MiRNA and TF co-regulatory network analysis for the pathology and recurrence of myocardial infarction

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Lin, Ying ^a   Sibanda, Vusumuzi Leroy ^a   Zhang, Hong Mei ^a   Hu, Hui ^a   Liu, Hui ^a   Guo, An Yuan ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; MIRN29 MICRORNA, HUMAN; TRANSCRIPTION FACTOR;

ANIMAL; BIOLOGY; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HEART INFARCTION; HUMAN; METABOLISM; PATHOLOGY; RECURRENT DISEASE; REPRODUCIBILITY; RNA INTERFERENCE; SIGNAL TRANSDUCTION;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; MYOCARDIAL INFARCTION; RECURRENCE; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE; RNA, MESSENGER; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 84928395051     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep09653     Document Type: Article

References (59)

1. D'Alessandra, Y., Pompilio, G. & Capogrossi, M. C. MicroRNAs and myocardial infarction. Curr Opin Cardiol 27, 228-235 (2012).
2. Yamada, Y., Ichihara, S. & Nishida, T. Molecular genetics of myocardial infarction. Genomic Med 2, 7-22 (2008).
3. Ouwehand, W. H., Bloodomics. & Cardiogenics, C. The discovery of genes implicated in myocardial infarction. Journal of thrombosis and haemostasis: JTH 7 Suppl 1, 305-307 (2009).
4. Erdmann, J., Linsel-Nitschke, P. & Schunkert, H. Genetic causes of myocardial infarction: new insights from genome-wide association studies. Dtsch Arztebl Int 107, 694-699 (2010).
5. Myocardial Infarction Genetics, C. et al. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nature genetics 41, 334-341 (2009).
6. Smolina, K., Wright, F. L., Rayner, M. & Goldacre, M. J. Long-term survival and recurrence after acute myocardial infarction in England, 2004 to 2010. Circulation Cardiovascular quality and outcomes 5, 532-540 (2012).
7. Thune, J. J. et al. Predictors and prognostic impact of recurrent myocardial infarction in patients with left ventricular dysfunction, heart failure, or both following a first myocardial infarction. European journal of heart failure 13, 148-153 (2011).
8. Kaya, M. G. et al. Potential role of plasma myeloperoxidase level in predicting long-term outcome of acute myocardial infarction. Tex Heart Inst J 39, 500-506 (2012).
9. Takahashi, S. et al. Phospholipase A2 expression in coronary thrombus is increased in patients with recurrent cardiac events after acute myocardial infarction. Int J Cardiol 168, 4214-4221 (2013).
10. Suresh, R. et al. Transcriptome from circulating cells suggests dysregulated pathways associated with long-term recurrent events following first-time myocardial infarction. J Mol Cell Cardiol 74, 13-21 (2014).
11. Zhang, H. M., Kuang, S., Xiong, X., Gao, T., Liu, C. & Guo, A. Y. Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases. Brief Bioinform 16, 45-58 (2015).
12. Zhu, H. & Fan, G. C. Role of microRNAs in the reperfused myocardium towards post-infarct remodelling. Cardiovascular research 94, 284-292 (2012).
13. Pan, Z. et al. MicroRNA-101 inhibited postinfarct cardiac fibrosis and improved left ventricular compliance via the FBJ osteosarcoma oncogene/transforming growth factor-beta1 pathway. Circulation 126, 840-850 (2012).
14. van Rooij, E. et al. Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis. Proc Natl Acad Sci U S A 105, 13027-13032 (2008).
15. Zhu, J. N. et al. Smad3 inactivation and MiR-29b upregulation mediate the effect of carvedilol on attenuating the acute myocardium infarction-induced myocardial fibrosis in rat. PLoS One 8, e75557 (2013).
16. Wei, C., Li, L. & Gupta, S. NF-kappaB-mediated miR-30b regulation in cardiomyocytes cell death by targeting Bcl-2. Mol Cell Biochem 387, 135-141 (2014).
