Journal of Molecular Medicine

, Volume 85, Issue 7, pp 733–743 | Cite as

Molecular defense mechanisms of Barrett’s metaplasia estimated by an integrative genomics

  • Jerzy Ostrowski
  • Michal Mikula
  • Jakub Karczmarski
  • Tymon Rubel
  • Lucjan S. Wyrwicz
  • Piotr Bragoszewski
  • Pawel Gaj
  • Michal Dadlez
  • Eugeniusz Butruk
  • Jaroslaw Regula
Original Article


Barrett’s esophagus is characterized by the replacement of squamous epithelium with specialized intestinal metaplastic mucosa. The exact mechanisms of initiation and development of Barrett’s metaplasia remain unknown, but a hypothesis of “successful adaptation” against noxious reflux components has been proposed. To search for the repertoire of adaptation mechanisms of Barrett’s metaplasia, we employed high-throughput functional genomic and proteomic methods that defined the molecular background of metaplastic mucosa resistance to reflux. Transcriptional profiling was established for 23 pairs of esophageal squamous epithelium and Barrett’s metaplasia tissue samples using Affymetrix U133A 2.0 GeneChips and validated by quantitative real-time polymerase chain reaction. Differences in protein composition were assessed by electrophoretic and mass-spectrometry-based methods. Among 2,822 genes differentially expressed between Barrett’s metaplasia and squamous epithelium, we observed significantly overexpressed metaplastic mucosa genes that encode cytokines and growth factors, constituents of extracellular matrix, basement membrane and tight junctions, and proteins involved in prostaglandin and phosphoinositol metabolism, nitric oxide production, and bioenergetics. Their expression likely reflects defense and repair responses of metaplastic mucosa, whereas overexpression of genes encoding heat shock proteins and several protein kinases in squamous epithelium may reflect lower resistance of normal esophageal epithelium than Barrett’s metaplasia to reflux components. Despite the methodological and interpretative difficulties in data analyses discussed in this paper, our studies confirm that Barrett’s metaplasia may be regarded as a specific microevolution allowing for accumulation of mucosal morphological and physiological changes that better protect against reflux injury.


Barrett’s esophagus Defense mechanisms Gene expression Microarrays Proteomics Integrative genomics 



This work was supported by grants from the Polish Committee for Scientific Research (PBZ-KBN-091/P05/2003/43, KBN-P05A-131-25 and PBZ-KBN-088/P04/2003 [for MD]). JO work was also supported by a scholar grant from the Foundation for Polish Science. LSW was supported by a Program for Young Researchers from the Foundation for Polish Science. We thank Drs. Janina Orlowska and Dorota Jarosz for the histological examination.

Supplementary material

109_2007_176_MOESM1_ESM.pdf (664 kb)
Supplementary Figures (PDF 679 kb)
109_2007_176_MOESM2_ESM.pdf (132 kb)
Supplementary materials (PDF 135 kb)
109_2007_176_MOESM3_ESM.pdf (551 kb)
Supplementary Tables (PDF 1.2 mb)


