Associate Professor Stanford University, California, United States
Congenital heart defects, the most common birth defects, are the clinical manifestation of anomalies in fetal heart development - a complex process involving dynamic spatiotemporal coordination among various precursor cell lineages. This complexity underlies the incomplete understanding of the genetic architecture of congenital heart disease (CHD). To define the multi-cellular epigenomic and transcriptional landscape of cardiac cellular development, we generated single-cell chromatin accessibility maps of human embryonic heart tissues. These data identified eight major differentiation trajectories involving primary cardiac cell types, each associated with an array of continuous transcription factor (TF) activity signatures. This atlas allowed molecular comparison of the regulatory similarities and differences between iPSC-derived cardiac cell types with their in vivo counterparts. We interpreted deep learning models that predict cell-type resolved, base-resolution chromatin accessibility profiles from DNA sequence to decipher underlying transcription factor motif syntax and infer the regulatory impact of noncoding variants observed in CHD trios. De novo mutations predicted to affect chromatin accessibility in arterial endothelial clusters were significantly enriched in CHD cases vs controls with 1.7-fold enrichment. We used CRISPR perturbations to validate three of the enhancers harboring nominated regulatory mutations from these models, linking them to effects on the expression of JARID2, NFATC1, and TFAP2A. Together, this work defines the cis-regulatory sequence determinants of heart development and identifies disruption of cell type-specific regulatory elements as a component of the genetic etiology of CHD.