Determination of the human cardiomyocyte mRNA and miRNA differentiation network by fine-scale profiling

Stem Cells and Development

Volumn 21, Issue 11, 2012, Pages 1956-1965

  Babiarz, Joshua E ^a   Ravon, Morgane ^b   Sridhar, Sriram ^c   Ravindran, Palanikumar ^c   Swanson, Brad ^d   Bitter, Hans ^c   Weiser, Thomas ^b   Chiao, Eric ^a   Certa, Ulrich ^b   Kolaja, Kyle L ^a  

^a Non Clinical Safety   (United States)

^b Non Clinical Safety   (Switzerland)

^c Bioinformatics and Biostatistics   (United States)

^d Cellular Dynamics International   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 1; MICRORNA 133A; MICRORNA 133B; MICRORNA 208A; MICRORNA 208B; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CELL ASSAY; CELL DIFFERENTIATION; CONTROLLED STUDY; FINE SCALE PROFILING; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; HEART DEVELOPMENT; HEART MUSCLE CELL; HUMAN; HUMAN CELL; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ADULT; BIOLOGICAL MARKERS; CELL DIFFERENTIATION; CELLS, CULTURED; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; FETUS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HEART; HUMANS; MICRORNAS; MYOCYTES, CARDIAC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PLURIPOTENT STEM CELLS; RNA, MESSENGER; TIME FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84863888089     PISSN: 15473287     EISSN: 15578534     Source Type: Journal    
DOI: 10.1089/scd.2011.0357     Document Type: Article

References (50)