  1. 1.
    Sampliner RE (2002) Updated guidelines for the diagnosis, surveillance, and therapy of Barrett’s esophagus. Am J Gastroenterol 97:1888–1895PubMedCrossRefGoogle Scholar
  2. 2.
    Orlando RC (2006) Mucosal defense in Barrett’s esophagus In: Sharma P, Sampliner RE (eds) Barrett’s esophagus and esophageal adenocarcinoma. Blackwell, Malden, MA, pp 60–72CrossRefGoogle Scholar
  3. 3.
    Cameron AJ, Zinsmeister AR, Ballard DJ, Carney JA (1990) Prevalence of columnar-lined (Barrett’s) esophagus. Comparison of population-based clinical and autopsy findings. Gastroenterology 99:918–922PubMedGoogle Scholar
  4. 4.
    Hameeteman W, Tytgat GN, Houthoff HJ, van den Tweel JG (1989) Barrett’s esophagus: development of dysplasia and adenocarcinoma. Gastroenterology 96:1249–1256PubMedGoogle Scholar
  5. 5.
    McArdle JE, Lewin KJ, Randall G, Weinstein W (1992) Distribution of dysplasias and early invasive carcinoma in Barrett’s esophagus. Human Pathol 23:479–482CrossRefGoogle Scholar
  6. 6.
    Rosenberg JC, Budev H, Edwards RC, Singal S, Steiger Z, Sundareson AS (1985) Analysis of adenocarcinoma in Barrett’s esophagus utilizing a staging system. Cancer 55:1353–1360PubMedCrossRefGoogle Scholar
  7. 7.
    Schmidt HG, Riddell RH, Walther B, Skinner DB, Riemann JF (1985) Dysplasia in Barrett’s esophagus. J Cancer Res Clin Oncol 110:145–152PubMedCrossRefGoogle Scholar
  8. 8.
    Ostrowski J, Rubel T, Wyrwicz LS, Mikula M, Bielasik A, Butruk E, Regula J (2006) Three clinical variants of gastroesophageal reflux disease form two distinct gene expression signatures. J Mol Med 84(10):872–882PubMedCrossRefGoogle Scholar
  9. 9.
    Schlemper RJ, Riddell RH, Kato Y, Borchard F, Cooper HS, Dawsey SM, Dixon MF, Fenoglio-Preiser CM, Flejou JF, Geboes K, Hattori T, Hirota T, Itabashi M, Iwafuchi M, Iwashita A, Kim YI, Kirchner T, Klimpfinger M, Koike M, Lauwers GY, Lewin KJ, Oberhuber G, Offner F, Price AB, Rubio CA, Shimizu M, Shimoda T, Sipponen P, Solcia E, Stolte M, Watanabe H, Yamabe H (2000) The Vienna classification of gastrointestinal epithelial neoplasia. Gut 47:251–255PubMedCrossRefGoogle Scholar
  10. 10.
    Mikula M, Dzwonek A, Karczmarski J, Rubel T, Dadlez M, Wyrwicz LS, Bomsztyk K, Ostrowski J (2006) Landscape of the hnRNP K protein–protein interactome. Proteomics 6:2395–2406PubMedCrossRefGoogle Scholar
  11. 11.
    Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J (2006) Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length. Biochim Biophys Acta 1764:299–306PubMedGoogle Scholar
  12. 12.
    Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261PubMedCrossRefGoogle Scholar
  13. 13.
    Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357PubMedCrossRefGoogle Scholar
  14. 14.
    Beisvag V, Junge FK, Bergum H, Jolsum L, Lydersen S, Gunther CC, Ramampiaro H, Langaas M, Sandvik AK, Laegreid A (2006) GeneTools-application for functional annotation and statistical hypothesis testing. BMC Bioinformatics 7:470PubMedCrossRefGoogle Scholar
  15. 15.
    Peano C, Severgnini M, Cifola I, De Bellis G, Battaglia C (2006) Transcriptome amplification methods in gene expression profiling. Expert Rev Mol Diagn 6:465–480PubMedCrossRefGoogle Scholar
  16. 16.
