Integrative single-cell multi-modal analyses reveal detailed spatial cellular organization directing human heart morphogenesis

The heart, which is the first organ to develop, is highly dependent on its
form to function. However, how diverse cardiac cell types spatially
coordinate to create complex morphological structures critical for heart
function remains to be elucidated. Here, we show that integration of
single cell RNA-sequencing with high-resolution multiplexed error-robust
fluorescent in situ hybridization (MERFISH) not only resolves the identity
of cardiac cell types developing the human heart but also provides a
spatial mapping of individual cells that enables illumination of their
organization into cellular communities forming distinct cardiac
structures. We discovered that many of these cardiac cell types further
specified into subpopulations exclusive to specific communities,
supporting their specialization according to cellular ecosystem and
anatomic region. In particular, ventricular cardiomyocyte subpopulations
displayed an unexpected complex laminar organization across the
ventricular wall and formed, with other cell subpopulations, several
cellular communities. Interrogating cell-cell interactions within these
communities revealed signaling pathways orchestrating the spatial
organization of cardiac cell subpopulations during ventricular wall
morphogenesis. In vivo conditional genetic mouse models and in
vitro human pluripotent stem cell studies confirmed an intricate
multicellular PLXN-SEMA crosstalk among specific ventricular
cardiomyocyte, fibroblast and endothelial cell subpopulations that directs
the compaction of the ventricular wall layers. Thus, these detailed
findings into the cellular social interactions and specialization of
cardiac cell types constructing and remodeling the human heart offer new
insights into structural heart diseases as well as engineering complex
multi-cellular tissues for human heart repair.