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. 2024 Aug 20;26(10):1790–1803. doi: 10.1038/s41556-024-01487-8

Fig. 6. Effects of perturbing BMP signalling on human RA-gastruloids.

Fig. 6

a, Schematic of perturbation of BMP signalling in human RA-gastruloids. CHIR, CHIR99021; LDN/BMP4, LDN193189 or BMP4. b, Representative images of untreated control, LDN-treated and BMP4-treated RA-gastruloids. The experiments were repeated independently three times with similar results. Scale bar, 100 µm. c, Morphometrics. From left to right: full length (µm) of 120 h RA-gastruloids, neural tube (NT) length (µm) measured with SOX2-mCit signal, neural tube/full-length ratio and somite pair counts. n = 6 and 11 for untreated and LDN treatment, respectively. d, UMAP visualization of co-embedded scRNA-seq data from untreated (grey) and LDN-treated (yellow) 120 h human RA-gastruloids (left). Same UMAP labelled by cell type annotation (right). e, Cell type composition changes upon LDN treatment of human RA-gastruloids. f, Marker gene expression in each cell type. g–i, The effects of BMP inhibition on neural lineages (NMP, neural tube, neural crest and neural progenitor cells). UMAP visualization of co-embedded scRNA-seq data (neural lineages only) from untreated (grey) and LDN-treated (yellow) 120 h human RA-gastruloids (g). Changes in marker gene expression with LDN treatment in neural lineages (h). Colour bars at left indicate the cell type(s) for which each gene is a marker. Dots indicate the ratio of average expression in LDN-treated versus control gastruloids. Data are presented as mean ± s.e.m. across pseudo-replicates (n = 3). Dots corresponding to increases or decreases larger than twofold are coloured red and blue, respectively. Same UMAP projection as g (i). Gene expression of three marker genes for each neural cell type are shown in each row. j–l, Same as g–i, but restricting instead to somitic lineages with pseudo-replicates (n = 3). Data are presented as mean ± s.e.m. m, Effects of LDN treatment on the proportion of endotome cells. Endotome cells are defined as the subset of somitic cells that are both KDR2+ and EBF2+. The bar chart shows the proportion of endotome cells, out of all somitic cells, in two experimental conditions.