Differential lncRNA-mRNA co-expression network analysis revealing the potential regulatory roles of lncRNAs in myocardial infarction

Molecular Medicine Reports

Volumn 13, Issue 2, 2016, Pages 1195-1203

  Wang, Ping ^a   Fu, Haiying ^b   Cui, Jiayue ^b   Chen, Xia ^b  

^a THE FIRST HOSPITAL OF JILIN UNIVERSITY   (China)

^b JILIN UNIVERSITY   (China)

Author keywords

Co expression network; LncRNA; Myocardial infarction; Network analysis; Pathway

Indexed keywords

ANGIOPOIETIN 2; CARTILAGE INTERMEDIATE LAYER PROTEIN 2; CLAUDIN; CLAUDIN 10; CLAUDIN 19; CORONIN 6; EPOXIDE HYDROLASE; EPOXIDE HYDROLASE 1; FK 506 BINDING PROTEIN; GONADORELIN; HEAT SHOCK PROTEIN 22; HUS1 CHECKPOINT HOMOLOG B; KHELLIN; LIPASE MATURATION FACTOR 2; LONG UNTRANSLATED RNA; MESSENGER RNA; MICROFIBRILLAR ASSOCIATED PROTEIN 4; MITOGEN ACTIVATED PROTEIN KINASE; PANCREAS POLYPEPTIDE; PANCREATIC POLYPEPTIDE RECEPTOR 1; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; PROSTACYCLIN; PROTEIN; RING FINGER PROTEIN; RING FINGER PROTEIN 207; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG;

ARTICLE; CALCIUM SIGNALING; CELL DIFFERENTIATION; CONGESTIVE CARDIOMYOPATHY; CONTROLLED STUDY; EXTRACELLULAR MATRIX; GENE EXPRESSION; HEART CONTRACTION; HEART FUNCTION; HEART INFARCTION; HEART RIGHT VENTRICLE DYSPLASIA; HUMAN; HYPERTROPHIC CARDIOMYOPATHY; REGULATORY MECHANISM; VASCULAR SMOOTH MUSCLE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; SIGNAL TRANSDUCTION;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MAP KINASE SIGNALING SYSTEM; MYOCARDIAL INFARCTION; RNA, LONG NONCODING; RNA, MESSENGER;

EID: 84956928737     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr.2015.4669     Document Type: Article

References (35)

