Fig. 3: scRNA-seq identifies dKO-associated remodelling of the NC-derived and immune compartments.
a, Dimension-reduced representation using uniform manifold approximation and projection (UMAP) of cell clusters in WT and dKO melanomas profiled by scRNA-seq at 35 DPI. Dots correspond to single cells from three independently processed tumours per genotype, coloured by cluster identity. b, Phylogenetic tree showing the degree of cell type and state similarity based on distances between clusters in principal component analysis space. See Supplementary Table 3 for a description of the cell-type acronyms used. c, Distribution of annotated spot types derived from ST analysis, overlaid on WT and dKO tumour histology. Insets are shown at ×2 magnification. d, Relative cell frequencies across clusters in individual melanomas profiled by scRNA-seq. Values shown are normalized to the total number of high-quality cells per sample included in the analysis. Names in colour represent clusters with significant differences between WT and dKO frequencies (two-tailed unpaired t-test < 0.05); red indicates more abundant in dKO, whereas blue indicates more abundant in WT. P values are provided as numerical source data. e, UMAP representation of differential abundance analysis performed using Milo. Cells are grouped into overlapping neighbourhoods based on their k-nearest neighbour graph position, depicted as circles proportional in size to the number of cells contained, coloured by the log fold change of abundance between genotypes. The graph edge thickness is proportional to the number of cells shared between adjacent neighbourhoods. f, Bee swarm plot of significant differences in e showing distributions of abundance log fold changes between dKO and WT samples in neighbourhoods belonging to the indicated clusters as in a. For e and f, neighbourhoods with significant differential abundance at a 5% false discovery rate are coloured. In f, non-significant neighbourhoods are not shown.