    Flucke U, Steinborn E, Dries V, Monig SP, Schneider PM, Thiele J, Holscher AH, Dienes HP, Baldus SE (2003) Immunoreactivity of cytokeratins (CK7, CK20) and mucin peptide core antigens (MUC1, MUC2, MUC5AC) in adenocarcinomas, normal and metaplastic tissues of the distal oesophagus, oesophago-gastric junction and proximal stomach. Histopathology 43:127–134PubMedCrossRefGoogle Scholar
  17. 17.
    Ormsby AH, Goldblum JR, Rice TW, Richter JE, Falk GW, Vaezi MF, Gramlich TL (1999) Cytokeratin subsets can reliably distinguish Barrett’s esophagus from intestinal metaplasia of the stomach. Human Pathol 30:288–294CrossRefGoogle Scholar
  18. 18.
    Bi LC, Kaunitz JD (2003) Gastroduodenal mucosal defense: an integrated protective response. Curr Opin Gastroenterol 19:526–532PubMedCrossRefGoogle Scholar
  19. 19.
    Shim JO, Shin CY, Lee TS, Yang SJ, An JY, Song HJ, Kim TH, Huh IH, Sohn UD (2002) Signal transduction mechanism via adenosine A1 receptor in the cat esophageal smooth muscle cells. Cell Signal 14:365–372PubMedCrossRefGoogle Scholar
  20. 20.
    Jaiswal K, Tello V, Lopez-Guzman C, Nwariaku F, Anthony T, Sarosi GA Jr (2004) Bile salt exposure causes phosphatidyl-inositol-3-kinase-mediated proliferation in a Barrett’s adenocarcinoma cell line. Surgery 136:160–168PubMedCrossRefGoogle Scholar
  21. 21.
    Kashiwagi M, Ohba M, Chida K, Kuroki T (2002) Protein kinase C eta (PKC eta): its involvement in keratinocyte differentiation. J Biochem (Tokyo) 132:853–857CrossRefGoogle Scholar
  22. 22.
    Nishio H, Hayashi Y, Terashima S, Takeuchi K (2006) Role of endogenous nitric oxide in mucosal defense of inflamed rat stomach following iodoacetamide treatment. Life Sci 79:1523–1530PubMedCrossRefGoogle Scholar
  23. 23.
    Wallace JL (1996) Cooperative modulation of gastrointestinal mucosal defence by prostaglandins and nitric oxide. Clin Invest Med 19:346–351PubMedGoogle Scholar
  24. 24.
    Das AM (2003) Regulation of the mitochondrial ATP-synthase in health and disease. Mol Genet Metab 79:71–82PubMedCrossRefGoogle Scholar
  25. 25.
    Mikula M, Dzwonek A, Hennig EE, Ostrowski J (2005) Increased mitochondrial gene expression during L6 cell myogenesis is accelerated by insulin. Int J Biochem Cell Biol 37:1815–1828PubMedCrossRefGoogle Scholar
  26. 26.
    Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31:19–20PubMedCrossRefGoogle Scholar
  27. 27.
    Kaunitz JD, Akiba Y (2004) Gastroduodenal mucosal defense: role of endogenous mediators. Curr Opin Gastroenterol 20:526–532PubMedCrossRefGoogle Scholar
  28. 28.
    Lichtenberger LM (1999) Gastroduodenal mucosal defense. Curr Opin Gastroenterol 15:463PubMedCrossRefGoogle Scholar
  29. 29.
    Levine DS, Rubin CE, Reid BJ, Haggitt RC (1989) Specialized metaplastic columnar epithelium in Barrett’s esophagus. A comparative transmission electron microscopic study. Lab Invest 60:418–432PubMedGoogle Scholar
  30. 30.
    Latchford A, Eksteen B, Jankowski J (2001) The continuing tale of cytokeratins in Barrett’s mucosa: as you like it. Gut 49:746–747PubMedCrossRefGoogle Scholar
  31. 31.
    Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S (2005) Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. BMC Bioinformatics 6:26PubMedCrossRefGoogle Scholar
  32. 32.
    Playford RJ, Ghosh S (2005) Cytokines and growth factor modulators in intestinal inflammation and repair. J Pathol 205:417–425PubMedCrossRefGoogle Scholar
  33. 33.
