Gene Expression Studies in Lung Development and Lung Stem Cell Biology

Current Topics in Developmental Biology

Volumn 64, Issue , 2004, Pages 57-71

  Mariani, Thomas J ^a   Kaminski, Naftali ^b  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CYTOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HISTOLOGY; LUNG; LUNG ALVEOLUS; LUNG TUMOR; METABOLISM; MORPHOGENESIS; PHYSIOLOGY; PRENATAL DEVELOPMENT; REVIEW; STEM CELL;

ANIMALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; LUNG; LUNG NEOPLASMS; MORPHOGENESIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PULMONARY ALVEOLI; STEM CELLS;

EID: 16644384915     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0070-2153(04)64004-X     Document Type: Article

References (50)

1. A.A. Alizadeh M.B. Eisen R.E. Davis C. Ma I.S. Lossos A. Rosenwald J.C. Boldrick H. Sabet T. Tran X. Yu J.I. Powell L. Yang G.E. Marti T. Moore J. Hudson Jr. L. Lu D.B. Lewis R. Tibshirani G. Sherlock W.C. Chan T.C. Greiner D.D. Weisenburger J.O. Armitage R. Warnke R. Levy W. Wilson M.R. Grever J.C. Byrd D. Botstein P.O. Brown L.M. Staudt Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 403 6769 2000 503 511
2. U. Alon Biological networks: The tinkerer as an engineer Science 301 5641 2003 1866 1867
3. M.N. Arbeitman E.E. Furlong F. Imam E. Johnson B.H. Null B.S. Baker M.A. Krasnow M.P. Scott R.W. Davis K.P. White Gene expression during the life cycle of Drosophila melanogaster Science 297 5590 2002 2270 2275
4. D.G. Beer S.L. Kardia C.C. Huang T.J. Giordano A.M. Levin D.E. Misek L. Lin G. Chen T.G. Gharib D.G. Thomas M.L. Lizyness R. Kuick S. Hayasaka J.M. Taylor M.D. Iannettoni M.B. Orringer S. Hanash Gene-expression profiles predict survival of patients with lung adenocarcinoma Nat. Med 8 8 2002 816 824
5. S. Bellusci J. Grindley H. Emoto N. Itoh B.L. Hogan Fibroblast growth factor 10 (FGF10) and branching morphogenesis in the embryonic mouse lung Development 124 23 1997 4867 4878
6. A. Bhattacharjee W. Richards J. Staunton C. Li S. Monti P. Vasa C. Ladd J. Beheshti R. Bueno M. Gillette M. Loda G. Weber E. Mark E. Lander W. Wong B. Johnson T. Golub D. Sugarbaker M. Meyerson Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc. Natl. Acad. Sci. USA 98 2001 13790 13795
7. A.C. Borczuk L. Gorenstein K.L. Walter A.A. Assaad L. Wang C.A. Powell Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways Am. J. Pathol 163 5 2003 1949 1960
8. H. Bostrom K. Willetts M. Pekny P. Leveen P. Lindahl H. Hedstrand M. Pekna M. Hellstrom S. Gebre-Medhin M. Schalling M. Nilsson S. Kurland J. Tornell J.K. Heath C. Betsholtz PDGF-A signaling is a critical event in lung alveolar myofibroblast development and alveogenesis Cell 85 6 1996 863 873
9. G.R. Burton Y. Guan R. Nagarajan R.E. McGehee Jr. Microarray analysis of gene expression during early adipocyte differentiation Gene 293 1–2 2002 21 31
10. W. Cardoso Lung morphogenesis revisited: Old facts, current ideas Dev. Dyn 219 2 2000 121 130
11. W.V. Cardoso Molecular regulation of lung development Annu. Rev. Physiol 63 2001 471 494
