Decoding enhancer usage and gene expression of human heart development in 3-D cardioids

The early steps of heart formation during embryogenesis require precise spatiotemporal coordination between different heart progenitors to join together to form a beating heart tube.

This complex biological process is regulated through an evolutionary conserved gene regulatory network (GRN) of transcription factors and cis-regulatory elements that integrate inductive signals from surrounding tissues to ensure correct heart development.

Yet, how this process is controlled during heart development, and how mutations impacting the cardiac GRN leads to cardiomyopathies, remains unclear. There is currently little or no information about human heart enhancers during these early stages of heart development.

Here, we will first determine the dynamic changes in the usage of regulatory elements and gene expression that accompanies human heart development using heart organoids (cardioids) derived from human induced pluripotent stem cells.

To uncover the underlying GRN, we will apply scRNA-seq and scATAC-seq to 3-D cardioids at different stages of development, which will allow us to map enhancer usage during cell fate transitions in human heart development for the first time in vitro. Moreover, we will study how developmental trajectories are altered in disease-relevant mutant 3-D cardioids models.

Last, we will study how perturbations of transcription factors influence enhancer function and gene expression by fine-tuning the nuclear level of key regulators using an optogenetic tool developed by the Furlong lab, which is extremely dynamic providing very precise temporal resolution, in the order of minutes.

The functional impact of these perturbations will be assessed by scRNA-seq and scATAC-seq to identify the transcription factors regulatory mechanisms.

Together, these findings will advance our understanding of gene regulation during cardiogenesis by identifying fundamental principles of enhancer usage and transcriptional changes during normal and diseased heart development.