Systems biology of autosomal dominant polycystic kidney disease (ADPKD): Computational identification of gene expression pathways and integrated regulatory networks

Human Molecular Genetics

Volumn 18, Issue 13, 2009, Pages 2328-2343

  Song, Xuewen ^a   Di Giovanni, Valeria ^b   He, Ning ^a   Wang, Kairong ^a   Ingram, Alistair ^c   Rosenblum, Norman D ^b   Pei, York ^a  

^a UNIVERSITY HEALTH NETWORK   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR; EPIDERMAL GROWTH FACTOR RECEPTOR; FIBROBLAST GROWTH FACTOR; FIBROCYSTIN; G PROTEIN COUPLED RECEPTOR; GENE PRODUCT; HEPATOCYTE NUCLEAR FACTOR 1BETA; PROTEIN CYS1; PROTEIN IFT88; SOMATOMEDIN; SOMATOMEDIN C RECEPTOR; UNCLASSIFIED DRUG; VASCULOTROPIN; WNT PROTEIN;

AGING; ARTICLE; CELL CYCLE PROGRESSION; CELL DEDIFFERENTIATION; CELL DIFFERENTIATION; CELL PROLIFERATION; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE COURSE; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; HUMAN; HUMAN TISSUE; HYPOXIA; IMMUNE RESPONSE; INFLAMMATION; KIDNEY EPITHELIUM; KIDNEY POLYCYSTIC DISEASE; MOLECULAR GENETICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TUMOR GROWTH; UPREGULATION;

CYSTS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYCYSTIC KIDNEY, AUTOSOMAL DOMINANT; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION FACTORS;

EID: 67249125789     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddp165     Document Type: Article

References (56)