    Ota H, Hayama M, Momose M, El-Zimaity HM, Matsuda K, Sano K, Maruta F, Okumura N, Katsuyama T (2006) Co-localization of TFF2 with gland mucous cell mucin in gastric mucous cells and in extracellular mucous gel adherent to normal and damaged gastric mucosa. Histochem Cell Biol 126(5):617–625PubMedCrossRefGoogle Scholar
  34. 34.
    Thim L, Madsen F, Poulsen SS (2002) Effect of trefoil factors on the viscoelastic properties of mucus gels. Eur J Clin Invest 32:519–527PubMedCrossRefGoogle Scholar
  35. 35.
    Basson MD (2003) Invited research review: Cell–matrix interactions in the gut epithelium. Surgery 133:263–267PubMedCrossRefGoogle Scholar
  36. 36.
    Asaoka D, Miwa H, Hirai S, Ohkawa A, Kurosawa A, Kawabe M, Hojo M, Nagahara A, Minoo T, Ohkura R, Ohkusa T, Sato N (2005) Altered localization and expression of tight-junction proteins in a rat model with chronic acid reflux esophagitis. J Gastroenterol 40:781–790PubMedCrossRefGoogle Scholar
  37. 37.
    Rahner C, Mitic LL, Anderson JM (2001) Heterogeneity in expression and subcellular localization of claudins 2, 3, 4, and 5 in the rat liver, pancreas, and gut. Gastroenterology 120:411–422PubMedCrossRefGoogle Scholar
  38. 38.
    Martin GR, Wallace JL (2006) Gastrointestinal inflammation: a central component of mucosal defense and repair. Exp Biol Medicine (Maywood) 231:130–137Google Scholar
  39. 39.
    Nusrat A, Turner JR, Madara JL (2000) Molecular physiology and pathophysiology of tight junctions. IV. Regulation of tight junctions by extracellular stimuli: nutrients, cytokines, and immune cells. Am J Physiol Gastrointest Liver Physiol 279:G851–G857PubMedGoogle Scholar
  40. 40.
    Wallace JL, Devchand PR (2005) Emerging roles for cyclooxygenase-2 in gastrointestinal mucosal defense. Br J Pharmacol 145:275–282PubMedCrossRefGoogle Scholar
  41. 41.
    Yamato M, Nagahama K, Kotani T, Kato S, Takeuchi K (2005) Biphasic effect of prostaglandin E2 in a rat model of esophagitis mediated by EP1 receptors: relation to pepsin secretion. Digestion 72:109–118PubMedCrossRefGoogle Scholar
  42. 42.
    Ishikawa T, Morris PL (2006) Interleukin-1β signals through a cJun-N-terminal kinase (JNK)-dependent inducible nitric oxide synthase and nitric oxide production pathway in Sertoli epithelial cells. Endocrinology 147(11):5424–5430PubMedCrossRefGoogle Scholar
  43. 43.
    Li H, Wallerath T, Forstermann U (2002) Physiological mechanisms regulating the expression of endothelial-type NO synthase. Nitric Oxide 7:132–147PubMedCrossRefGoogle Scholar
  44. 44.
    Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJ, Marra MA (2006) Sequence biases in large scale gene expression profiling data. Nucleic Acids Res 34:e83PubMedCrossRefGoogle Scholar
  45. 45.
    Ostrowski J, Wocial T, Skurzak H, Bartnik W (2003) Do altering in ornithine decarboxylase activity and gene expression contribute to antiproliferative properties of COX inhibitors? Br J Cancer 88:1143–1151PubMedCrossRefGoogle Scholar
  46. 46.
    Huang Z, Tunnacliffe A (2004) Response of human cells to desiccation: comparison with hyperosmotic stress response. J Physiol 558:181–191PubMedCrossRefGoogle Scholar
  47. 47.
    Souza RF, Shewmake K, Pearson S, Sarosi GA Jr, Feagins LA, Ramirez RD, Terada LS, Spechler SJ (2004) Acid increases proliferation via ERK and p38 MAPK-mediated increases in cyclooxygenase-2 in Barrett’s adenocarcinoma cells. Am J Physiol Gastrointest Liver Physiol 287:G743–G748PubMedCrossRefGoogle Scholar
