Deciphering Cardiac Biology and Disease by Single-Cell Transcriptomic Profiling

Figure 1. Topics commonly studied by scRNA-seq in the mammalian heart. (a) Embryonic heart development: the role of cardiac progenitor cells during in vivo cardiogenesis and critical transcription factors determining cardiac cell fates [12,14,17,20,21,22,23,24,25]. (b) Adult heart in health and disease: cellular heterogeneity and intercellular crosstalk, the role of specific cell subtypes in cardiac diseases, and potential therapeutic opportunities [8,9,13,15,16,26,27,28,29,30,31,32,33]. (c) Induced pluripotent stem-cell-derived cardiomyocytes: ways of improving modeling (maturation and reprogramming efficiency), patient-specific cells to understand genetic heart diseases, and in vitro modeling of embryonic heart development [18,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51]. (d) ScRNA-seq can be used to explore cellular heterogeneity, identify rare cell types, deduce intercellular communications, establish regulatory networks, and construct lineage trajectories.

Figure 2. Cellular heterogeneity and gene expression during cardiac differentiation from hiPSC-CMs defined by single-cell transcriptomic profiling. On day 2, the differentiating population comprises cells corresponding to the mesoderm (MESP1), definitive endoderm (SOX17), and mesendoderm (EOMES). By day 5, cardiac precursors (TNNI1) and endothelial cells (TALI), and a persistent cluster of definitive endoderm are defined. On day 15 of cardiac differentiation, the population comprises 3 clusters, two expressing TNNT2, ACTC1, and cell cycle genes, representing early stage proliferative CMs; and a cluster of non-cardiomyocytes expressing genes enriched in processes, such as extracellular matrix deposition, motility, and cell adhesion (THY1, PITX2, and BMP4). The population on day 30 is composed of 2 clusters of mid-stage cardiomyocytes and a cluster of non-cardiomyocytes. By day 45, 2 mature CM clusters expressed sarcomeric (MYH6, MYL2, TNNT2, and MYBPC3) and calcium handling genes (RYR2, PLN). It is worth noting that the ventricular subsets marked by MYL2 only appeared at the later stage of differentiation (D30–D90), in contrast to the atrial subsets (MYL7) that appeared earlier. This…