17. Zhang, H. M. et al. AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. Nucleic acids research 43, D76-81 (2015).
18. Zhang, T. et al. Bioinformatics analysis of time series gene expression in left ventricle (LV) with acute myocardial infarction (AMI). Gene 543, 259-267 (2014).
19. Guo, A. Y., Sun, J., Jia, P. & Zhao, Z. A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst Biol 4, 10 (2010).
20. Ye, H. et al. MicroRNA and transcription factor co-regulatory network analysis reveals miR-19 inhibits CYLD in T-cell acute lymphoblastic leukemia. Nucleic acids research 40, 5201-5214 (2012).
21. Su, N.,Wang, Y., Qian, M. & Deng, M. Combinatorial regulation of transcription factors and microRNAs. BMC Syst Biol 4, 150 (2010).
22. Tsang, J., Zhu, J. & van Oudenaarden, A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26, 753-767 (2007).
23. Banai, S., Shweiki, D., Pinson, A., Chandra, M., Lazarovici, G. & Keshet, E. Upregulation of vascular endothelial growth factor expression induced by myocardial ischaemia: implications for coronary angiogenesis. Cardiovasc Res 28, 1176-1179 (1994).
24. Hattori, R. et al. An essential role of the antioxidant gene Bcl-2 in myocardial adaptation to ischemia: an insight with antisense Bcl-2 therapy. Antioxid Redox Signal 3, 403-413 (2001).
25. Devaux, Y. et al. A panel of 4 microRNAs facilitates the prediction of left ventricular contractility after acute myocardial infarction. PLoS One 8, e70644 (2013).
26. Keyes, K. T., Xu, J., Long, B., Zhang, C., Hu, Z. & Ye, Y. Pharmacological inhibition of PTEN limits myocardial infarct size and improves left ventricular function postinfarction. Am J Physiol Heart Circ Physiol 298, H1198-1208 (2010).
27. Sutton, M. G. & Sharpe, N. Left ventricular remodeling after myocardial infarction: pathophysiology and therapy. Circulation 101, 2981-2988 (2000).
28. Krijnen, P. A., Nijmeijer, R., Meijer, C. J., Visser, C. A., Hack, C. E. & Niessen, H. W. Apoptosis in myocardial ischaemia and infarction. J Clin Pathol 55, 801-811 (2002).
29. Barry, S. P. & Townsend, P. A. What causes a broken heart - molecular insights into heart failure. Int Rev Cell Mol Biol 284, 113-179 (2010).
30. Cheng, Z., DiMichele, L. A., Hakim, Z. S., Rojas, M., Mack, C. P. & Taylor, J. M. Targeted focal adhesion kinase activation in cardiomyocytes protects the heart from ischemia/reperfusion injury. Arterioscler Thromb Vasc Biol 32, 924-933 (2012).
31. Hong, D., Zeng, X., Xu, W., Ma, J., Tong, Y. & Chen, Y. Altered profiles of gene expression in curcumin-treated rats with experimentally induced myocardial infarction. Pharmacol Res 61, 142-148 (2010).
32. Pietenpol, J. A., Holt, J. T., Stein, R. W.&Moses, H. L. Transforming growth factor beta 1 suppression of c-myc gene transcription: role in inhibition of keratinocyte proliferation. Proc Natl Acad Sci U S A 87, 3758-3762 (1990).
33. McDonald, K. Diastolic heart failure in the elderly: underlying mechanisms and clinical relevance. Int J Cardiol 125, 197-202 (2008).
34. Bostjancic, E. & Glavac, D. miRNome in myocardial infarction: Future directions and perspective. World J Cardiol 6, 939-958 (2014).
35. Ye, Y., Perez-Polo, J. R., Qian, J. & Birnbaum, Y. The role of microRNA in modulating myocardial ischemia-reperfusion injury. Physiol Genomics 43, 534-542 (2011).
