microRNAs and mRNAs genes associated with the development of myocardial infarction
84 24
Keywords:
miRNA, mRNA, binding sites, target genes, myocardial infarction.Abstract
In the analysis of interaction between 2564 miRNAs with mRNAs of 185 genes, participating in the development of human myocardial infarction, there was identified 304 miRNAs binding sites with their mRNAs in 5'-UTR, CDS and 3'-UTR. For 54 miRNA involved in the development of human myocardial infarction, there was identified 17 target genes from 17510 genes. Five miRNA bind with mRNA of LRP1, LRP8 genes. Seven miRNA bind with mRNA of CYP1A2 and DNASE1 genes. Nine miRNA bind with mRNA of CCL5 and SP1 genes. mRNA of TFAM and SP1 genes have multiple binding sites with miR-466. mRNA of ADRB1 gene has multiple binding sites with miR-3960. mRNA of CD40LG, CDKN2B and IGF genes have multiple binding sites with miR-574-5р. The identified miR-762, has multiple binding sites with mRNA of CDKN1C. The unique miRNAs, having more than 300 binding sites is miR-619, miR-5095, miR-5096, miR-3960, miR-1322 and some miRNAs from miR-1273 family has binding sites in mRNA of many genes, participating in the development of myocardial infarction. miR-619-5р has 14 target genes, miR-5585-3p has 12 target genes, miR-5095 and miR-5096 have eight and six target genes. The family miR-1273a,c,d,e,f,g,h have 34 binding sites, including 19 binding sites of miR-1273g-3p in mRNA of 14 genes. The identified associations between miRNA and their target genes, which allow the use of it as diagnostic markers in myocardial infarction. As associations of miRNAs with target genes for diagnosis it is preferable to use associations of one miRNA with mRNA of several genes or multiple miRNA with the mRNA of one gene. The association of miR-149-3p with each of its target genes HNRNPA0, KCNJ6, MAP3K10, SHISA3 can be used for the diagnosis of MI. As candidates for the diagnosis recommended the associations of miR-619-5p with GSTCD and IL23R genes, having a ΔG/ΔGm value equal to 96%, and also associations of miR-4257 and C4B, miR-326 and NFKBIL1, miR-4300 and LAMA3 either having the ΔG/ΔGm value equal to 96%. The recommended associations of miRNA and mRNA of genes with high free energy of miRNA-mRNA interaction: miR-3960, miR-466, miR-574-5p together with their target genes pairs - PDE4D and SCAP, GSN and TNFSF4, CD40LG and OLR1. The unique miR-619-5p and miR-5095 have binding sites in mRNA of CCL5, DNASE1, F2R, IL6R, LDLR, MTHFR, STAT3, which is the basis for their use in diagnosis. The participation of miRNA of miR-1273 family necessary to control the expression of genes: ADIPOQ, CYP1A2, ENPP1, IGF1, KCNJ11, MEF2A, PPIA, TFAM. It is recommended miRNA and mRNA genes with a high value of the free energy of interaction at the binding sites. This pairs are miR-1273d, miR-4758-5p and miR-4763-5p binding with mRNA of PPIA, NFKB1 and SH2B1 genes. miR-1226-5p with mRNA of ALDH2 gene, miR-1183 with mRNA of THBS1 gene, and miR-6089-5p with mRNA of ADAM8, IL6R and TFAM genes.
References
Литература
1 American Heart Association. Heart and Stroke Statistical Update. - National Center. - 2012.- 43 р.
2 Abd El-Aziz T.A., Rezk N.A. Relation of PAI-1 and TPA genes polymorphisms to acute myocardial infarction and its outcomes in Egyptian patients // Cell Biochemistry & Biophysics.- 2015.- V.71(1).- P.227-234.
3 Шевченко А.В., Коненков В.И., Прокофьев В.Ф., Покушалов Е.А. Анализ комбинаций генотипов по полиморфным точкам промоторных участков трех матричных металлопротеиназ и гена эндотелия сосудов у больного с историей острого инфаркта миокарда // Терапевтический архив.- 2014.- №.86(4).- С.19-24.
