Genetics meets epigenetics: Genetic variants that modulate noncoding RNA in cardiovascular diseases

Journal of Molecular and Cellular Cardiology

Volumn 89, Issue , 2015, Pages 27-34

  Calore, Martina ^a   De Windt, Leon J ^a   Rampazzo, Alessandra ^b  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b UNIVERSITY OF PADOVA   (Italy)

Author keywords

Cardiovascular diseases; Common genetic variants; Long noncoding RNAs; MiRNAs

Indexed keywords

5,10 METHYLENETETRAHYDROFOLATE REDUCTASE (FADH2); ANGIOPOIETIN 1; ANGIOTENSINOGEN; CHROMOGRANIN A; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; GELATINASE B; LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA; MICRORNA 147; MICRORNA 149; MICRORNA 22; MICRORNA 224; ORGANIC CATION TRANSPORTER 3; POTASSIUM CHANNEL KCNQ1; TOLL LIKE RECEPTOR 4; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

3' UNTRANSLATED REGION; AGT GENE; ATP6V0A1 GENE; ATRIAL FIBRILLATION; CARDIOMETABOLIC SYNDROME; CARDIOVASCULAR DISEASE; CARDIOVASCULAR RISK; CDKN2A GENE; CDKN2B GENE; CHGA GENE; CORONARY ARTERY DISEASE; EPIGENETICS; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCUS; GENE TARGETING; GENETIC ASSOCIATION; GENETIC REGULATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENETICS; HUMAN; KCNQ1 GENE; LONG QT SYNDROME; MMP9 GENE; MTHFR GENE; NONHUMAN; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SLC22A3 GENE; TCF21 GENE; TRANSCRIPTION REGULATION; ANIMAL; GENETIC EPIGENESIS; GENETIC VARIATION; METABOLISM;

ANIMALS; CARDIOVASCULAR DISEASES; EPIGENESIS, GENETIC; GENETIC VARIATION; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, UNTRANSLATED;

EID: 84952683413     PISSN: 00222828     EISSN: 10958584     Source Type: Journal    
DOI: 10.1016/j.yjmcc.2015.10.028     Document Type: Review

References (66)

