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Review

Epigenomics of Idiopathic Pulmonary Fibrosis

Pages 195-203 | Published online: 27 Mar 2012

References

  • Gross TJ , HunninghakeGW. Idiopathic pulmonary fibrosis. N. Engl. J. Med.345(7) , 517–525 (2001).
  • Raghu G , WeyckerD, EdelsbergJ, BradfordWZ, OsterG. Incidence and prevalence of idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med.174(7) , 810–816 (2006).
  • Olson AL , SwigrisJJ, LezotteDC, NorrisJM, WilsonCG, BrownKK. Mortality from pulmonary fibrosis increased in the United States from 1992 to 2003. Am. J. Respir. Crit. Care Med.176(3) , 277–284 (2007).
  • King T , CostabelU, 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.161(2 Pt 1) , 646–664 (2000).
  • King TE . Interstitial Lung Disease (5th Edition). King TE, Schwarz MI (Eds). People‘s Medical Publishing House, Shelton, CT, USA, 895–943 (2010).
  • Willis BC , LieblerJM, Luby-PhelpsK et al. Induction of epithelial-mesenchymal transition in alveolar epithelial cells by transforming growth factor-beta1: potential role in idiopathic pulmonary fibrosis. Am. J. Pathol. 166(5) , 1321–1332 (2005).
  • Kim KK , KuglerMC, WoltersPJ et al. Alveolar epithelial cell mesenchymal transition develops in vivo during pulmonary fibrosis and is regulated by the extracellular matrix. Proc. Natl Acad. Sci. USA 103(35) , 13180–13185 (2006).
  • Tanjore H , XuXC, PolosukhinVV et al. Contribution of epithelial-derived fibroblasts to bleomycin-induced lung fibrosis. Am. J. Respir. Crit. Care Med. 180(7) , 657–665 (2009).
  • Farkas L , GauldieJ, VoelkelNF, KolbM. Pulmonary hypertension and idiopathic pulmonary fibrosis: a tale of angiogenesis, apoptosis, and growth factors. Am. J. Respir. Cell Mol. Biol.45(1) , 1–15 (2011).
  • Fattman CL . Apoptosis in pulmonary fibrosis: too much or not enough? Antioxid. Redox Signal.10(2) , 379–385 (2008).
  • Thannickal VJ , HorowitzJC. Evolving concepts of apoptosis in idiopathic pulmonary fibrosis. Proc. Am. Thorac. Soc.3(4) , 350–356 (2006).
  • Hecker L , VittalR, JonesT et al. NADPH oxidase-4 mediates myofibroblast activation and fibrogenic responses to lung injury. Nat. Med. 15(9) , 1077–1081 (2009).
  • Lawson WE , ChengDS, DegryseAL et al. Endoplasmic reticulum stress enhances fibrotic remodeling in the lungs. Proc. Natl Acad. Sci. USA 108(26) , 10562–10567 (2011).
  • Tanjore H , ChengDS, DegryseAL et al. Alveolar epithelial cells undergo epithelial-to-mesenchymal transition in response to endoplasmic reticulum stress. J. Biol. Chem. 286(35) , 30972–30980 (2011).
  • Tsakiri KD , CronkhiteJT, KuanPJ et al. Adult-onset pulmonary fibrosis caused by mutations in telomerase. Proc. Natl Acad. Sci. USA 104(18) , 7552–7557 (2007).
  • Alder JK , ChenJJ, LancasterL et al. Short telomeres are a risk factor for idiopathic pulmonary fibrosis. Proc. Natl Acad. Sci. USA 105(35) , 13051–13056 (2008).
  • Cronkhite JT , XingC, RaghuG et al. Telomere shortening in familial and sporadic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 178(7) , 729–737 (2008).
  • Chilosi M , DoglioniC, MurerB, PolettiV. Epithelial stem cell exhaustion in the pathogenesis of idiopathic pulmonary fibrosis. Sarcoidosis Vasc. Diffuse Lung Dis.27(1) , 7–18 (2010).
  • Scotton CJ , KrupiczojcMA, KonigshoffM et al. Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury. J. Clin. Invest. 119(9) , 2550–2563 (2009).
  • Seibold MA , WiseAL, SpeerMC et al. A common MUC5B promoter polymorphism and pulmonary fibrosis. N. Engl. J. Med. 364(16) , 1503–1512 (2011).
  • Boucher RC . Idiopathic pulmonary fibrosis – a sticky business. N. Engl. J. Med.364(16) , 1560–1561 (2011).
  • Garcia CK . Idiopathic pulmonary fibrosis: update on genetic discoveries. Proc. Am. Thorac. Soc.8(2) , 158–162 (2011).
