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Application of systems biology to the study of chronic kidney disease

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Author:: No author available

Journal Title:: Chinese Medical Journal

Issue:: 14

DOI:: 10.3760/cma.j.issn.0366-6999.2012.14.036

Key Word:: systems biology;chronic kidney disease;microarray analysis;genome-wide association study;serial analysis ofgene expression

Abstract： Chronic kidney disease (CKD) is a major public health problem that affects about 10％ of the general population.Current approaches to characterize the category and progression of CKD are normally based on renal histopathological results and clinical parameters.However,this information is not sufficient to predict CKD progression risk reliably or to guide preventive interventions.Nowadays,the appearance of systems biology has brought forward the concepts of "-omics"technologies,including genomics,transcriptomics,proteomics,and metabolomics.Systems biology,together with molecular analysis approaches such as microarray analysis,genome-wide association studies (GWAS),and serial analysis of gene expression (SAGE),has provided the framework for a comprehensive analysis of renal disease and serves as a starting point for generating novel molecular diagnostic tools for use in nephrology.In particular,analysis of urinary mRNA and protein levels is rapidly evolving as a non-invasive approach for CKD monitoring.All these systems biological molecular approaches are required for application of the concept of "personalized medicine" to progressive CKD,which will result in tailoring therapy for each patient,in contrast to the "one-size-fits-all" therapies currently in use.

