Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation

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Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenotype during differentiation. We performed epigenomic profiling in conjunction with transcriptomic profiling using in vitro differentiation of human primary alveolar epithelial cells (AEC). This model recapitulates an in vivo process in which AEC transition from one differentiated cell type to another during regeneration following lung injury. Interrogation of histone marks over time revealed enrichment of specific transcription factor binding motifs within regions of changing chromatin structure. Cross-referencing of these motifs with pathways showing transcriptional changes revealed known regulatory pathways of distal alveolar differentiation, such as the WNT and transforming growth factor beta (TGFB) pathways, and putative novel regulators of adult AEC differentiation including hepatocyte nuclear factor 4 alpha (HNF4A), and the retinoid X receptor (RXR) signaling pathways. Inhibition of the RXR pathway confirmed its functional relevance for alveolar differentiation. Our incorporation of epigenetic data allowed specific identification of transcription factors that are potential direct upstream regulators of the differentiation process, demonstrating the power of this approach. Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation.

Vyšlo v časopise: Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation. PLoS Genet 9(6): e32767. doi:10.1371/journal.pgen.1003513
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003513

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Zdroje

1. SharmaS, KellyTK, JonesPA (2010) Epigenetics in cancer. Carcinogenesis 31 : 27–36.

2. VasanthiD, MishraRK (2008) Epigenetic regulation of genes during development: a conserved theme from flies to mammals. J Genet Genomics 35 : 413–429.

3. BernsteinBE, MeissnerA, LanderES (2007) The mammalian epigenome. Cell 128 : 669–681.

4. HirschhornJN, BrownSA, ClarkCD, WinstonF (1992) Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev 6 : 2288–2298.

5. GuentherMG, LevineSS, BoyerLA, JaenischR, YoungRA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130 : 77–88.

6. JiaL, ShenHC, WantrobaM, KhalidO, WangQ, et al. (2006) Locus-wide chromatin remodeling and enhanced androgen receptor-mediated transcription in recurrent prostate tumor cells. Mol Cell Bio 26 : 7331–7341.

7. WanH, DingleS, XuY, BesnardV, KaestnerKH, et al. (2005) Compensatory roles of Foxa1 and Foxa2 during lung morphogenesis. J Biol Chem 280 : 13809–13816.

8. MaiA, MassaS, RotiliD, CerbaraI, ValenteS, et al. (2005) Histone deacetylation in epigenetics: an attractive target for anticancer therapy. Med Res Rev 25 : 261–309.

9. SaraivaNZ, OliveiraCS, GarciaJM (2010) Histone acetylation and its role in embryonic stem cell differentiation. World J Stem Cells 2 : 121–126.

10. BoegerH, GriesenbeckJ, StrattanJS, KornbergRD (2003) Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 11 : 1587–1598.

11. SparmannA, van LohuizenM (2006) Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer 6 : 846–856.

12. MüllerJ, HartCM, FrancisNJ, VargasML, SenguptaA, et al. (2002) Histone methyltransferase activity of a Drosophila polycomb group repressor complex. Cell 111 : 197–208.

13. SchwartzYB, PirrottaV (2008) Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20 : 266–273.

14. MurryCE, KellerG (2008) Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell 132 : 661–680.

15. FuchsS, HollinsAJ, LaueM, SchaeferUF, RoemerK, et al. (2003) Differentiation of human alveolar epithelial cells in primary culture: morphological characterization and synthesis of caveolin-1 and surfactant protein-C. Cell Tissue Res 311 : 31–45.

16. ZhouB, AnnDK, FlodbyP, MinooP, LieblerJM, et al. (2008) Rat aquaporin-5 4.3-kb 5′-flanking region differentially regulates expression in salivary gland and lung in vivo. Am J Physiol Cell Physiol 295: C111–C120.

17. FehrenbachH (2001) Alveolar epithelial type II cell: defender of the alveolus revisited. Respir Res 2 : 33–46.

18. ChapmanHA, LiX, AlexanderJP, BrumwellA, LorizioW, et al. (2011) Integrin α6β4 identifies an adult distal epithelial population with regenerative potential in mice. J Clin Invest 121 : 2855–2862.

19. BorokZ, DantoSI, LubmanRL, CaoY, WilliamsMC, et al. (1998) Modulation of t1α expression with alveolar epithelial cell phenotype in vitro. Am J Physiol Lung Cell Mol Physiol 275: L155–164.

20. FangX, SongY, ZemansR, HirschJ, MatthayMA (2004) Fluid transport across cultured rat alveolar epithelial cells: a novel in vitro system. Am J Physiol Lung Cell Mol Physiol 287: L104–10.

21. FlodbyP, BorokZ, BanfalviA, ZhouB, GaoD, et al. (2010) Directed expression of Cre in alveolar epithelial type 1 cells. Am J Respir Cell Mol Biol 43 : 173–178.

