期刊论文详细信息
Respiratory Research
Application of microarray technology in pulmonary diseases
Demosthenes Bouros1  George Patlakas1  Argyris Tzouvelekis1 
[1] Department of Pneumonology, Medical School, Democritus University of Thrace, Greece
关键词: pulmonary diseases;    sarcoidosis;    pulmonary edema;    acute lung injury;    chronic obstructive pulmonary disease;    asthma;    pulmonary fibrosis;    Microarrays;   
Others  :  1227350
DOI  :  10.1186/1465-9921-5-26
 received in 2004-09-26, accepted in 2004-12-07,  发布年份 2004
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【 摘 要 】

Microarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives.

【 授权许可】

   
2004 Tzouvelekis et al; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Schena M, Shalon D, Davis R, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
  • [2]Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-11.
  • [3]Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y: Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci USA 2001, 98:2199-204.
  • [4]Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I: The transcriptional program of sporulation in budding yeast. Science 1998, 282:699-705.
  • [5]Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D: Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 2002, 13:1977-2000.
  • [6]van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009.
  • [7]Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA: Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci USA 2002, 99:972-7.
  • [8]Wang T, Hopkins D, Schmidt C, Silva S, Houghton R, Takita H, Repasky E, Reed SG: Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis. Oncogene 2000, 19:1519-28.
  • [9]Eisen MB, Brown PO: DNA arrays for analysis of Gene Expression. Methods Enzymol 1999, 303:179-205.
  • [10]Cojocaru GS, Rechavi G, Kaminski N: The use of microarrays in medicine. Isr Med Assoc J 2001, 3:292-296.
  • [11]Alam R, Gorska M: Genomic microarrays: arraying order in biological chaos? Am J Respir Cell Mol Biol 2001, 25:405-8.
  • [12]Kaminski N, Friedman N: Practical approaches to analyzing results of microarray experiments. Am J Respir Cell Mol Biol 2002, 27:125-32.
  • [13]Kraft P, Horvath S: The genetics of gene expression and gene mapping. Trends Biotechnol 2003, 21:377-8.
  • [14]Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH: Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422:297-302.
  • [15]Deyholos MK, Galbraith DW: High-density microarrays for gene expression analysis. Cytometry 2001, 43:229-38.
  • [16]Lopez F, Rougemont J, Loriod B, Bourgeois A, Loi L, Bertucci F, Hingamp P, Houlgatte R, Granjeaud S: Feature extraction and signal processing for nylon DNA microarrays. BMC Genomics 2004, 5:38. BioMed Central Full Text
  • [17]Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM: Expression profiling using cDNA microarrays. Nat Genet 1999, 21:10-4.
  • [18]Bertucci F, Bernard K, Loriod B, Chang YC, Granjeaud S, Birnbaum D, Nguyen C, Peck K, Jordan BR: Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Hum Mol Genet 1999, 8:1715-22.
  • [19]Chambers RC: Gene expression profiling: good housekeeping and a clean message. Thorax 2002, 57:754-6.
  • [20]Dopazo J, Zanders E, Dragoni I, Amphlett G, Falciani F: Methods and approaches in the analysis of gene expression data. J Immunol Methods 2001, 250:93-112.
  • [21]Costabel U, King TE: International consensus statement on idiopathic pulmonary fibrosis. Eur Respir J 2001, 17:163-7.
  • [22]Zuo F, Kaminski N, Eugui E, Allard J, Yakhini Z, Ben-Dor A, Lollini L, Morris D, Kim Y, DeLustro B, Sheppard D, Pardo A, Selman M, Heller RA: 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.
  • [23]Kaminski N, Allard JD, Pittet JF, Zuo F, Griffiths MJ, Morris D, Huang X, Sheppard D, Heller RA: Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc Natl Acad Sci USA 2000, 97:1778-83.
  • [24]Katsuma S, Nishi K, Tanigawara K, Ikawa H, Shiojima S, Takagaki K, Kaminishi Y, Suzuki Y, Hirasawa A, Ohgi T, Yano J, Murakami Y, Tsujimoto G: Molecular monitoring of bleomycin-induced pulmonary fibrosis by cDNA microarray-based gene expression profiling. Biochem Biophys Res Commun 2001, 288:747-51.
