Expression of microRNAs and their target mRNAs in human stem cell-derived cardiomyocyte clusters and in heart tissue

Physiological Genomics

Volumn 43, Issue 10, 2011, Pages 581-594

  Synnergren, Jane ^a,b   Améen, Caroline ^c   Lindahl, Anders ^b   Olsson, Björn ^a   Sartipy, Peter ^c  

^a UNIVERSITY OF SKÖVDE   (Sweden)

^b SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

^c Cellartis   (Sweden)

Author keywords

Cardiac; Differentiation; Gene expression; Human embryonic stem cells

Indexed keywords

MESSENGER RNA; MICRORNA;

ADULT; ARTICLE; CELL DIFFERENTIATION; EMBRYO; EMBRYONIC STEM CELL; FETUS; GENE IDENTIFICATION; HEART DEVELOPMENT; HEART MUSCLE CELL; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PREDICTION; PRIORITY JOURNAL; RNA SYNTHESIS;

ADULT; ALGORITHMS; CELL DIFFERENTIATION; CELLS, CULTURED; CLUSTER ANALYSIS; EMBRYONIC STEM CELLS; FETUS; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; MYOCARDIUM; MYOCYTES, CARDIAC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER;

EID: 79957660025     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00074.2010     Document Type: Article

References (51)

