Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China.
State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, China.
Stem Cell Res Ther. 2023 Sep 13;14(1):247. doi: 10.1186/s13287-023-03442-0.
Dissecting complex interactions among transcription factors (TFs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are central for understanding heart development and function. Although computational approaches and platforms have been described to infer relationships among regulatory factors and genes, current approaches do not adequately account for how highly diverse, interacting regulators that include noncoding RNAs (ncRNAs) control cardiac gene expression dynamics over time.
To overcome this limitation, we devised an integrated framework, cardiac gene regulatory modeling (CGRM) that integrates LogicTRN and regulatory component analysis bioinformatics modeling platforms to infer complex regulatory mechanisms. We then used CGRM to identify and compare the TF-ncRNA gene regulatory networks that govern early- and late-stage cardiomyocytes (CMs) generated by in vitro differentiation of human pluripotent stem cells (hPSC) and ventricular and atrial CMs isolated during in vivo human cardiac development.
Comparisons of in vitro versus in vivo derived CMs revealed conserved regulatory networks among TFs and ncRNAs in early cells that significantly diverged in late staged cells. We report that cardiac genes ("heart targets") expressed in early-stage hPSC-CMs are primarily regulated by MESP1, miR-1, miR-23, lncRNAs NEAT1 and MALAT1, while GATA6, HAND2, miR-200c, NEAT1 and MALAT1 are critical for late hPSC-CMs. The inferred TF-miRNA-lncRNA networks regulating heart development and contraction were similar among early-stage CMs, among individual hPSC-CM datasets and between in vitro and in vivo samples. However, genes related to apoptosis, cell cycle and proliferation, and transmembrane transport showed a high degree of divergence between in vitro and in vivo derived late-stage CMs. Overall, late-, but not early-stage CMs diverged greatly in the expression of "heart target" transcripts and their regulatory mechanisms.
In conclusion, we find that hPSC-CMs are regulated in a cell autonomous manner during early development that diverges significantly as a function of time when compared to in vivo derived CMs. These findings demonstrate the feasibility of using CGRM to reveal dynamic and complex transcriptional and posttranscriptional regulatory interactions that underlie cell directed versus environment-dependent CM development. These results with in vitro versus in vivo derived CMs thus establish this approach for detailed analyses of heart disease and for the analysis of cell regulatory systems in other biomedical fields.
解析转录因子（TFs）、微小 RNA（miRNAs）和长链非编码 RNA（lncRNAs）之间的复杂相互作用，是理解心脏发育和功能的关键。尽管已经描述了用于推断调控因子和基因之间关系的计算方法和平台，但当前的方法并不能充分说明包括非编码 RNA（ncRNAs）在内的高度多样化的相互作用调控因子如何随时间控制心脏基因表达动力学。
为了克服这一限制，我们设计了一个综合框架，即心脏基因调控建模（CGRM），该框架集成了 LogicTRN 和调控成分分析生物信息学建模平台，以推断复杂的调控机制。然后，我们使用 CGRM 来识别和比较体外分化人类多能干细胞（hPSC）产生的早期和晚期心肌细胞（CM）以及体内人类心脏发育过程中分离的心室和心房 CM 所调控的 TF-ncRNA 基因调控网络。
比较体外和体内来源的 CM 发现，早期细胞中 TF 和 ncRNA 之间存在保守的调控网络，而晚期细胞中的这些网络则显著分化。我们报告说，在早期 hPSC-CM 中表达的心脏基因（“心脏靶标”）主要受 MESP1、miR-1、miR-23、lncRNAs NEAT1 和 MALAT1 调控，而 GATA6、HAND2、miR-200c、NEAT1 和 MALAT1 则对晚期 hPSC-CM 至关重要。调节心脏发育和收缩的推断 TF-miRNA-lncRNA 网络在早期 CM 之间、单个 hPSC-CM 数据集之间以及体外和体内样本之间相似。然而，与凋亡、细胞周期和增殖以及跨膜转运相关的基因在体外和体内衍生的晚期 CM 之间表现出高度的差异。总的来说，与体内衍生的晚期 CM 相比，晚期 CM 的“心脏靶标”转录物及其调控机制的表达差异很大。
总之，我们发现 hPSC-CM 在早期发育过程中以细胞自主的方式受到调控，与体内衍生的 CM 相比，随着时间的推移，其调控方式会发生显著变化。这些发现证明了使用 CGRM 揭示细胞定向和环境依赖的 CM 发育背后的动态和复杂转录和转录后调控相互作用的可行性。因此，体外与体内衍生的 CM 的这些结果为详细分析心脏病以及分析其他生物医学领域的细胞调控系统奠定了基础。