4 Xu X., Wang L.H., Liu H.B. Association of chemokines and their receptors genes polymorphisms with risk of myocardial infarction // Zhonghua Yi Xue Yi Chuan Xue Za Zhi.- 2013.- V.30(5).- P.601-607.
5 Helseth R., Seljeflot I., Opstad T. Genes expressed in coronary thrombi are associated with ischemic time in patients with acute myocardial infarction // Thromb Research.- 2015.- №135(2).- P.329-333.
6 Kovacs V., Gasz B., Balatonyi B. Polymorphisms in glutathione S-transferase are risk factors for perioperative acute myocardial infarction after cardiac surgery: a preliminary study // Molecular & Cell Biochemistry.- 2014.- V.389(1-2).- P.79-84.
7 Sakowicz A., Fendler W., Lelonek M., Sakowicz B., Pietrucha T. Genetic polymorphisms and the risk of myocardial infarction in patients under 45 years of age // Biochemical Genetics.- 2013.- V.51(3-4).- P.230-242.
8 Wang Y., Wang L., Liu X., Zhang Y. Genetic variants associated with myocardial infarction and the risk factors in Chinese population // Public Library of Science One.- 2014.- V.9(1).- P.863.
9 Zhang T., Zhao L.L., Zhang Z.R., Fu P.D., Su Z.D., Qi L.C., Li X.Q., Dong Y.M. Interaction network analysis revealed biomarkers in myocardial infarction // Molecular Biology Report.- 2014.- V.41(8).- P.4997-5003.
10 Liu Q., Du G.Q., Zhu Z.T. Identification of apoptosis-related microRNAs and their target genes in myocardial infarction post-transplantation with skeletal myoblasts // Journal of Translational Medicine.- 2015.- V.19.- P.13-27.
11 Wang N., Zhou Z., Liao X., Zhang T. Role of microRNAs in cardiac hypertrophy and heart failure // International Union of Biochemistry and Molecular Biology (IUBMB) Life.- 2009.- V.61(6).- P.566-571.
12 Ye Y., Perez-Polo J.R., Qian J., Birnbaum Y. The role of microRNA in modulating myocardial ischemia-reperfusion injury // Physiological Genomics.- 2011.- V.43(10).- P.534-542.
13 Ono K., Kuwabara Y., Han J. MicroRNAs and cardiovascular diseases // Federation of European Biochemical Societies Journal.- 2011.- V.278(10).- P.1619-1633.
14 Xiao H., Lis J.T. Germline transformation used to define key features of heat-shock response elements // Science.- 1988.- V.239.- P.1139–1142.
15 Benjamin I.J., McMillan D.R. Stress (heat shock) proteins: molecular chaperones in cardiovascular biology and disease // Circulation research.- 1988.- V.83(2).- P.117–132.
16 Li S.P., Liu B., Song B., Wang C.X., Zhou Y.C. MiR-28 promotes cardiac ischemia by targeting mitochondrial aldehyde dehydrogenase 2 (ALDH2) in Mus musculus cardiac myocytes // European Review for Medical and Pharmacological Sciences.- 2015.- V.19.- P.752–758.
17 Rouzier C., Vanatka R., Bannwarth S. A novel homozygous MMP2 mutation in a family with Winchester syndrome // Clinical Genetics.- 2016.- V.69(3).- P.271–276.
18 Joladarashi D., Srikanth G.V., Thandavarayan R.A., Verma S.K., Mackie A.R., Khan M. Enhanced cardiac regenerative ability of stem cells after ischemia-reperfusion injury: role of human CD34(þ) cells deficient in MicroRNA-377 // Journal of the American College of Cardiology.- 2015.- V.66.- P.2214–2226.
19 Аулик И.В. Определение физической работоспособности в клинике и спорте // Медицина.- 1979.- С.192.
