Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus

BMC Medical Genomics

Volumn 3, Issue , 2010, Pages

  Bell, Christopher G ^a   Teschendorff, Andrew E ^a   Rakyan, Vardhman K ^b   Maxwell, Alexander P ^c   Beck, Stephan ^a   Savage, David A ^c  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^c QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CYTOSINE; GENOMIC DNA; PROTEIN UNC13B; UNCLASSIFIED DRUG; UPSTREAM STIMULATORY FACTOR; NERVE PROTEIN; UNC13B PROTEIN, HUMAN;

ADULT; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DIABETIC NEPHROPATHY; DISEASE DURATION; DNA FINGERPRINTING; DNA METHYLATION; FEMALE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC CORRELATION; GENETIC EPIGENESIS; GENETIC RISK; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; INTRON; IRELAND; MALE; MICROCHIP ANALYSIS; ONSET AGE; PRIORITY JOURNAL; PROMOTER REGION; SEX DIFFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION INITIATION SITE; CASE CONTROL STUDY; GENETIC PREDISPOSITION; GENETICS; HUMAN GENOME; MIDDLE AGED;

ADULT; CASE-CONTROL STUDIES; CPG ISLANDS; DIABETES MELLITUS, TYPE 1; DIABETIC NEPHROPATHIES; DNA METHYLATION; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HUMANS; MALE; MIDDLE AGED; NERVE TISSUE PROTEINS; TRANSCRIPTION INITIATION SITE;

EID: 77955205559     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-3-33     Document Type: Article

References (45)

