Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution

Heart maturation and remodelling during the foetal and early postnatal period are critical for proper survival and growth of the foetus, yet our knowledge of the molecular processes involved are lacking for many cardiac cell types. To gain a deeper understanding of the transcriptional dynamics of the heart during the perinatal period, we performed single-cell RNA-seq on E14.5, E16.5, E18.5, P0, P4 and P7 mouse hearts to establish a catalogue of 49,769 cells. Gene regulatory network and pathway activity analyses underscored that heart maturation is strongly associated with regulation of cell growth and proliferation via pathways such as TGF. We additionally identified a common, cell type-independent signature for imprinted genes over time. Surprisingly, bioinformatics analyses and confirmation with RNAscope confirmed that while lncRNA H19 expression decreased over time in multiple cardiac cell types, it remained stably expressed in endocardial cells between E14.5 and P7. This suggests a differential requirement for H19 in the endocardium, and points towards an endocardium-specific maturation process when compared to other cardiac cell types. We envision this dataset to serve as a resource for better understanding perinatal heart maturation at the transcriptomic level, and to help bridge the gap between early developmental and adult heart stages for single-cell transcriptomics. Drop-seq was performed on single-cell suspensions from a total of 30 mouse hearts. We sampled 5 different time points during the perinatal period (E16.5,E18.5,P0,P4,P7) with 6 biological replicates per time point, from mice on a C57Bl/6NJ background. The raw UMI matrix contains a further 6 replicates from a previous study for E14.5 hearts (GSE109247).胎儿期与出生早期的心脏成熟与重塑，是保障胎儿正常存活与生长发育的关键环节，然而当前我们对诸多心脏细胞类型所涉及的分子调控机制仍缺乏系统认知。为深入解析围产期心脏的转录动态变化，我们对胚胎期14.5天（E14.5）、16.5天（E16.5）、18.5天（E18.5）以及出生后0天（P0）、4天（P4）、7天（P7）的小鼠心脏开展单细胞RNA测序（single-cell RNA-seq），最终构建了包含49769个细胞的细胞图谱。基因调控网络与通路活性分析结果表明，心脏成熟过程与细胞生长及增殖调控紧密相关，该调控主要通过转化生长因子（TGF）等通路实现。此外，我们还鉴定出一组随时间变化、不依赖于细胞类型的印记基因（imprinted genes）共表达特征。令人意外的是，生物信息学分析结合RNAscope验证结果显示：尽管长链非编码RNA（long non-coding RNA, lncRNA）H19在多种心脏细胞类型中的表达水平随时间推移逐渐下调，但在E14.5至P7期间的心脏心内膜细胞（endocardial cells）中，其表达始终保持稳定。这表明H19在心内膜细胞中存在差异化的功能需求，同时也提示，相较于其他心脏细胞类型，心内膜细胞存在其特有的成熟调控过程。我们期望本数据集可作为一项重要资源，助力学界从转录组层面深入理解围产期心脏成熟机制，并为填补单细胞转录组学中早期心脏发育与成体心脏阶段之间的研究空白提供支持。本研究通过液滴单细胞测序（Drop-seq）技术，对总计30个小鼠心脏的单细胞悬液开展测序。我们选取了C57Bl/6NJ背景的小鼠，在围产期的5个时间点（E16.5、E18.5、P0、P4、P7）进行采样，每个时间点设置6个生物学重复。原始唯一分子标识符（unique molecular identifier, UMI）矩阵还包含了一项既往研究中针对E14.5天小鼠心脏的6个额外生物学重复数据（数据集编号：GSE109247）。