Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Campanaro, Stefano ^a   Picelli, Simone ^a   Torregrossa, Rossella ^a   Colluto, Laura ^a   Ceol, Monica ^a   Del Prete, Dorella ^a   D'Angelo, Angela ^a   Valle, Giorgio ^a   Anglani, Franca ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; RAS PROTEIN; SMAD PROTEIN; TRANSFORMING GROWTH FACTOR BETA1;

APOPTOSIS; ARTICLE; CELL CYCLE REGULATION; CELL DIFFERENTIATION; CELL FATE; CELL INTERACTION; CELL MATURATION; CELL PROLIFERATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; EPITHELIUM CELL; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENETIC REGULATION; GROWTH REGULATION; HUMAN; HUMAN CELL; IN VITRO STUDY; KIDNEY DEVELOPMENT; KIDNEY TUBULE EPITHELIUM; MESENCHYME CELL; MORPHOGENESIS; NUCLEOTIDE SEQUENCE; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; UNINDEXED SEQUENCE; UPREGULATION; CELL CULTURE; CYTOLOGY; DRUG EFFECT; GENOME; KIDNEY TUBULE; MESODERM; METABOLISM;

CELL DIFFERENTIATION; CELLS, CULTURED; EPITHELIAL CELLS; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; KIDNEY TUBULES; MESODERM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSFORMING GROWTH FACTOR BETA1;

EID: 37749046446     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-383     Document Type: Article

References (50)

