Figure EV2. scRNA-seq in AOM/DSS and orthotopic models show reduced CAF diversity and impaired subtype-specific gene expression in Fib^ΔZeb1 tumors.

(A) Phenotypic annotation of AOM/DSS CAFs (n = 3 mice per genotype; corresponding to Fig. 2) upon integrated clustering by scoring of iCAF/myCAF/apCAF/mCAF/vCAF gene signatures (Bartoschek et al, 2018; Elyada et al, 2019) and displayed on UMAP Leiden clusters, pooled according to the determined scores. Note that ‘i/myCAFs’ share features of iCAFs and myCAFs and that the identities of 3 cell clusters could not be determined (ND) using these gene sets. (B) Genotype distribution of cells in AOM/DSS CAFs in DA regions (please refer to Fig. 2). The fraction of Fib^Ctrl and Fib^ΔZeb1 CAFs in each DA region or among all CAFs is shown. (C, D) Gene set enrichment analysis using Enrichr of marker genes from DAseq region 1 (C) and 3 (D) as compared to all other CAFs (Benjamini-Hochburg corrected Fisher’s exact test). (E) t-SNE sub-clustering of fibroblasts separately in Fib^Ctrl (left) and Fib^ΔZeb1 mice (right) of the orthotopic model showing less clusters in Fib^ΔZeb1. (F) Cluster similarities defined by cluster annotations based on ‘SingleR’ scores (see "Methods" for details) (Aran et al, 2019). Grayscale shows the log₂-transformed number of cells across clusters. Note the low similarity of Fib^ΔZeb1 cells with Fib^Ctrl clusters 2 and 5. (G) Heatmap showing the similarity (annotation scores) of gene expression in CAF clusters with published gene sets. Note, the high scores of Fib^Ctrl clusters 2 and 5 when compared with ‘iCAF’ and ‘myCAF’ signatures, respectively, and absence in Fib^ΔZeb1. Source data are available online for this figure.