20 Read A.P., Strachan T. Human molecular genetics 2. - New York: Wiley.- 1999.- 576 р.
21 Sinnaeve P.R., Donahue M.P., Grass P., Seo D., Vonderscher J., Chibout S.D., Kraus W.E., Sketch M.J., Nelson C., Ginsburg G.S. Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease // Public Library of Science One.- 2009.- V.4.- P.70-73.
22 Sondermeijer B.M., Bakker A., Halliani A., de Ronde M.W., Marquart A.A., Tijsen A.J., Mulders T.A., Kok M.G., Battjes S., Maiwald S. Platelets in patients with premature coronary artery disease exhibit upregulation of miRNA340-3p and miRNA624-5p // Public Library of Science One.- 2011.- V.6.- P.46-59.
23 Patterson T.A., Lobenhofer E.K., Fulmer-Smentek S.B., Collins P.J., Chu T.M., Bao W., Fang H., Kawasaki E.S., Hager J., Tikhonova I.R. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project // Natural Biotechnology.- 2016.- V.24.- P.1140–1150.
24 Иващенко А.Т., Атамбаева С., Ниязова Р.Е., Пинский И. Гены связанные с развитием инфаркта миокарда // Вестник КазНУ, биологическая серия.- 2015.- №3(65).- С.124-132.
25 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R. Binding Sites of miR-1273 Family on the mRNA of Target Genes // Biomed Research International.- 2014.- V.2014.- P.1-11.
26 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. The properties of binding sites of miR-619-5p, miR-5095, miR-5096 and miR-5585-3p in the mRNAs of human genes // Biomed Research International.- 2014.- V.2014.- P.1-8.
27 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. MiR-3960 binding sites with mRNA of human genes // Bioinformation.- 2014.- V.10(7).- P.423-427.
28 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. The binding sites of unique miRNAs in the human mRNAs // Journal of Biotechnology.- 2014.- V.185S.- P.S37–S125.
29 Атамбаева С., Ниязова Р.Е., Берилло О., Иващенко А.Т. Особенности сайтов связывания mir-574-5р и mir-574-3р с mrna генов-мишеней // Вестник КазНУ, биологическая серия.- 2015.- №1(63).- С.349-354.
30 Niyazova R., Berillo O., Atambayeva S., Pyrkova A., Alybaeva A., Ivashchenko A. miR-1322 Binding Sites in Paralogous and Orthologous Genes // Biomed Research International.- 2015.- V.2015.- p.1-7.
31 Niyazova R., Atambayeva S., Akimniyazova A., Pinsky I., Alybaeva A., Faye B., Ivashchenko A.T. Features of mir-466-3p binding sites in mRNA genes with different functions // International Journal of Biology and Chemistry.- 2015.- V.8(2).- P.44- 51
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13 Ono K, Kuwabara Y, Han J (2011) MicroRNAs and cardiovascular diseases, Federation of European Biochemical Societies Journal, 278(10):1619-1633. DOI: 10.1111/j.1742-4658.2011.08090.x
14 Xiao H, Lis JT (1988) Germline transformation used to define key features of heat-shock response elements, Science, 239:1139–1142. DOI: 10.1126/science.3125608
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17 Rouzier C, Vanatka R, Bannwarth S (2016) A novel homozygous MMP2 mutation in a family with Winchester syndrome, Clinical Genetics, 69(3):271–276. DOI: 10.1111/j.1399-0004.2006.00584.x
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21 Sinnaeve PR, Donahue MP, Grass P, Seo D, Vonderscher J, Chibout SD, Kraus WE, Sketch MJ, Nelson C, Ginsburg GS (2009) Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease, Public Library of Science One, 4:70-73. DOI: ΔG/ΔGm 10.1371/journal.pone.0007037
