A comparison of genome-wide DNA methylation patterns between different vascular tissues from patients with coronary heart disease

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Nazarenko, Maria S ^a,b   Markov, Anton V ^a,b   Lebedev, Igor N ^a,b   Freidin, Maxim B ^a   Sleptcov, Aleksei A ^a,b   Koroleva, Iuliya A ^a   Frolov, Aleksei V ^c   Popov, Vadim A ^c   Barbarash, Olga L ^c   Puzyrev, Valery P ^a,b  

^a RESEARCH INSTITUTE OF MEDICAL GENETICS   (Russian Federation)

^b TOMSK STATE UNIVERSITY   (Russian Federation)

^c RESEARCH INSTITUTE FOR COMPLEX ISSUES OF CARDIOVASCULAR DISEASES   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; ATHEROSCLEROTIC PLAQUE; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; CORONARY ARTERY ATHEROSCLEROSIS; CORONARY ARTERY BYPASS GRAFT; CPG ISLAND; DNA METHYLATION; GENE; GENE CONTROL; GENE FUNCTION; GENE ONTOLOGY; GENE SEQUENCE; GENETIC ASSOCIATION; GRAFT PATENCY; HOX GENE; HOXD4 GENE; HUMAN; HUMAN TISSUE; INFLAMMATION; INTERNAL MAMMARY ARTERY; ISCHEMIC HEART DISEASE; MALE; MIDDLE AGED; MIR10B GENE; PROMOTER REGION; PYROSEQUENCING; RIGHT CORONARY ARTERY; SAPHENOUS VEIN; AGED; ANTIBODY SPECIFICITY; ATHEROSCLEROSIS; CORONARY ARTERY DISEASE; CORONARY BLOOD VESSEL; FEMALE; GENETIC EPIGENESIS; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MAMMARY ARTERY; METABOLISM; MOLECULAR GENETICS; PATHOLOGY;

HOMEODOMAIN PROTEIN; MICRORNA; MIRN10 MICRORNA, HUMAN;

AGED; ATHEROSCLEROSIS; CORONARY DISEASE; CORONARY VESSELS; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENOME-WIDE ASSOCIATION STUDY; HOMEODOMAIN PROTEINS; HUMANS; MALE; MAMMARY ARTERIES; MICRORNAS; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; ORGAN SPECIFICITY; PLAQUE, ATHEROSCLEROTIC; SAPHENOUS VEIN;

EID: 84929455757     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0122601     Document Type: Article

References (34)

