TY - JOUR
T1 - Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation
AU - Poon, Ellen Ngar Yun
AU - Hao, Baixia
AU - Guan, Daogang
AU - Li, Mulin Jun
AU - Lu, Jun
AU - Yang, Yong
AU - Wu, Binbin
AU - Wu, Stanley Chun Ming
AU - Webb, Sarah E.
AU - Liang, Yan
AU - Miller, Andrew L.
AU - Yao, Xiaoqiang
AU - Wang, Junwen
AU - Yan, Bin
AU - Boheler, Kenneth R.
N1 - Funding Information:
This work has been supported by Theme-based Research Scheme Hong Kong Research Grant Council [T13-706/11] to K.R.B., Small Project Funding Scheme of the University of Hong Kong [grant no. 201309176210] to E.P., Seed Funding for Basic Research of the University of Hong Kong [grant nos. 201606159002 and RCGAS0768448734] to B.Y., Guangdong Scientific and Technological Development Program of China [grant no. 2016A020214015] to B.Y., General Research Fund from Hong Kong Research Grant Council [grant no. 17121414 M] to J.W.
Publisher copyright:
© The Author(s) 2018.
PY - 2018/5/1
Y1 - 2018/5/1
N2 - Aims MicroRNAs (miRNAs) are crucial for the post-Transcriptional control of protein-encoding genes and together with transcription factors (TFs) regulate gene expression; however, the regulatory activities of miRNAs during cardiac development are only partially understood. In this study, we tested the hypothesis that integrative computational approaches could identify miRNAs that experimentally could be shown to regulate cardiomyogenesis. Methods and results We integrated expression profiles with bioinformatics analyses of miRNA and TF regulatory programs to identify candidate miRNAs involved with cardiac development. Expression profiling showed that miR-200c, which is not normally detected in adult heart, is progressively down-regulated both during cardiac development and in vitro differentiation of human embryonic stem cells (hESCs) to cardiomyocytes (CMs). We employed computational methodologies to predict target genes of both miR-200c and five key cardiac TFs to identify co-regulated gene networks. The inferred cardiac networks revealed that the cooperative action of miR-200c with these five key TFs, including three (GATA4, SRF and TBX5) targeted by miR-200c, should modulate key processes and pathways necessary for CM development and function. Experimentally, over-expression (OE) of miR-200c in hESC-CMs reduced the mRNA levels of GATA4, SRF and TBX5. Cardiac expression of Ca 2+, K + and Na + ion channel genes (CACNA1C, KCNJ2 and SCN5A) were also significantly altered by knockdown or OE of miR-200c. Luciferase reporter assays validated miR-200c binding sites on the 3′ untranslated region of CACNA1C. In hESC-CMs, elevated miR-200c increased beating frequency, and repressed both Ca 2+ influx, mediated by the L-Type Ca 2+ channel and Ca 2+ transients. Conclusions Our analyses demonstrate that miR-200c represses hESC-CM differentiation and maturation. The integrative computation and experimental approaches described here, when applied more broadly, will enhance our understanding of the interplays between miRNAs and TFs in controlling cardiac development and disease processes.
AB - Aims MicroRNAs (miRNAs) are crucial for the post-Transcriptional control of protein-encoding genes and together with transcription factors (TFs) regulate gene expression; however, the regulatory activities of miRNAs during cardiac development are only partially understood. In this study, we tested the hypothesis that integrative computational approaches could identify miRNAs that experimentally could be shown to regulate cardiomyogenesis. Methods and results We integrated expression profiles with bioinformatics analyses of miRNA and TF regulatory programs to identify candidate miRNAs involved with cardiac development. Expression profiling showed that miR-200c, which is not normally detected in adult heart, is progressively down-regulated both during cardiac development and in vitro differentiation of human embryonic stem cells (hESCs) to cardiomyocytes (CMs). We employed computational methodologies to predict target genes of both miR-200c and five key cardiac TFs to identify co-regulated gene networks. The inferred cardiac networks revealed that the cooperative action of miR-200c with these five key TFs, including three (GATA4, SRF and TBX5) targeted by miR-200c, should modulate key processes and pathways necessary for CM development and function. Experimentally, over-expression (OE) of miR-200c in hESC-CMs reduced the mRNA levels of GATA4, SRF and TBX5. Cardiac expression of Ca 2+, K + and Na + ion channel genes (CACNA1C, KCNJ2 and SCN5A) were also significantly altered by knockdown or OE of miR-200c. Luciferase reporter assays validated miR-200c binding sites on the 3′ untranslated region of CACNA1C. In hESC-CMs, elevated miR-200c increased beating frequency, and repressed both Ca 2+ influx, mediated by the L-Type Ca 2+ channel and Ca 2+ transients. Conclusions Our analyses demonstrate that miR-200c represses hESC-CM differentiation and maturation. The integrative computation and experimental approaches described here, when applied more broadly, will enhance our understanding of the interplays between miRNAs and TFs in controlling cardiac development and disease processes.
KW - Bioinformatics methods
KW - Gene regulatory network
KW - miRNA-200c
KW - Pluripotent stem cell-derived cardiomyocyte differentiation and maturation
KW - Transcription factor
UR - http://www.scopus.com/inward/record.url?scp=85047108776&partnerID=8YFLogxK
U2 - 10.1093/cvr/cvy019
DO - 10.1093/cvr/cvy019
M3 - Journal article
C2 - 29373717
AN - SCOPUS:85047108776
SN - 0008-6363
VL - 114
SP - 894
EP - 906
JO - Cardiovascular Research
JF - Cardiovascular Research
IS - 6
ER -