22 Sondermeijer BM, Bakker A, Halliani A, de Ronde MW, Marquart AA, Tijsen AJ, Mulders TA, Kok MG, Battjes S, Maiwald S (2011) Platelets in patients with premature coronary artery disease exhibit upregulation of miRNA340-3p and miRNA624-5p, Public Library of Science One. 6:46-59. DOI: 10.1371/journal.pone.0025946
23 Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR (2016) Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project, Natural Biotechnology, 24:1140–1150. DOI:10.1038/nbt1242
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25 Ivashchenko A, Berillo O, Pyrkova A, Niyazova R (2014) Binding Sites of miR-1273 Family on the mRNA of Target Genes, Biomed Research International, 2014: 1-11. DOI:10.1155/2014/620530
26 Ivashchenko A, Berillo O, Pyrkova A, Niyazova R, Atambayeva S (2014) The properties of binding sites of miR-619-5p, miR-5095, miR-5096 and miR-5585-3p in the mRNAs of human genes, Biomed Research International, 2014:1-8. DOI:10.1155/2014/720715
27 Ivashchenko A, Berillo O, Pyrkova A, Niyazova R, Atambayeva S (2014) MiR-3960 binding sites with mRNA of human genes, Bioinformation, 10(7):423-427. DOI:10.6026/97320630010423
28 Ivashchenko A, Berillo O, Pyrkova A, Niyazova R, Atambayeva S (2014) The binding sites of unique miRNAs in the human mRNAs, Journal of Biotechnology, 185S:S37–S125.
29 Atambayeva S, Niyazova R, Berillo O, Ivashchenko A (2015) Futures of miR-574-5р and miR-574-3р binding sites with mRNA of target genes. Vestnik KazNU, biological series [Osobennosti saitov svyazyvaniya miR-574-5р i miR-574-3р s mRNA genov-misheney. Vestnik KazNU, biologicheskaya seriya] 1 (63):349-354. (In Russian)
30 Niyazova R, Berillo O, Atambayeva S, Pyrkova A, Alybaeva A, Ivashchenko A (2015) miR-1322 Binding Sites in Paralogous and Orthologous Genes, Biomed Research International, 2015:1-7. DOI:10.1155/2015/962637
31 Niyazova R, Atambayeva S, Akimniyazova A, Pinsky I, Alybaeva A, Faye B, Ivashchenko AT (2015) Features of mir-466-3p binding sites in mRNA genes with different functions, International Journal of Biology and Chemistry, 8 (2):44- 51.
1 American Heart Association. Heart and Stroke Statistical Update. - National Center. - 2012.- 43 р.
2 Abd El-Aziz T.A., Rezk N.A. Relation of PAI-1 and TPA genes polymorphisms to acute myocardial infarction and its outcomes in Egyptian patients // Cell Biochemistry & Biophysics.- 2015.- V.71(1).- P.227-234.
3 Шевченко А.В., Коненков В.И., Прокофьев В.Ф., Покушалов Е.А. Анализ комбинаций генотипов по полиморфным точкам промоторных участков трех матричных металлопротеиназ и гена эндотелия сосудов у больного с историей острого инфаркта миокарда // Терапевтический архив.- 2014.- №.86(4).- С.19-24.
4 Xu X., Wang L.H., Liu H.B. Association of chemokines and their receptors genes polymorphisms with risk of myocardial infarction // Zhonghua Yi Xue Yi Chuan Xue Za Zhi.- 2013.- V.30(5).- P.601-607.
5 Helseth R., Seljeflot I., Opstad T. Genes expressed in coronary thrombi are associated with ischemic time in patients with acute myocardial infarction // Thromb Research.- 2015.- №135(2).- P.329-333.
6 Kovacs V., Gasz B., Balatonyi B. Polymorphisms in glutathione S-transferase are risk factors for perioperative acute myocardial infarction after cardiac surgery: a preliminary study // Molecular & Cell Biochemistry.- 2014.- V.389(1-2).- P.79-84.
7 Sakowicz A., Fendler W., Lelonek M., Sakowicz B., Pietrucha T. Genetic polymorphisms and the risk of myocardial infarction in patients under 45 years of age // Biochemical Genetics.- 2013.- V.51(3-4).- P.230-242.
