Developmental Dynamics of Human Cardiogenesis: A multi-omic reference and its disruption in Trisomy 21

Developmental dynamics involve the specification of diverse cell types and their spatial organization into multicellular niches. Here, we combine single-cell and spatial multiomics to define 19 distinct tissue niches in the developing heart, leading to the development of a context-aware, resolution-agnostic niche classification tool ( TissueTypist ). Applying high-resolution spatial profiling to the developing sinoatrial node, we resolve three pacemaker cell subtypes arrayed along a linear axis. First trimester subpopulations, such as the pacemaker cells in the sinus horn and sinoatrial node head region, display neuro-attractant programmes and interact with parasympathetic neurons via interactions including Semaphorin-Plexin signalling. Temporal trajectories map maturation of atrial and ventricular cardiomyocytes, uncovering a lipid-metabolic switch and potential key regulators of cell type identity. In the ventricle, we identify cellular and transcriptional gradients along both pseudotime and transmural axes, offering new molecular insights into myocardial compaction and maturation. Comparative profiling of euploid and trisomy 21 hearts shows a depletion of compact cardiomyocytes and heightened apoptosis, validated in isogenic-matched trisomy 21 and euploid iPSC-derived cardiomyocytes. This implicates disrupted myocardial growth may be a mechanism for Down’s syndrome-associated congenital heart disease. Overall, we deliver a spatially resolved framework of human cardiac development, enabling systematic exploration of developmental niches in health and disease.