12. L.B. Clerch A.S. Baras G.D. Massaro E.P. Hoffman D. Massaro DNA microarray analysis of neonatal mouse lung connects regulation of KDR with dexamethasone-induced inhibition of alveolar formation Am. J. Physiol. Lung Cell Mol. Physiol 286 2 2004 L411 L419
13. R.H. Costa V.V. Kalinichenko L. Lim Transcription factors in mouse lung development and function Am. J. Physiol. Lung Cell Mol. Physiol 280 5 2001 L823 L838
14. B. Dekel Profiling gene expression in kidney development Nephron. Exp. Nephrol 95 1 2003 E1 E6
15. A. Erez M. Perelman S.M. Hewitt G. Cojacaru I. Goldberg I. Shahar P. Yaron I. Muler S. Campaner N. Amariglio G. Rechavi I.R. Kirsch M. Krupsky N. Kaminski S. Izraeli Sil overexpression in lung cancer characterizes tumors with increased mitotic activity Oncogene 23 31 2004 5371 5377
16. E. Huang S.H. Cheng H. Dressman J. Pittman M.H. Tsou C.F. Horng A. Bild E.S. Iversen M. Liao C.M. Chen M. West J.R. Nevins A.T. Huang Gene expression predictors of breast cancer outcomes Lancet 361 9369 2003 1590 1596
17. N.B. Ivanova J.T. Dimos C. Schaniel J.A. Hackney K.A. Moore I.R. Lemischka A stem cell molecule signature Science 298 5593 2002 601 604
18. S. Izraeli L.A. Lowe V.L. Bertness D.J. Good D.W. Dorward I.R. Kirsch M.R. Kuehn The SIL gene is required for mouse embryonic axial development and left-right specification Nature 399 6737 1999 691 694
19. S. Izraeli L.A. Lowe V.L. Bertness S. Campaner H. Hahn I.R. Kirsch M.R. Kuehn Genetic evidence that Sil is required for the Sonic Hedgehog response pathway Genesis 31 2 2001 72 77
20. F. Kaplan J. Comber R. Sladek T.J. Hudson L.J. Muglia T. Macrae S. Gagnon M. Asada J.A. Brewer N.B. Sweezey The growth factor midkine is modulated by both glucocorticoid and retinoid in fetal lung development Am. J. Respir. Cell Mol. Biol 28 1 2003 33 41
21. S.K. Kim J. Lund M. Kiraly K. Duke M. Jiang J.M. Stuart A. Eizinger B.N. Wylie G.S. Davidson A gene expression map for Caenorhabditis elegans Science 293 5537 2001 2087 2092
22. D.W. Koh J.D. Roby B. Starcher R.M. Senior R.A. Pierce Postpneumonectomy lung growth: A model of reinitiation of tropoelastin and type I collagen production in a normal pattern in adult rat lung Am. J. Respir Cell Mol. Biol 15 5 1996 611 623
23. E.S. Lander L.M. Linton B. Birren C. Nusbaum M.C. Zody J. Baldwin K. Devon K. Dewar M. Doyle W. FitzHugh R. Funke D. Gage K. Harris A. Heaford J. Howland L. Kann J. Lehoczky R. LeVine P. McEwan K. McKernan J. Meldrim J.P. Mesirov C. Miranda W. Morris J. Naylor C. Raymond M. Rosetti R. Santos A. Sheridan C. Sougnez N. Stange-Thomann N. Stojanovic A. Subramanian D. Wyman J. Rogers J. Sulston R. Ainscough S. Beck D. Bentley J. Burton C. Clee N. Carter A. Coulson R. Deadman P. Deloukas A. Dunham I. Dunham R. Durbin L. French D. Grafham S. Gregory T. Hubbard S. Humphray A. Hunt M. Jones C. Lloyd A. McMurray L. Matthews S. Mercer S. Milne J.C. Mullikin A. Mungall R. Plumb M. Ross R. Shownkeen S. Sims R.H. Waterston R.K. Wilson L.W. Hillier J.D. McPherson