1. Harris, P.C. and Torres, V.E. (2009) Polycystic kidney disease. Annu. Rev. Med., 60, 321-337.
2. Ong, A.C. and Harris, P.C. (2005) Molecular pathogenesis of ADPKD: The polycystin complex gets complex. Kidney Int., 67, 1234-1247.
3. Paterson, A.D., Magistroni, R., He, N., Wang, K., Johnson, A., Fain, P.R., Dicks, E., Parfrey, P., St George-Hyslop, P. and Pei, Y. (2005) Progressive loss of renal function is an age-dependent heritable trait in type 1 autosomal dominant polycystic kidney disease. J. Am. Soc. Nephrol., 16, 755-762.
4. Grantham, J.J., Geiser, J.L. and Evan, A.P. (1987) Cyst formation and growth in autosomal dominant polycystic kidney disease. Kidney Int. 31, 1145-1152.
5. Pei, Y. (2001) A 'two-hit' model of cystogenesis in autosomal dominant polycystic kidney disease? Trends Mol. Med., 7, 151-156.
6. Nauli, S.M., Rossetti, S., Kolb, R.J., Alenghat, F.J., Consugar, M.B., Harris, P.C., Ingber, D.E., Loghman-Adham, M. and Zhou, J. (2006) Loss of polycystin-1 in human cyst-lining epithelia leads to ciliary dysfunction. J. Am. Soc. Nephrol., 17, 1015-1025.
7. Grantham, J.J., Torres, V.E., Chapman, A.B., Guay-Woodford, L.M., Bae, K.T., King, B.F. Jr, Wetzel, L.H., Baumgarten, D.A., Kenney, P.J., Harris, P.C. et al. (2006) Volume progression in polycystic kidney disease. N. Engl. J. Med., 354, 2122-2130.
8. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
9. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
10. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
11. Dennis, G. Jr, Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. (2003) DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol., 4, 3 p.
12. Mrug, M., Zhou, J., Woo, Y., Cui, X., Szalai, A.J., Novak, J., Churchill, G.A. and Guay-Woodford, L.M. (2008) Overexpression of innate immune response genes in a model of recessive polycystic kidney disease. Kidney Int., 73, 63-76.
13. Chabardes-Garonne, D., Mejean, A., Aude, J.C., Cheval, L., Di Stefano, A., Gaillard, M.C., Imbert-Teboul, M., Wittner, M., Balian, C., Anthouard, V. et al. (2003) A panoramic view of gene expression in the human kidney. Proc. Natl Acad. Sci. USA, 100, 13710-13715.
14. Gresh, L., Fischer, E., Reimann, A., Tanguy, M., Garbay, S., Shao, X., Hiesberger, T., Fiette, L., Igarashi, P., Yaniv, M. et al. (2004) A transcriptional network in polycystic kidney disease. EMBO J., 23, 1657-1668.
15. Senkel, S., Lucas, B., Klein-Hitpass, L. and Ryffel, G.U. (2005) Identification of target genes of the transcription factor HNF1beta and HNF1alpha in a human embryonic kidney cell line. Biochem. Biophys. Acta, 1731, 179-190.
16. Rebouissou, S., Vasiliu, V., Thomas, C., Bellanne-Chantelot, C., Bui, H., Chretien, Y., Timsit, J., Rosty, C., Laurent-Puig, P., Chauveau, D. et al. (2005) Germline hepatocyte nuclear factor 1alpha and 1beta mutations in renal cell carcinomas. Hum. Mol. Genet., 14, 603-614.
17. Ma, Z., Gong, Y., Patel, V., Karner, C.M., Fischer, E., Hiesberger, T., Carroll, T.J., Pontoglio, M. and Igarashi, P. (2007) Mutations of HNF-1beta inhibit epithelial morphogenesis through dysregulation of SOCS-3. Proc. Natl Acad. Sci. USA, 104, 20386-20391.
18. Roxburgh, S.A., Murphy, M., Pollock, C.A. and Brazil, D.P. (2006) Recapitulation of embryological programmes in renal fibrosis - the importance of epithelial cell plasticity and developmental genes. Nephron Physiol., 103, 139-148.
19. El-Nahas, A.M. (2003) Plasticity of kidney cells: Role in kidney remodeling and scarring. Kidney Int., 64, 1553-1563.
20. Gill, P.S. and Rosenblum, N.D. (2006) Control of murine kidney development by sonic hedgehog and its GLI effectors. Cell Cycle, 5, 1426-1430.
