Liu Qing, Jiang Chao, Xu Jin, Zhao Ming-Tao, Van Bortle Kevin, Cheng Xun, Wang Guangwen, Chang Howard Y, Wu Joseph C, Snyder Michael P
From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA.
Circ Res. 2017 Aug 4;121(4):376-391. doi: 10.1161/CIRCRESAHA.116.310456. Epub 2017 Jun 29.
Recent advances have improved our ability to generate cardiomyocytes from human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). However, our understanding of the transcriptional regulatory networks underlying early stages (ie, from mesoderm to cardiac mesoderm) of cardiomyocyte differentiation remains limited.
To characterize transcriptome and chromatin accessibility during early cardiomyocyte differentiation from hiPSCs and hESCs.
We profiled the temporal changes in transcriptome and chromatin accessibility at genome-wide levels during cardiomyocyte differentiation derived from 2 hiPSC lines and 2 hESC lines at 4 stages: pluripotent stem cells, mesoderm, cardiac mesoderm, and differentiated cardiomyocytes. Overall, RNA sequencing analysis revealed that transcriptomes during early cardiomyocyte differentiation were highly concordant between hiPSCs and hESCs, and clustering of 4 cell lines within each time point demonstrated that changes in genome-wide chromatin accessibility were similar across hiPSC and hESC cell lines. Weighted gene co-expression network analysis (WGCNA) identified several modules that were strongly correlated with different stages of cardiomyocyte differentiation. Several novel genes were identified with high weighted connectivity within modules and exhibited coexpression patterns with other genes, including noncoding RNA and uncharacterized RNA in the module related to the mesoderm stage; E-box-binding homeobox 1 () in the module correlated with postcardiac mesoderm. We further demonstrated that ZEB1 is required for early cardiomyocyte differentiation. In addition, based on integrative analysis of both WGCNA and transcription factor motif enrichment analysis, we determined numerous transcription factors likely to play important roles at different stages during cardiomyocyte differentiation, such as and eomesodermin (; mesoderm), lymphoid enhancer-binding factor 1 () and mesoderm posterior BHLH transcription factor 1 (; from mesoderm to cardiac mesoderm), meis homeobox 1 () and GATA-binding protein 4 () (postcardiac mesoderm), and families, and (cardiomyocyte).
Both hiPSCs and hESCs share similar transcriptional regulatory mechanisms underlying early cardiac differentiation, and our results have revealed transcriptional regulatory networks and new factors (eg, ZEB1) controlling early stages of cardiomyocyte differentiation.
最近的进展提高了我们从人诱导多能干细胞（hiPSC）和人胚胎干细胞（hESC）生成心肌细胞的能力。然而，我们对心肌细胞分化早期阶段（即从中胚层到心脏中胚层）潜在的转录调控网络的理解仍然有限。
表征hiPSC和hESC早期心肌细胞分化过程中的转录组和染色质可及性。
我们在4个阶段对来自2种hiPSC系和2种hESC系的心肌细胞分化过程中全基因组水平的转录组和染色质可及性的时间变化进行了分析：多能干细胞、中胚层、心脏中胚层和分化的心肌细胞。总体而言，RNA测序分析显示，hiPSC和hESC之间早期心肌细胞分化过程中的转录组高度一致，每个时间点内4种细胞系的聚类表明，全基因组染色质可及性的变化在hiPSC和hESC细胞系中相似。加权基因共表达网络分析（WGCNA）确定了几个与心肌细胞分化不同阶段密切相关的模块。在模块内鉴定出几个具有高加权连通性的新基因，并与其他基因呈现共表达模式，包括中胚层阶段相关模块中的非编码RNA和未表征的RNA；与心脏中胚层后阶段相关模块中的E盒结合同源框1（ZEB1）。我们进一步证明ZEB1是早期心肌细胞分化所必需的。此外，基于WGCNA和转录因子基序富集分析的综合分析，我们确定了许多可能在心肌细胞分化不同阶段发挥重要作用的转录因子，如叉头框A2（FOXA2；中胚层）、胚外中胚层决定因子（EOMES；中胚层）、淋巴细胞增强因子结合因子1（LEF1）和中胚层后部BHLH转录因子1（MESPB；从中胚层到心脏中胚层）、肌细胞增强因子2（MEF2）家族和GATA结合蛋白4（GATA4；心脏中胚层后）、NKX家族和TBX家族（心肌细胞）。
hiPSC和hESC在早期心脏分化过程中共享相似的转录调控机制，我们的结果揭示了控制心肌细胞分化早期阶段的转录调控网络和新因子（如ZEB1）。