8 Wang Y., Wang L., Liu X., Zhang Y. Genetic variants associated with myocardial infarction and the risk factors in Chinese population // Public Library of Science One.- 2014.- V.9(1).- P.863.
9 Zhang T., Zhao L.L., Zhang Z.R., Fu P.D., Su Z.D., Qi L.C., Li X.Q., Dong Y.M. Interaction network analysis revealed biomarkers in myocardial infarction // Molecular Biology Report.- 2014.- V.41(8).- P.4997-5003.
10 Liu Q., Du G.Q., Zhu Z.T. Identification of apoptosis-related microRNAs and their target genes in myocardial infarction post-transplantation with skeletal myoblasts // Journal of Translational Medicine.- 2015.- V.19.- P.13-27.
11 Wang N., Zhou Z., Liao X., Zhang T. Role of microRNAs in cardiac hypertrophy and heart failure // International Union of Biochemistry and Molecular Biology (IUBMB) Life.- 2009.- V.61(6).- P.566-571.
12 Ye Y., Perez-Polo J.R., Qian J., Birnbaum Y. The role of microRNA in modulating myocardial ischemia-reperfusion injury // Physiological Genomics.- 2011.- V.43(10).- P.534-542.
13 Ono K., Kuwabara Y., Han J. MicroRNAs and cardiovascular diseases // Federation of European Biochemical Societies Journal.- 2011.- V.278(10).- P.1619-1633.
14 Xiao H., Lis J.T. Germline transformation used to define key features of heat-shock response elements // Science.- 1988.- V.239.- P.1139–1142.
15 Benjamin I.J., McMillan D.R. Stress (heat shock) proteins: molecular chaperones in cardiovascular biology and disease // Circulation research.- 1988.- V.83(2).- P.117–132.
16 Li S.P., Liu B., Song B., Wang C.X., Zhou Y.C. MiR-28 promotes cardiac ischemia by targeting mitochondrial aldehyde dehydrogenase 2 (ALDH2) in Mus musculus cardiac myocytes // European Review for Medical and Pharmacological Sciences.- 2015.- V.19.- P.752–758.
17 Rouzier C., Vanatka R., Bannwarth S. A novel homozygous MMP2 mutation in a family with Winchester syndrome // Clinical Genetics.- 2016.- V.69(3).- P.271–276.
18 Joladarashi D., Srikanth G.V., Thandavarayan R.A., Verma S.K., Mackie A.R., Khan M. Enhanced cardiac regenerative ability of stem cells after ischemia-reperfusion injury: role of human CD34(þ) cells deficient in MicroRNA-377 // Journal of the American College of Cardiology.- 2015.- V.66.- P.2214–2226.
19 Аулик И.В. Определение физической работоспособности в клинике и спорте // Медицина.- 1979.- С.192.
20 Read A.P., Strachan T. Human molecular genetics 2. - New York: Wiley.- 1999.- 576 р.
21 Sinnaeve P.R., Donahue M.P., Grass P., Seo D., Vonderscher J., Chibout S.D., Kraus W.E., Sketch M.J., Nelson C., Ginsburg G.S. Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease // Public Library of Science One.- 2009.- V.4.- P.70-73.
22 Sondermeijer B.M., Bakker A., Halliani A., de Ronde M.W., Marquart A.A., Tijsen A.J., Mulders T.A., Kok M.G., Battjes S., Maiwald S. Platelets in patients with premature coronary artery disease exhibit upregulation of miRNA340-3p and miRNA624-5p // Public Library of Science One.- 2011.- V.6.- P.46-59.
23 Patterson T.A., Lobenhofer E.K., Fulmer-Smentek S.B., Collins P.J., Chu T.M., Bao W., Fang H., Kawasaki E.S., Hager J., Tikhonova I.R. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project // Natural Biotechnology.- 2016.- V.24.- P.1140–1150.
24 Иващенко А.Т., Атамбаева С., Ниязова Р.Е., Пинский И. Гены связанные с развитием инфаркта миокарда // Вестник КазНУ, биологическая серия.- 2015.- №3(65).- С.124-132.
