Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy

Journal of Biological Chemistry

Volumn 279, Issue 28, 2004, Pages 29670-29680

  Sadlier, Denise M ^a   Connolly, Susan B ^a   Kieran, Niamh E ^a   Roxburgh, Sarah ^a   Brazil, Derek P ^a   Kairaitis, Lukas ^b   Wang, Y ^b   Harris, David C H ^b   Doran, Peter ^a   Brady, Hugh R ^a  

^a MATER MISERICORDIAE UNIVERSITY HOSPITAL   (Ireland)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASES; GENES; RNA;

MICROARRAY TECHNOLOGY; NEPHROPATHY;

BIOCHEMISTRY;

CLUSTERIN; DOXORUBICIN; ENDOGLIN; FIBRONECTIN; GELSOLIN; OSTEONECTIN; SCLEROPROTEIN; TRANSFORMING GROWTH FACTOR BETA1;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA MICROARRAY; EXTRACELLULAR MATRIX; FIBROGENESIS; GENE CLUSTER; GENE EXPRESSION PROFILING; KIDNEY FIBROSIS; KIDNEY TUBULE EPITHELIUM; MALE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ANIMALS; ANTIBIOTICS, ANTINEOPLASTIC; CELLS, CULTURED; CLUSTER ANALYSIS; DISEASE MODELS, ANIMAL; DOXORUBICIN; EPITHELIAL CELLS; EXTRACELLULAR MATRIX; EXTRACELLULAR MATRIX PROTEINS; FIBROSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; KIDNEY DISEASES; KIDNEY TUBULES; MALE; MICE; MICE, INBRED BALB C; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC;

ANIMALIA; EUKARYOTA; MURINAE;

EID: 3142676670     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M313408200     Document Type: Article

References (66)