1. Loop FD. Internal-thoracic-artery grafts. Biologically better coronary arteries. N Engl J Med. 1996; 334: 263-265. PMID: 8532006
2. Webster AL, Yan MS, Marsden PA. Epigenetics and cardiovascular disease. Can J Cardiol. 2013; 29: 46-57. doi: 10.1016/j.cjca.2012.10.023 PMID: 23261320
3. Zaina S. Unraveling the DNA methylome of atherosclerosis. Curr Opin Lipidol. 2014; 25: 148-153. doi: 10.1097/MOL.0000000000000059 PMID: 24535282
4. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012; 13: 484-492. doi: 10.1038/nrg3230 PMID: 22641018
5. Post WS, Goldschmidt-Clermont PJ, Wilhide CC, Heldman AW, Sussman MS, Ouyang P, et al. Methylation of the estrogen receptor gene is associated with aging and atherosclerosis in the cardiovascular system. Cardiovasc Res. 1999; 43: 985-991. PMID: 10615426
6. Hiltunen MO, Turunen MP, Hakkinen TP, Rutanen J, Hedman M, Makinen K, et al. DNA hypomethylation and methyltransferase expression in atherosclerotic lesions. Vasc Med. 2002; 7: 5-11. PMID: 12083735
7. Zhu S, Goldschmidt-Clermont PJ, Dong C. Inactivation of monocarboxylate transporter MCT3 by DNA methylation in atherosclerosis. Circulation. 2005; 112: 1353-1361. PMID: 16116050
8. Kim J, Kim JY, Song KS, Lee YH, Seo JS, Jelinek J, et al. Epigenetic changes in estrogen receptor beta gene in atherosclerotic cardiovascular tissues and in-vitro vascular senescence. Biochim Biophys Acta. 2007; 1772: 72-80. PMID: 17110088
9. Zawadzki C, Chatelain N, Delestre M, Susen S, Quesnel B, Juthier F, et al. Tissue factor pathway inhibitor-2 gene methylation is associated with low expression in carotid atherosclerotic plaques. Atherosclerosis. 2009; 204: e4-14. doi: 10.1016/j.atherosclerosis.2008.10.009 PMID: 19081094
10. Castillo-Diaz SA, Garay-Sevilla ME, Hernandez-Gonzalez MA, Solis-Martinez MO, Zaina S. Extensive demethylation of normally hypermethylated CpG islands occurs in human atherosclerotic arteries. Int J Mol Med. 2010; 26: 691-700. PMID: 20878091
11. Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012; 22: 407-419. doi: 10.1101/gr.119867.110 PMID: 21613409
12. Nazarenko MS, Markov AV, Lebedev IN, Sleptsov AA, Frolov AV, Barbash OL, et al. DNA methylation profiling of the vascular tissues in the setting of atherosclerosis. Molecular Biology. 2013; 47: 352-357. doi: 10.3109/14017431.2013.845307 PMID: 24131200
13. Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013; 14: R115. PMID: 24138928
14. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium assay. Epigenomics. 2009; 1: 177-200. doi: 10.2217/epi.09.14 PMID: 22122642
15. Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008; 24: 1547-1548. doi: 10.1093/bioinformatics/btn224 PMID: 18467348
16. Smyth GK. Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and Computational Biology Solutions using R and Bioconductor. New York: Springer; 2005. pp. 397-420.
17. Wang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013; 41: W77-83. doi: 10.1093/nar/gkt439 PMID: 23703215
18. Muto A, Model L, Ziegler K, Eghbalieh SD, Dardik A. Mechanisms of vein graft adaptation to the arterial circulation: insights into the neointimal algorithm and management strategies. Circ J. 2010; 74: 1501-1512. PMID: 20606326
19. Goldschmidt-Clermont PJ, Dong C, Seo DM, Velazquez OC. Atherosclerosis, inflammation, genetics, and stem cells: 2012 update. Curr Atheroscler Rep. 2012; 14: 201-210. doi: 10.1007/s11883-012-0244-1 PMID: 22476914
20. Bijnens AP, Lutgens E, Ayoubi T, Kuiper J, Horrevoets AJ, Daemen MJ. Genome-wide expression studies of atherosclerosis: critical issues in methodology, analysis, interpretation of transcriptomics data. Arterioscler Thromb Vasc Biol. 2006; 26: 1226-1235. PMID: 16574897
21. Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A. 2010; 107: 1757-1764. doi: 10.1073/pnas.0906183107 PMID: 20080672
22. Davies PF, Manduchi E, Stoeckert CJ, Jimenez JM, Jiang YZ. Emerging topic: flow-related epigenetic regulation of endothelial phenotype through DNA methylation. Vascul Pharmacol. 2014; 62: 88-93. doi: 10.1016/j.vph.2014.05.007 PMID: 24874278
23. Shah N, Sukumar S. The Hox genes and their roles in oncogenesis. Nat Rev Cancer. 2010; 10: 361-371. doi: 10.1038/nrc2826 PMID: 20357775
24. Seo D, Wang T, Dressman H, Herderick EE, Iversen ES, Dong C, et al. Gene expression phenotypes of atherosclerosis. Arterioscler Thromb Vasc Biol. 2004; 24: 1922-1927. PMID: 15297278
25. Ma L, Teruya-Feldstein J, Weinberg RA. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature. 2007; 449: 682-688. PMID: 17898713
26. Shen X, Fang J, Lv X, Pei Z, Wang Y, Jiang S, et al. Heparin impairs angiogenesis through inhibition of microRNA-10b. J Biol Chem. 2011; 286: 26616-26627. doi: 10.1074/jbc.M111.224212 PMID: 21642433
27. Bidzhekov K, Gan L, Denecke B, Rostalsky A, Hristov M, Koeppel TA, et al. microRNA expression signatures and parallels between monocyte subsets and atherosclerotic plaque in humans. Thromb Haemost. 2012; 107: 619-625. doi: 10.1160/TH11-09-0607 PMID: 22370758
28. Gorski DH, Walsh K. The role of homeobox genes in vascular remodeling and angiogenesis. Circ Res. 2000; 87: 865-872. PMID: 11073881
29. Zhu Y, Cuevas IC, Gabriel RA, Su H, Nishimura S, Gao P, et al. Restoring transcription factor HoxA5 expression inhibits the growth of experimental hemangiomas in the brain. J Neuropathol Exp Neurol. 2009; 68: 626-632. doi: 10.1097/NEN.0b013e3181a491ce PMID: 19458547
30. Dunn J, Qiu H, Kim S, Jjingo D, Hoffman R, Kim CW, et al. Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis. J Clin Invest. 2014; 124: 3187-3199. doi: 10.1172/JCI74792 PMID: 24865430
31. Olson FJ, Sihlbom C, Davidsson P, Hulthe J, Fagerberg B, Bergstrom G. Consistent differences in protein distribution along the longitudinal axis in symptomatic carotid atherosclerotic plaques. Biochem Biophys Res Commun. 2010; 401: 574-580. doi: 10.1016/j.bbrc.2010.09.103 PMID: 20888797
32. Okuda M, Inoue N, Azumi H, Seno T, Sumi Y, Hirata Ki, et al. Expression of glutaredoxin in human coronary arteries: its potential role in antioxidant protection against atherosclerosis. Arterioscler Thromb Vasc Biol. 2001; 21: 1483-1487. PMID: 11557676
33. Archacki SR, Angheloiu G, Moravec CS, Liu H, Topol EJ, Wang QK. Comparative gene expression analysis between coronary arteries and internal mammary arteries identifies a role for the TES gene in endothelial cell functions relevant to coronary artery disease. Hum Mol Genet. 2012; 21: 1364-1373. doi: 10.1093/hmg/ddr574 PMID: 22156939
34. Chen YA, Choufani S, Ferreira JC, Grafodatskaya D, Butcher DT, Weksberg R. Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray. Genomics. 2011; 97: 214-222. doi: 10.1016/j.ygeno.2010.12.004 PMID: 21211562