  48. 48.
    Toivola DM, Zhou Q, English LS, Omary MB (2002) Type II keratins are phosphorylated on a unique motif during stress and mitosis in tissues and cultured cells. Mol Biol Cell 13:1857–1870PubMedCrossRefGoogle Scholar
  49. 49.
    Petrof EO, Ciancio MJ, Chang EB (2004) Role and regulation of intestinal epithelial heat shock proteins in health and disease. Chinese Journal of Digestive Diseases 5:45–50PubMedCrossRefGoogle Scholar
  50. 50.
    Guillem PG (2005) How to make a Barrett esophagus: pathophysiology of columnar metaplasia of the esophagus. Dig Dis Sci 50:415–424PubMedCrossRefGoogle Scholar
  51. 51.
    Gomes LI, Esteves GH, Carvalho AF, Cristo EB, Hirata R Jr, Martins WK, Marques SM, Camargo LP, Brentani H, Pelosof A, Zitron C, Sallum RA, Montagnini A, Soares FA, Neves EJ, Reis LF (2005) Expression profile of malignant and nonmalignant lesions of esophagus and stomach: differential activity of functional modules related to inflammation and lipid metabolism. Cancer Res 65:7127–7136PubMedCrossRefGoogle Scholar
  52. 52.
    Wang S, Zhan M, Yin J, Abraham JM, Mori Y, Sato F, Xu Y, Olaru A, Berki AT, Li H, Schulmann K, Kan T, Hamilton JP, Paun B, Yu MM, Jin Z, Cheng Y, Ito T, Mantzur C, Greenwald BD, Meltzer SJ (2006) Transcriptional profiling suggests that Barrett’s metaplasia is an early intermediate stage in esophageal adenocarcinogenesis. Oncogene 25:3346–3356PubMedCrossRefGoogle Scholar
  53. 53.
    Barrett MT, Yeung KY, Ruzzo WL, Hsu L, Blount PL, Sullivan R, Zarbl H, Delrow J, Rabinovitch PS, Reid BJ (2002) Transcriptional analyses of Barrett’s metaplasia and normal upper GI mucosae. Neoplasia 4:121–128PubMedCrossRefGoogle Scholar
  54. 54.
    El-Serag HB, Nurgalieva Z, Souza RF, Shaw C, Darlington G (2006) Is genomic evaluation feasible in endoscopic studies of Barrett’s esophagus? A pilot study. Gastrointest Endosc 64:17–26PubMedCrossRefGoogle Scholar
  55. 55.
    van Baal JW, Milano F, Rygiel AM, Bergman JJ, Rosmolen WD, van Deventer SJ, Wang KK, Peppelenbosch MP, Krishnadath KK (2005) A comparative analysis by SAGE of gene expression profiles of Barrett’s esophagus, normal squamous esophagus, and gastric cardia. Gastroenterology 129:1274–1281PubMedCrossRefGoogle Scholar
  56. 56.
    Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207PubMedCrossRefGoogle Scholar
  57. 57.
    Godovac-Zimmermann J, Kleiner O, Brown LR, Drukier AK (2005) Perspectives in spicing up proteomics with splicing. Proteomics 5:699–709PubMedCrossRefGoogle Scholar
  58. 58.
    Greenbaum D, Colangelo C, Williams K, Gerstein M (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biology 4:117PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Jerzy Ostrowski
    • 1
  • Michal Mikula
    • 1
  • Jakub Karczmarski
    • 1
  • Tymon Rubel
    • 2
  • Lucjan S. Wyrwicz
    • 1
  • Piotr Bragoszewski
    • 1
  • Pawel Gaj
    • 1
  • Michal Dadlez
    • 3
  • Eugeniusz Butruk
    • 1
  • Jaroslaw Regula
    • 1
  1. 1.Department of Gastroenterology, Medical Center for Postgraduate EducationMaria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyWarsawPoland
  2. 2.Institute of RadioelectronicsWarsaw University of TechnologyWarsawPoland
  3. 3.Department of Biophysics, Institute of Biochemistry and BiophysicsPASWarsawPoland

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