M.A. Marra E.R. Mardis L.A. Fulton A.T. Chinwalla K.H. Pepin W.R. Gish S.L. Chissoe M.C. Wendl K.D. Delehaunty T.L. Miner A. Delehaunty J.B. Kramer L.L. Cook R.S. Fulton D.L. Johnson P.J. Minx S.W. Clifton T. Hawkins E. Branscomb P. Predki P. Richardson S. Wenning T. Slezak N. Doggett J.F. Cheng A. Olsen S. Lucas C. Elkin E. Uberbacher M. Frazier R.A. Gibbs D.M. Muzny S.E. Scherer J.B. Bouck E.J. Sodergren K.C. Worley C.M. Rives J.H. Gorrell M.L. Metzker S.L. Naylor R.S. Kucherlapati D.L. Nelson G.M. Weinstock Y. Sakaki A. Fujiyama M. Hattori T. Yada A. Toyoda T. Itoh C. Kawagoe H. Watanabe Y. Totoki T. Taylor J. Weissenbach R. Heilig W. Saurin F. Artiguenave P. Brottier T. Bruls E. Pelletier C. Robert P. Wincker D.R. Smith L. Doucette-Stamm M. Rubenfield K. Weinstock H.M. Lee J. Dubois A. Rosenthal M. Platzer G. Nyakatura S. Taudien A. Rump H. Yang J. Yu J. Wang G. Huang J. Gu L. Hood L. Rowen A. Madan S. Qin R.W. Davis N.A. Federspiel A.P. Abola M.J. Proctor R.M. Myers J. Schmutz M. Dickson J. Grimwood D.R. Cox M.V. Olson R. Kaul N. Shimizu K. Kawasaki S. Minoshima G.A. Evans M. Athanasiou R. Schultz B.A. Roe F. Chen H. Pan J. Ramser H. Lehrach R. Reinhardt W.R. McCombie M. de la Bastide N. Dedhia H. Blocker K. Hornischer G. Nordsiek R. Agarwala L. Aravind J.A. Bailey A. Bateman S. Batzoglou E. Birney P. Bork D.G. Brown C.B. Burge L. Cerutti H.C. Chen D. Church M. Clamp R.R. Copley T. Doerks S.R. Eddy E.E. Eichler T.S. Furey J. Galagan J.G. Gilbert C. Harmon Y. Hayashizaki D. Haussler H. Hermjakob K. Hokamp W. Jang L.S. Johnson T.A. Jones S. Kasif A. Kaspryzk S. Kennedy W.J. Kent P. Kitts E.V. Koonin I. Korf D. Kulp D. Lancet T.M. Lowe A. McLysaght T. Mikkelsen J.V. Moran N. Mulder V.J. Pollara C.P. Ponting G. Schuler J. Schultz G. Slater A.F. Smit J. Stupka J. Szustakowski D. Thierry-Mieg J. Thierry-Mieg L. Wagner J. Wallis R. Wheeler A. Williams Y.I. Wolf K.H. Wolfe S.P. Yang R.F. Yeh F. Collins M.S. Guyer J. Peterson A. Felsenfeld K.A. Wetterstrand A. Patrinos M.J. Morgan J. Szustakowki P. de Jong J.J. Catanese K. Osoegawa H. Shizuya S. Choi Y.J. Chen Initial sequencing and analysis of the human genome Nature 409 6822 2001 860 921
24. P. Lindahl L. Karlsson M. Hellstrom S. Gebre-Medhin K. Willetts J.K. Heath C. Betsholtz Alveogenesis failure in PDGF-A- deficient mice is coupled to lack of distal spreading of alveolar smooth muscle cell progenitors during lung development Development 124 20 1997 3943 3953
25. S. Malpel C. Mendelsohn W.V. Cardoso Regulation of retinoic acid signaling during lung morphogenesis Development 127 14 2000 3057 3067
26. T. Mariani Regulation of alveogenesis by reciprocal proximo-distal FGF and retinoic acid signaling Am. J. Respir. Cell Mol. Biol 31 2004 552 557
27. T. Mariani J. Reed S. Shapiro Expression profiling of the developing mouse lung Am. J. Resp. Cell. Mol. Biol 26 2002 541 548
28. T.J. Mariani S. Sandefur R.A. Pierce Elastin in lung development Exp. Lung. Res 23 2 1997 131 145