21. Lal, M., Song, X., Pluznick, J.L., Di Giovanni, V., Merrick, D.M., Rosenblum, N.D., Chauvet, V., Gottardi, C.J., Pei, Y. and Caplan, M.J. (2008) Polycystin-1 C-terminal tail associates with beta-catenin and inhibits canonical Wnt signaling. Hum. Mol. Genet., 17, 3105-3117.
22. Hildebrandt, F., Attanasio, M. and Otto, E. (2009) Nephronophthisis: disease mechanisms of a ciliopathy. J. Am. Soc. Nephrol., 20 23-35.
23. Martinelli, D.C. and Fan, C.M. (2007) The role of Gas1 in embryonic development and its implications for human disease. Cell Cycle, 6, 2650-2655.
24. Schlessinger, J. (2000) Cell signaling by receptor tyrosine kinases. Cell, 103, 211-225.
25. Omori, S., Hida, M., Fujita, H., Takahashi, H., Tanimura, S., Kohno, M. and Awazu, M. (2006) Extracellular signal-regulated kinase inhibition slows disease progression in mice with polycystic kidney disease. J. Am. Soc. Nephrol., 17, 1604-1614.
26. Parker, E., Newby, L.J., Sharpe, C.C., Rossetti, S., Streets, A.J., Harris, P.C., O'Hare, M.J. and Ong, A.C. (2007) Hyperproliferation of PKD1 cystic cells is induced by insulin-like growth factor-1 activation of the Ras/Raf signalling system. Kidney Int., 72, 157-165.
27. Shillingford, J.M., Murcia, N.S., Larson, C.H., Low, S.H., Hedgepeth, R., Brown, N., Flask, C.A., Novick, A.C., Goldfarb, D.A., Kramer-Zucker, A. et al. (2006) The mTOR pathway is regulated by polycystin-1, and its inhibition reverses renal cystogenesis in polycystic kidney disease. Proc. Natl Acad. Sci. USA, 103, 5466-5471.
28. Rozengurt, E. (2007) Mitogenic signaling pathways induced by G protein-coupled receptors. J. Cell Physiol., 213, 589-602.
29. Schlaepfer, D.D. and Mitra, S.K. (2004) Multiple connections link FAK to cell motility and invasion. Curr. Opin. Genet. Dev., 14, 92-101.
30. Yamaguchi, T., Hempson, S.J., Reif, G.A., Hedge, A.M. and Wallace, D.P. (2006) Calcium restores a normal proliferation phenotype in human polycystic kidney disease epithelial cells. J. Am. Soc. Nephrol., 17, 178-187.
31. Elberg, G., Elberg, D., Lewis, T.V., Guruswamy, S., Chen, L., Logan, C.J., Chan, M.D. and Turman, M.A. (2007) EP2 receptor mediates PGE2-induced cystogenesis of human renal epithelial cells. Am. J. Physiol. Renal Physiol., 293, F1622-F1632.
32. Hao, C.M. and Breyer, M.D. (2008) Physiological regulation of prostaglandins in the kidney. Annu. Rev. Physiol., 70, 357-377.
33. Puri, S., Magenheimer, B.S., Maser, R.L., Ryan, E.M., Zien, C.A., Walker, D.D., Wallace, D.P., Hempson, S.J. and Calvet, J.P. (2004) Polycystin-1 activates the calcineurin/NFAT (nuclear factor of activated T-cells) signaling pathway. J. Biol. Chem., 279, 55455-55464.
34. Buchholz, M. and Ellenrieder, V. (2007) An emerging role for Ca2+/ calcineurin/NFAT signaling in cancerogenesis. Cell Cycle, 6, 16-19.
35. Le, N.H., van der Wal, A., van der Bent, P., Lantinga-van Leeuwen, I.S., Breuning, M.H., van Dam, H., de Heer, E. and Peters, D.J. (2005) Increased activity of activator protein-1 transcription factor components ATF2, c-Jun, and c-Fos in human and mouse autosomal dominant polycystic kidney disease. J. Am. Soc. Nephrol., 16, 2724-2731.
36. Bhunia, A.K., Piontek, K., Boletta, A., Liu, L., Qian, F., Xu, P.N., Germino, F.J. and Germino, G.G. (2002) PKD1 induces p21(waf1) and regulation of the cell cycle via direct activation of the JAK-STAT signaling pathway in a process requiring PKD2. Cell, 109, 157-168.
37. Battini, L., Macip, S., Fedorova, E., Dikman, S., Somlo, S., Montagna, C. and Gusella, G.L. (2008) Loss of polycystin-1 causes centrosome amplification and genomic instability. Hum. Mol. Genet., 17, 2819-2833.
38. Kuro-o, M. (2008) Klotho as a regulator of oxidative stress and senescence. Biol. Chem., 389, 233-241.