  • [25]Chambers RC, Leoni P, Kaminski N, Laurent GJ, Heller RA: Global expression profiling of fibroblast responses to transforming growth factor-beta1 reveals the induction of inhibitor of differentiation-1 and provides evidence of smooth muscle cell phenotypic switching. Am J Pathol 2003, 162:533-46.
  • [26]Liu T, Dhanasekaran SM, Jin H, Hu B, Tomlins SA, Chinnaiyan AM Phan SH: FIZZ1 stimulation of myofibroblast differentiation. Am J Pathol 2004, 164:1315-26.
  • [27]Crystal RG, Bitterman PB, Mossman B, Schwarz MI, Sheppard D, Almasy L, Chapman HA, Friedman SL, King TE Jr, Leinwand LA, Liotta L, Martin GR, Schwartz DA, Schultz GS, Wagner CR, Musson RA: Future research directions in idiopathic pulmonary fibrosis: summary of a National Heart, Lung, and Blood Institute working group. Am J Respir Crit Care Med 2002, 15(166):236-46.
  • [28]Manian P: Genetics of asthma: a review. Chest 1997, 112:1397-408.
  • [29]Cookson W: The alliance of genes and environment in asthma and allergy. Nature 1999, 402:B5-B11.
  • [30]Barnes KC: Atopy and asthma genes-where do we stand? Allergy 2000, 55:803-817.
  • [31]Borish L: Genetics of allergy and asthma. Ann Allergy Asthma Immunol 1999, 82:413-424.
  • [32]Zou J, Young S, Zhu F, Gheyas F, Skeans S, Wan Y, Wang L, Ding W, Billah M, McClanahan T, Coffman RL, Egan R, Umland S: Microarray profile of differentially expressed genes in a monkey model of allergic asthma. Genome Biol 2002, 3(5):research 0020. BioMed Central Full Text
  • [33]Brutsche MH, Joos L, Carlen Brutsche IE, Bissinger R, Tamm M, Custovic A, Woodcock A: Array-based diagnostic gene-expression score for atopy and asthma. J Allergy Clin Immunol 2002, 109:271-3.
  • [34]Lee JH, Kaminski N, Dolganov G, Grunig G, Koth L, Solomon C, Erle DJ, Sheppard D: Interleukin-13 induces dramatically different transcriptional programs in three human airway cell types. Am J Respir Cell Mol Biol 2001, 25:474-85.
  • [35]Temple R, Allen E, Fordham J, Phipps S, Schneider HC, Lindauer K, Hayes I, Lockey J, Pollock K, Jupp R: Microarray analysis of eosinophils reveals a number of candidate survival and apoptosis genes. Am J Respir Cell Mol Biol 2001, 25:425-33.
  • [36]Hakonarson H, Halapi E, Whelan R, Gulcher J, Stefansson K, Grunstein MM: Association between IL-1beta/TNF-alpha-induced glucocorticoid-sensitive changes in multiple gene expression and altered responsiveness in airway smooth muscle. Am J Respir Cell Mol Biol 2001, 25:761-71.
  • [37]Laprise C, Sladek R, Ponton A, Bernier MC, Hudson TJ, Laviolette M: Functional classes of bronchial mucosa genes that are differentially expressed in asthma. BMC Genomics 2004, 5:21. BioMed Central Full Text
  • [38]Sayama K, Diehn M, Matsuda K, Lunderius C, Tsai M, Tam SY, Botstein D, Brown PO, Galli SJ: Transcriptional response of human mast cells stimulated via the Fc (epsilon) RI and identification of mast cells as a source of IL-11. BMC Immunol 2002, 3(1):5. BioMed Central Full Text
  • [39]Nakajima T, Matsumoto K, Suto H, Tanaka K, Ebisawa M, Tomita H, Yuki K, Katsunuma T, Akasawa A, Hashida R, Sugita Y, Ogawa H, Ra C, Saito H: Gene expression screening of human mast cells and eosinophils using high-density oligonucleotide probe arrays: abundant expression of major basic protein in mast cells. Blood 2001, 98:1127-34.