  • Seibold MA , SchwartzDA. The lung: the natural boundary between nature and nurture. Annu. Rev. Physiol.73 , 457–478 (2011).
  • Taskar VS , CoultasDB. Is idiopathic pulmonary fibrosis an environmental disease? Proc. Am. Thorac. Soc.3(4) , 293–298 (2006).
  • Ding Q , LuckhardtT, HeckerL et al. New insights into the pathogenesis and treatment of idiopathic pulmonary fibrosis. Drugs 71(8) , 981–1001 (2011).
  • Chua F , GauldieJ, LaurentGJ. Pulmonary fibrosis: searching for model answers. Am. J. Respir. Cell Mol. Biol.33(1) , 9–13 (2005).
  • Kaminski N . Microarray analysis of idiopathic pulmonary fibrosis. Am. J. Respir. Cell Mol. Biol.29(Suppl. 3) , S32–S36 (2003).
  • Konishi K , GibsonKF, LindellKO et al. Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 180(2) , 167–175 (2009).
  • Selman M , CarrilloG, EstradaA et al. Accelerated variant of idiopathic pulmonary fibrosis: clinical behavior and gene expression pattern. PLoS One 2(5) , e482 (2007).
  • Selman M , PardoA, BarreraL et al. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Am. J. Respir. Crit. Care Med. 173(2) , 188–198 (2006).
  • Zuo F , KaminskiN, EuguiE et al. Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Proc. Natl Acad. Sci. USA 99(9) , 6292–6297 (2002).
  • Yang IV , BurchLH, SteeleMP et al. Gene expression profiling distinguishes familial and non-familial forms of pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 175 , 45–54 (2005).
  • Boon K , BaileyNW, YangJ et al. Molecular phenotypes distinguish patients with relatively stable from progressive idiopathic pulmonary fibrosis (IPF). PLoS ONE 4(4) , e5134 (2009).
  • Garcia-Sancho Figueroa MC , CarrilloG, Perez-PadillaR et al. Risk factors for idiopathic pulmonary fibrosis in a Mexican population. A case–control study. Respir. Med. 104(2) , 305–309 (2010).
  • Antoniou KM , HansellDM, RubensMB et al. Idiopathic pulmonary fibrosis: outcome in relation to smoking status. Am. J. Respir. Crit. Care Med. 177(2) , 190–194 (2008).
  • King TE , Jr., Tooze JA, Schwarz MI, Brown KR, Cherniack RM. Predicting survival in idiopathic pulmonary fibrosis: scoring system and survival model. Am. J. Respir. Crit. Care Med.164(7) , 1171–1181 (2001).
  • Jirtle RL , SkinnerMK. Environmental epigenomics and disease susceptibility. Nat. Rev. Genet.8(4) , 253–262 (2007).
  • Waterland RA , JirtleRL. Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol. Cell. Biol.23(15) , 5293–5300 (2003).
  • Anway MD , CuppAS, UzumcuM, SkinnerMK. Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science308(5727) , 1466–1469 (2005).
  • Baccarelli A , WrightRO, BollatiV et al. Rapid DNA methylation changes after exposure to traffic particles. Am. J. Respir. Crit. Care Med. 179(7) , 572–578 (2009).
  • Fraga MF , BallestarE, PazMF et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl Acad. Sci. USA 102(30) , 10604–10609 (2005).
  • Kim DH , NelsonHH, WienckeJK et al. p16(INK4a) and histology-specific methylation of CpG islands by exposure to tobacco smoke in non-small cell lung cancer. Cancer Res. 61(8) , 3419–3424 (2001).
  • Launay JM , Del Pino M, Chironi G et al. Smoking induces long-lasting effects through a monoamine-oxidase epigenetic regulation. PLoS ONE4(11) , e7959 (2009).
  • Liu F , KillianJK, YangM et al. Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate. Oncogene 29(25) , 3650–3664 (2010).
  • Phillips JM , GoodmanJI. Inhalation of cigarette smoke induces regions of altered DNA methylation (RAMs) in SENCAR mouse lung. Toxicology260(1–3) , 7–15 (2009).
  • Schembri F , SridharS, PerdomoC et al. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc. Natl Acad. Sci. USA 106(7) , 2319–2324 (2009).
  • Izzotti A , CalinGA, SteeleVE, CroceCM, De Flora S. Relationships of microRNA expression in mouse lung with age and exposure to cigarette smoke and light. FASEB J.23(9) , 3243–3250 (2009).
