPG ISLAND; DATA ANALYSIS; DNA HYBRIDIZATION; DNA METHYLATION; DNA MICROARRAY; FIBROSING ALVEOLITIS; GENE; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC VARIABILITY; HIST1H2AH GENE; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; LUNG CANCER; MOLECULAR DYNAMICS; MORPHOGENESIS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REGULATORY MECHANISM; RETROPOSON; STK17B GENE; STK3 GENE; VALIDATION PROCESS; ADENOCARCINOMA; AGED; FEMALE; GENETIC EPIGENESIS; GENETICS; LUNG; LUNG TUMOR; MALE; METABOLISM; MIDDLE AGED; PATHOLOGY;

ADENOCARCINOMA; AGED; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION; HUMANS; IDIOPATHIC PULMONARY FIBROSIS; LUNG; LUNG NEOPLASMS; MALE; MIDDLE AGED;

EID: 84859626233     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033770     Document Type: Article

References (71)

1. American Thoracic Society (2000) 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 161: 646-664.
2. Gross TJ, Hunninghake GW, (2001) Idiopathic pulmonary fibrosis. N Engl J Med 345: 517-525.
3. Katzenstein AL, Myers JL, (1998) Idiopathic pulmonary fibrosis: clinical relevance of pathologic classification. Am J Respir Crit Care Med 157: 1301-1315.
4. Selman M, King TE, Pardo A, (2001) Idiopathic pulmonary fibrosis: prevailing and evolving hypotheses about its pathogenesis and implications for therapy. Ann Intern Med 134: 136-151.
5. Collard HR, King TE Jr, (2001) Treatment of idiopathic pulmonary fibrosis: the rise and fall of corticosteroids. Am J Med 110: 326-328.
6. Taskar VS, Coultas DB, (2006) Is idiopathic pulmonary fibrosis an environmental disease? Proc Am Thorac Soc 3: 293-298.
7. Taskar V, Coultas D, (2008) Exposures and idiopathic lung disease. Semin Respir Crit Care Med 29: 670-679.
8. Pandit KV, Corcoran D, Yousef H, Yarlagadda M, Tzouvelekis A, et al. (2010) Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 182: 220-229.
9. Liu G, Friggeri A, Yang Y, Milosevic J, Ding Q, et al. (2010) miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis. J Exp Med 207: 1589-1597.
10. Rajkumar R, Konishi K, Richards TJ, Ishizawar DC, Wiechert AC, et al. (2010) Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension. Am J Physiol Heart Circ Physiol 298: H1235-1248.
11. Selman M, Pardo A, Barrera L, Estrada A, Watson SR, et al. (2006) Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Am J Respir Crit Care Med 173: 188-198.
12. Selman M, Carrillo G, Estrada A, Mejia M, Becerril C, et al. (2007) Accelerated variant of idiopathic pulmonary fibrosis: clinical behavior and gene expression pattern. PLoS One 2: e482.
13. Rosas IO, Richards TJ, Konishi K, Zhang Y, Gibson K, et al. (2008) MMP1 and MMP7 as potential peripheral blood biomarkers in idiopathic pulmonary fibrosis. PLoS Med 5: e93.
14. Konishi K, Gibson KF, Lindell KO, Richards TJ, Zhang Y, et al. (2009) Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 180: 167-175.
15. Scotton CJ, Krupiczojc MA, Konigshoff M, Mercer PF, Lee YC, et al. (2009) Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury. J Clin Invest 119: 2550-2563.
16. Thannickal VJ, Horowitz JC, (2006) Evolving concepts of apoptosis in idiopathic pulmonary fibrosis. Proc Am Thorac Soc 3: 350-356.
17. Fattman CL, (2008) Apoptosis in pulmonary fibrosis: too much or not enough? Antioxid Redox Signal 10: 379-385.
18. Hecker L, Vittal R, Jones T, Jagirdar R, Luckhardt TR, et al. (2009) NADPH oxidase-4 mediates myofibroblast activation and fibrogenic responses to lung injury. Nat Med 15: 1077-1081.
