DNA methylation map of human atherosclerosis

Circulation: Cardiovascular Genetics

Volumn 7, Issue 5, 2014, Pages 692-700

  Zaina, Silvio ^a   Heyn, Holger ^b   Carmona, F Javier ^b   Varol, Nuray ^b   Sayols, Sergi ^b   Condom, Enric ^b,c   Ramírez Ruz, José ^c   Gomez, Antonio ^b   Gonçalves, Isabel ^d   Moran, Sebastian ^b   Esteller, Manel ^b,c,e,f  

^a UNIVERSITY OF GUANAJUATO   (Mexico)

^b HOSPITAL UNIVERSITARI DE BELLVITGE   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

^d LUND UNIVERSITY   (Sweden)

^e INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^f BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; TRANSFER RNA; UNTRANSLATED RNA; HYDROGEN SULFITE; SULFITE;

AORTA; AORTA ATHEROSCLEROSIS; ARTERY CALCIFICATION; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; MUSCLE FUNCTION; PRIORITY JOURNAL; PROMOTER REGION; PYROSEQUENCING; QUANTITATIVE TRAIT LOCUS; REAL TIME POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; SMOOTH MUSCLE; ATHEROSCLEROSIS; CHEMISTRY; CHROMOSOME MAP; CLUSTER ANALYSIS; DIET; DISEASE COURSE; FEMALE; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; LIFESTYLE; METABOLISM; PATHOLOGY; PROCEDURES; RISK FACTOR;

AORTA; ATHEROSCLEROSIS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; CPG ISLANDS; DIET; DISEASE PROGRESSION; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION REGULATION; HUMANS; LIFE STYLE; RISK FACTORS; SULFITES;

EID: 84917721547     PISSN: 1942325X     EISSN: 19423268     Source Type: Journal    
DOI: 10.1161/CIRCGENETICS.113.000441     Document Type: Article

References (54)