1. Dvash T and N Benvenisty. (2004). Human embryonic stem cells as a model for early human development. Best Pract Res Clin Obstet Gynaecol 18:929-940. (Pubitemid 40012028)
2. Stadtfeld M and K Hochedlinger. Induced pluripotency: history, mechanisms, and applications. Genes Dev 24:2239-2263.
3. Pouton CW and JM Haynes. (2007). Embryonic stem cells as a source of models for drug discovery. Nat Rev Drug Discov 6:605-616. (Pubitemid 47202486)
4. Babiarz JE and R Blelloch. (2009). Small RNAs-their biogenesis, regulation and function in embryonic stem cells. In: StemBook. The Stem Cell Research Community, ed. doi/10.3824/stembook.1.47.1
5. Bernstein E, SY Kim, MA Carmell, EP Murchison, H Alcorn, MZ Li, AA Mills, SJ Elledge, KV Anderson and GJ Hannon. (2003). Dicer is essential for mouse development. Nat Genet 35:215-217. (Pubitemid 37363172)
6. Wang Y, R Medvid, C Melton, R Jaenisch and R Blelloch. (2007). DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet 39:380-385. (Pubitemid 46328490)
7. Bartel DP. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136:215-233.
8. Cordes KR and D Srivastava. (2009). MicroRNA regulation of cardiovascular development. Circ Res 104:724-732.
9. Kartha RV and S Subramanian. (2010). MicroRNAs in cardiovascular diseases: biology and potential clinical applications. J Cardiovasc Transl Res 3:256-270.
10. Zhao Y, JF Ransom, A Li, V Vedantham, M von Drehle, AN Muth, T Tsuchihashi, MT McManus, RJ Schwartz and D Srivastava. (2007). Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 129:303-317. (Pubitemid 46574975)
11. Zhang J, GF Wilson, AG Soerens, CH Koonce, J Yu, SP Palecek, JA Thomson and TJ Kamp. (2009). Functional cardiomyocytes derived from human induced pluripotent stem cells. Circ Res 104:e30-e41.
12. Bu L, X Jiang, S Martin-Puig, L Caron, S Zhu, Y Shao, DJ Roberts, PL Huang, IJ Domian and KR Chien. (2009). Human ISL1 heart progenitors generate diverse multipotent cardiovascular cell lineages. Nature 460:113-117.
13. Yang L, MH Soonpaa, ED Adler, TK Roepke, SJ Kattman, M Kennedy, E Henckaerts, K Bonham, GW Abbott, et al. (2008). Human cardiovascular progenitor cells develop from a KDR+ embryonic-stem-cell-derived population. Nature 453:524-528. (Pubitemid 351733312)
14. Braam SR, L Tertoolen, A van de Stolpe, T Meyer, R Passier and CL Mummery. (2010). Prediction of drug-induced cardiotoxicity using human embryonic stem cell-derived cardiomyocytes. Stem Cell Res 4:107-116.
15. Hattori F, H Chen, H Yamashita, S Tohyama, YS Satoh, S Yuasa, W Li, H Yamakawa, T Tanaka, et al. (2010). Nongenetic method for purifying stem cell-derived cardiomyocytes. Nat Methods 7:61-66.
16. Xu XQ, SY Soo, W Sun and R Zweigerdt. (2009). Global expression profile of highly enriched cardiomyocytes derived from human embryonic stem cells. Stem Cells 27:2163-2174.
17. Braam SR, R Passier and CL Mummery. (2009). Cardiomyocytes from human pluripotent stem cells in regenerative medicine and drug discovery. Trends Pharmacol Sci 30:536-545.
18. Ma J, L Guo, SJ Fiene, BD Anson, JA Thomson, TJ Kamp, KL Kolaja, BJ Swanson and CT January. (2011). High purity human induced pluripotent stem cell (hiPSC) derived cardiomyocytes: electrophysiological properties of action potentials and ionic currents. Am J Physiol Heart Circ Physiol 301:H2006-2017.
19. Yu J, MA Vodyanik, K Smuga-Otto, J Antosiewicz-Bourget, JL Frane, S Tian, J Nie, GA Jonsdottir, V Ruotti, et al. (2007). Induced pluripotent stem cell lines derived from human somatic cells. Science 318:1917-1920.
20. Klug MG, MH Soonpaa, GY Koh and LJ Field. (1996). Genetically selected cardiomyocytes from differentiating embronic stem cells form stable intracardiac grafts. J Clin Invest 98:216-224. (Pubitemid 26243839)
21. Donnelly ML, G Luke, A Mehrotra, X Li, LE Hughes, D Gani and MD Ryan. (2001). Analysis of the aphthovirus 2A/2B polyprotein 'cleavage' mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal 'skip'. J Gen Virol 82:1013-1025. (Pubitemid 32454602)
22. Pfaffl MW. (2001). A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45.
23. Tai YC and TP Speed. (2009). On gene ranking using replicated microarray time course data. Biometrics 65:40-51.
24. Lu Y, PY Liu, P Xiao and HW Deng. (2005). Hotelling's T2 multivariate profiling for detecting differential expression in microarrays. Bioinformatics 21:3105-3113. (Pubitemid 41418463)