1. Anglani F Forino M Del Prete D Tosetto E Torregrossa R D'Angelo A; In search of adult renal stem cells. J Cell Mol Med 2004, 8:474-487. 10.1111/j.1582-4934.2004.tb00472.x 15601576
2. Stahl PJ Felsen D: Transforming growth factor-beta, basement membrane, and epithelial-mesenchymal transdifferentiation: Implications for fibrosis in kidney disease. Am J Pathol 2001, 159:1187-1192. 1850494 11583944
3. Iwano M Plieth D Danoff TM Xue C Okada H Neilson EG Evidence that fibroblasts derive from epithelium during tissue fibrosis J Clin Invest 2002, 110:341-350. 151091 12163453 10.1172/JCI200215518
4. Massague J Wotton D Transcriptional control by the TGF-beta/Smad signaling system EMBO J 2000, 19:1745-1754. 302010 10775259 10.1093/ emboj/19.8.1745
5. Zavadil J Bottinger EP TGF-beta and epithelial-to-mesenchymal transitions Oncogene 2005, 24:5764-5774. 10.1038/sj.onc.1208927 16123809
6. Forino M Torregrossa R Ceol M Murer L Vella MD Prete DD D'Angelo A Anglani F TGFbeta1 induces epithelial-mesenchymal transition, but not myofibroblast transdifferentiation of human kidney tubular epithelial cells in primary culture Int J Exp Pathol 2006, 87:197-208. 10.1111/ j.1365-2613.2006.00479.x 16709228
7. Zavadil J Bitzer M Liang D Yang YC Massimi A Kneitz S Piek E Bottinger EP Genetic programs of epithelial cell plasticity directed by transforming growth factor-beta Proc Natl Acad Sci USA 2001, 98:6686-6691. 34413 11390996 10.1073/pnas.111614398
8. Derynck R Zhang YE Smad-dependent and Smad-independent pathways in TGF-beta family signaling Nature 2003, 425:577-584. 10.1038/nature02006 14534577
9. Bottinger EP Bitzer M TGF-beta signaling in renal disease J Am Soc Nephrol 2002, 13:2600-2610. 10.1097/01.ASN.0000033611.79556.AE 12239251
10. Yip KY Yu H Kim PM Schultz M Gerstein M The tYNA platform for comparative interactomics: A web tool for managing, comparing and mining multiple networks Bioinformatics 2006, 22:2968-2970. 10.1093/ bioinformatics/btl488 17021160
11. Sampogna RV Nigam SK Implications of gene networks for understanding resilience and vulnerability in the kidney branching program Physiology (Bethesda) 2004, 19:339-347. 15546851
12. Han JD Bertin N Hao T Goldberg DS Berriz GF Zhang LV Dupuy D Walhout AJ Cusick ME Roth FP Vidal M Evidence for dynamically organized modularity in the yeast protein-protein interaction network Nature 2004, 430:88-93. 10.1038/nature02555 15190252
13. Li S Armstrong CM Bertin N Ge H Milstein S Boxem M Vidalain PO Han JD Chesneau A Hao T Goldberg DS Li N Martinez M Rual JF Lamesch P Xu L Tewari M Wong SL Zhang LV Berriz GF Jacotot L Vaglio P Reboul J Hirozane-Kishikawa T Li Q Gabel HW Elewa A Baumgartner B Rose DJ Yu H Bosak S Sequerra R Fraser A Mango SE Saxton WM Strome S Van Den Heuvel S Piano F Vandenhaute J Sardet C Gerstein M Doucette-Stamm L Gunsalus KC Harper JW Cusick ME Roth FP Hill DE Vidal M A map of the interactome network of the metazoan C. elegans Science 2004, 303:540-543. 1698949 14704431 10.1126/science.1091403
14. Daniel C Wiede J Krutzsch HC Ribeiro SM Roberts DD Murphy-Ullrich JE Hugo C Thrombospondin-1 is a major activator of TGF-beta in fibrotic renal disease in the rat in vivo Kidney Int 2004, 65:459-468. 10.1111/ j.1523-1755.2004.00395.x 14717916
15. Horster MF Braun GS Huber SM Embryonic renal epithelia: Induction, nephrogenesis, and cell differentiation Physiol Rev 1999, 79:1157-1191. 10508232
16. Zoppi N Gardella R De Paepe A Barlati S Colombi M Human fibroblasts with mutations in COL5A1 and COL3A1 genes do not organize collagens and fibronectin in the extracellular matrix, down-regulate alpha2beta1 integrin, and recruit alphavbeta3 instead of alpha5beta1 integrin J Biol Chem 2004, 279:18157-18168. 10.1074/jbc.M312609200 14970208
17. Tiger CF Fougerousse F Grundstrom G Velling T Gullberg D alpha11beta1 integrin is a receptor for interstitial collagens involved in cell migration and collagen reorganization on mesenchymal nonmuscle cells Dev Biol 2001, 237:116-29. 10.1006/dbio.2001.0363 11518510
18. Kitamura S Yamasaki Y Kinomura M Sugaya T Sugiyama H Maeshima Y Makino H Establishment and characterization of renal progenitor-like cells from S3 segment of nephron in rat adult kidney FASEB J 2005, 19:1789-1797. 10.1096/fj.05-3942com 16260649
19. Maeshima A Sakurai H Nigam SK Adult kidney tubular cell population showing phenotypic plasticity, tubulogenic capacity, and integration capability into developing kidney J Am Soc Nephrol 2006, 17:188-198. 10.1681/ASN.2005040370 16338966
20. Bussolati B Bruno S Grange C Buttiglieri S Deregibus MC Cantino D Camusi G Isolation of renal progenitor cells from adult human kidney Am J Pathol 2005, 166:545-555. 1602314 15681837
21. Florek M Haase M Marzesco AM Freund D Ehninger G Huttner WB Corbeil D Prominin-1/CD133, a neural and hematopoietic stem cell marker, is expressed in adult human differentiated cells and certain types of kidney cancer Cell Tissue Res 2005, 319:15-26. 10.1007/s00441-004-1018-z 15558321
22. Scheld A Hastie ND Cross-talk in kidney development Curr Opin Genet Dev 2000, 10:543-549. 10.1016/S0959-437X(00)00125-8 10980433
