Application of systems biology to the study of chronic kidney disease

Chinese Medical Journal

Volumn 125, Issue 14, 2012, Pages 2603-2609

  Cao, Yu Han ^a   Lü, Lin Li ^a   Zhang, Jian Dong ^a   Liu, Bi Cheng ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

Chronic kidney disease; Genome wide association study; Microarray analysis; Serial analysis of gene expression; Systems biology

Indexed keywords

MESSENGER RNA;

ARTICLE; CHRONIC KIDNEY DISEASE; DISEASE COURSE; GENETIC ASSOCIATION; GENOMICS; HUMAN; METABOLOMICS; MICROARRAY ANALYSIS; MOLECULAR DIAGNOSIS; NONHUMAN; PERSONALIZED MEDICINE; PROTEIN URINE LEVEL; PROTEOMICS; RISK; SERIAL ANALYSIS OF GENE EXPRESSION; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; HUMANS; RENAL INSUFFICIENCY, CHRONIC; SYSTEMS BIOLOGY;

EID: 84864241870     PISSN: 03666999     EISSN: None     Source Type: Journal    
DOI: 10.3760/cma.j.issn.0366-6999.2012.14.036     Document Type: Article

References (67)

1. Eddy AA, Neilson EG. Chronic kidney disease progression. J Am Soc Nephrol 2006; 17: 2964-2966.
2. Zhang L, Wang F, Wang L, Wang W, Liu B, Liu J, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet 2012; 379: 815-822.
3. Boor P, Ostendorf T, Floege J. Renal fibrosis: novel insights into mechanisms and therapeutic targets. Nat Rev Nephrol 2010; 6: 643-656.
4. Rule AD, Amer H, Cornell LD, Taler SJ, Cosio FG, Kremers WK, et al. The association between age and nephrosclerosis on renal biopsy among healthy adults. Ann Intern Med 2010; 152: 561-567.
5. Yasuda Y, Cohen CD, Henger A, Kretzler M. Gene expression profiling analysis in nephrology: towards molecular definition of renal disease. Clin Exp Nephrol 2006; 10: 91-98.
6. Abu-Asab MS, Chaouchi M, Alesci S, Galli S, Laassri M, Cheema AK, et al. Biomarkers in the age of omics: time for a systems biology approach. Omics 2011; 15: 105-112.
7. Aebersold R. Molecular systems biology: a new journal for a new biology? Mol Syst Biol 2005; 1: 2005. 0005.
8. Neusser MA, Lindenmeyer MT, Kretzler M, Cohen CD. Genomic analysis in nephrology: towards systems biology and systematic medicine? Nephrol Ther 2008; 4: 306-311.
9. Yang L, Guo S, Li Y, Zhou S, Tao S. Protein microarrays for systems biology. Acta Biochim Biophys Sin 2011; 43: 161-171.
10. Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2001; 2: 343-372.
11. Schmid H, Henger A, Kretzler M. Molecular approaches to chronic kidney disease. Curr Opin Nephrol Hypertens 2006; 15: 123-129.
12. Kurella M, Hsiao LL, Yoshida T, Randall JD, Chow G, Sarang SS, et al. DNA microarray analysis of complex biologic processes. J Am Soc Nephrol 2001; 12: 1072-1078.
13. Boger CA, Heid IM. Chronic kidney disease: novel insights from genome-wide association studies. Kidney Blood Press Res 2011; 34: 225-234.
14. Hayden PS, El-Meanawy A, Schelling JR, Sedor JR. DNA expression analysis: serial analysis of gene expression, microarrays and kidney disease. Curr Opin Nephrol Hypertens 2003; 12: 407-414.
15. Luttropp K, Lindholm B, Carrero JJ, Glorieux G, Schepers E, Vanholder R, et al. Genetics/Genomics in chronic kidney disease--towards personalized medicine? Semin Dial 2009; 22: 417-422.
16. Bowden DW. Genetics of kidney disease. Kidney Int Suppl 2003; 83: S8-S12.
17. Kottgen A, Kao WH, Hwang SJ, Boerwinkle E, Yang Q, Levy D, et al. Genome-wide association study for renal traits in the Framingham Heart and Atherosclerosis Risk in Communities Studies. BMC Med Genet 2008; 9: 49.
18. de Souza CM, Braosi AP, Luczyszyn SM, Avila AR, de Brito RB, Ignacio SA, et al. Association between vitamin D receptor gene polymorphisms and susceptibility to chronic kidney disease and periodontitis. Blood Purif 2007; 25: 411-419.
19. Huang HD, Lin FJ, Li XJ, Wang LR, Jiang GR. Genetic polymorphisms of the renin-angiotensin-aldosterone system in Chinese patients with end-stage renal disease secondary to IgA nephropathy. Chin Med J 2011; 123: 3238-3242.
20. Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD. Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS One 2009; 4: e4702.