29. S.R. Master J.L. Hartman C.M. D'Cruz S.E. Moody E.A. Keiper S.I. Ha J.D. Cox G.K. Belka L.A. Chodosh Functional microarray analysis of mammary organogenesis reveals a developmental role in adaptive thermogenesis Mol. Endocrinol 16 6 2002 1185 1203
30. M. Mody Y. Cao Z. Cui K.Y. Tay A. Shyong E. Shimizu K. Pham P. Schultz D. Welsh J.Z. Tsien Genome-wide gene expression profiles of the developing mouse hippocampus Proc. Natl. Acad. Sci. USA 98 15 2001 8862 8867
31. S.J. O'Brien W.J. Murphy Genomics. A dog's breakfast? Science 301 5641 2003 1854 1855
32. D. Pan X. Zhe S. Jakkaraju G.A. Taylor L. Schuger P311 induces a TGF-betal-independent, nonfibrogenic myofibroblast phenotype J. Clin. Invest 110 9 2002 1349 1358
33. C.V. Pepicelli P.M. Lewis A.P. McMahon Sonic hedgehog regulates branching morphogenesis in the mammalian lung Curr. Biol 8 19 1998 1083 1086
34. A.K. Perl J.A. Whitsett Molecular mechanisms controlling lung morphogenesis Clin. Genet 56 1 1999 14 27
35. K. Peters S. Werner X. Liao S. Wert J. Whitsett L. Williams Targeted expression of a dominant negative FGF receptor blocks branching morphogenesis and epithelial differentiation of the mouse lung EMBO J 13 14 1994 3296 3301
36. R. Pierce J. Shipley Retinoid-enhanced alveolization: Identifying relevant downstream targets Am. J. Respir. Cell Mol. Biol 23 2000 137 141
37. R.A. Pierce K.H. Albertine B.C. Starcher J.F. Bohnsack D.P. Carlton R.D. Bland Chronic lung injury in preterm lambs: Disordered pulmonary elastin deposition Am. J. Physiol 272 3 Pt 1 1997 L452 L460
38. R.A. Pierce T.J. Mariani R.M. Senior Elastin in lung development and disease Ciba Found Symp 192 1995 199 212 discussion 212–214
39. R.A. Pierce W.I. Mariencheck S. Sandefur E.C. Crouch W.C. Parks Glucocorticoids upregulate tropoelastin expression during late stages of fetal lung development Am. J. Physiol 268 3 pt 1 1995 L491 L500
40. S. Ramaswamy K.N. Ross E.S. Lander T.R. Golub A molecular signature of metastasis in primary solid tumors Nat. Genet 33 1 2003 49 54
41. G.M. Rubin E.B. Lewis A brief history of Drosophila's contributions to genome research Science 287 5461 2000 2216 2218
42. G.E. Sandusky K.S. Mintze S.E. Pratt A.H. Dantzig Expression of multidrug resistance-associated protein 2 (MRP2) in normal human tissues and carcinomas using tissue microarrays Histopathology 41 1 2002 65 74
43. K. Schwab L.T. Patterson B.J. Aronow R. Luckas H.C. Liang S.S. Potter A catalogue of gene expression in the developing kidney Kidney Int 64 5 2003 1588 1604
44. L. Smith A. Greenfield DNA microarrays and development Hum. Mol. Genet 12 Spec No 1 2003 R1 R8
45. M.H. Swee W.C. Parks R.A. Pierce Developmental regulation of elastin production. Expression of tropoelastin pre-mRNA persists after down-regulation of steady-state mRNA levels J. Biol. Chem 270 25 1995 14899 14906
46. L.J. van't Veer H. Dai M.J. van de Vijver Y.D. He A.A. Hart M. Mao H.L. Peterse K. van der Kooy M.J. Marton A.T. Witteveen G.J. Schreiber R.M. Kerkhoven C. Roberts P.S. Linsley R. Bernards S.H. Friend Gene expression profiling predicts clinical outcome of breast cancer Nature 415 6871 2002 530 536