  • Izzotti A , CalinGA, ArrigoP, SteeleVE, CroceCM, De Flora S. Downregulation of microRNA expression in the lungs of rats exposed to cigarette smoke. FASEB J.23(3) , 806–812 (2009).
  • Breton CV , ByunHM, WentenM, PanF, YangA, GillilandFD. Prenatal tobacco smoke exposure affects global and gene-specific DNA methylation. Am. J. Respir. Crit. Care Med.180(5) , 462–467 (2009).
  • Guerrero-Preston R , GoldmanLR, Brebi-MievilleP et al. Global DNA hypomethylation is associated with in utero exposure to cotinine and perfluorinated alkyl compounds. Epigenetics 5(6) , 539–546 (2010).
  • Suter M , MaJ, HarrisAS et al. Maternal tobacco use modestly alters correlated epigenome-wide placental DNA methylation and gene expression. Epigenetics 6(11) , 1284–1294 (2011).
  • Maccani MA , Avissar-WhitingM, BanisterCE, McGonnigalB, PadburyJF, MarsitCJ. Maternal cigarette smoking during pregnancy is associated with downregulation of miR-16, miR-21, and miR-146a in the placenta. Epigenetics5(7) , 583–589 (2010).
  • Cuddapah S , BarskiA, ZhaoK. Epigenomics of T cell activation, differentiation, and memory. Curr. Opin. Immunol.22(3) , 341–347 (2010).
  • Lee GR , KimST, SpilianakisCG, FieldsPE, FlavellRA. T helper cell differentiation: regulation by cis elements and epigenetics. Immunity24(4) , 369–379 (2006).
  • Lal G , BrombergJS. Epigenetic mechanisms of regulation of Foxp3 expression. Blood114(18) , 3727–3735 (2009).
  • Wei B , PeiG. microRNAs: critical regulators in Th17 cells and players in diseases. Cell. Mol. Immunol.7(3) , 175–181 (2010).
  • Mukasa R , BalasubramaniA, LeeYK et al. Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Immunity 32(5) , 616–627 (2010).
  • Xiao C , RajewskyK. MicroRNA control in the immune system: basic principles. Cell136(1) , 26–36 (2009).
  • Parra ER , KairallaRA, Ribeiro De Carvalho CR, Eher E, Capelozzi VL. Inflammatory cell phenotyping of the pulmonary interstitium in idiopathic interstitial pneumonia. Respiration74(2) , 159–169 (2007).
  • Feghali-Bostwick CA , TsaiCG, ValentineVG et al. Cellular and humoral autoreactivity in idiopathic pulmonary fibrosis. J. Immunol. 179(4) , 2592–2599 (2007).
  • Kotsianidis I , NakouE, BouchliouI et al. Global impairment of CD4+CD25+FOXP3+ regulatory T cells in idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 179(12) , 1121–1130 (2009).
  • Gilani SR , VugaLJ, LindellKO et al. CD28 down-regulation on circulating CD4 T-cells is associated with poor prognoses of patients with idiopathic pulmonary fibrosis. PLoS ONE 5(1) , e8959 (2010).
  • Coward WR , WattsK, Feghali-BostwickCA, KnoxA, PangL. Defective histone acetylation is responsible for the diminished expression of cyclooxygenase 2 in idiopathic pulmonary fibrosis. Mol. Cell. Biol.29(15) , 4325–4339 (2009).
  • Coward WR , WattsK, Feghali-BostwickCA, JenkinsG, PangL. Repression of IP-10 by interactions between histone deacetylation and hypermethylation in idiopathic pulmonary fibrosis. Mol. Cell. Biol.30(12) , 2874–2886 (2010).
  • Sanders YY , PardoA, SelmanM et al. Thy-1 promoter hypermethylation: a novel epigenetic pathogenic mechanism in pulmonary fibrosis. Am. J. Respir. Cell Mol. Biol. 39(5) , 610–618 (2008).
  • Sanders YY , TollefsbolTO, VariscoBM, HagoodJS. Epigenetic regulation of Thy-1 by histone deacetylase inhibitor in rat lung fibroblasts. Am. J. Respir. Cell Mol. Biol.45(1) , 16–23 (2010).
  • Hu B , Gharaee-KermaniM, WuZ, PhanSH. Epigenetic regulation of myofibroblast differentiation by DNA methylation. Am. J. Pathol.177(1) , 21–28 (2010).
  • Hu B , Gharaee-KermaniM, WuZ, PhanSH. Essential role of MeCP2 in the regulation of myofibroblast differentiation during pulmonary fibrosis. Am. J. Pathol.178(4) , 1500–1508 (2011).
