Li Guang, Xu Adele, Sim Sopheak, Priest James R, Tian Xueying, Khan Tooba, Quertermous Thomas, Zhou Bin, Tsao Philip S, Quake Stephen R, Wu Sean M
Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
Dev Cell. 2016 Nov 21;39(4):491-507. doi: 10.1016/j.devcel.2016.10.014. Epub 2016 Nov 10.
Embryonic gene expression intricately reflects anatomical context, developmental stage, and cell type. To address whether the precise spatial origins of cardiac cells can be deduced solely from their transcriptional profiles, we established a genome-wide expression database from 118, 949, and 1,166 single murine heart cells at embryonic day 8.5 (e8.5), e9.5, and e10.5, respectively. We segregated these cells by type using unsupervised bioinformatics analysis and identified chamber-specific genes. Using a random forest algorithm, we reconstructed the spatial origin of single e9.5 and e10.5 cardiomyocytes with 92.0% ± 3.2% and 91.2% ± 2.8% accuracy, respectively (99.4% ± 1.0% and 99.1% ± 1.1% if a ±1 zone margin is permitted) and predicted the second heart field distribution of Isl-1-lineage descendants. When applied to Nkx2-5 cardiomyocytes from murine e9.5 hearts, we showed their transcriptional alteration and lack of ventricular phenotype. Our database and zone classification algorithm will enable the discovery of novel mechanisms in early cardiac development and disease.
胚胎基因表达复杂地反映了解剖学背景、发育阶段和细胞类型。为了探究心脏细胞的确切空间起源是否仅能从其转录谱中推断出来，我们分别从胚胎第8.5天（e8.5）、e9.5和e10.5的118949个和1166个单鼠心脏细胞建立了全基因组表达数据库。我们使用无监督生物信息学分析按类型对这些细胞进行了分类，并鉴定出特定腔室的基因。使用随机森林算法，我们分别以92.0%±3.2%和91.2%±2.8%的准确率重建了单个e9.5和e10.5心肌细胞的空间起源（如果允许±1区域边界，则分别为99.4%±1.0%和99.1%±1.1%），并预测了Isl-1谱系后代的第二心脏场分布。当应用于来自小鼠e9.5心脏的Nkx2-5心肌细胞时，我们展示了它们的转录改变和缺乏心室表型。我们的数据库和区域分类算法将有助于发现早期心脏发育和疾病中的新机制。