1. Ambros V. The functions of animal microRNAs. Nature 2004, 431:350-355.
2. Kim V.N. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 2005, 6:376-385.
3. Geisler S., Coller J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 2013, 14:699-712.
4. Cammaerts S., Strazisar M., De Rijk P., Del Favero J. Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. Front. Genet. 2015, 6:186. 10.3389/fgene.2015.00186.
5. Mencia A., Modamio-Hoybjor S., Redshaw N., Morin M., Mayo-Merino F., Olavarrieta L., et al. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat. Genet. 2009, 41:609-613.
6. Calin G.A., Dumitru C.D., Shimizu M., Bichi R., Zupo S., Noch E., et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl. Acad. Sci. 2002, 99:15524-15529. 10.1073/pnas.242606799.
7. Hughes A.E., Bradley D.T., Campbell M., Lechner J., Dash D.P., Simpson D.A., et al. Mutation altering the miR-184 seed region causes familial keratoconus with cataract. Am. J. Hum. Genet. 2011, 89:628-633. 10.1016/j.ajhg.2011.09.014.
8. Damani S.B., Topol E.J. Emerging genomic applications in coronary artery disease. J. Am. Coll. Cardiol. Intv. 2011, 4:473-482. 10.1016/j.jcin.2010.12.016.
9. Wu C., Gong Y., Sun A., Zhang Y., Zhang C., Zhang W., et al. The human MTHFR rs4846049 polymorphismincreases coronary heart disease risk through modifying miRNA binding. Nutr. Metab. Cardiovasc. Dis. 2013, 23:693-698. 10.1016/j.numecd.2012.02.009.
10. Antoniades C., Shirodaria C., Warrick N., Cai S., de Bono J., Lee J., et al. 5-methyltetrahydrofolate rapidly improves endothelial function and decreases superoxide production in human vessels: effects on vascular tetrahydrobiopterin availability and endothelial nitric oxide synthase coupling. Circulation 2006, 114:1193-1201. 10.1161/CIRCULATIONAHA.106.612325.
11. Deloukas P., Kanoni S., Willenborg C., Farrall M., Assimes T.L., Thompson J.R., et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat. Genet. 2013, 45:25-33.
12. Miller C.L., Haas U., Diaz R., Leeper N.J., Kundu R.K., Patlolla B., et al. Coronary heart disease-associated variation in TCF21 disrupts a miR-224 binding site and miRNA-mediated regulation. PLoS Genet. 2014, 10.
13. Schneider E., Machavoine F., Pléau J.-M., Bertron A.-F., Thurmond R.L., Ohtsu H., et al. Organic cation transporter 3 modulates murine basophil functions by controlling intracellular histamine levels. J. Exp. Med. 2005, 202:387-393. 10.1084/jem.20050195.
14. Li L., He M., Zhou L., Miao X., Wu F., Huang S., et al. A solute carrier family 22 member 3 variant rs3088442 G→a associated with coronary heart disease inhibits lipopolysaccharide-induced inflammatory response. J. Biol. Chem. 2015, 290:5328-5340. 10.1074/jbc.M114.584953.
15. Shaw S.Y., Cheng S., Cupples L.A., Larson M.G., McCabe E.L., Ngwa J.S., et al. Genetic and clinical correlates of early-outgrowth colony-forming units. Circ. Cardiovasc. Genet. 2011, 4:296-304. 10.1161/CIRCGENETICS.110.958470.
16. Chen Y., Rao F., Rodriguez-Flores J.L., Mahapatra N.R., Mahata M., Wen G., et al. Common genetic variants in the chromogranin a promoter alter autonomic activity and blood pressure. Kidney Int. 2008, 74:115-125.
17. Salem R.M., Cadman P.E., Chen Y., Rao F., Wen G., Hamilton B.A., et al. Chromogranin a polymorphisms are associated with hypertensive renal disease. J. Am. Soc. Nephrol. 2008, 19:600-614. 10.1681/ASN.2007070754.
18. Luft F.C. Molecular genetics of human hypertension. J. Hypertens. 1998, 16:1871-1878.