25. Su AI, T Wiltshire, S Batalov, H Lapp, KA Ching, D Block, J Zhang, R Soden, M Hayakawa, et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101:6062-6067. (Pubitemid 38520528)
26. Chang JT and JR Nevins. (2006). GATHER: a systems approach to interpreting genomic signatures. Bioinformatics 22:2926-2933. (Pubitemid 44811565)
27. Reich M, T Liefeld, J Gould, J Lerner, P Tamayo and JP Mesirov. (2006). GenePattern 2.0. Nat Genet 38:500-501.
28. Friedman RC, KK Farh, CB Burge and DP Bartel. (2009). Most mammalian mRNAs are conserved targets of micro-RNAs. Genome Res 19:92-105.
29. Bader GD and CW Hogue. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2.
30. Kim J, J Chu, X Shen, J Wang and SH Orkin. (2008). An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132:1049-1061. (Pubitemid 351381745)
31. Peng JC, A Valouev, T Swigut, J Zhang, Y Zhao, A Sidow and J Wysocka. (2009). Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139:1290-1302.
32. Stennard F, K Ryan and JB Gurdon. (1997). Markers of vertebrate mesoderm induction. Curr Opin Genet Dev 7:620-627. (Pubitemid 27491426)
33. Tada S, T Era, C Furusawa, H Sakurai, S Nishikawa, M Kinoshita, K Nakao and T Chiba. (2005). Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture. Development 132:4363-4374. (Pubitemid 41576697)
34. Cao F, RA Wagner, KD Wilson, X Xie, JD Fu, M Drukker, A Lee, RA Li, SS Gambhir, et al. (2008). Transcriptional and functional profiling of human embryonic stem cell-derived cardiomyocytes. PLoS One 3:e3474.
35. Liu J, DK Lieu, CW Siu, JD Fu, HF Tse and RA Li. (2009). Facilitated maturation of Ca2 + handling properties of human embryonic stem cell-derived cardiomyocytes by calsequestrin expression. Am J Physiol Cell Physiol 297:C152-C159.
36. Goldfarb LG and MC Dalakas. (2009). Tragedy in a heartbeat: malfunctioning desmin causes skeletal and cardiac muscle disease. J Clin Invest 119:1806-1813.
37. Duprey P and D Paulin. (1995). What can be learned from intermediate filament gene regulation in the mouse embryo. Int J Dev Biol 39:443-457.
38. Bachman NJ, PK Riggs, N Siddiqui, GJ Makris, JE Womack and MI Lomax. (1997). Structure of the human gene (COX6A2) for the heart/muscle isoform of cytochrome c oxidase subunit VIa and its chromosomal location in humans, mice, and cattle. Genomics 42:146-151. (Pubitemid 27215135)
39. Laurent LC, J Chen, I Ulitsky, FJ Mueller, C Lu, R Shamir, JB Fan and JF Loring. (2008). Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence. Stem Cells 26:1506-1516.
40. Suh MR, Y Lee, JY Kim, SK Kim, SH Moon, JY Lee, KY Cha, HM Chung, HS Yoon, et al. (2004). Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270:488-498. (Pubitemid 38748567)
41. Bar M, SK Wyman, BR Fritz, J Qi, KS Garg, RK Parkin, EM Kroh, A Bendoraite, PS Mitchell, et al. (2008). MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 26:2496-2505.
42. Morin RD, MD O'Connor, M Griffith, F Kuchenbauer, A Delaney, AL Prabhu, Y Zhao, H McDonald, T Zeng, et al. (2008). Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18:610-621. (Pubitemid 351482785)
43. Melton C and R Blelloch. (2010). MicroRNA Regulation of Embryonic Stem Cell Self-Renewal and Differentiation. Adv Exp Med Biol 695:105-117.
44. van Rooij E, LB Sutherland, N Liu, AH Williams, J McAnally, RD Gerard, JA Richardson and EN Olson. (2006). A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci U S A 103:18255-18260. (Pubitemid 44871645)
45. Adachi T, M Nakanishi, Y Otsuka, K Nishimura, G Hirokawa, Y Goto, H Nonogi and N Iwai. Plasma microRNA 499 as a biomarker of acute myocardial infarction. Clin Chem 56:1183-1185.
46. Wang GK, JQ Zhu, JT Zhang, Q Li, Y Li, J He, YW Qin and Q Jing. Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans. Eur Heart J 31:659-666.
47. Guo H, NT Ingolia, JS Weissman and DP Bartel. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-840.
48. Griffiths-Jones S, A Bateman, M Marshall, A Khanna and SR Eddy. (2003). Rfam: an RNA family database. Nucleic Acids Res 31:439-441. (Pubitemid 36150423)
49. Miska EA, E Alvarez-Saavedra, AL Abbott, NC Lau, AB Hellman, SM McGonagle, DP Bartel, VR Ambros and HR Horvitz. (2007). Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3:e215.
50. Doench JG, CP Petersen and PA Sharp. (2003). siRNAs can function as miRNAs. Genes Dev 17:438-442. (Pubitemid 36258757)