22. NielsenS, KingLS, ChristensenBM, AgreP (1997) Aquaporins in complex tissues. II. Subcellular distribution in respiratory and glandular tissues of rat. Am J Physiol Cell Physiol 273: C1549–C1561.

23. CampbellL, HollinsAJ, Al-EidA, NewmanGR, von RuhlandC, et al. (1999) Caveolin-1 expression and caveolae biogenesis during cell transdifferentiation in lung alveolar epithelial primary cultures. Biochem Biophys Res Commun 262 : 744–751.

24. NewmanDR, ZhangH, BortoffK, BonnerJC, SannesPL (2010) Alveolar epithelial differentiation during repair involves FoxA1, Wnt7A, and TGF-β. Proc Am Thorac Soc 7 : 155–156.

25. RamirezMI, MillienG, HindsA, CaoY, SeldinDC, et al. (2003) T1alpha, a lung type I cell differentiation gene, is required for normal lung cell proliferation and alveolus formation at birth. Dev Biol 256 : 61–72.

26. MillienG, SpiraA, HindsA, WangJ, WilliamsMC, et al. (2006) Alterations in gene expression in T1α null lung: a model of deficient alveolar sac development. BMC Dev Biol 6 : 35.

27. MasonRJ, WilliamsMC, WiddicombeJH, SandersMJ, MisfeldtDS, et al. (1982) Transepithelial transport by pulmonary alveolar type II cells in primary culture. Proc Natl Acad Sci U S A 79 : 6033–6037.

28. QiaoR, ZhouB, LieblerJM, LiX, CrandallED, et al. (2003) Identification of three genes of known function expressed by alveolar epithelial type I cells. Am J Respir Cell Mol Biol 29 : 98–105.

29. BallardPL, LeeJW, FangX, ChapinC, AllenL, et al. (2010) Regulated gene expression in cultured type II cells of adult human lung. Am J Physiol Lung Cell Mol Physiol 299: L36–50.

30. CheekJM, EvansMJ, CrandallED (1989) Type I cell-like morphology in tight alveolar epithelial monolayers. Exp Cell Res 184 : 375–387.

31. CheekJM, KimKJ, CrandallED (1989) Tight monolayers of rat alveolar epithelial cells: bioelectric properties and active sodium transport. Am J Physiol 256: C688–93.

32. WangJ, EdeenK, ManzerR, ChangY, WangS, et al. (2007) Differentiated human alveolar epithelial cells and reversibility of their phenotype in vitro. Am J Respir Cell Mol Biol 36 : 661–668.

33. ZhouB, FrancisTA, YangH, TsengW, ZhongQ, et al. (2008) GATA-6 mediates transcriptional activation of aquaporin-5 through interactions with Sp1. Am J Physiol Cell Physiol 295: C1141–C1150.

34. HeinzS, BennerC, SpannN, BertolinoE, LinYC, et al. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38 : 576–589.

35. FlozakAS, LamAP, RussellS, JainM, PeledON, et al. (2010) Beta-catenin/T cell factor signaling is activated during lung injury and promotes the survival and migration of alveolar epithelial cells. J Biol Chem 285 : 3157–3167.

36. NewmanGR, CampbellL, von RuhlandC, JasaniB, GumbletonM (1999) Caveolin and its cellular and subcellular immunolocalisation in lung alveolar epithelium: implications for alveolar epithelial type I cell function. Cell Tissue Res 295 : 111–120.

37. FosterC, AktarA, KopfD, ZhangP, GuttentagS (2004) Pepsinogen C: a type 2 cell-specific protease. Am J Physiol Lung Cell Mol Physiol 286: L382–L387.

38. MucenskiML, WertSE, NationJM, LoudyDE, HuelskenJ, et al. (2003) β-catenin is required for specification of proximal/distal cell fate during lung morphogenesis. J Biol Chem 278 : 40231–40238.

39. TebarM, DestreeO, de VreeWJ, Ten Have-OpbroekAA (2001) Expression of Tcf/Lef and sFrp and localization of beta-catenin in the developing mouse lung. Mech Dev 109 : 437–440.

40. LefebvreP, BenomarY, StaelsB (2010) Retinoid X receptors: common heterodimerization partners with distinct functions. Trends Endocrinol Metabol 21 : 676–683.

41. McGowanS, JacksonSK, Jenkins-MooreM, DaiHH, ChambonP, et al. (2000) Mice bearing deletions of retinoic acid receptors demonstrate reduced lung elastin and alveolar numbers. Am J Respir Cell Mol Biol 23 : 162–167.

42. SimonDM, MarianiTJ (2007) Role of PPARs and retinoid X receptors in the regulation of lung maturation and development. PPAR Res 2007 : 91240.