1. UK Renal Registry Annual Report. D Ansell J Feehally D Fogarty CRV Tomsom AJ Williams G Warwick, Bistol 2008 2009/06/30 edn
2. US Renal Data System 2008 Annual Data Report. U.S Renal Data System, Atlas of Chronic Kidney Disease and End Stage Renal Disease in the United States Bethesda, MD: National Institutes of Health, National Institutes of Diabetes and Digestive and Kidney Diseases 2008 (National Institutes of Health NIoDaDaKD
3. Diabetic nephropathy. HN Ibrahim TH Hostetter, J Am Soc Nephrol 1997 8 487 493 9071718
4. Diabetes and the kidney. AS O'Connor JR Schelling, Am J Kidney Dis 2005 46 766 773 10.1053/j.ajkd.2005.05.032 16183435
5. Familial clustering of diabetic kidney disease. Evidence for genetic susceptibility to diabetic nephropathy. ER Seaquist FC Goetz S Rich J Barbosa, N Engl J Med 1989 320 1161 1165 10.1056/NEJM198905043201801 2710189
6. Familial factors determine the development of diabetic nephropathy in patients with IDDM. M Quinn MC Angelico JH Warram AS Krolewski, Diabetologia 1996 39 940 945 10.1007/BF00403913 8858216
7. Recent advancement of understanding pathogenesis of type 1 diabetes and potential relevance to diabetic nephropathy. K Ichinose E Kawasaki K Eguchi, Am J Nephrol 2007 27 554 564 10.1159/000107758 17823503
8. AP-1 proteins mediate hyperglycemia-induced activation of the human TGF-beta1 promoter in mesangial cells. C Weigert U Sauer K Brodbeck A Pfeiffer HU Haring ED Schleicher, J Am Soc Nephrol 2000 11 2007 2016 11053476
9. High glucose blunts vascular endothelial growth factor response to hypoxia via the oxidative stress-regulated hypoxia-inducible factor/hypoxia-responsible element pathway. P Katavetin T Miyata R Inagi T Tanaka R Sassa JR Ingelfinger T Fujita M Nangaku, J Am Soc Nephrol 2006 17 1405 1413 10.1681/ASN.2005090918 16597689
10. The role of inflammatory cytokines in diabetic nephropathy. JF Navarro-Gonzalez C Mora-Fernandez, J Am Soc Nephrol 2008 19 433 442 10.1681/ASN.2007091048 18256353
11. Association of genetic variants at 3 q22 with nephropathy in patients with type 1 diabetes mellitus. B He AM Osterholm A Hoverfalt C Forsblom EE Hjorleifsdottir AS Nilsson M Parkkonen J Pitkaniemi A Hreidarsson C Sarti,, et al. Am J Hum Genet 2009 84 5 13 10.1016/j.ajhg.2008.11.012 19084216
12. High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach. JJ Rogus GD Poznik MG Pezzolesi AM Smiles J Dunn W Walker K Wanic D Moczulski L Canani S Araki,, et al. Diabetes 2008 57 2519 2526 10.2337/db07-1086 18559660
13. G/T substitution in intron 1 of the UNC13B gene is associated with increased risk of nephropathy in patients with type 1 diabetes. DA Tregouet PH Groop S McGinn C Forsblom S Hadjadj M Marre HH Parving L Tarnow R Telgmann T Godefroy,, et al. Diabetes 2008 57 2843 2850 10.2337/db08-0073 18633107
14. Multiple superoxide dismutase 1/splicing factor serine alanine 15 variants are associated with the development and progression of diabetic nephropathy: the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Genetics study. H Al-Kateb AP Boright L Mirea X Xie R Sutradhar A Mowjoodi B Bharaj M Liu JM Bucksa VL Arends,, et al. Diabetes 2008 57 218 228 10.2337/db07-1059 17914031
15. Variants in intron 13 of the ELMO1 gene are associated with diabetic nephropathy in African Americans. TS Leak PS Perlegas SG Smith KL Keene PJ Hicks CD Langefeld JC Mychaleckyj SS Rich JK Kirk BI Freedman,, et al. Ann Hum Genet 2009 73 152 159 10.1111/j.1469-1809.2008.00498.x 19183347
16. confirmation of genetic associations at ELMO1 in the GoKinD collection supports its role as a susceptibility gene in diabetic nephropathy. MG Pezzolesi P Katavetin M Kure GD Poznik J Skupien JC Mychaleckyj SS Rich JH Warram AS Krolewski, Diabetes 2009 58 2698 2702 10.2337/db09-0641 19651817
17. Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes. MG Pezzolesi GD Poznik JC Mychaleckyj AD Paterson MT Barati JB Klein DP Ng G Placha LH Canani J Bochenski,, et al. Diabetes 2009 58 1403 1410 10.2337/db08-1514 19252134
18. Inherited epigenetic variation - revisiting soft inheritance. EJ Richards, Nat Rev Genet 2006 7 395 401 10.1038/nrg1834 16534512
19. Altered gene expression related to glomerulogenesis and podocyte structure in early diabetic nephropathy of db/db mice and its restoration by pioglitazone. H Makino Y Miyamoto K Sawai K Mori M Mukoyama K Nakao Y Yoshimasa S Suga, Diabetes 2006 55 2747 2756 10.2337/db05-1683 17003339
20. Epigenetics: new concepts of old phenomena in vascular physiology. B Krause L Sobrevia P Casanello, Curr Vasc Pharmacol 2009 7 513 520 10.2174/157016109789043883 19485890
21. Epigenetics and atherosclerosis. MP Turunen E Aavik S Yla-Herttuala, Biochim Biophys Acta 2009 1790 886 891 19233248