1. Waddington CH. Introduction to Modern Genetics. New York: Macmillan; 1939
2. Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol. 2010;28:1057-1068
3. Bock C. Analysing and interpreting DNA methylation data. Nat Rev Genet. 2012;13:705-719
4. Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet. 2012;13:679-692
5. Urdinguio RG, Sanchez-Mut JV, Esteller M. Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies. Lancet Neurol. 2009;8:1056-1072
6. Bruneau BG. Epigenetic regulation of the cardiovascular system: introduction to a review series. Circ Res. 2010;107:324-326
7. Shirodkar AV, Marsden PA. Epigenetics in cardiovascular disease. Curr Opin Cardiol. 2011;26:209-215
8. Churko JM, Mantalas GL, Snyder MP, Wu JC. Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res. 2013;112:1613-1623
9. Movassagh M, Choy MK, Knowles DA, Cordeddu L, Haider S, Down T, et al. Distinct epigenomic features in end-stage failing human hearts. Circulation. 2011;124:2411-2422
10. Mathers CD, Loncar D. Projections of global mortality and burden of disease from 2002 to 2030. PLoS Med. 2006;3:e442
11. Marian AJ, Belmont J. Strategic approaches to unraveling genetic causes of cardiovascular diseases. Circ Res. 2011;108:1252-1269
12. Dubé JB, Hegele RA. Genetics 100 for cardiologists: basics of genomewide association studies. Can J Cardiol. 2013;29:10-17
13. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484-492
14. Lund G, Zaina S. Atherosclerosis: an epigenetic balancing act that goes wrong. Curr Atheroscler Rep. 2011;13:208-214
15. Findeisen HM, Kahles FK, Bruemmer D. Epigenetic regulation of vascular smooth muscle cell function in atherosclerosis. Curr Atheroscler Rep. 2013;15:319
16. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43:768-775
17. Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2012;44:40-46
18. Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res. 2010;20:170-179
19. Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, et al. Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis. PLoS Genet. 2011;7:e1002300
20. Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A. 2012;109:10522-10527
21. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315-322
22. Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6:692-702
23. Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics. 2010;11:587
24. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet. 2010;6:e1000952
25. Baccarelli A, Tarantini L, Wright RO, Bollati V, Litonjua AA, Zanobetti A, et al. Repetitive element DNA methylation and circulating endothelial and inflammation markers in the VA normative aging study. Epigenetics. 2010;5:222-228
26. Barrachina M, Ferrer I. DNA methylation of Alzheimer disease and tauopathy-related genes in postmortem brain. J Neuropathol Exp Neurol. 2009;68:880-891
27. Stylianou IM, Bauer RC, Reilly MP, Rader DJ. Genetic basis of atherosclerosis: insights from mice and humans. Circ Res. 2012;110:337-355
28. Lehtinen AB, Cox AJ, Ziegler JT, Voruganti VS, Xu J, Freedman BI, et al. Genetic mapping of vascular calcified plaque loci on chromosome 16p in European Americans from the diabetes heart study. Ann Hum Genet. 2011;75:222-235
29. Smolock EM, Trappanese DM, Chang S, Wang T, Titchenell P, Moreland RS. siRNA-mediated knockdown of h-caldesmon in vascular smooth muscle. Am J Physiol Heart Circ Physiol. 2009;297:H1930-H1939
30. Laumanns IP, Fink L, Wilhelm J, Wolff JC, Mitnacht-Kraus R, Graef-Hoechst S, et al. The noncanonical WNT pathway is operative in idiopathic pulmonary arterial hypertension. Am J Respir Cell Mol Biol. 2009;40:683-691
31. Gomez Sandoval YH, Lévesque LO, Li Y, Anand-Srivastava MB. Role of epidermal growth factor receptor transactivation in endothelin-1-induced enhanced expression of Gi protein and proliferation in A10 vascular smooth muscle cells. Can J Physiol Pharmacol. 2013;91:221-227
32. Van Herck JL, De Meyer GR, Martinet W, Van Hove CE, Foubert K, Theunis MH, et al. Impaired fibrillin-1 function promotes features of plaque instability in apolipoprotein E-deficient mice. Circulation. 2009;120:2478-2487
33. Trivedi CM, Patel RC, Patel CV. Homeobox gene HOXA9 inhibits nuclear factor-kappa B dependent activation of endothelium. Atherosclerosis. 2007;195:e50-e60
34. Chung N, Jee BK, Chae SW, Jeon YW, Lee KH, Rha HK. HOX gene analysis of endothelial cell differentiation in human bone marrow-derived mesenchymal stem cells. Mol Biol Rep. 2009;36:227-235
35. Kwan HY, Shen B, Ma X, Kwok YC, Huang Y, Man YB, et al. TRPC1 associates with BK(Ca) channel to form a signal complex in vascular smooth muscle cells. Circ Res. 2009;104:670-678
36. Li XC, Hopfer U, Zhuo JL. AT1 receptor-mediated uptake of angiotensin II and NHE-3 expression in proximal tubule cells through a microtubule-dependent endocytic pathway. Am J Physiol Renal Physiol. 2009;297:F1342-F1352
37. Zhou Q, Gallagher R, Ufret-Vincenty R, Li X, Olson EN, Wang S. Regulation of angiogenesis and choroidal neovascularization by members of microRNA-23~27~24 clusters. Proc Natl Acad Sci U S A. 2011;108:8287-8292
38. Bond JE, Bergeron A, Thurlow P, Selim MA, Bowers EV, Kuang A, et al. Angiotensin-II mediates nonmuscle myosin II activation and expression and contributes to human keloid disease progression. Mol Med. 2011;17:1196-1203
39. Wågsäter D, Zhu C, Björck HM, Eriksson P. Effects of PDGF-C and PDGF-D on monocyte migration and MMP-2 and MMP-9 expression. Atherosclerosis. 2009;202:415-423
40. Ait-Oufella H, Herbin O, Lahoute C, Coatrieux C, Loyer X, Joffre J, et al. Group X secreted phospholipase A2 limits the development of atherosclerosis in LDL receptor-null mice. Arterioscler Thromb Vasc Biol. 2013;33:466-473
41. Welling TH, Huber TS, Messina LM, Stanley JC. Tissue plasminogen activator increases canine endothelial cell proliferation rate through a plasmin-independent, receptor-mediated mechanism. J Surg Res. 1996;66:36-42
42. Wang Y, Bai Y, Qin L, Zhang P, Yi T, Teesdale SA, et al. Interferon-gamma induces human vascular smooth muscle cell proliferation and intimal expansion by phosphatidylinositol 3-kinase dependent mammalian target of rapamycin raptor complex 1 activation. Circ Res. 2007;101:560-569
43. Williams HC, San Martín A, Adamo CM, Seidel-Rogol B, Pounkova L, Datla SR, et al. Role of coronin 1B in PDGF-induced migration of vascular smooth muscle cells. Circ Res. 2012;111:56-65
44. Yoshida T, Hoofnagle MH, Owens GK. Myocardin and Prx1 contribute to angiotensin II-induced expression of smooth muscle alpha-actin. Circ Res. 2004;94:1075-1082
45. Lugano R, Peña E, Badimon L, Padró T. Aggregated low-density lipoprotein induce impairment of the cytoskeleton dynamics through urokinase-type plasminogen activator/urokinase-type plasminogen activator receptor in human vascular smooth muscle cell. J Thromb Haemost. 2012;10:2158-2167
46. Bai YP, Hu CP, Yuan Q, Peng J, Shi RZ, Yang TL, et al. Role of VPO1, a newly identified heme-containing peroxidase, in ox-LDL induced endothelial cell apoptosis. Free Radic Biol Med. 2011;51:1492-1500
47. Mendonça MC, Koles N, Doi SQ, Sellitti DF. Transforming growth factorbeta1 regulation of C-type natriuretic peptide expression in human vascular smooth muscle cells: dependence on TSC22D1. Am J Physiol Heart Circ Physiol. 2010;299:H2018-H2027
48. Kim M, Long TI, Arakawa K, Wang R, Yu MC, Laird PW. DNA methylation as a biomarker for cardiovascular disease risk. PLoS One. 2010;5:e9692
49. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011;333:1303-1307
50. Liu R, Jin Y, Tang WH, Qin L, Zhang X, Tellides G, Hwa J, Yu J, Martin KA. Ten-eleven translocation-2 (TET2) is a master regulator of smooth muscle cell plasticity. Circulation. 2013;128:2047-2057
51. Yoo T, Yoon YS, Ryu SH, Ahn JY, Kim S, Ha TY, et al. Hypermethylation of repetitive DNA elements in livers of mice fed an atherogenic diet. Nutrition. 2012;28:127-130
52. Rangel-Salazar R, Wickström-Lindholm M, Aguilar-Salinas CA, Alvarado-Caudillo Y, Døssing KB, Esteller M, et al. Human native lipoprotein-induced de novo DNA methylation is associated with repression of inflammatory genes in THP-1 macrophages. BMC Genomics. 2011;12:582
53. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013;45:1127-1133
54. Sandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, et al. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. J Clin Oncol. 2013;31:4140-4147.