1. Wang Y, Zhang H, Chai F, Liu X and Berk M: The effects of escitalopram on myocardial apoptosis and the expression of Bax and Bcl-2 during myocardial ischemia/reperfusion in a model of rats with depression. BMC Psychiatry 14: 349, 2014.
2. Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M and Herrmann BG: The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24: 206-214, 2013.
3. Yang KC, Yamada KA, Patel AY, Topkara VK, George I, Cheema FH, Ewald GA, Mann DL and Nerbonne JM: Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support. Circulation 129: 1009-1021, 2014.
4. Batista PJ and Chang HY: Long noncoding RNAs: Cellular address codes in development and disease. Cell 152: 1298-1307, 2013.
5. Mitra SA, Mitra AP and Triche TJ: A central role for long non-coding RNA in cancer. Front Genet 3: 17, 2012.
6. Wang KC and Chang HY: Molecular mechanisms of long noncoding RNAs. Mol Cell 43: 904-914, 2011.
7. Wang K, Liu F, Zhou LY, Long B, Yuan SM, Wang Y, Liu CY, Sun T, Zhang XJ and Li PF: The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 114: 1377-1388, 2014.
8. Gupta SK, Piccoli MT and Thum T: Non-coding RNAs in cardiovascular ageing. Ageing Res Rev 17: 79-85, 2014.
9. Ounzain S, Micheletti R, Beckmann T, Schroen B, Alexanian M, Pezzuto I, Crippa S, Nemir M, Sarre A, Johnson R, et al: Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J 36: 353-368a, 2015.
10. Kino T, Hurt DE, Ichijo T, Nader N and Chrousos GP: Noncoding RNA gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3: ra8, 2010.
11. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, et al: A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419, 2010.
12. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, et al: Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 43: 621-629, 2011.
13. Lee S, Choi E, Cha MJ, Park AJ, Yoon C and Hwang KC: Impact of miRNAs on cardiovascular aging. J Geriatr Cardiol 12: 569-574, 2015.
14. Calore M, De Windt LJ and Rampazzo A: Genetics meets epigenetics: Genetic variants that modulate noncoding RNA in cardiovascular diseases. J Mol Cell Cardiol: Nov 3, 2015 (Epub ahead of print).
15. Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, Zhao G, Luo H, Bu D, Zhao H, et al: Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res 39: 3864-3878, 2011.
16. Suresh R, Li X, Chiriac A, Goel K, Terzic A, Perez-Terzic C and Nelson TJ: 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.
17. Liao Q, Xiao H, Bu D, Xie C, Miao R, Luo H, Zhao G, Yu K, Zhao H, Skogerbø G, et al: ncFANs: A web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 39: W118-W124, 2011.
18. Huang da W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57, 2009.
19. Eisen MB, Spellman PT, Brown PO and Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868, 1998.
20. Da Sacco L, Baldassarre A and Masotti A: Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis. Int J Mol Sci 13: 97-114, 2012.
21. Luptáková L, Benčová D, Siváková D and Cvíčelová M: Association of CILP2 and ACE gene polymorphisms with cardiovascular risk factors in Slovak midlife women. Biomed Res Int 2013: 634207, 2013.
22. Nakayama T: Genetic polymorphisms of prostacyclin synthase gene and cardiovascular disease. Int Angiol 29 (Suppl 2): S33-S42, 2010.
23. Zhao Y, Hu HY, Sun DR, Feng R, Sun XF, Guo F and Hao LY: Dynamic alterations in the CaV1.2/CaM/CaMKII signaling pathway in the left ventricular myocardium of ischemic rat hearts. DNA Cell Biol 33: 282-290, 2014.
24. Marx N, Bourcier T, Sukhova GK, Libby P and Plutzky J: PPARgamma activation in human endothelial cells increases plasminogen activator inhibitor type-1 expression: PPARgamma as a potential mediator in vascular disease. Arterioscler Thromb Vasc Biol 19: 546-551, 1999.
25. Wei N, Zhang C, He H, Wang T, Liu Z, Liu G, Sun Z, Zhou Z, Bai C and Yuan D: Protective effect of saponins extract from Panax japonicus on myocardial infarction: Involvement of NF-kB, Sirt1 and mitogen-activated protein kinase signalling pathways and inhibition of inflammation. J Pharm Pharmacol 66: 1641-1651, 2014.
26. Eltit JM, Franzini-Armstrong C and Perez CF: Amino acid residues 489-503 of dihydropyridine receptor (DHPR) beta1a subunit are critical for structural communication between the skeletal muscle DHPR complex and Type-1 ryanodine receptor. J Biol Chem 289: 36116-36124, 2014.
27. Viola HM, Adams AM, Davies SM, Fletcher S, Filipovska A and Hool LC: Impaired functional communication between the L-type calcium channel and mitochondria contributes to metabolic inhibition in the mdx heart. Proc Natl Acad Sci USA 111: E2905-E2914, 2014.
28. Sluijter JP, Verhage V, Deddens JC, van den Akker F and Doevendans PA: Microvesicles and exosomes for intracardiac communication. Cardiovasc Res 102: 302-311, 2014.
29. Lax A, Sanchez-Mas J, Asensio-Lopez MC, Fernandez-Del Palacio MJ, Caballero L, Garrido IP, Pastor-Perez FJ, Januzzi JL and Pascual-Figal DA: Mineralocorticoid receptor antagonists modulate galectin-3 and interleukin-33/ST2 signaling in left ventricular systolic dysfunction after acute myocardial infarction. JACC Heart Fail 3: 50-58, 2015.
30. Javadov S, Jang S and Agostini B: Crosstalk between mitogen-activated protein kinases and mitochondria in cardiac diseases: Therapeutic perspectives. Pharmacol Ther 144: 202-225, 2014.
31. Muslin AJ: MAPK signalling in cardiovascular health and disease: Molecular mechanisms and therapeutic targets. Clin Sci (Lond) 115: 203-218, 2008.
32. Foltz IN, Gerl RE, Wieler JS, Luckach M, Salmon RA and Schrader JW: Human mitogen-activated protein kinase kinase 7 (MKK7) is a highly conserved c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK) activated by environmental stresses and physiological stimuli. J Biol Chem 273: 9344-9351, 1998.
33. Bueno OF, De Windt LJ, Tymitz KM, Witt SA, Kimball TR, Klevitsky R, Hewett TE, Jones SP, Lefer DJ, Peng CF, et al: The MEK1-ERK1/2 signaling pathway promotes compensated cardiac hypertrophy in transgenic mice. EMBO J 19: 6341-6350, 2000.
34. Shi X, Sun M, Liu H, Yao Y and Song Y: Long non-coding RNAs: A new frontier in the study of human diseases. Cancer Lett 339: 159-166, 2013.
35. Yamaguchi O, Higuchi Y, Hirotani S, Kashiwase K, Nakayama H, Hikoso S, Takeda T, Watanabe T, Asahi M, Taniike M, et al: Targeted deletion of apoptosis signal-regulating kinase 1 attenuates left ventricular remodeling. Proc Natl Acad Sci USA 100: 15883-15888, 2003.