19. Helle K. Chromogranins A and B and Secretogranin II as Prohormones for Regulatory Peptides from the Diffuse Neuroendocrine System. Cell. Pept. Horm. Synth. Secret. Pathways SE - 26 2010, vol. 50:45-62. Springer, Berlin Heidelberg. 10.1007/400_2009_26. J.F. Rehfeld, J.R. Bundgaard (Eds.).
20. Mahapatra N.R. Catestatin is a novel endogenous peptide that regulates cardiac function and blood pressure. Cardiovasc. Res. 2008, 80:330-338.
21. Taupenot L., Harper K.L., O'Connor D.T. The chromogranin-secretogranin family. N. Engl. J. Med. 2003, 348:1134-1149. 10.1056/NEJMra021405.
22. Friese R.S., Altshuler A.E., Zhang K., Miramontes-Gonzalez J.P., Hightower C.M., Jirout M.L., et al. MicroRNA-22 and promoter motif polymorphisms at the chga locus in genetic hypertension: functional and therapeutic implications for gene expression and the pathogenesis of hypertension. Hum. Mol. Genet. 2013, 22:3624-3640. 10.1093/hmg/ddt213.
23. O'Connor D.T., Zhu G., Rao F., Taupenot L., Fung M.M., Das M., et al. Heritability and genome-wide linkage in US and Australian twins identify novel genomic regions controlling chromogranin a: implications for secretion and blood pressure. Circulation 2008, 118:247-257. 10.1161/CIRCULATIONAHA.107.709105.
24. Wei Z., Biswas N., Wang L., Courel M., Zhang K., Soler-Jover A., et al. A common genetic variant in the 3'-UTR of vacuolar H+-ATPase ATP6V0A1 creates a micro-RNA motif to alter chromogranin a processing and hypertension risk. Circ. Cardiovasc. Genet. 2011, 4:381-389. 10.1161/CIRCGENETICS.111.959767.
25. Mopidevi B., Ponnala M., Kumar A. Human angiotensinogen +11525 C/a polymorphism modulates its gene expression through microRNA binding. Physiol. Genomics 2013, 45:901-906. 10.1152/physiolgenomics.00056.2013.
26. Kretowski A., McFann K., Hokanson J.E., Maahs D., Kinney G., Snell-Bergeon J.K., et al. Polymorphisms of the renin-angiotensin system genes predict progression of subclinical coronary atherosclerosis. Diabetes 2007, 56:863-871. 10.2337/db06-1321.
27. Rasmussen-Torvik L.J., North K.E., Gu C.C., Lewis C.E., Wilk J.B., Chakravarti A., et al. A population association study of angiotensinogen polymorphisms and haplotypes with left ventricular phenotypes. Hypertension 2005, 46:1294-1299. 10.1161/01.HYP.0000192653.17209.84.
28. Jain S., Tillinger A., Mopidevi B., Pandey V.G., Chauhan C.K., Fiering S.N., et al. Transgenic mice with -6A haplotype of the human angiotensinogen gene have increased blood pressure compared with -6G haplotype. J. Biol. Chem. 2010, 285:41172-41186. 10.1074/jbc.M110.167585.
29. Nejatizadeh A., Kumar R., Stobdan T., Goyal A.K., Gupta M., Javed S., et al. Significance of angiotensinogen gene haplotypes and genotypes combinations in hypertension. J. Hypertens. 2008, 26:1094-1101. 10.1097/HJH.0b013e3282fad951.
30. Iwai N., Shimoike H., Ohmichi N., Kinoshita M. Angiotensinogen gene and blood pressure in the Japanese population. Hypertension 1995, 25:688-693. 10.1161/01.HYP.25.4.688.
31. Roden D.M. Long-QT syndrome. N. Engl. J. Med. 2008, 358:169-176. 10.1056/NEJMcp0706513.
32. Zhao Y., Ransom J.F., Li A., Vedantham V., von Drehle M., Muth A.N., et al. Dysregulation of Cardiogenesis, Cardiac Conduction, and Cell Cycle in Mice Lacking miRNA-1-2. Cell 2007, 129:303-317. 10.1016/j.cell.2007.03.030.
33. Xiao L., Xiao J., Luo X., Lin H., Wang Z., Nattel S. Feedback remodeling of cardiac potassium current expression: a novel potential mechanism for control of repolarization reserve. Circulation 2008, 118:983-992. 10.1161/CIRCULATIONAHA.107.758672.