  • [40]Leiferman KM, Gleich GJ, Kephart GM, Haugen HS, Hisamatsu K, Proud D, Lichtenstein LM, Ackerman SJ: Differences between basophils and mast cells: failure to detect Charcot-Leyden crystal protein (lysophospholipase) and eosinophil granule major basic protein in human mast cells. J Immunol 1986, 136:852-5.
  • [41]Brutsche MH, Brutsche IC, Wood P, Brass A, Morrison N, Rattay M, Mogulkoc N, Simler N, Craven M, Custovic A, Egan JJ, Woodcock A: Apoptosis signals in atopy and asthma measured with cDNA arrays. Clin Exp Immunol 2001, 123:181-7.
  • [42]Syed F, Blakemore SJ, Wallace DM, Trower MK, Johnson M, Markham AF, Morrison JF: CCR7 (EBI1) receptor down-regulation in asthma: differential gene expression in human CD4+ T lymphocytes. QJM 1999, 92:463-71.
  • [43]Banerjee SK, Young HW, Volmer JB, Blackburn MR: Gene expression profiling in inflammatory airway disease associated with elevated adenosine. Am J Physiol Lung Cell Mol Physiol 2002, 282:L169-L182.
  • [44]Petty TL: COPD in perspective. Chest 2002, 121:116S-120S.
  • [45]Koike E, Hirano S, Furuyama A, Kobayashi T: cDNA microarray analysis of rat alveolar epithelial cells following exposure to organic extract of diesel exhaust particles. Toxicol Appl Pharmacol 2004, 201:178-85.
  • [46]Yamanaka Y, Tamari M, Nakahata T, Nakamura Y: Gene expression profiles of human small airway epithelial cells treated with low doses of 14- and 16-membered macrolides. Biochem Biophys Res Commun 2001, 287:198-203.
  • [47]Fuke S, Betsuyaku T, Nasuhara Y, Morikawa T, Katoh H, Nishimura M: Chemokines in bronchiolar epithelium in the development of chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol 2004, 31:405-12.
  • [48]Vuillemenot BR, Rodriguez JF, Hoyle GW: Lymphoid tissue and emphysema in the lungs of transgenic mice inducibly expressing tumor necrosis factor-alpha. Am J Respir Cell Mol Biol 2004, 30:438-48.
  • [49]Sethi JM, Rochester CL: Smoking and chronic obstructive pulmonary disease. Clin Chest Med 2000, 21:67-86.
  • [50]Hackett NR, Heguy A, Harvey BG, O'Connor TP, Luettich K, Flieder DB, Kaplan R, Crystal RG: Variability of antioxidant-related gene expression in the airway epithelium of cigarette smokers. Am J Respir Cell Mol Biol 2003, 29:331-43.
  • [51]Sheppard D, Roger S: Mitchell lecture. Uses of expression microarrays in studies of pulmonary fibrosis, asthma, acute lung injury, and emphysema. Chest 2002, 121:21S-25S.
  • [52]Morris DG, Huang X, Kaminski N, Wang Y, Shapiro SD, Dolganov G, Glick A, Sheppard D: Loss of integrin alpha (v) beta6-mediated TGF-beta activation causes Mmp12-dependent emphysema. Nature 2003, 422:169-73.
  • [53]Golpon HA, Geraci MW, Moore MD, Miller HL, Miller GJ, Tuder RM, Voelkel NF: HOX genes in human lung: altered expression in primary pulmonary hypertension and emphysema. Am J Pathol 2001, 158(3):955-66.
  • [54]Lewis JF, Jobe AH: Surfactant and the adult respiratory distress syndrome. Am Rev Respir Dis 1993, 147:218-33.
  • [55]Pittet JF, Mackersie RC, Martin TR, Matthay MA: Biological markers of acute lung injury: prognostic and pathogenetic significance. Am J Respir Crit Care Med 1997, 155:1187-205.
