Uncovering neuromesodermal progenitor contributions to neural crest derivatives in vivo

Abstract

The neural crest (NC) is a multipotent embryonic cell population contributing to craniofacial skeleton, peripheral nervous system (PNS), and body pigmentation in vertebrate embryos. NC cells delaminate from the dorsal neural tube, and their fate is dictated by their anterior-posterior axis location. Neuromesodermal progenitors (NMPs) are a distinct posterior embryonic cell population giving rise to paraxial mesoderm and central nervous system (CNS) lineages. In vitro studies using pluripotent stem cells show that trunk-like NC derivatives require an intermediate state expressing both NC and NMP markers. The in vivo link between trunk NC and NMPs remains elusive, raising questions about the role of NMPs in specifying trunk peripheral neuronal populations, traditionally thought to derive from NC. We employed a Cre-Lox based genetic lineage tracing approach to track NMP derivatives in the zebrafish embryo and larva at a high resolution through constitutive labelling. We performed single-cell and single-nuclear RNA-sequencing to generate a comprehensive time-resolved single-cell atlas of NMP derivatives in the zebrafish larva. We identify an unprecedented range of NMP derivatives. NMPs differentiate into CNS neurons and glia, skeletal and muscle elements, myeloid, vasculature and many others. Notably, we discover contributions to the PNS, including sympathetic, enteric, and autonomic neurons and a Schwann cell precursor population, previously thought to be entirely NC-derived. We identify and characterize specific neuronal populations based on their marker gene expression through integrative analysis with publicly available scRNA-seq datasets. Therefore, in this study, we uncover the broad developmental potential of NMPs and establish NMPs as a paradigm for studying complex cell fate decisions, which would have implications on advancing regenerative cell therapies.