1. Devarajan, P., and Spitzer, A. (2002) Am. J. Kidney Dis. 39, 625-636
2. Anders, H. J., Vielhauer, V., and Schlondorff, D. (2003) Kidney Int. 63, 401-415
3. Crean, J. K., Lappin, D., Godson, C., and Brady, H. R. (2001) Expert Opin. Ther. Targets 5, 519-530
4. Eikmans, M., Baelde, J. J., De Heer, E., and Bruijn, J. A. (2003) J. Pathol. 200, 526-536
5. Sanchez-Lozada, L. G., Tapia, E., Johnson, R. J., Rodriguez-Iturbe, B., and Herrera-Acosta, J. (2003) Kidney Int. 64, Suppl. 86, 9-14
6. Okada, H., Strutz, F., Danoff, T. M., Kalluri, R., and Neilson, E. G. (1996) Contrib. Nephrol. 118, 147-154
7. Strutz, F., and Muller, G. A. (2000) Nephrol. Dial. Transplant. 15, 1729-1731
8. Wang, Y., Wang, Y. P., Tay, Y. C., and Harris, D. C. (2000) Kidney Int. 58, 1797-1804
9. Haverty, T. P., Kelly, C. J., Hines, W. H., Amenta, P. S., Watanabe, M., Harper, R. A., Kefalides, N. A., and Neilson, E. G. (1988) J. Cell Biol. 107, 1359-1368
10. Kieran, N. E., Doran, P. P., Connolly, S. B., Greenan, M. C., Higgins, D. F., Leonard, M., Godson, C., Taylor, C. T., Henger, A., Kretzler, M., Burne, M. J., Rabb, H., and Brady, H. R. (2003) Kidney Int. 64, 480-492
11. Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003) Bioinformatics 19, 185-193
12. Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B., and Speed, T. P. (2003) Nucleic Acids Res. 31, e15
13. Quackenbush, J. (2002) Nat. Genet. 32, (suppl.) 496-501
14. Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 5116-5121
15. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 14863-14868
16. Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D., and Brown, P. O. (2000) Nat. Genet. 24, 227-235R. M.
17. Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., Houstis, N., Daly, M. J., Patterson, N., Mesirov, J. P., Golub, T. R., Tamayo, P., Spiegelman, B., Lander, E. S., Hirschhorn, J. N., Altshuler, D., and Groop, L. C. (2003) Nat. Genet. 34, 267-273
18. Gene Ontology Consortium (2001) Genome Res. 11, 1425-1433
19. Draghici, S., Khatri, P., Bhavsar, P., Shah, A., Krawetz, S. A., and Tainsky, M. A. (2003) Nucleic Acids Res. 31, 3775-3781
20. 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, J. L., Eisen, M. B., Iyer, V. R., Brown, P. O., Muramatsu, M., Shimada, H., Okazaki, Y., and Hayashizaki, Y. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 2199-2204
21. Atula, T., Hedstrom, J., Finne, P., Leivo, I., Markkanen-Leppanen, M., and Haglund, C. (2003) Anticancer Res. 23, 3051-3056
22. Sarwal, M., Chua, M. S., Kambham, N., Hsieh, S. C., Satterwhite, T., Masek, M., and Salvatierra, O., Jr. (2003) N. Engl. J. Med. 349, 125-138
23. Francki, A., and Sage, E. H. (2001) Trends Cardiovasc. Med. 11, 32-37
24. Motamed, K., Funk, S. E., Koyama, H., Ross, R., Raines, E. W., and Sage, E. H. (2002) J. Cell. Biochem. 84, 759-771
25. Floege, J., Johnson, R. J., Alpers, C. E., Fatemi-Nainie, S., Richardson, C. A., Gordon, K., and Couser, W. G. (1993) Am. J. Pathol. 142, 637-650
26. Pichler, R. H., Bassuk, J. A., Hugo, C., Reed, M. J., Eng, E., Gordon, K. L., Pippin, J., Alpers, C. E., Couser, W. G., Sage, E. H., and Johnson, R. J. (1996) Am. J. Pothol. 148, 1153-1167
27. Taneda, S., Pippin, J. W., Sage, E. H., Hudkins, K. L., Takeuchi, Y., Couser, W. G., and Alpers, C. E. (2003) J. Am. Soc. Nephrol. 14, 968-980
28. Francki, A., Bradshaw, A. D., Bassuk, J. A., Howe, C. C., Couser, W. G., and Sage, E. H. (1999) J. Biol. Chem. 274, 32145-32152
29. Gupta, S., Clarkson, M. R., Duggan, J., and Brady, H. R. (2000) Kidney Int. 58, 1389-1399
30. Jahkola, T., Toivonen, T., Virtanen, I., von Smitten, K., Nordling, S., von Boguslawski, K., Haglund, C., Nevanlinna, H., and Blomqvist, C. (1998) Br. J. Cancer 78, 1507-1513
31. Truong, L. D., Foster, S. V., Barrios, R., D'Agati, V., Verani, R. R., Gonzalez, J. M., and Suki, W. N. (1996) Nephron 72, 579-586
32. Gore-Hyer, E., Shegogue, D., Markiewicz, M., Lo, S., Hazen-Martin, D., Greene, E. L., Grotendorst, G., and Trojanowska, M. (2002) Am. J. Physiol. 283, F707-F716
33. Timpl, R., Sasaki, T., Kostka, G., and Chu, M. L. (2003) Nat. Rev. Mol. Cell. Biol. 4, 479-489
34. Twal, W. O., Czirok, A., Hegedus, B., Knaak, C., Chintalapudi, M. R., Okagawa, H., Sugi, Y., and Argraves, W. S. (2001) J. Cell Sci. 114, 4587-4598