23. Plisov SY Ivanov SV Yoshino K Dove LF Plisova TM Higinbotham KG Karavanova I Lerman M Perantoni AO Mesenchymal-epithelial transition in the developing metanephric kidney: Gene expression study by differential display Genesis 2000, 27:22-31. 10.1002/ 1526-968X(200005)27:1<22::AID-GENE40>3.0.CO;2-V 10862152
24. Widelitz R Wnt signaling through canonical and non-canonical pathways: recent progress Growth Factors 2005, 23:111-116. 10.1080/ 08977190500125746 16019432
25. Osafune K Takasato M Kispert A Asashima M Nishinakamura R Identification of multipotent progenitors in the embryonic mouse kidney by a novel colony-forming assay. Development. 2006 Jan;133(1):151-61. Development 2006, 133:151-61. 10.1016/j.ceca.2005.06.022 16099039
26. Masszi A Fan L Rosivall L McCulloch CA Rotstein OD Mucsi I Kapus A Integrity of cell-cell contacts is a critical regulator of TGF-beta 1-induced epithelial-to-myofibroblast transition: Role for beta-catenin Am J Pathol 2004, 165:1955-67. 1618715 15579439
27. Nicolas FJ Lehmann K Warne PH Hill CS Downward J Kondo M Epithelial to mesenchymal transition in Madin-Darby canine kidney cells is accompanied by down-regulation of Smad3 expression, leading to resistance to transforming growth factor-beta-induced growth arrest J Biol Chem 2003, 278:3251-6. 10.1074/jbc.M209019200 12435725
28. Cubillo E Tobiume K Shirakihara T Fukuda N Suzuki H Shimizu K Takehara K Cano A Saitoh M Miyazono K A role for Id in the regulation of TGF-beta-induced epithelial-mesenchymal transdifferentiation Cell Death Differ 2004, 11:1092-1101. 10.1038/sj.cdd.4401467 15181457
29. Kowanetz M Valcourt U Bergstrom R Heldin CH Moustakas A Id2 and Id3 define the potency of cell proliferation and differentiation responses to transforming growth factor beta and bone morphogenetic protein Mol Cell Biol 2004, 24:4241-4254. 400464 15121845 10.1128/ MCB.24.10.4241-4254.2004
30. Mehlen P Mille F Thibert C Morphogens and cell survival during development J Neurobiol 2005, 64:357-366. 10.1002/neu.20167 16041752
31. Bhowmick NA Zent R Ghiassi M McDonnell M Moses HL Integrin beta 1 signaling is necessary for transforming growth factor-beta activation of p38MAPK and epithelial plasticity J Biol Chem 2001, 276:46707-46713. 10.1074/jbc.M106176200 11590169
32. Yang YC Piek E Zavadil J Liang D Xie D Heyer J Pavlidis P Kucherlapati R Roberts AB Bottinger EP; Hierarchical model of gene regulation by transforming growth factor beta. Proc Natl Acad Sci USA 2003, 100: 10269-10274. 193550 12930890 10.1073/pnas.1834070100
33. Xie L Law BK Chytil AM Brown KA Aakre ME Moses HL: Activation of the Erk pathway is required for TGF-beta1-induced EMT in vitro. Neoplasia 2004, 6:603-610. 1531665 15548370 10.1593/neo.04241
34. Saeed AI Sharov V White J Li J Liang W Bhagabati N Braisted J Klapa M Currier T Thiagarajan M Sturn A Snuffin M Rezantsev A Popov D Ryltsov A Kostukovich E Borisovsky I Liu Z Vinsavich A Trush V Quackenbush J: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378. 12613259
35. Yang IV Chen E Hasseman JP Liang W Frank BC Wang S Sharov V Saeed AI White J Li A Lee NH Yeatman TJ Quackenbush J: Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 2002, 3:rEsearch0062.1 0062.12. 10.1186/ gb-2002-3-11-research0062
36. Bussey KJ Kane D Sunshine M Narasimhan S Nishizuka S Reinhold WC Zeeberg B AjayAW Weinstein JN: MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol 2003, 4:R27. 154578 12702208 10.1186/gb-2003-4-4-r27
37. Kent WJ Sugnet CW Furey TS Roskin KM Pringle TH Zahler AM Haussler D: The Human Genome Browser at UCSC. Genome Res 2002, 12:996-1006. 186604 12045153 10.1101/gr.229102. Article published online before print in May 2002
38. NCBI ftp site "gene info" file ftp://ftp.ncbi.nlm.nih.gov/gene/ DATA/
39. Zeeberg BR Feng W Wang G Wang MD Fojo AT Sunshine M Narasimhan S Kane DW Reinhold WC Lababidi S Bussey KJ Riss J Barrett JC Weinstein JN; GoMiner: A Resource for Biological Interpretation of Genomic and Proteomic. Data Genome Biol 2003, 4:R28. 154579 12702209 10.1186/ gb-2003-4-4-r28
40. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G: Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000. 25:25-29. 10.1038/75556 10802651
41. Ogata H Goto S Sato K Fujibuchi W Bono H Kanehisa M: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 148090 9847135 10.1093/nar/27.1.29
42. Color Objects in KEGG Pathways http://www.genome.jp/kegg/tool/ color_pathway.html
43. NCBI ftp site "interactions" file ftp://ftp.ncbi.nlm.nih.gov/ gene/GeneRIF/
44. The BioGRID File download http://www.thebiogrid.org/downloads.php
45. Biomolecular Interaction Network Database http://bond.unleashedinformatics.com/
46. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N SchwiAowski B Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 403769 14597658 10.1101/gr.1239303
47. MAere S Heymans K Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449. 10.1093/bioinformatics/bti551 15972284
48. tYNA http://tyna.gersteinlab.org/tyna/
49. ArrayExpress http://www.ebi.ac.uk/arrayexpress/
50. OPERON [http://www.operon.com/arrays/omad.php?]