34. Splawski I., Shen J., Timothy K.W., Lehmann M.H., Priori S., Robinson J.L., et al. Spectrum of mutations in long-QT syndrome genes: KVLQT1, HERG, SCN5A, KCNE1, and KCNE2. Circulation 2000, 102:1178-1185. 10.1161/01.CIR.102.10.1178.
35. Amin A.S., Giudicessi J.R., Tijsen A.J., Spanjaart A.M., Reckman Y.J., Klemens C.A., et al. Variants in the 3' untranslated region of the KCNQ1-encoded Kv7.1 potassium channel modify disease severity in patients with type 1 long QT syndrome in an allele-specific manner. Eur. Heart J. 2012, 33:714-723. 10.1093/eurheartj/ehr473.
36. Consortium G.L.G. Discovery and refinement of loci associated with lipid levels. Nat. Genet. 2013, 45:1274-1283.
37. Scott R.A., Lagou V., Welch R.P., Wheeler E., Montasser M.E., Luan J., et al. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. Nat. Genet. 2012, 44:991-1005.
38. Grundy S.M., Cleeman J.I., Daniels S.R., Donato K.A., Eckel R.H., Franklin B.A., et al. Diagnosis and management of the metabolic syndrome: an American heart association/national heart, lung, and blood institute scientific statement: executive summary. Crit. Pathw. Cardiol. 2005, 4:198-203.
39. Ghanbari M., Franco O.H., de Looper H.W.J., Hofman A., Erkeland S.J., Dehghan A. Genetic variations in MicroRNA-binding sites affect MicroRNA-mediated regulation of several genes associated with cardio-metabolic phenotypes. Circ. Cardiovasc. Genet. 2015, 8:473-486. 10.1161/CIRCGENETICS.114.000968.
40. Yuan M., Zhan Q., Duan X., Song B., Zeng S., Chen X., et al. A functional polymorphism at miR-491-5p binding site in the 3'-UTR of MMP-9 gene confers increased risk for atherosclerotic cerebral infarction in a Chinese population. Atherosclerosis 2013, 226:447-452. 10.1016/j.atherosclerosis.2012.11.026.
41. Andersen K.K., Olsen T.S., Dehlendorff C., Kammersgaard L.P. Hemorrhagic and ischemic strokes compared: stroke severity, mortality, and risk factors. Stroke 2009, 40:2068-2072. 10.1161/STROKEAHA.108.540112.
42. Kuwashiro T., Sugimori H., Ago T., Kamouchi M., Kitazono T. Risk factors predisposing to stroke recurrence within one year of non-cardioembolic stroke onset: the Fukuoka stroke registry. Cerebrovasc. Dis. 2012, 33:141-149. 10.1159/000334190.
43. Newby A.C. Dual role of matrix metalloproteinases (matrixins) in intimal thickening and atherosclerotic plaque rupture. Physiol. Rev. 2004, 85:1-31.
44. Mitsios N., Gaffney J., Kumar P., Krupinski J., Kumar S., Slevin M. Pathophysiology of acute ischaemic stroke: an analysis of common signalling mechanisms and identification of new molecular targets. Pathobiology 2006, 73:159-175. 10.1159/000096017.
45. Elkind M.S.V. Inflammation, atherosclerosis, and stroke. Neurologist 2006, 12:140-148. 10.1097/01.nrl.0000215789.70804.b0.
46. Chen J., Yang T., Yu H., Sun K., Shi Y., Song W., et al. A functional variant in the 3'-UTR of angiopoietin-1 might reduce stroke risk by interfering with the binding efficiency of microRNA 211. Hum. Mol. Genet. 2010, 19:2524-2533. 10.1093/hmg/ddq131.
47. Bai Y., Nie S., Jiang G., Zhou Y., Zhou M., Zhao Y., et al. Regulation of CARD8 expression by ANRIL and association of CARD8 single nucleotide polymorphism rs2043211 (p.C10X) with ischemic stroke. Stroke 2014, 45:383-388. 10.1161/STROKEAHA.113.003393.
48. Paramel G.V., Folkersen L., Strawbridge R.J., Elmabsout A.A., Särndahl E., Lundman P., et al. CARD8 gene encoding a protein of innate immunity is expressed in human atherosclerosis and associated with markers of inflammation. Clin. Sci. 2013, 125:401-407.