21. Keller B, Martini S, Sedor J, Kretzler M. Linking variants from genome-wide association analysis to function via transcriptional network analysis. Semin Nephrol 2010; 30: 177-184.
22. Vuylsteke M, Peleman JD, van Eijk MJ. AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis. Nat Protoc 2007; 2: 1399-1413.
23. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008; 5: 621-68.
24. Perco P, Muhlberger I, Mayer G, Oberbauer R, Lukas A, Mayer B. Linking transcriptomic and proteomic data on the level of protein interaction networks. Electrophoresis 2010; 31: 1780-1789.
25. Rudnicki M, Eder S, Perco P, Enrich J, Scheiber K, Koppelstatter C, et al. Gene expression profiles of human proximal tubular epithelial cells in proteinuric nephropathies. Kidney Int 2007; 71: 325-335.
26. Zheng M, Lv LL, Ni J, Ni HF, Li Q, Ma KL, et al. Urinary podocyte-associated mRNA profile in various stages of diabetic nephropathy. PLoS One 2011; 6: e20431.
27. Zheng M, Lv LL, Cao YH, Zhang JD, Wu M, Ma KL, et al. Urinary mRNA markers of epithelial-mesenchymal transition correlate with progression of diabetic nephropathy. Clin Endocrinol (Oxf) 2012; 76: 657-664.
28. Anderson NL, Anderson NG. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 1998; 19: 1853-1861.
29. Lawrance IC, Klopcic B, Wasinger VC. Proteomics: an overview. Inflamm Bowel Dis 2005; 11: 927-936.
30. Klein JB, Thongboonkerd V. Overview of proteomics. Contrib Nephrol 2004; 141: 1-10.
31. Liu BC, Lu LL. Novel biomarkers for progression of chronic kidney disease. Chin Med J 2010; 123: 1789-1792.
32. Ngai HH, Sit WH, Jiang PP, Xu RJ, Wan JM, Thongboonkerd V. Serial changes in urinary proteome profile of membranous nephropathy: implications for pathophysiology and biomarker discovery. J Proteome Res 2006; 5: 3038-3047.
33. Rossing K, Mischak H, Dakna M, Zurbig P, Novak J, Julian BA, et al. Urinary proteomics in diabetes and CKD. J Am Soc Nephrol 2008; 19: 1283-1290.
34. Liu JM, Li Y, Jiang Y, Yan XP. Gold nanoparticles amplified ultrasensitive quantification of human urinary protein by capillary electrophoresis with on-line inductively coupled plasma mass spectroscopic detection. J Proteome Res 2010; 9: 3545-3550.
35. Andersen S, Mischak H, Zurbig P, Parving HH, Rossing P. Urinary proteome analysis enables assessment of renoprotective treatment in type 2 diabetic patients with microalbuminuria. BMC Nephrol 2010; 11: 29.
36. Martin GB, Mansion F, Servais AC, Debrus B, Rozet E, Hubert P, et al. CE-MS method development for peptides analysis, especially hepcidin, an iron metabolism marker. Electrophoresis 2009; 30: 2624-2631.
37. Devarajan P. The use of targeted biomarkers for chronic kidney disease. Adv Chronic Kidney Dis 2010; 17: 469-479.
38. Liu BC, Zhang L, Lv LL, Wang YL, Liu DG, Zhang XL. Application of antibody array technology in the analysis of urinary cytokine profiles in patients with chronic kidney disease. Am J Nephrol 2006; 26: 483-490.
39. Wishart DS. Proteomics and the human metabolome project. Expert Rev Proteomics 2007; 4: 333-335.
40. Boudonck KJ, Rose DJ, Karoly ED, Lee DP, Lawton KA, Lapinskas PJ. Metabolomics for early detection of drug-induced kidney injury: review of the current status. Bioanalysis 2009; 1: 1645-1663.
41. Goldsmith P, Fenton H, Morris-Stiff G, Ahmad N, Fisher J, Prasad KR. Metabonomics: a useful tool for the future surgeon. J Surg Res 2010; 160: 122-132.
42. Portilla D, Schnackenberg L, Beger RD. Metabolomics as an extension of proteomic analysis: study of acute kidney injury. Semin Nephrol 2007; 27: 609-620.
43. Robertson DG. Metabonomics in toxicology: a review. Toxicol Sci 2005; 85: 809-822.
44. Wishart DS. Metabolomics: the principles and potential applications to transplantation. Am J Transplant 2005; 5: 2814-2820.
45. Bell JD, Lee JA, Lee HA, Sadler PJ, Wilkie DR, Woodham RH. Nuclear magnetic resonance studies of blood plasma and urine from subjects with chronic renal failure: identification of trimethylamine-N-oxide. Biochim Biophys Acta 1991; 1096: 101-107.
