Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation

Ellen Ngar Yun Poon, Baixia Hao, Daogang Guan, Mulin Jun Li, Jun Lu, Yong Yang, Binbin Wu, Stanley Chun Ming Wu, Sarah E. Webb, Yan Liang, Andrew L. Miller, Xiaoqiang Yao, Junwen Wang, Bin Yan, Kenneth R. Boheler

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)894-906
Number of pages13
JournalCardiovascular Research
Volume114
Issue number6
DOIs
StatePublished - May 1 2018

Fingerprint

Pluripotent Stem Cells
MicroRNAs
Cardiac Myocytes
Transcription Factors
Gene Regulatory Networks
3' Untranslated Regions
Computational Biology
Luciferases
Ion Channels
Genes
Cell Differentiation
Heart Diseases
Binding Sites
Gene Expression
Messenger RNA
Human Embryonic Stem Cells
Proteins

Keywords

  • Bioinformatics methods
  • Gene regulatory network
  • miRNA-200c
  • Pluripotent stem cell-derived cardiomyocyte differentiation and maturation
  • Transcription factor

ASJC Scopus subject areas

  • Physiology
  • Cardiology and Cardiovascular Medicine
  • Physiology (medical)

Cite this

Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation. / Poon, Ellen Ngar Yun; Hao, Baixia; Guan, Daogang; Jun Li, Mulin; Lu, Jun; Yang, Yong; Wu, Binbin; Wu, Stanley Chun Ming; Webb, Sarah E.; Liang, Yan; Miller, Andrew L.; Yao, Xiaoqiang; Wang, Junwen; Yan, Bin; Boheler, Kenneth R.

In: Cardiovascular Research, Vol. 114, No. 6, 01.05.2018, p. 894-906.

Research output: Contribution to journalArticle

Poon, ENY, Hao, B, Guan, D, Jun Li, M, Lu, J, Yang, Y, Wu, B, Wu, SCM, Webb, SE, Liang, Y, Miller, AL, Yao, X, Wang, J, Yan, B & Boheler, KR 2018, 'Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation', Cardiovascular Research, vol. 114, no. 6, pp. 894-906. https://doi.org/10.1093/cvr/cvy019
Poon, Ellen Ngar Yun ; Hao, Baixia ; Guan, Daogang ; Jun Li, Mulin ; Lu, Jun ; Yang, Yong ; Wu, Binbin ; Wu, Stanley Chun Ming ; Webb, Sarah E. ; Liang, Yan ; Miller, Andrew L. ; Yao, Xiaoqiang ; Wang, Junwen ; Yan, Bin ; Boheler, Kenneth R. / Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation. In: Cardiovascular Research. 2018 ; Vol. 114, No. 6. pp. 894-906.
@article{cd6f29c7bd3548f5872bd5431b780981,
title = "Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation",
abstract = "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.",
keywords = "Bioinformatics methods, Gene regulatory network, miRNA-200c, Pluripotent stem cell-derived cardiomyocyte differentiation and maturation, Transcription factor",
author = "Poon, {Ellen Ngar Yun} and Baixia Hao and Daogang Guan and {Jun Li}, Mulin and Jun Lu and Yong Yang and Binbin Wu and Wu, {Stanley Chun Ming} and Webb, {Sarah E.} and Yan Liang and Miller, {Andrew L.} and Xiaoqiang Yao and Junwen Wang and Bin Yan and Boheler, {Kenneth R.}",
year = "2018",
month = "5",
day = "1",
doi = "10.1093/cvr/cvy019",
language = "English (US)",
volume = "114",
pages = "894--906",
journal = "Cardiovascular Research",
issn = "0008-6363",
publisher = "Oxford University Press",
number = "6",

}

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 - Jun Li, Mulin

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.

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

UR - http://www.scopus.com/inward/citedby.url?scp=85047108776&partnerID=8YFLogxK

U2 - 10.1093/cvr/cvy019

DO - 10.1093/cvr/cvy019

M3 - Article

C2 - 29373717

AN - SCOPUS:85047108776

VL - 114

SP - 894

EP - 906

JO - Cardiovascular Research

JF - Cardiovascular Research

SN - 0008-6363

IS - 6

ER -