19. Kim KK, Kugler MC, Wolters PJ, Robillard L, Galvez MG, et al. (2006) Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix. Proc Natl Acad Sci U S A 103: 13180-13185.
20. Willis BC, Borok Z, (2007) TGF-beta-induced EMT: mechanisms and implications for fibrotic lung disease. Am J Physiol Lung Cell Mol Physiol 293: L525-534.
21. Kim KK, Wei Y, Szekeres C, Kugler MC, Wolters PJ, et al. (2009) Epithelial cell alpha3beta1 integrin links beta-catenin and Smad signaling to promote myofibroblast formation and pulmonary fibrosis. J Clin Invest 119: 213-224.
22. Selman M, Pardo A, Kaminski N, (2008) Idiopathic pulmonary fibrosis: aberrant recapitulation of developmental programs? PLoS Med 5: e62.
23. Vuga LJ, Ben-Yehudah A, Kovkarova-Naumovski E, Oriss T, Gibson KF, et al. (2009) WNT5A is a regulator of fibroblast proliferation and resistance to apoptosis. Am J Respir Cell Mol Biol 41: 583-589.
24. Schwartz DA, (2010) Epigenetics and environmental lung disease. Proc Am Thorac 7 (2): 123-125.
25. Suzuki MM, Bird A, (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
26. Toyota M, Suzuki H, Yamashita T, Hirata K, Imai K, et al. (2009) Cancer epigenomics: implications of DNA methylation in personalized cancer therapy. Cancer Sci 100: 787-791.
27. Waterland RA, Jirtle RL, (2004) Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases. Nutrition 20: 63-68.
28. Dolinoy DC, Jirtle RL, (2008) Environmental epigenomics in human health and disease. Environ Mol Mutagen 49: 4-8.
29. Jones PA, Takai D, (2001) The role of DNA methylation in mammalian epigenetics. Science 293: 1068-1070.
30. Slotkin RK, Martienssen R, (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
31. Jones PA, Baylin SB, (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3: 415-428.
32. Li E, Beard C, Jaenisch R, (1993) Role for DNA methylation in genomic imprinting. Nature 366: 362-365.
33. Ting AH, McGarvey KM, Baylin SB, (2006) The cancer epigenome-components and functional correlates. Genes Dev 20: 3215-3231.
34. Pfeifer GP, Rauch TA, (2009) DNA methylation patterns in lung carcinomas. Semin Cancer Biol 19: 181-187.
35. Rauch T, Wang Z, Zhang X, Zhong X, Wu X, et al. (2007) Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci U S A 104: 5527-5532.
36. Rauch TA, Zhong X, Wu X, Wang M, Kernstine KH, et al. (2008) High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci U S A 105: 252-257.
37. Vancheri C, Failla M, Crimi N, Raghu G, (2010) Idiopathic pulmonary fibrosis: a disease with similarities and links to cancer biology. Eur Respir J 35: 496-504.
38. Lababede O, Meziane MA, Rice TW, (1999) TNM staging of lung cancer: a quick reference chart. Chest 115: 233-235.
39. Mohn F, Weber M, Schubeler D, Roloff TC, (2009) Methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 507: 55-64.
40. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: 853-862.
41. Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, et al. (2009) Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16: 564-571.
42. Yamashita S, Hosoya K, Gyobu K, Takeshima H, Ushijima T, (2009) Development of a novel output value for quantitative assessment in methylated DNA immunoprecipitation-CpG island microarray analysis. DNA Res 16: 275-286.
43. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, et al. (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A 102: 15785-15790.
44. Chomczynski P, Sacchi N, (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156-159.
45. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
46. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I, (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.
47. Segal E, Friedman N, Koller D, Regev A, (2004) A module map showing conditional activity of expression modules in cancer. Nat Genet 36: 1090-1098.
48. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
49. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
50. Jaenisch R, Bird A, (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl pp. 245-254.
51. Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, et al. (2005) Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 33: 6823-6836.
52. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: 178-186.
53. Klug M, Heinz S, Gebhard C, Schwarzfischer L, Krause SW, et al. (2010) Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels. Genome Biol 11: R63.
54. Choi JK, (2010) Contrasting chromatin organization of CpG islands and exons in the human genome. Genome Biol 11: R70.
55. Dudziec E, Miah S, Choudhry HM, Owen HC, Blizard S, et al. (2011) Hypermethylation of CpG Islands and Shores around Specific MicroRNAs and Mirtrons Is Associated with the Phenotype and Presence of Bladder Cancer. Clin Cancer Res 17: 1287-1296.
56. Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, et al. (2011) Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res 21: 1028-1041.
57. Sanjo H, Kawai T, Akira S, (1998) DRAKs, novel serine/threonine kinases related to death-associated protein kinase that trigger apoptosis. J Biol Chem 273: 29066-29071.
58. Pang M, Zhuang S, (2010) Histone deacetylase: a potential therapeutic target for fibrotic disorders. J Pharmacol Exp Ther 335: 266-272.
59. Liu T, Hu B, Choi YY, Chung M, Ullenbruch M, et al. (2009) Notch1 signaling in FIZZ1 induction of myofibroblast differentiation. Am J Pathol 174: 1745-1755.
60. Boon K, Bailey NW, Yang J, Steel MP, Groshong S, et al. (2009) Molecular phenotypes distinguish patients with relatively stable from progressive idiopathic pulmonary fibrosis (IPF). PLoS One 4: e5134.
61. Keane MP, Belperio JA, Moore TA, Moore BB, Arenberg DA, et al. (1999) Neutralization of the CXC chemokine, macrophage inflammatory protein-2, attenuates bleomycin-induced pulmonary fibrosis. J Immunol 162: 5511-5518.
62. Ozawa Y, Suda T, Naito T, Enomoto N, Hashimoto D, et al. (2009) Cumulative incidence of and predictive factors for lung cancer in IPF. Respirology 14: 723-728.
63. Le Jeune I, Gribbin J, West J, Smith C, Cullinan P, et al. (2007) The incidence of cancer in patients with idiopathic pulmonary fibrosis and sarcoidosis in the UK. Respiratory medicine 101: 2534-2540.
64. Wilson AS, Power BE, Molloy PL, (2007) DNA hypomethylation and human diseases. Biochim Biophys Acta 1775: 138-162.
65. Chalitchagorn K, Shuangshoti S, Hourpai N, Kongruttanachok N, Tangkijvanich P, et al. (2004) Distinctive pattern of LINE-1 methylation level in normal tissues and the association with carcinogenesis. Oncogene 23: 8841-8846.
66. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41: 563-571.
67. Estecio MR, Gharibyan V, Shen L, Ibrahim AE, Doshi K, et al. (2007) LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability. PLoS One 2: e399.
68. Han JS, Szak ST, Boeke JD, (2004) Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429: 268-274.
69. Howard G, Eiges R, Gaudet F, Jaenisch R, Eden A, (2008) Activation and transposition of endogenous retroviral elements in hypomethylation induced tumors in mice. Oncogene 27: 404-408.
70. Huang SK, Fisher AS, Scruggs AM, White ES, Hogaboam CM, et al. (2010) Hypermethylation of PTGER2 confers prostaglandin E2 resistance in fibrotic fibroblasts from humans and mice. Am J Pathol 177: 2245-2255.
71. Sanders YY, Pardo A, Selman M, Nuovo GJ, Tollefsbol TO, et al. (2008) Thy-1 promoter hypermethylation: a novel epigenetic pathogenic mechanism in pulmonary fibrosis. Am J Respir Cell Mol Biol 39: 610-618.