49. Den Hoed M., Eijgelsheim M., Esko T., Brundel B.J.J.M., Peal D.S., Evans D.M., et al. Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat. Genet. 2013, 45:621-631.
50. Thomas I., Sorrentino M. Bleeding risk prediction models in atrial fibrillation. Curr. Cardiol. Rep. 2013, 16:1-8. 10.1007/s11886-013-0432-9.
51. Wang Z., Lu Y., Yang B. MicroRNAs and atrial fibrillation: new fundamentals. Cardiovasc. Res. 2011, 89:710-721.
52. Luo X., Yang B., Nattel S. MicroRNAs and atrial fibrillation: mechanisms and translational potential. Nat. Rev. Cardiol. 2015, 12:80-90.
53. Girmatsion Z., Biliczki P., Bonauer A., Wimmer-Greinecker G., Scherer M., Moritz A., et al. Changes in microRNA-1 expression and IK1 up-regulation in human atrial fibrillation. Heart Rhythm. 2009, 6:1802-1809. 10.1016/j.hrthm.2009.08.035.
54. Xiao J., Liang D., Zhang Y., Liu Y., Zhang H., Liu Y., et al. MicroRNA expression signature in atrial fibrillation with mitral stenosis. Physiol. Genomics 2011, 43:655-664.
55. Cooley N., Cowley M.J., Lin R.C.Y., Marasco S., Wong C., Kaye D.M., et al. Influence of atrial fibrillation on microRNA expression profiles in left and right atria from patients with valvular heart disease. Physiol. Genomics 2012, 44:211-219.
56. Ohanian M., Humphreys D.T., Anderson E., Preiss T., Fatkin D. A heterozygous variant in the human cardiac miR-133 gene, MIR133A2, alters miRNA duplex processing and strand abundance. BMC Genet. 2013, 14:18. 10.1186/1471-2156-14-18.
57. Roldán V., Arroyo A.B., Salloum-Asfar S., Manzano-Fernández S., García-Barberá N., Marín F., et al. Prognostic role of MIR146A polymorphisms for cardiovascular events in atrial fibrillation. Thromb. Haemost. 2014, 112:781-788. 10.1160/TH14-01-0092.
58. Taganov K.D., Boldin M.P., Chang K.-J., Baltimore D. NF-κB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc. Natl. Acad. Sci. 2006, 103:12481-12486. 10.1073/pnas.0605298103.
59. Ishii N., Ozaki K., Sato H., Mizuno H., Saito S., Takahashi A., et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J. Hum. Genet. 2006, 51:1087-1099.
60. Ip J.Y., Nakagawa S. Long non-coding RNAs in nuclear bodies. Develop. Growth Differ. 2012, 54:44-54. 10.1111/j.1440-169X.2011.01303.x.
61. Helgadottir A., Thorleifsson G., Manolescu A., Gretarsdottir S., Blondal T., Jonasdottir A., et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 2007, 316:1491-1493. 10.1126/science.1142842.
62. Dandona S., Stewart A.F.R., Chen L., Williams K., So D., O'Brien E., et al. Gene dosage of the common variant 9p21 predicts severity of coronary artery disease. J. Am. Coll. Cardiol. 2010, 56:479-486. 10.1016/j.jacc.2009.10.092.
63. Jarinova O., Stewart A.F.R., Roberts R., Wells G., Lau P., Naing T., et al. Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus. Arterioscler. Thromb. Vasc. Biol. 2009, 29:1671-1677. 10.1161/ATVBAHA.109.189522.
64. Burd C.E., Jeck W.R., Liu Y., Sanoff H.K., Wang Z., Sharpless N.E. Expression of linear and novel circular forms of an INK4/ARF-associated Non-coding RNA correlates with atherosclerosis risk. PLoS Genet. 2010, 6. 10.1371/journal.pgen.1001233.
65. Motterle A., Pu X., Wood H., Xiao Q., Gor S., Liang Ng F., et al. Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells. Hum. Mol. Genet. 2012, 21:4021-4029. 10.1093/hmg/dds224.
66. Congrains A., Kamide K., Oguro R., Yasuda O., Miyata K., Yamamoto E., et al. Genetic variants at the 9p21 locus contribute to atherosclerosis through modulation of ANRIL and CDKN2A/B. Atherosclerosis 2012, 220:449-455. 10.1016/j.atherosclerosis.2011.11.017.