Fig. 2: Single-cell transcriptomic analysis reveals ATF4-dependent changes in CAFs in B16F10 tumours.

a, UMAP plot of cells from two biologically independent samples pooled from small B16F10 tumours (150 mm³) from each genotype. Different cell type clusters are colour coded. TAMs, tumour-associated macrophages. b, Dot plot displaying selected gene markers across all clusters. The colour intensity represents the average expression and the size of dots indicates the percentage of cells expressing each gene. c, Violin plots showing the expression of Acta2, Pdgfrb, Col1a1 and Col1a2 at the CAF cluster identified in B16F10 tumours. The y axis shows the mean expression level. Red (KO) and blue (WT) represent Atf4^Δ/Δ and Atf4^WT/WT, respectively. FC, fold change. d, Bar plot displaying the negative log₁₀(false discovery rate (FDR)) of the ten most significantly upregulated gene ontology terms enriched in WT (left) or KO (right) CAFs. e, UMAP plot after reclustering of the CAF cell type in the dataset from a. f, Violin plots of the expression levels of the indicated CAF markers in the CAF subclusters. g, Bar plot of the normalized log₂(FC) (WT/KO) of CAF subclusters in tumours grown in each genotype. h, Violin plots of Col1a1 and Col1a2 expression in the vCAF subcluster. i, UMAP plot of reclustered CAFs from merged small and large B16F10 tumours. j, Slingshot-based pseudo-time ordering suggests that mCAFs move along a differentiation trajectory to become vCAFs, cCAFs and melCAFs.