47. D. Warburton M. Lee Current concepts on lung development Curr. Opin. Pediatr 11 3 1999 188 192
48. D. Warburton M. Schwarz D. Tefft G. Flores-Delgado K. Anderson W.C. WV The molecular basis of lung morphogenesis Mech. Dev 92 1 2000 55 81
49. R.H. Waterston K. Lindblad-Toh E. Birney J. Rogers J.F. Abril P. Agarwal R. Agarwala R. Ainscough M. Alexandersson P. An S.E. Antonarakis J. Attwood R. Baertsch J. Bailey K. Barlow S. Beck E. Berry B. Birren T. Bloom P. Bork M. Botcherby N. Bray M.R. Brent D.G. Brown S.D. Brown C. Bult J. Burton J. Butler R.D. Campbell P. Carninci S. Cawley F. Chiaromonte A.T. Chinwalla D.M. Church M. Clamp C. Clee F.S. Collins L.L. Cook R.R. Copley A. Coulson O. Couronne J. Cuff V. Curwen T. Cutts M. Daly R. David J. Davies K.D. Delehaunty J. Deri E.T. Dermitzakis C. Dewey N.J. Dickens M. Diekhans S. Dodge I. Dubchak D.M. Dunn S.R. Eddy L. Elnitski R.D. Emes P. Eswara E. Eyras A. Felsenfeld G.A. Fewell P. Flicek K. Foley W.N. Frankel L.A. Fulton R.S. Fulton T.S. Furey D. Gage R.A. Gibbs G. Glusman S. Gnerre N. Goldman L. Goodstadt D. Grafham T.A. Graves E.D. Green S. Gregory R. Guigo M. Guyer R.C. Hardison D. Haussler Y. Hayashizaki L.W. Hillier A. Hinrichs W. Hlavina T. Holzer F. Hsu A. Hua T. Hubbard A. Hunt I. Jackson D.B. Jaffe L.S. Johnson M. Jones T.A. Jones A. Joy M. Kamal E.K. Karlsson D. Karolchik A. Kasprzyk J. Kawai E. Keibler C. Kells W.J. Kent A. Kirby D.L. Kolbe I. Korf R.S. Kucherlapati E.J. Kulbokas D. Kulp T. Landers J.P. Leger S. Leonard I. Letunic R. Levine J. Li M. Li C. Lloyd S. Lucas B. Ma D.R. Maglott E.R. Mardis L. Matthews E. Mauceli J.H. Mayer M. McCarthy W.R. McCombie S. McLaren K. McLay J.D. McPherson J. Meldrim B. Meredith J.P. Mesirov W. Miller T.L. Miner E. Mongin K.T. Montgomery M. Morgan R. Mott J.C. Mullikin D.M. Muzny W.E. Nash J.O. Nelson M.N. Nhan R. Nicol Z. Ning C. Nusbaum M.J. O'Connor Y. Okazaki K. Oliver E. Overton-Larty L. Pachter G. Parra K.H. Pepin J. Peterson P. Pevzner R. Plumb C.S. Pohl A. Poliakov T.C. Ponce C.P. Ponting S. Potter M. Quail A. Reymond B.A. Roe K.M. Roskin E.M. Rubin A.G. Rust R. Santos V. Sapojnikov B. Schultz J. Schultz M.S. Schwartz S. Schwartz C. Scott S. Seaman S. Searle T. Sharpe A. Sheridan R. Shownkeen S. Sims J.B. Singer G. Slater A. Smit D.R. Smith B. Spencer A. Stabenau N. Stange-Thomann C. Sugnet M. Suyama G. Tesler J. Thompson D. Torrents E. Trevaskis J. Tromp C. Ucla A. Ureta-Vidal J.P. Vinson A.C. Von Niederhausern C.M. Wade M. Wall R.J. Weber R.B. Weiss M.C. Wendl A.P. West K. Wetterstrand R. Wheeler S. Whelan J. Wierzbowski D. Willey S. Williams R.K. Wilson E. Winter K.C. Worley D. Wyman S. Yang S.P. Yang E.M. Zdobnov M.C. Zody E.S. Lander Initial sequencing and comparative analysis of the mouse genome Nature 420 6915 2002 520 562
50. Z.X. Xu C.J. Viviano S.A. Rooney Glucocorticoid stimulation of fatty-acid synthase gene transcription in fetal lung: Antagonism by retinoic acid Am. J. Physiol 268 4 Pt1 1995 L683 L690