  • [56]McDowell SA, Gammon K, Bachurski CJ, Wiest JS, Leikauf JE, Prows DR, Leikauf GD: Differential gene expression in the initiation and progression of nickel-induced acute lung injury. Am J Respir Cell Mol Biol 2000, 23:466-74.
  • [57]Jobe AH, Ikegami M: Surfactant and acute lung injury. Proc Assoc Am Physicians 1998, 110:489-95.
  • [58]Olman MA, White KE, Ware LB, Cross MT, Zhu S, Matthay MA: Microarray analysis indicates that pulmonary edema fluid from patients with acute lung injury mediates inflammation, mitogen gene expression, and fibroblast proliferation through bioactive interleukin-1. J Immunol 2004, 172:2668-77.
  • [59]Abraham E, Carmody A, Shenkar R, Arcaroli J: Neutrophils as early immunologic effectors in hemorrhage- or endotoxemia-induced acute lung injury. Am J Physiol Lung Cell Mol Physiol 2000, 279:L1137-45.
  • [60]Blackwell TS, Blackwell TR, Holden EP, Christman BW, Christman JW: In vivo antioxidant treatment suppresses nuclear factor-kappa B activation and neutrophilic lung inflammation. J Immunol 1996, 157:1630-7.
  • [61]Kupfner JG, Arcaroli JJ, Yum HK, Nadler SG, Yang KY, Abraham E: Role of NF-kappaB in endotoxemia-induced alterations of lung neutrophil apoptosis. J Immunol 2001, 167:7044-51.
  • [62]Cher CD, Armugam A, Lachumanan R, Coghlan MW, Jeyaseelan K: Pulmonary inflammation and edema induced by phospholipase A2: global gene analysis and effects on aquaporins and Na+/K+-ATPase. J Biol Chem 2003, 278:31352-60.
  • [63]Sabbadini M, Barisani D, Conforti E, Marozzi A, Ginelli E, Miserocchi G, Meneveri R: Gene expression analysis in interstitial lung edema induced by saline infusion. Biochim Biophys Acta 2003, 1638:149-56.
  • [64]Perkowski S, Sun J, Singhal S, Santiago J, Leikauf GD, Albelda SM: Gene expression profiling of the early pulmonary response to hyperoxia in mice. Am J Respir Cell Mol Biol 2003, 28:682-96.
  • [65]Chinnaiyan AM Huber-Lang M, Kumar-Sinha C, Barrette TR, Shankar-Sinha S, Sarma VJ, Padgaonkar VA, Ward PA: Molecular signatures of sepsis: multiorgan gene expression profiles of systemic inflammation. Am J Pathol 2001, 159:1199-209.
  • [66]Joint Statement of the American Thoracic Society (ATS), the European Respiratory Society and the World Association of Sarcoidosis and Other Granulomatous Disorders (WASOG): Statement on Sarcoidosis adopted by the ATS Board of Directors and by the ERS Executive Commitee, February 1999 Am J Respir Crit Care Med 1999, 160:736-755.
  • [67]Haslett C, Savill JS, Whyte MK, Stern M, Dransfield I, Meagher LC: Granulocyte apoptosis and the control of inflammation. Philos Trans R Soc Lond B Biol Sci 1994, 345:327-33.
  • [68]Rutherford RM, Kehren J, Staedtler F, Chibout SD, Egan JJ, Tamm M, Gilmartin JJ, Brutsche MH: Functional genomics in sarcoidosis – reduced or increased apoptosis? Swiss Med Wkly 2001, 131:459-70.
  • [69]Sabounchi-Schutt F, Astrom J, Hellman U, Eklund A, Grunewald J: Changes in bronchoalveolar lavage fluid proteins in sarcoidosis: a proteomics approach. Eur Respir J 2003, 21:414-20.
  • [70]MacBeath G: Protein microarrays and proteomics. Nat Genet 2002, 32:526-32.
  • [71]Aitman TJ: DNA microarrays in medical practice. BMJ 2001, 323:611-5.
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