To gain insight into the molecular regulation of human heart development, a detailed comparison of the mRNA and miRNA transcriptomes across differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes and biopsies from fetal, adult, and hypertensive human hearts was performed. Gene ontology analysis of the mRNA expression levels of the hiPSCs differentiating into cardiomyocytes revealed 3 distinct groups of genes: pluripotent specific, transitional cardiac specification, and mature cardiomyocyte specific. Hierarchical clustering of the mRNA data revealed that the transcriptome of hiPSC cardiomyocytes largely stabilizes 20 days after initiation of differentiation. Nevertheless, analysis of cells continuously cultured for 120 days indicated that the cardiomyocytes continued to mature toward a more adult-like gene expression pattern. Analysis of cardiomyocyte-specific miRNAs (miR-1, miR-133a/b, and miR-208a/b) revealed an miRNA pattern indicative of stem cell to cardiomyocyte specification. A biostatistitical approach integrated the miRNA and mRNA expression profiles revealing a cardiomyocyte differentiation miRNA network and identified putative mRNAs targeted by multiple miRNAs. Together, these data reveal the miRNA network in human heart development and support the notion that overlapping miRNA networks re-enforce transcriptional control during developmental specification.
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References
1.
DvashT, BenvenistyN. 2004. Human embryonic stem cells as a model for early human development. Best Pract Res Clin Obstet Gynaecol, 18:929–940.
PoutonCW, HaynesJM. 2007. Embryonic stem cells as a source of models for drug discovery. Nat Rev Drug Discov, 6:605–616.
4.
BabiarzJE, BlellochR. 2009. Small RNAs–their biogenesis, regulation and function in embryonic stem cells. StemBook. The Stem Cell Research Community doi/10.3824/stembook.1.47.1
5.
BernsteinE, KimSY, CarmellMA, MurchisonEP, AlcornH, LiMZ, MillsAA, ElledgeSJ, AndersonKV, HannonGJ. 2003. Dicer is essential for mouse development. Nat Genet, 35:215–217.
6.
WangY, MedvidR, MeltonC, JaenischR, BlellochR. 2007. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet, 39:380–385.
7.
BartelDP. 2009. MicroRNAs: target recognition and regulatory functions. Cell, 136:215–233.
YangL, SoonpaaMH, AdlerED, RoepkeTK, KattmanSJ, KennedyM, HenckaertsE, BonhamK, AbbottGWet al. 2008. Human cardiovascular progenitor cells develop from a KDR+ embryonic-stem-cell-derived population. Nature, 453:524–528.
14.
BraamSR, TertoolenL, van de StolpeA, MeyerT, PassierR, MummeryCL. 2010. Prediction of drug-induced cardiotoxicity using human embryonic stem cell-derived cardiomyocytes. Stem Cell Res, 4:107–116.
XuXQ, SooSY, SunW, ZweigerdtR. 2009. Global expression profile of highly enriched cardiomyocytes derived from human embryonic stem cells. Stem Cells, 27:2163–2174.
17.
BraamSR, PassierR, MummeryCL. 2009. Cardiomyocytes from human pluripotent stem cells in regenerative medicine and drug discovery. Trends Pharmacol Sci, 30:536–545.
18.
MaJ, GuoL, FieneSJ, AnsonBD, ThomsonJA, KampTJ, KolajaKL, SwansonBJ, JanuaryCT. 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.
DonnellyML, LukeG, MehrotraA, LiX, HughesLE, GaniD, RyanMD. 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.
22.
PfafflMW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res, 29:e45.
23.
TaiYC, SpeedTP. 2009. On gene ranking using replicated microarray time course data. Biometrics, 65:40–51.
24.
LuY, LiuPY, XiaoP, DengHW. 2005. Hotelling's T2 multivariate profiling for detecting differential expression in microarrays. Bioinformatics, 21:3105–3113.
25.
SuAI, WiltshireT, BatalovS, LappH, ChingKA, BlockD, ZhangJ, SodenR, HayakawaMet al. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A, 101:6062–6067.
26.
ChangJT, NevinsJR. 2006. GATHER: a systems approach to interpreting genomic signatures. Bioinformatics, 22:2926–2933.
TadaS, EraT, FurusawaC, SakuraiH, NishikawaS, KinoshitaM, NakaoK, ChibaT. 2005. Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture. Development, 132:4363–4374.
34.
CaoF, WagnerRA, WilsonKD, XieX, FuJD, DrukkerM, LeeA, LiRA, GambhirSSet al. 2008. Transcriptional and functional profiling of human embryonic stem cell-derived cardiomyocytes. PLoS One, 3:e3474.
35.
LiuJ, LieuDK, SiuCW, FuJD, TseHF, LiRA. 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.
GoldfarbLG, DalakasMC. 2009. Tragedy in a heartbeat: malfunctioning desmin causes skeletal and cardiac muscle disease. J Clin Invest, 119:1806–1813.
37.
DupreyP, PaulinD. 1995. What can be learned from intermediate filament gene regulation in the mouse embryo. Int J Dev Biol, 39:443–457.
38.
BachmanNJ, RiggsPK, SiddiquiN, MakrisGJ, WomackJE, LomaxMI. 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.
39.
LaurentLC, ChenJ, UlitskyI, MuellerFJ, LuC, ShamirR, FanJB, LoringJF. 2008. Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence. Stem Cells, 26:1506–1516.
40.
SuhMR, LeeY, KimJY, KimSK, MoonSH, LeeJY, ChaKY, ChungHM, YoonHSet al. 2004. Human embryonic stem cells express a unique set of microRNAs. Dev Biol, 270:488–498.
41.
BarM, WymanSK, FritzBR, QiJ, GargKS, ParkinRK, KrohEM, BendoraiteA, MitchellPSet al. 2008. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells, 26:2496–2505.
42.
MorinRD, O'ConnorMD, GriffithM, KuchenbauerF, DelaneyA, PrabhuAL, ZhaoY, McDonaldH, ZengT. et al. 2008. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res, 18:610–621.
43.
MeltonC, BlellochR. 2010. MicroRNA Regulation of Embryonic Stem Cell Self-Renewal and Differentiation. Adv Exp Med Biol, 695:105–117.
44.
van RooijE, SutherlandLB, LiuN, WilliamsAH, McAnallyJ, GerardRD, RichardsonJA, OlsonEN. 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.
45.
AdachiT, NakanishiM, OtsukaY, NishimuraK, HirokawaG, GotoY, NonogiH, IwaiN. Plasma microRNA 499 as a biomarker of acute myocardial infarction. Clin Chem, 56:1183–1185.
46.
WangGK, ZhuJQ, ZhangJT, LiQ, LiY, HeJ, QinYW, JingQ. Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans. Eur Heart J, 31:659–666.
Griffiths-JonesS, BatemanA, MarshallM, KhannaA, EddySR. 2003. Rfam: an RNA family database. Nucleic Acids Res, 31:439–441.
49.
MiskaEA, Alvarez-SaavedraE, AbbottAL, LauNC, HellmanAB, McGonagleSM, BartelDP, AmbrosVR, HorvitzHR. 2007. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet, 3:e215.
50.
DoenchJG, PetersenCP, SharpPA. 2003. siRNAs can function as miRNAs. Genes Dev, 17:438–442.
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