A toolkit for mapping cell identities in relation to neighbors reveals conserved patterning of neuromesodermal progenitor populations
Fig 3
Mapping the spatial distribution of Neuro-Mesodermal Progenitors.
A: Manifold projection of nuclei centroids in an example 4-somite-pair embryo showing SOX2+ TBXT+ cells (orange) and the regions in the lateral epiblast (Lt1-2) and node-streak border (B) defined by grafting experiments [34,35] as having neural and mesodermal potency (bifated regions: black boxes). SOX2 + TBXT+ are not restricted to the known N-M-bi-fated regions and instead map onto a broader spatial region. B: Iterative kernel averaging spatially smooths TF intensity values, shown by an example 4-somite-pair embryo. C: (i) PCA dimension reduction of the smoothed TF values in order to identify cell states. PCA loadings per TF indicated by arrow direction and magnitude (n = 19 embryos). (ii) The pseudotime tool Slingshot [44] identifies a path between the SOX2 high and the TBX6 high regions to create a pseudo-space continuum (n = 19 embryos). D: The pseudo-space continuum values (corresponding to cell states as defined by expression of TBXT, SOX2, and TBX6) mapped back onto the manifold projection of the four-somite-pair epiblast. Excluded cells (gray) are determined as described in the methods section. Pseudo-space values within known N-M-bifated regions are likely to correspond to NMP identities. E: The boundary between cells excluded because they fall outside the domain of potential neural/mesoderm fate (gray) and domains containing mono-fated, neural OR mesoderm cells (blue) is determined as described in the methods section. Red nuclei correspond to cells with pseudospace values defined in (Cii, D: see also main text) as corresponding to likely NMP identities (‘NMP-like cells’). These map to a U-shaped region that extends beyond the boundaries of the known N-M-bifated regions (black boxes: based on functional grafting experiments [34,35]. Data for Fig 3 (A-E): Data file 1, https://doi.org/10.5281/zenodo.15802710.