39. Kurosu, H., Yamamoto, M., Clark, J.D., Pastor, J.V., Nandi, A., Gurnani, P., McGuinness, O.P., Chikuda, H., Yamaguchi, M., Kawaguchi, H. et al (2005) Suppression of aging in mice by the hormone Klotho. Science, 309, 1829-1833.
40. Liu, H., Fergusson, M.M., Castilho, R.M., Liu, J., Cao, L., Chen, J., Malide, D., Rovira, I.I., Schimel, D., Kuo, C.J. et al. (2007) Augmented Wnt signaling in a mammalian model of accelerated aging. Science, 317, 803-806.
41. Elkon, R., Linhart, C., Sharan, R., Shamir, R. and Shiloh, Y. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
42. Bukanov, N.O., Smith, L.A., Klinger, K.W., Ledbetter, S.R. and Ibraghimov-Beskrovnaya, O. (2006) Long-lasting arrest of murine polycystic kidney disease with CDK inhibitor roscovitine. Nature, 444, 949-952.
43. Qian, Q., Du, H., King, B.F., Kumar, S., Dean, P.G., Cosio, F.G. and Torres, V.E. (2008) Sirolimus reduces polycystic liver volume in ADPKD patients. J. Am. Soc. Nephrol., 19, 631-638.
44. Torres, V.E., Wang, X., Qian, Q., Somlo, S., Harris, P.C. and Gattone, V.H. 2nd (2004) Effective treatment of an orthologous model of autosomal dominant polycystic kidney disease. Nat. Med., 10, 363-364.
45. Castellone, M.D., Teramoto, H. and Gutkind, J.S. (2006) Cyclooxygenase-2 and colorectal cancer chemoprevention: The beta-catenin connection. Cancer Res., 66, 11085-11088.
46. Pai, R., Soreghan, B., Szabo, I.L., Pavelka, M., Baatar, D. and Tarnawski, A.S. (2002) Prostaglandin E2 transactivates EGF receptor: A novel mechanism for promoting colon cancer growth and gastrointestinal hypertrophy. Nat. Med., 8, 289-293.
47. Saadi-Kheddouci, S., Berrebi, D., Romagnolo, B., Cluzeaud, F., Peuchmaur, M., Kahn, A., Vandewalle, A. and Perret, C. (2001) Early development of polycystic kidney disease in transgenic mice expressing an activated mutant of the beta-catenin gene. Oncogene, 20, 5972-5981.
48. Koh, N., Fujimori, T., Nishiguchi, S., Tamori, A., Shiomi, S., Nakatani, T., Sugimura, K., Kishimoto, T., Kinoshita, S., Kuroki, T. et al. (2001) Severely reduced production of klotho in human chronic renal failure kidney. Biochem. Biophys. Res. Commun., 280, 1015-1020.
49. Haruna, Y., Kashihara, N., Satoh, M., Tomita, N., Namikoshi, T., Sasaki, T., Fujimori, T., Xie, P. and Kanwar, Y.S. (2007) Amelioration of progressive renal injury by genetic manipulation of Klotho gene. Proc. Natl Acad. Sci. USA, 104, 2331-2336.
50. Mitani, H., Ishizaka, N., Aizawa, T., Ohno, M., Usui, S., Suzuki, T., Amaki, T., Mori, I., Nakamura, Y., Sato, M. et al. (2002) In vivo klotho gene transfer ameliorates angiotensin II-induced renal damage. Hypertension, 39, 838-843.
51. Wei, W., Popov, V., Walocha, J.A., Wen, J. and Bello-Reuss, E. (2006) Evidence of angiogenesis and microvascular regression in autosomal-dominant polycystic kidney disease kidneys: A corrosion cast study. Kidney Int., 70, 1261-1268.
52. Tao, Y., Kim, J., Yin, Y., Zafar, I., Falk, S., He, Z., Faubel, S., Schrier, R.W. and Edelstein, C.L. (2007) VEGF receptor inhibition slows the progression of polycystic kidney disease. Kidney Int., 72 1358-1366.
53. Chai, J. and Tarnawski, A.S. (2002) Serum response factor: Discovery, biochemistry, biological roles and implications for tissue injury healing. J. Physiol. Pharmacol., 53, 147-157.
54. Posern, G. and Treisman, R. (2006) Actin' together: Serum response factor, its cofactors and the link to signal transduction. Trends Cell Biol., 16, 588-596.
55. Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. and Speed, T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
56. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A. and Speleman, F. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol., 3, RESEARCH0034.