46. Xu EY, Perlina A, Vu H, Troth SP, Brennan RJ, Aslamkhan AG, et al. Integrated pathway analysis of rat urine metabolic profiles and kidney transcriptomic profiles to elucidate the systems toxicology of model nephrotoxicants. Chem Res Toxicol 2008; 21: 1548-1561.
47. Piddocke MP, Fazio A, Vongsangnak W, Wong ML, Heldt-Hansen HP, Workman C, et al. Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using "-omics" techniques. Microb Cell Fact 2011; 10: 27.
48. Young RA. Biomedical discovery with DNA arrays. Cell 2000; 102: 9-15.
49. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997; 278: 680-686.
50. Henger A, Kretzler M, Doran P, Bonrouhi M, Schmid H, Kiss E, et al. Gene expression fingerprints in human tubulointerstitial inflammation and fibrosis as prognostic markers of disease progression. Kidney Int 2004; 65: 904-917.
51. Alexander JJ, Saxena AK, Bao L, Jacob A, Haas M, Quigg RJ. Prominent renal expression of a murine leukemia retrovirus in experimental systemic lupus erythematosus. J Am Soc Nephrol 2002; 13: 2869-2877.
52. Hilpert J, Wogensen L, Thykjaer T, Wellner M, Schlichting U, Orntoft TF, et al. Expression profiling confirms the role of endocytic receptor megalin in renal vitamin D3 metabolism. Kidney Int 2002; 62: 1672-1681
53. Kretzler M, Cohen CD, Doran P, Henger A, Madden S, Grone EF, et al. Repuncturing the renal biopsy: strategies for molecular diagnosis in nephrology. J Am Soc Nephrol 2002; 13: 1961-1972.
54. Kottgen A, Glazer NL, Dehghan A, Hwang SJ, Katz R, Li M, et al. Multiple loci associated with indices of renal function and chronic kidney disease. Nat Genet 2009; 41: 712-717.
55. Kottgen A, Pattaro C, Boger CA, Fuchsberger C, Olden M, Glazer NL, et al. New loci associated with kidney function and chronic kidney disease. Nat Genet 2010; 42: 376-384.
56. Tanaka N, Babazono T, Saito S, Sekine A, Tsunoda T, Haneda M, et al. Association of solute carrier family 12 (sodium/chloride) member 3 with diabetic nephropathy, identified by genome-wide analyses of single nucleotide polymorphisms. Diabetes 2003; 52: 2848-2853.
57. Maeda S, Kobayashi MA, Araki S, Babazono T, Freedman BI, Bostrom MA, et al. A single nucleotide polymorphism within the acetyl-coenzyme A carboxylase beta gene is associated with proteinuria in patients with type 2 diabetes. PLoS Genet 2010; 6: e1000842.
58. Shimazaki A, Kawamura Y, Kanazawa A, Sekine A, Saito S, Tsunoda T, et al. Genetic variations in the gene encoding ELMO1 are associated with susceptibility to diabetic nephropathy. Diabetes 2005; 54: 1171-1178.
59. Boger CA, Chen MH, Tin A, Olden M, Kottgen A, de Boer IH, et al. CUBN is a gene locus for albuminuria. J Am Soc Nephrol 2011; 22: 555-570.
60. Stanescu HC, Arcos-Burgos M, Medlar A, Bockenhauer D, Kottgen A, Dragomirescu L, et al. Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy. N Engl J Med 2011; 364: 616-626.
61. Gharavi AG, Kiryluk K, Choi M, Li Y, Hou P, Xie J, et al. Genome-wide association study identifies susceptibility loci for IgA nephropathy. Nat Genet 2011; 43: 321-327.
62. Yu XQ, Li M, Zhang H, Low HQ, Wei X, Wang JQ, et al. A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. Nat Genet 2011.
63. Adams MD. Serial analysis of gene expression: ESTs get smaller. Bioessays 1996; 18: 261-262.
64. van Ruissen F, Jansen BJ, de Jongh GJ, van Vlijmen-Willems IM, Schalkwijk J. Differential gene expression in premalignant human epidermis revealed by cluster analysis of serial analysis of gene expression (SAGE) libraries. FASEB J 2002; 16: 246-248.
65. Virlon B, Cheval L, Buhler JM, Billon E, Doucet A, Elalouf JM. Serial microanalysis of renal transcriptomes. Proc Natl Acad Sci U S A 1999; 96: 15286-15291.
66. Chabardes-Garonne D, Mejean A, Aude JC, Cheval L, Di Stefano A, Gaillard MC, et al. A panoramic view of gene expression in the human kidney. Proc Natl Acad Sci U S A 2003; 100: 13710-13715.
67. El-Meanawy MA, Schelling JR, Pozuelo F, Churpek MM, Ficker EK, Iyengar S, et al. Use of serial analysis of gene expression to generate kidney expression libraries. Am J Physiol Renal Physiol 2000; 279: F383-F392.