36. Zouein, F. A., Kurdi, M. & Booz, G. W. LIF and the heart: just another brick in the wall? Eur Cytokine Netw 24, 11-19 (2013).
37. Robertson, G. A. Endocytic control of ion channel density as a target for cardiovascular disease. J Clin Invest 119, 2531-2534 (2009).
38. Chablais, F. & Jazwinska, A. The regenerative capacity of the zebrafish heart is dependent on TGFbeta signaling. Development 139, 1921-1930 (2012).
39. He, Y., Zhou, X., Zheng, X. & Jiang, X. Exogenous high-mobility group box 1 protein prevents postinfarction adverse myocardial remodeling through TGFbeta/ Smad signaling pathway. J Cell Biochem 114, 1634-1641 (2013).
40. Cui, Q., Yu, Z., Pan, Y., Purisima, E. O. & Wang, E. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun 352, 733-738 (2007).
41. Cui, Q., Yu, Z., Purisima, E. O.&Wang, E. Principles of microRNA regulation of a human cellular signaling network. Mol Syst Biol 2, 46 (2006).
42. Icli, B., Dorbala, P. & Feinberg, M. W. An emerging role for the miR-26 family in cardiovascular disease. Trends Cardiovasc Med 24, 241-248 (2014).
43. Vicari, D., Foy, K. C., Liotta, E. M. & Kaumaya, P. T. Engineered conformation-dependent VEGF peptide mimics are effective in inhibiting VEGF signaling pathways. J Biol Chem 286, 13612-13625 (2011).
44. Li, D. Y., Tao, L., Liu, H., Christopher, T. A., Lopez, B. L.&Ma, X. L. Role of ERK1/ 2 in the anti-apoptotic and cardioprotective effects of nitric oxide after myocardial ischemia and reperfusion. Apoptosis: an international journal on programmed cell death 11, 923- 930 (2006).
45. Liu, H. et al. CADgene: a comprehensive database for coronary artery disease genes. Nucleic acids research 39, D991-996 (2011).
46. Sabater-Lleal, M. et al. Multiethnic meta-analysis of genome-wide association studies in > 100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease. Circulation 128, 1310-1324 (2013).
47. Kessler, T., Erdmann, J. & Schunkert, H. Genetics of coronary artery disease and myocardial infarction - 2013. Curr Cardiol Rep 15, 368 (2013).
48. Wauters, E. et al. Influence of 23 coronary artery disease variants on recurrent myocardial infarction or cardiac death: the GRACE Genetics Study. Eur Heart J 34, 993-1001 (2013).
49. Jiang, Q. et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic acids research 37, D98-104 (2009).
50. Lu,M. et al. An analysis of human microRNA and disease associations. PLoS One 3, e3420 (2008).
51. Bostjancic, E., Zidar, N. & Glavac, D. MicroRNA microarray expression profiling in human myocardial infarction. Dis Markers 27, 255-268 (2009).
52. Fiedler, J. & Thum, T. MicroRNAs in myocardial infarction. Arterioscler Thromb Vasc Biol 33, 201-205 (2013).
53. Port, J. D., Walker, L. A., Polk, J., Nunley, K., Buttrick, P. M. & Sucharov, C. C. Temporal expression of miRNAs and mRNAs in a mouse model of myocardial infarction. Physiol Genomics 43, 1087-1095 (2011).
54. Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X. & Li, T. miRecords: an integrated resource for microRNA-target interactions. Nucleic acids research 37, D105-110 (2009).
55. Betel, D., Wilson, M., Gabow, A., Marks, D. S. & Sander, C. The microRNA. org resource: targets and expression. Nucleic acids research 36, D149-153 (2008).
56. Vergoulis, T. et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic acids research 40, D222-229 (2012).
57. Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
58. Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L.& Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432 (2011).
59. Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57 (2009).