1. Ameen C, Strehl R, Bjorquist P, Lindahl A, Hyllner J, Sartipy P. Human embryonic stem cells: current technologies and emerging industrial applications. Crit Rev Oncol Hematol 65: 54-80, 2008.
2. Appasani K. MicroRNAs: from basic science to disease biology. New York, Cambridge University Press, 2008.
3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29, 2000.
4. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, function. Cell 116: 281-297, 2004.
5. Castellano L, Giamas G, Jacob J, Coombes RC, Lucchesi W, Thiruchelvam P, Barton G, Jiao LR, Wait R, Waxman J, Hannon GJ, Stebbing J. The estrogen receptor-alpha-induced microRNA signature regulates itself and its transcriptional response. Proc Natl Acad Sci USA 106: 15732-15737, 2009.
6. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, Muth AN, Lee TH, Miano JM, Ivey KN, Srivastava D. miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460: 705-710, 2009.
7. Czubryt MP, McAnally J, Fishman GI, Olson EN. Regulation of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1 alpha) and mitochondrial function by MEF2 and HDAC5. Proc Natl Acad Sci USA 100: 1711-1716, 2003.
8. Dela Pompa JL, Timmerman LA, Takimoto H, Yoshida H, Elia AJ, Samper E, Potter J, Wakeham A, Marengere L, Langille BL, Crabtree GR, Mak TW. Role of the NF-ATc transcription factor in morphogenesis of cardiac valves and septum. Nature 392: 182-186, 1998.
9. Gangaraju VK, Lin H. MicroRNAs: key regulators of stem cells. Nat Rev Mol Cell Biol 10: 116-125, 2009.
10. Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y, Goodall GJ. The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol 10: 593-601, 2008.
11. Hayes B, Fagerlie SR, Ramakrishnan A, Baran S, Harkey M, Graf L, Bar M, Bendoraite A, Tewari M, Torok-Storb B. Derivation, characterization, and in vitro differentiation of canine embryonic stem cells. Stem Cells 26: 465-473, 2008.
12. Ivey KN, Muth A, Arnold J, King FW, Yeh RF, Fish JE, Hsiao EC, Schwartz RJ, Conklin BR, Bernstein HS, Srivastava D. MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2: 219-229, 2008.
13. 2+ channels (CaV1.2a,b) by protein kinases. Am J Physiol Cell Physiol 281: C1743-C1756, 2001.
14. Keller G. Embryonic stem cell differentiation: emergence of a new era in biology and medicine. Genes Dev 19: 1129-1155, 2005.
15. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18: 1165-1178, 2004.
16. Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864, 2001.
17. Leivonen SK, Makela R, Ostling P, Kohonen P, Haapa-Paananen S, Kleivi K, Enerly E, Aakula A, Hellstrom K, Sahlberg N, Kristensen VN, Borresen-Dale AL, Saviranta P, Perala M, Kallioniemi O. Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines. Oncogene 28: 3926-3936, 2009.
18. Li SS, Yu SL, Kao LP, Tsai ZY, Singh S, Chen BZ, Ho BC, Liu YH, Yang PC. Target identification of microRNAs expressed highly in human embryonic stem cells. J Cell Biochem 106: 1020-1030, 2009.
19. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773, 2005.
20. Morimoto T, Hasegawa K, Wada H, Kakita T, Kaburagi S, Yanazume T, Sasayama S. Calcineurin-GATA4 pathway is involved in beta-adrenergic agonist-responsive endothelin-1 transcription in cardiac myocytes. J Biol Chem 276: 34983-34989, 2001.
21. Parsons JT. Focal adhesion kinase: the first ten years. J Cell Sci 116: 1409-1416, 2003.
22. Petit V, Thiery JP. Focal adhesions: structure and dynamics. Biol Cell 92: 477-494, 2000.
23. Protasi F. Structural interaction between RYRs and DHPRs in calcium release units of cardiac and skeletal muscle cells. Front Biosci 7: d650-d658, 2002.
24. Puceat M, Ballis A. Embryonic stem cells: from bench to bedside. Clin Pharmacol Ther 82: 337-339, 2007.
25. Rane S, He M, Sayed D, Vashistha H, Malhotra A, Sadoshima J, Vatner DE, Vatner SF, Abdellatif M. Downregulation of miR-199a derepresses hypoxia-inducible factor-1alpha and Sirtuin 1 and recapitulates hypoxia preconditioning in cardiac myocytes. Circ Res 104: 879-886, 2009.
26. Samarel AM. Costameres, focal adhesions, and cardiomyocyte mecha-notransduction. Am J Physiol Heart Circ Physiol 289: H2291-H2301, 2005.
27. Sartipy P, Björquist P, Strehl R, Hyllner J. The application of human embryonic stem cell technologies to drug discovery. Drug Discov Today 12: 688-699, 2007.
28. Sartipy P, Olsson B, Hyllner J, Synnergren J. Regulation of 'stem-ness' and stem cell differentiation by microRNAs. IDrugs 12: 492-496, 2009.
29. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 5: R13, 2004.
30. Sluijter JP, van Mil A, van Vliet P, Metz CH, Liu J, Doevendans PA, Goumans MJ. MicroRNA-1 and -499 regulate differentiation and proliferation in human-derived cardiomyocyte progenitor cells. Arterioscler Thromb Vasc Biol 30: 859-868, 2010.
31. Sun Q, Zhang Y, Yang G, Chen X, Cao G, Wang J, Sun Y, Zhang P, Fan M, Shao N, Yang X. Transforming growth factor-beta-regulated miR-24 promotes skeletal muscle differentiation. Nucleic Acids Res 36: 2690-2699, 2008.
32. Synnergren J, Akesson K, Dahlenborg K, Vidarsson H, Ameen C, Steel D, Lindahl A, Olsson B, Sartipy P. Molecular signature of cardiomyocyte clusters derived from human embryonic stem cells. Stem Cells 26: 1831-1840, 2008.
33. Thum T, Catalucci D, Bauersachs J. MicroRNAs: novel regulators in cardiac development and disease. Cardiovasc Res 79: 562-570, 2008.
34. Thum T, Gross C, Fiedler J, Fischer T, Kissler S, Bussen M, Galuppo P, Just S, Rottbauer W, Frantz S, Castoldi M, Soutschek J, Kotelian-sky V, Rosenwald A, Basson MA, Licht JD, Pena JT, Rouhanifard SH, Muckenthaler MU, Tuschl T, Martin GR, Bauersachs J, Engelhardt S. MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts. Nature 456: 980-984, 2008.
35. Tian Y, Cohen ED, Morrisey EE. The importance of Wnt signaling in cardiovascular development. Pediatr Cardiol 31: 342-348, 2010.
36. Tsai ZY, Singh S, Yu SL, Kao LP, Chen BZ, Ho BC, Yang PC, Li SS. Identification of microRNAs regulated by activin A in human embryonic stem cells. J Cell Biochem 109: 93-102, 2010.
37. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121, 2001.
38. VanRooij E, Marshall WS, Olson EN. Toward microRNA-based therapeutics for heart disease: the sense in antisense. Circ Res 103: 919-928, 2008.
39. VanRooij E, Olson EN. MicroRNAs: powerful new regulators of heart disease and provocative therapeutic targets. J Clin Invest 117: 2369-2376, 2007.
40. VanRooij E, Sutherland LB, Liu N, Williams AH, McAnally J, Gerard RD, Richardson JA, Olson EN. A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci USA 103: 18255-18260, 2006.
41. VanRooij E, Sutherland LB, Qi X, Richardson JA, Hill J, Olson EN. Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 316: 575-579, 2007.
42. Vasudevan S, Tong Y, Steitz JA. Switching from repression to activation: microRNAs can up-regulate translation. Science 318: 1931-1934, 2007.
43. Vidarsson H, Hyllner J, Sartipy P. Differentiation of Human Embryonic Stem Cells to Cardiomyocytes for In Vitro and In Vivo Applications. Stem Cell Rev 6:108-120, 2010.
44. Wang Y, Keys DN, Au-Young JK, Chen C. MicroRNAs in embryonic stem cells. J Cell Physiol 218: 251-255, 2009.
45. Wong CF, Tellam RL. MicroRNA-26a targets the histone methyltrans-ferase Enhancer of Zeste homolog 2 during myogenesis. J Biol Chem 283: 9836-9843, 2008.
46. Wu L, Belasco JG. Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells. Mol Cell Biol 25: 9198-9208, 2005.
47. Yeligar S, Tsukamoto H, Kalra VK. Ethanol-induced expression of ET-1 and ET-BR in liver sinusoidal endothelial cells and human endothe-lial cells involves hypoxia-inducible factor-1alpha and microRNA-199. J Immunol 183: 5232-5243, 2009.
48. Yue J, Sheng Y, Orwig KE. Identification of novel homologous microRNA genes in the rhesus macaque genome. BMC Genomics 9: 8, 2008.
49. Zhang C. MicroRNAs: role in cardiovascular biology and disease. Clin Sci (Lond) 114: 699-706, 2008.
50. Zhao Y, Samal E, Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220, 2005.
51. Zhou Y, Ferguson J, Chang JT, Kluger Y. Inter- and intra-combinatorial regulation by transcription factors and microRNAs. BMC Genomics 8: 396, 2007.