22. Epigenetics in hyperhomocysteinemic states. A special focus on uremia. D Ingrosso AF Perna, Biochim Biophys Acta 2009 1790 892 899 19245874
23. The epigenetic conductor: a genomic orchestrator in chronic kidney disease complications? TJ Ekstrom P Stenvinkel, J Nephrol 2009 22 442 449 19662598
24. Atherosclerosis risk factors can impose aberrant DNA methylation patterns: a tale of traffic and homocysteine. G Lund S Zaina, Curr Opin Lipidol 2009 20 448 449 10.1097/MOL.0b013e3283309928 19741342
25. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. BH Ramsahoye D Biniszkiewicz F Lyko V Clark AP Bird R Jaenisch, Proc Natl Acad Sci USA 2000 97 5237 5242 10.1073/pnas.97.10.5237 10805783
26. Human DNA methylomes at base resolution show widespread epigenomic differences. R Lister M Pelizzola RH Dowen RD Hawkins G Hon J Tonti-Filippini JR Nery L Lee Z Ye QM Ngo,, et al. Nature 2009 462 315 322 10.1038/nature08514 19829295
27. The methylome: approaches for global DNA methylation profiling. S Beck VK Rakyan, Trends Genet 2008 24 231 237 10.1016/j.tig.2008.01.006 18325624
28. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. S Saxonov P Berg DL Brutlag, Proc Natl Acad Sci USA 2006 103 1412 1417 10.1073/pnas.0510310103 16432200
29. Genome-wide DNA methylation profiling using Infinium assay. M Bibikova J Le B Barnes S Saedinia-Melnyk L Zhou R Shen K Gunderson, Epigenomics 2009 1 177 200 10.2217/epi.09.14
30. GoldenGate assay for DNA methylation profiling. M Bibikova JB Fan, Methods Mol Biol 2009 507 149 163 full-text 18987813
31. An epigenetic signature in peripheral blood predicts active ovarian cancer. AE Teschendorff U Menon A Gentry-Maharaj SJ Ramus SA Gayther S Apostolidou A Jones M Lechner S Beck IJ Jacobs M Widschwendter, PLoS One 2009 4 8274 10.1371/journal.pone.0008274 20019873
32. A common variant on chromosome 9p21 affects the risk of myocardial infarction. A Helgadottir G Thorleifsson A Manolescu S Gretarsdottir T Blondal A Jonasdottir A Sigurdsson A Baker A Palsson G Masson,, et al. Science 2007 316 1491 1493 10.1126/science.1142842 17478679 (Pubitemid 46906618)
33. A genome-wide association study identifies novel risk loci for type 2 diabetes. R Sladek G Rocheleau J Rung C Dina L Shen D Serre P Boutin D Vincent A Belisle S Hadjadj,, et al. Nature 2007 445 881 885 10.1038/nature05616 17293876
34. R: A Language for Data Analysis and Graphics. R Ihaka R Gentleman, Journal of Computational and Graphical Statistics 1996 5 299 314 10.2307/1390807
35. Bioconductor: open software development for computational biology and bioinformatics. RC Gentleman VJ Carey DM Bates B Bolstad M Dettling S Dudoit B Ellis L Gautier Y Ge J Gentry,, et al. Genome Biol 2004 5 80 10.1186/gb-2004-5-10-r80 15461798
36. The elements of statistical learning: data mining, inference, and prediction: with 200 full-color illustrations. T Hastie R Tibshirani JH Friedman, New York: Springer 2001
37. Capturing heterogeneity in gene expression studies by surrogate variable analysis. JT Leek JD Storey, PLoS Genet 2007 3 1724 1735 10.1371/journal.pgen. 0030161 17907809
38. Remarks on Parallel Analysis. A Buja N Eyuboglu, Multivariate Behavioral Research 1992 27 509 540 10.1207/s15327906mbr2704-2
39. Statistical significance for genomewide studies. JD Storey R Tibshirani, Proc Natl Acad Sci USA 2003 100 9440 9445 10.1073/pnas.1530509100 12883005
40. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. A Subramanian P Tamayo VK Mootha S Mukherjee BL Ebert MA Gillette A Paulovich SL Pomeroy TR Golub ES Lander JP Mesirov, Proc Natl Acad Sci USA 2005 102 15545 15550 10.1073/pnas.0506580102 16199517
41. Rab34 and its effector munc13-2 constitute a new pathway modulating protein secretion in the cellular response to hyperglycemia. NM Goldenberg M Silverman, Am J Physiol Cell Physiol 2009 297 1053 1058 10.1152/ajpcell.00286. 2009 19641095
42. DNA methylation landscapes: provocative insights from epigenomics. MM Suzuki A Bird, Nat Rev Genet 2008 9 465 476 10.1038/nrg2341 18463664
43. DNA methylation profiling of human chromosomes 6, 20 and 22. F Eckhardt J Lewin R Cortese VK Rakyan J Attwood M Burger J Burton TV Cox R Davies TA Down,, et al. Nat Genet 2006 38 1378 1385 10.1038/ng1909 17072317
44. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. RA Irizarry C Ladd-Acosta B Wen Z Wu C Montano P Onyango H Cui K Gabo M Rongione M Webster,, et al. Nat Genet 2009 41 178 186 10.1038/ng.298 19151715
45. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. TA Down VK Rakyan DJ Turner P Flicek H Li E Kulesha S Graf N Johnson J Herrero EM Tomazou,, et al. Nat Biotechnol 2008 26 779 785 10.1038/nbt1414 18612301