35. Frank, S., Schulthess, T., Landwehr, R., Lustig, A., Mini, T., Jeno, P., Engel, J., and Kammerer, R. A. (2002) J. Biol. Chem. 277, 19071-19079
36. Piecha, D., Muratoglu, S., Morgelin, M., Hauser, N., Studer, D., Kiss, I., Paulsson, M., and Deak, F. (1999) J. Biol. Chem. 274, 13353-13361
37. Klatt, A. R., Nitsche, D. P., Kobbe, B., Macht, M., Paulsson, M., and Wagener, R. (2001) J. Biol. Chem. 276, 17267-17275
38. Piecha, D., Wiberg, C., Morgelin, M., Reinhardt, D. P., Deak, F., Maurer, P., and Paulsson, M. (2002) Biochem. J. 367, 715-721
39. Jones, S. E., and Jomary, C. (2002) Int. J. Biochem. Cell Biol. 34, 427-431
40. Jomary, C., Murphy, B. F., Neal, M. J., and Jones, S. E. (1993) Brain Res. Mol. Brain Res. 20, 274-278
41. Yoshida, T., Kurella, M., Beato, F., Min, H., Ingelfinger, J. R., Stears, R. L., Swinford, R. D., Gullans, S. R., and Tang, S. S. (2002) Kidney Int. 61, 1646-1654
42. Aoyama, I., Shimokata, K., and Niwa, T. (2002) Nephron 92, 635-651
43. Santilli, G., Aronow, B. J., and Sala, A. (2003) J. Biol. Chem. 278, 38214-38219
44. Gougos, A., and Letarte, M. (1988) J. Immunol. 141, 1925-1933
45. McAllister, K. A., Grogg, K. M., Johnson, D. W., Gallione, C. J., Baldwin, M. A., Jackson, C. E., Helmbold, E. A., Markel, D. S., McKinnon, W. C., and Murrell, J. (1994) Nat. Genet. 8, 345-351
46. Guerrero-Esteo, M., Sanchez-Elsner, T., Letamendia, A., and Bernabeu, C. (2002) J. Biol. Chem. 277, 29197-29209
47. Letamendia, A., Lastres, P., Botella, L. M., Raab, U., Langa, C., Velasco, B., Attisano, L., and Bernabeu, C. (1998) J. Biol. Chem. 273, 33011-33019
48. Rodriguez-Pena, A., Prieto, M., Duwel, A., Rivas, J. V., Eleno, N., Perez-Barriocanal, F., Arevalo, M., Smith, J. D., Vary, C. P., Bernabeu, C., and Lopez-Novoa, J. M. (2001) Nephrol. Dial. Transplant. 16, Suppl. 1, 34-39
49. Rodriguez-Pena, A., Eleno, N., Duwell, A., Arevalo, M., Perez-Barriocanal, F., Flores, O., Docherty, N., Bernabeu, C., Letarte, M., and Lopez-Novoa, J. M. (2002) Hypertension 40, 713-720
50. Rodriguez-Barbero, A., Obreo, J., Eleno, N., Rodriguez-Pena, A., Duwel, A., Jerkic, M., Sanchez-Rodriguez, A., Bernabeu, C., and Lopez-Novoa, J. M. (2001) Biochem. Biophys. Res. Commun. 282, 142-147
51. dos Remedios, C. G., Chhabra, D., Kekic, M., Dedova, I. V., Tsubakihara, M., Berry, D. A., and Nosworthy, N. J. (2003) Physiol. Rev. 83, 433-473
52. Sun, H. Q., Yamamoto, M., Mejillano, M., and Yin, H. L. (1999) J. Biol. Chem. 274, 33179-33182
53. de la Chapelle, A., Tolvanen, R., Boysen, G., Santavy, J., Bleeker-Wagemakers, L., Maury, C. P., and Kere, J. (1992) Nat. Genet. 2, 157-160
54. Maury, C. P., Kere, J., Tolvanen, R., and de la Chapelle, A. (1990) FEBS Lett. 276, 75-77
55. Visapaa, H., Bui, M., Huang, Y., Seligson, D., Tsai, H., Pantuck, A., Figlin, R., Rao, J. Y., Belldegrun, A., Horvath, S., and Palotie, A. (2003) Urology 61, 845-850
56. Okamoto, Y., Chaves, A., Chen, J., Kelley, R., Jones, K., Weed, H. G., Gardner, K. L., Gangi, L., Yamaguchi, M., Klomkleaw, W., Nakayama, T., Hamlin, R. L., Carnes, C., Altschuld, R., Bauer, J., and Hai, T. (2001) Am. J. Pathol. 159, 639-650
57. Yin, T., Sandhu, G., Wolfgang, C. D., Burrier, A., Webb, R. L., Rigel, D. F., Hai, T., and Whelan, J. (1997) J. Biol. Chem. 272, 19943-19950
58. Chen, B. P., Wolfgang, C. D., and Hai, T. (1996) Mol. Cell. Biol. 16, 1157-1168
59. Wolfgang, C. D., Chen, B. P., Martindale, J. L., Holbrook, N. J., and Hai, T. (1997) Mol. Cell. Biol. 17, 6700-6707
60. Jin, K., Mao, X. O., Eshoo, M. W., del Rio, G., Rao, R., Chen, D., Simon, R. P., and Greenberg, D. A. (2002) Neurochem. Res. 27, 1105-1112
61. Rees, W. D., Hay, S. M., Fontanier-Razzaq, N. C., Antipatis, C., and Harries, D. N. (1999) J. Nutr. 129, 1532-1536
62. Leuenberger, B., Hahn, D., Pischitzis, A., Hansen, M. K., and Sterchi, E. E. (2003) Biochem. J. 369, 659-665
63. Spangenberg, C., Winterpacht, A., Zabel, B. U., and Lobbert, R. W. (1998) Genomics 48, 178-185
64. Kruse, M. N., Becker, C., Lottaz, D., Kohler, D., Yiallouros, I., Krell, H. W., Sterchi, E. E., and Stocker, W. (2003) Biochem. J. 378, 383-389
65. Ricardo, S. D., Bond, J. S., Johnson, G. D., Kaspar, J., and Diamond, J. R. (1996) Am. J. Physiol. 270, F669-F676
66. Miyamori, H., Takino, T., Kobayashi, Y., Tokai, H., Itoh, Y., Seiki, M., and Sato, H. (2001) J. Biol. Chem. 276, 28204-28211