Comparison of mRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes, biopsies from fetal, adult and hypertensive human hearts and primary cardiomyocytes

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 a 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. Comparison of mRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes, biopsies from fetal, adult and hypertensive human hearts and primary cardiomyocytes

为深入解析人类心脏发育的分子调控机制，本研究对人类诱导多能干细胞（human-induced pluripotent stem cell, hiPSC）分化而来的心肌细胞，以及胎儿、成人与高血压患者心脏活检样本的信使RNA（messenger RNA, mRNA）与微小RNA（microRNA, miRNA）转录组开展了全面比较分析。针对向心肌细胞分化的hiPSC的mRNA表达水平开展基因本体论（Gene Ontology, GO）分析，共鉴定出3类特征基因：多能性特异性基因、过渡态心脏定向分化基因以及成熟心肌细胞特异性基因。对mRNA数据进行分层聚类分析后发现，hiPSC来源心肌细胞的转录组在分化启动后约20天基本趋于稳定。尽管如此，对持续培养120天的细胞进行分析后发现，心肌细胞仍会持续成熟，逐步趋近于成人样基因表达模式。针对心肌细胞特异性miRNA（miR-1、miR-133a/b及miR-208a/b）的分析结果显示，其表达模式符合干细胞向心肌细胞定向分化的特征。通过整合miRNA与mRNA表达谱的生物统计学分析方法，本研究构建了心肌细胞分化相关的miRNA调控网络，并鉴定出多个miRNA所靶向的潜在mRNA靶点。综上，本研究揭示了人类心脏发育过程中的miRNA调控网络，并支持以下观点：在发育定向分化阶段，重叠的miRNA调控网络可增强转录调控效应。本研究同时对分化得到的hiPSC来源心肌细胞、胎儿、成人及高血压患者心脏活检样本与原代心肌细胞的mRNA表达谱进行了比较分析。