Single-cell roadmap of cardiac differentiation identifies roles for ZNF711 and retinoic acid in balanced epicardial and cardiomyocyte lineage commitment

Abstract

SUMMARYStem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. We constructed a single-cell roadmap of atrial and ventricular differentiation conditions, enabling direct comparisons of monolayer, cardiac embryoid body, and engineered heart tissue trajectories. Using a multiomic approach and gene-regulatory network inference, we focused on the regulators of the epicardial, atrial and ventricular cardiomyocyte lineages. We identifiedZNF711as a regulatory switch and safe-guard for cardiomyocyte commitment. We show thatZNF711ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation, showing an interplay betweenZNF711and retinoic in cardiac lineage commitment.HIGHLIGHTSWe present an atlas of cardiac differentiation under different culture conditions, showing progenitor trajectories and cell states reminiscent of the fetal heart.Multiome and chromatin accessibility analysis identified candidate regulators of cardiomyocyte and non-cardiomyocyte lineages.Distinct trajectories of lineage commitment and differentiation under different culture conditions shows plasticity of first and second heart field progenitors and different ratios of cardiomyocyte and non-myocyte lineages.ZNF711 is required for balanced commitment to epicardial and ventricular cardiomyocyte lineages. Retinoic acid rescues a requirement for ZNF711 in cardiomyocyte differentiation, promoting both atrial cardiomyocyte and epicardial differentiation.Graphical Abstract