Reference

[1]LIU Bi-cheng,L(U) Lin-li.Novel biomarkers for progression of chronic kidney disease[J].2010,(13).
[2]HUANG Hai-dong,LIN Fu-jun,LI Xin-juan,etc.Genetic polymorphisms of the renin-angiotensin-aldosterone system in Chinese patients with end-stage renal disease secondary to IgA nephropathy[J].2010,(22).
[3]Schmid H,Kretzler M,Henger A.Molecular approaches to chronic kidney disease.[J].2006,15(2).
[4]Min Zheng,Lin-Li Lv,Jie Ni,etc.Urinary Podocyte-Associated mRNA profile in Various Stages of Diabetic Nephropathy.[J].2011,6(5).
[5]Hong Zhang,Ming Li,Xue Qing Yu,etc.A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy[J].2012,44(2).
[6]Abbas Dehghan,Ronit Katz,Man Li,etc.Multiple loci associated with indices of renal function and chronic kidney disease[J].2009,41(6).
[7]Wishart DS.Metabolomics: the principles and potential applications to transplantation.[J].2005,5(12).
[8]Portilla D,Beger RD,Schnackenberg L.Metabolomics as an extension of proteomic analysis: study of acute kidney injury.[J].2007,27(6).
[9]Zhang,J.-D.,Ma,K.-L.,Phillips,A.O.,etc.Urinary mRNA markers of epithelial-mesenchymal transition correlate with progression of diabetic nephropathy[J].2012,76(5).
[10]M A, El-Meanawy,J R, Schelling,F, Pozuelo,etc.Use of serial analysis of gene expression to generate kidney expression libraries.[J].2000,279(2).
[11]David S, Wishart.Proteomics and the human metabolome project.[J].2007,4.
[12]Lina Yang,hujuan Guo,Ang LI,etc.Protein microarrays for systems biology[J].2011,(3).
[13]Anna Kottgen,Wen Hong L Kao,Shih-Jen Hwang,etc.Genome-wide association study for renal traits in the Framingham Heart and Atherosclerosis Risk in Communities Studies[J].2008,9(1).
[14]Taler SJ,Rule AD,Cosio FG,etc.The association between age and nephrosclerosis on renal biopsy among healthy adults.[J].2010,152(9).
[15]Arnaud Mejean,Veronique Anthouard,Danielle Chabardes-Garonne,etc.A panoramic view of gene expression in the human kidney[J].2003,100(23).
[16]Kretzler M,Grone HJ,Doran P,etc.Repuncturing the renal biopsy: strategies for molecular diagnosis in nephrology.[J].2002,13(7).
[17]Virlon B,Elalouf JM,Cheval L,etc.Serial microanalysis of renal transcriptomes.[J].1999,96(26).
[18]Masakazu Haneda,Yasushi Tanaka,Akihiro Sekine,etc.Association of Solute Carrier Family 12 (Sodium/Chloride) Member 3 With Diabetic Nephropathy, Identified by Genome-Wide Analyses of Single Nucleotide Polymorphisms[J].2003,52(11).
[19]Ideker T,Galitski T,Hood L.A new approach to decoding life: systems biology.[J].2001,2(0).
[20]Tarnow L,Zurbig P,Rossing P,etc.Urinary proteomics in diabetes and CKD.[J].2008,19(7).
[21]Jiang, Y.,Li, Y.,Liu, J.-M.,etc.Gold nanoparticles amplified ultrasensitive quantification of human urinary protein by capillary electrophoresis with on-line inductively coupled plasma mass spectroscopic detection[J].2010,9(7).
[22]van Ruissen F,Jansen BJ,de Jongh GJ,etc.Differential gene expression in premalignant human epidermis revealed by cluster analysis of serial analysis of gene expression (SAGE) libraries.[J].2002,16(2).
[23]J L, DeRisi,V R, Iyer,P O, Brown.Exploring the metabolic and genetic control of gene expression on a genomic scale.[J].1997,278(5338).
[24]Martin GB,Servais AC,Mansion F.CE-MS method development for peptides analysis, especially hepcidin, an iron metabolism marker.[J].2009,30(15).
[25]Jessy J, Alexander,Amit K, Saxena,Lihua, Bao,etc.Prominent renal expression of a murine leukemia retrovirus in experimental systemic lupus erythematosus.[J].2002,13.
[26]Robertson DG.Metabonomics in toxicology: a review.[J].2005,85(2).
[27]Kurt J, Boudonck,Donald J, Rose,Edward D, Karoly,etc.Metabolomics for early detection of drug-induced kidney injury: review of the current status.[J].2009,1.
[28]Maya P Piddocke,Alessandro Fazio,Wanwipa Vongsangnak,etc.Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using "-omics" techniques[J].2011,10(1).
[29]Oberbauer R,Perco P,Lukas A,etc.Linking transcriptomic and proteomic data on the level of protein interaction networks.[J].2010,31(11).
[30]Ian Craig Lawrance,Borut Klopcic,Valerie C Wasinger.Proteomics: An overview[J].2005,11(10).
[31]Ostendorf T,Boor P,Floege J.Renal fibrosis: novel insights into mechanisms and therapeutic targets.[J].2010,6(11).
[32]Schlichting U,Thykjaer T,Willnow TE,etc.Expression profiling confirms the role of endocytic receptor megalin in renal vitamin D3 metabolism.[J].2002,62(5).
[33]Schlondorff D,Henger A,Kiss E,etc.Gene expression fingerprints in human tubulointerstitial inflammation and fibrosis as prognostic markers of disease progression.[J].2004,65(3).
[34]Nakamura Y,Kanazawa A,Omachi S,etc.Genetic variations in the gene encoding ELMO1 are associated with susceptibility to diabetic nephropathy.[J].2005,54(4).
[35]Martini S,Kretzler M,Keller B,etc.Linking variants from genome-wide association analysis to function via transcriptional network analysis.[J].2010,30(2).
[36]Mortazavi A,Williams BA,Mccue K,etc.Mapping and quantifying mammalian transcriptomes by RNA-Seq[J].2008,5(7).
[37]Adams MD..Serial Analysis of Gene Expression - Ests Get Smaller[J].1996,18(4).
[38]Brennan RJ,Vu H,Xu Q,etc.Integrated pathway analysis of rat urine metabolic profiles and kidney transcriptomic profiles to elucidate the systems toxicology of model nephrotoxicants.[J].2008,21(8).
[39]Schelling JR,Hayden PS,Sedor JR,etc.DNA expression analysis: serial analysis of gene expression, microarrays and kidney disease.[J].2003,12(4).
[40]Randall JD,Chow G,Kurella M,etc.DNA microarray analysis of complex biologic processes.[J].2001,12(5).
[41]Maeda, Shiro,Kobayashi, Masa-aki,Araki, Shin-ichi,etc.A Single Nucleotide Polymorphism within the Acetyl-Coenzyme A Carboxylase Beta Gene Is Associated with Proteinuria in Patients with Type 2 Diabetes.[J].2010,6(2).
[42]Goldsmith P,Fenton H,Morris Stiff G,etc.Metabonomics: a useful tool for the future surgeon.[J].2010,160(1).
[43]B?ger,C.A.,Heid,I.M..Chronic kidney disease: Novel insights from genome-wide association studies[J].2011,34(4).
[44]Carrero JJ,Luttropp K,Lindholm B.Genetics/Genomics in chronic kidney disease--towards personalized medicine?[J].2009,22(4).
[45]Mones S. Abu-Asab,Mohamed Chaouchi,Salvatore Alesci,etc.Biomarkers in the Age of Omics: Time for a Systems Biology Approach.[J].2011,15(3).
[46]Klein, J. B.,Thongboonkerd, V..Overview of Proteomics[J].2004,141(1).
[47]Devarajan P.The use of targeted biomarkers for chronic kidney disease.[J].2010,17(6).
[48]Marnik, Vuylsteke,Johan D, Peleman,Michiel J T, van Eijk.AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis.[J].2007,2(6).
[49]J D, Bell,J A, Lee,H A, Lee,etc.Nuclear magnetic resonance studies of blood plasma and urine from subjects with chronic renal failure: identification of trimethylamine-N-oxide.[J].1991,1096.
[50]N L, Anderson,N G, Anderson.Proteome and proteomics: new technologies, new concepts, and new words.[J].1998,19(11).
[51]Schratzberger G,Oberbauer R,Perco P,etc.Gene expression profiles of human proximal tubular epithelial cells in proteinuric nephropathies.[J].2007,71(4).
[52]Carsten A, B?ger,Ming-Huei, Chen,Adrienne, Tin,etc.CUBN is a gene locus for albuminuria.[J].2011,22.
[53]Ghiggeri GM,Bertinetto F,Lugani F,etc.Genome-wide association study identifies susceptibility loci for IgA nephropathy.[J].2011,43(4).
[54]Braosi AP,Avila AR,de-Brito-RB Jr,etc.Association between vitamin D receptor gene polymorphisms and susceptibility to chronic kidney disease and periodontitis.[J].2007,25(5).
[55]Stanescu HC,Arcos Burgos M,Medlar A,etc.Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.[J].2011,364(7).
[56]Kretzler M,Yasuda Y,Cohen CD,etc.Gene expression profiling analysis in nephrology: towards molecular definition of renal disease.[J].2006,10(2).
[57]Sten Andersen,Harald Mischak,Petra Zürbig,etc.Urinary proteome analysis enables assessment of renoprotective treatment in type 2 diabetic patients with microalbuminuria[J].2010,11(1).