43. ZhangH, GarberSJ, CuiZ, FoleyJP, MohanGS, et al. (2009) The angiogenic factor midkine is regulated by dexamethasome and retinoic acid during alveolarization and in alveolar epithelial cells. Respir Res 10 : 77.

44. KimuraY, SuzukiT, KanekoC, DarnelAD, MoriyaT, et al. (2002) Retinoid receptors in the developing human lung. Clin Sci 103 : 613–621.

45. HindM, MadenM (2004) Retinoic acid induces alveolar regeneration in the adult mouse lung. Eur Respir J 23 : 20–27.

46. SugimotoK, TakayasuH, NakazawaN, MontedonicoS, PuriP (2008) Prenatal treatment with retinoic acid accelerates type 1 alveolar cell proliferation of the hypoplastic lung in the nitrofen model of congenital diaphragmatic hernia. J Pediatr Surg 43 : 367–372.

47. MontedocinoS, SugimotoK, FelleP, BanniganJ, PuriP (2008) Prenatal treatment with retinoic acid promotes pulmonary alveologenesis in the nitrofen model of congenital diaphragmatic hernia. J Pediatr Surg 43 : 500–507.

48. BaybuttRC, SmithBW, DonskayaEV, HuL, LiT, et al. (2010) The proliferative effects of retinoic acid on primary cultures of adult rat type II pneumocytes depend upon cell density. In Vitro Cell Dev Biol Anim 46 : 20–27.

49. PerezE, BourguetW, GronemeyerH, de LeraAR (2012) Modulation of RXR function through ligand design. Biochim Biophys Acta 1821 : 57–69.

50. NahoumV, PérezE, GermainP, Rodríquez-BarriosF, ManzoF, et al. (2007) Modulators of the structural dynamics of the retinoid X receptor to reveal receptor function. Proc Natl Acad Sci U S A 104 : 17323–17328.

51. FujinoN, KuboH, OtaC, SuzukiT, SuzukiS, et al. (2012) A novel method for isolating individual cellular components from the adult human distal lung. Am J Respir Cell Mol Biol 46 : 442–430.

52. SugaharaK, SadoharaT, SugitaM, IyamaK, TakiguchiM (1999) Differential expression of CCAAT enhancer binding protein family in rat alveolar epithelial cell proliferation and in acute lung injury. Cell Tissue Res 297 : 261–270.

53. BalciO, OzdemirS, MahmoudAS, AcarA, ColakogluMC (2010) The effect of antenatal steroids on fetal lung maturation between the 34th and 36th week of pregnancy. Gynecol Obstet Invest 70 : 95–99.

54. OikonomouN, HarokoposV, ZalevskyJ, ValavanisC, KotanidouA, et al. (2006) Soluble TNF mediates the transition from pulmonary inflammation to fibrosis. PLoS One 1: e108.

55. BesnardV, WertSE, KaestnerKH, WhitsettJA (2005) Stage-specific regulation of respiratory epithelial cell differentiation by Foxa1. Am J Physiol Lung Cell Mol Physiol 289: L750–L759.

56. KelAE, GösslingE, ReuterI, CheremushkinE, Kel-MargoulisOV, et al. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31 : 3576–3579.

57. ZhouB, ZhongQ, MinooP, LiC, AnnDK, et al. (2008) Foxp2 inhibits Nkx2.1-mediated transcription of SP-C via interactions with the Nkx2.1 homeodomain. Am J Respir Cell Mol Biol 38 : 750–758.

58. DuP, KibbeWA, LinSM (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24 : 1547–1548.

59. SmythGK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3 Article 3.

60. BenjaminiY, HochbergY (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57 : 289–300.

61. HuangDW, ShermanBT, LempickiRA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc 4 : 44–57.

62. HuangDW, ShermanBT, LempickiRA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37 : 1–13.

63. Mouse Genome Informatics (MGI) Web, The Jackson Laboratory, Bar Harbor, Maine. (URL: http://www.informatics.jax.org). [retrieved 2/2011].

64. JiaL, KimJ, ShenH, ClarkPE, TilleyWD, et al. (2003) Androgen receptor activity at the prostate specific antigen locus: steroidal and non-steroidal mechanisms. Mol Cancer Res 1 : 385–392.

65. ZangC, SchonesDE, ZengC, CuiK, ZhaoK, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-seq data. Bioinformatics 25 : 1952–1958.

66. HeintzmanND, StuartRK, HonG, FuY, ChingCW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39 : 311–318.

67. BarskiA, CuddapahS, CuiK, RohTY, SchonesDE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129 : 823–837.

68. MikkelsenTS, KuM, JaffeDB, IssacB, LiebermanE, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 : 553–560.

69. PanG, TianS, NieJ, YangC, RuottiV, et al. (2007) Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1 : 299–312.

70. ZhaoXD, HanX, ChewJL, LiuJ, ChiuKP, et al. (2007) Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1 : 286–298.