  • Hawkins RD , HonGC, RenB. Next-generation genomics: an integrative approach. Nat. Rev. Genet.11(7) , 476–486 (2010).
  • Schones DE , ZhaoK. Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet.9(3) , 179–191 (2008).
  • Yang IV , SchwartzDA. Epigenetic control of gene expression in the lung. Am. J. Respir. Crit. Care Med.183(10) , 1295–1301 (2011).
  • Rabinovich E , YakhiniZ, BenosP et al. Human CpG islands arrays reveal changes in global methylation patterns in idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 181 , A2017 (2010).
  • Irizarry RA , Ladd-AcostaC, WenB et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41(2) , 178–186 (2009).
  • Irizarry RA , Ladd-AcostaC, CarvalhoB et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18(5) , 780–790 (2008).
  • Yang I , HennessyC, DavidsonE et al. Genome-wide DNA methylation patterns in interstitial lung disease (ILD) and chronic obstructive lung disease (COPD). Am. J. Respir. Crit. Care Med. 183 , A1049 (2011).
  • 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. USA107(32) , 14309–14314 (2010).
  • Konigshoff M , KramerM, BalsaraN et al. WNT1-inducible signaling protein-1 mediates pulmonary fibrosis in mice and is upregulated in humans with idiopathic pulmonary fibrosis. J. Clin. Invest. 119(4) , 772–787 (2009).
  • Zhou B , LiuY, KahnM et al. β-catenin/CBP-dependent regulation of TGF-beta-mediated epithelial-mesenchymal transition (EMT) by SMAD3. J. Biol. Chem. doi:10.1074/jbc.M111.276311 (2012) (Epub ahead of print).
  • Pandit KV , CorcoranD, YousefH et al. Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 182(2) , 220–229 (2010).
  • Liu G , FriggeriA, YangY et al. miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis. J. Exp. Med. 207(8) , 1589–1597 (2010).
  • Cushing L , KuangPP, QianJ et al. miR-29 is a major regulator of genes associated with pulmonary fibrosis. Am. J. Respir. Cell Mol. Biol. 45(2) , 287–294 (2011).
  • Pottier N , MaurinT, ChevalierB et al. Identification of keratinocyte growth factor as a target of microRNA-155 in lung fibroblasts: implication in epithelial-mesenchymal interactions. PLoS ONE 4(8) , e6718 (2009).
  • Oak SR , MurrayL, HerathA et al. A micro RNA processing defect in rapidly progressing idiopathic pulmonary fibrosis. PLoS ONE 6(6) , e21253 (2011).
  • Pandit KV , MilosevicJ, KaminskiN. MicroRNAs in idiopathic pulmonary fibrosis. Transl. Res.157(4) , 191–199 (2011).
  • Shen-Orr SS , TibshiraniR, KhatriP et al. Cell type-specific gene expression differences in complex tissues. Nat. Methods 7(4) , 287–289 (2010).
  • Cedar H , BergmanY. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet.10(5) , 295–304 (2009).
  • Chodavarapu RK , FengS, BernatavichuteYV et al. Relationship between nucleosome positioning and DNA methylation. Nature 466(7304) , 388–392 (2010).
  • Hu JL , ZhouBO, ZhangRR, ZhangKL, ZhouJQ, XuGL. The N-terminus of histone H3 is required for de novo DNA methylation in chromatin. Proc. Natl Acad. Sci. USA106(52) , 22187–22192 (2009).
  • Ooi SK , QiuC, BernsteinE et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448(7154) , 714–717 (2007).
  • Milosavljevic A . Emerging patterns of epigenomic variation. Trends Genet.27(6) , 242–250 (2011).
  • Esteller M . Non-coding RNAs in human disease. Nat. Rev. Genet.12(12) , 861–874 (2011).
  • Tycko B . Allele-specific DNA methylation: beyond imprinting. Hum. Mol. Genet.19(R2) , R210–R220 (2010).
  • Sankaranarayanapillai M , TongWP, YuanQ et al. Monitoring histone deacetylase inhibition in vivo: noninvasive magnetic resonance spectroscopy method. Mol. Imaging 7(2) , 92–100 (2008).
  • Boumber Y , IssaJP. Epigenetics in cancer: what‘s the future? Oncology25(3) , 220–226, 228 (2011).
  • Furdas SD , KannanS, SipplW, JungM. Small molecule inhibitors of histone acetyltransferases as epigenetic tools and drug candidates. Arch. Pharm. (Weinheim)345(1) , 7–21 (2012).
  • Watts JK , CoreyDR. Silencing disease genes in the laboratory and the clinic. J. Pathol.226(2) , 365–379 (2012).

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