25 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R. Binding Sites of miR-1273 Family on the mRNA of Target Genes // Biomed Research International.- 2014.- V.2014.- P.1-11.
26 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. The properties of binding sites of miR-619-5p, miR-5095, miR-5096 and miR-5585-3p in the mRNAs of human genes // Biomed Research International.- 2014.- V.2014.- P.1-8.
27 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. MiR-3960 binding sites with mRNA of human genes // Bioinformation.- 2014.- V.10(7).- P.423-427.
28 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. The binding sites of unique miRNAs in the human mRNAs // Journal of Biotechnology.- 2014.- V.185S.- P.S37–S125.
29 Атамбаева С., Ниязова Р.Е., Берилло О., Иващенко А.Т. Особенности сайтов связывания mir-574-5р и mir-574-3р с mrna генов-мишеней // Вестник КазНУ, биологическая серия.- 2015.- №1(63).- С.349-354.
30 Niyazova R., Berillo O., Atambayeva S., Pyrkova A., Alybaeva A., Ivashchenko A. miR-1322 Binding Sites in Paralogous and Orthologous Genes // Biomed Research International.- 2015.- V.2015.- p.1-7.
31 Niyazova R., Atambayeva S., Akimniyazova A., Pinsky I., Alybaeva A., Faye B., Ivashchenko A.T. Features of mir-466-3p binding sites in mRNA genes with different functions // International Journal of Biology and Chemistry.- 2015.- V.8(2).- P.44- 51
References
1 American Heart Association (2012) Heart and Stroke Statistical Update, National Center, 43 P. DOI: 10.1161/CIR.0b013e31823ac046
2 Abd El-Aziz TA, Rezk NA (2015) Relation of PAI-1 and TPA genes polymorphisms to acute myocardial infarction and its outcomes in Egyptian patients, Cell Biochemistry & Biophysics, 71(1):227-234. DOI: 10.1007/s12013-014-0188-x
3 Shevchenko AV, Konenkov VI, Prokof'ev VF, Pokushalov EA (2014) Analysis of genotype combinations at the polymorphic points of the promoter regions of the genes of three matrix metalloproteinases and the gene of vascular endothelial growth factor (VEGF) in patients with history of acute myocardial infarction. Therapeutic archives [Analiz kombinacii genotipov po polimorfnym tochkam promotornyh uchastkov treh matrichnyh metalloproteinaz i gena faktora endoteliya sosudov u bolnogo s istoriei ostrogo infarkta miokarda, Terapevticheskii Arkhiv] 86(4):19-24. (In Russian)
4 Xu X, Wang LH, Liu HB (2013) Association of chemokines and their receptors genes polymorphisms with risk of myocardial infarction, Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 30(5):601-607. DOI: 10.3760/cma.j.issn.1003-9406.2013.05.021
5 Helseth R, Seljeflot I, Opstad T (2015) Genes expressed in coronary thrombi are associated with ischemic time in patients with acute myocardial infarction, Thromb Research, 135(2):329-333. DOI: 10.1016/j.thromres.2014.11.028
6 Kovacs V, Gasz B, Balatonyi B (2014) Polymorphisms in glutathione S-transferase are risk factors for perioperative acute myocardial infarction after cardiac surgery: a preliminary study, Molecular & Cell Biochemistry, 389(1-2):79-84. DOI: 10.1007/s11010-013-1929-7
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Ivashchenko, A. T., Niyazova, R. Y., Atambayeva, S. A., Pyrkova, A. Y., Pinsky, I. V., Alybayeva, A. Z., Akimniyazova, A. N., Mamirova, A. A., & Makashev, E. K. (2016). microRNAs and mRNAs genes associated with the development of myocardial infarction. Experimental Biology, 67(2), 82–93. Retrieved from https://bb.kaznu.kz/index.php/biology/article/view/1184
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МOLECULAR BIOLOGY AND GENETICS
