Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells

• Published in: Developmental cell Vol. 39; no. 4; pp. 491 - 507
• Main Authors: 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.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.11.2016
• Subjects: Algorithms; Animals; Biomarkers - metabolism; cardiac development; cardiomyocyte; Cell Lineage - genetics; Cell Separation; congenital heart disease; Embryo, Mammalian - cytology; Embryoid Bodies - cytology; Gene Expression Profiling; Gene Expression Regulation, Developmental; Heart - embryology; Integrases - metabolism; Mice; Models, Biological; Myocardium - metabolism; Myocytes, Cardiac - cytology; Myocytes, Cardiac - metabolism; Nkx2-5; Polymerase Chain Reaction; Reproducibility of Results; Sequence Analysis, RNA; Single-Cell Analysis; single-cell RNA sequencing; single-cell RNA sequencing; congenital heart disease; Nkx2-5; cardiac development; cardiomyocyte
• ISSN: 1534-5807; 1878-1551
• DOI: 10.1016/j.devcel.2016.10.014

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. [Display omitted] •Single-cell RNA-seq uncovers chamber-specific genes in the embryonic mouse heart•Machine learning can infer anatomical context from single-cell transcriptional data•Nkx2-5−/− embryonic mouse cardiomyocytes lack a ventricular transcriptional profile•Embryonic ventricular myocardium display trabecular-compact expression gradients Cardiogenesis is orchestrated by cell-type- and chamber-specific transcription. Li et al. collected 2,233 single-cell RNA-seq samples from embryonic mouse hearts. This data resource uncovers anatomical patterns of gene expression that enable the deduction of a single-cell sample's anatomical origin, providing insight into developmental perturbations in congenital heart defect models.