Figure 1

Single-cell RNA-seq identified transcriptional variability in multiple models of breast cancer. (a) Schematic for molecular and functional characterization of single-cell RNA-seq data in various model systems. (b) UMAP projection of single cell RNAseq data from MDA-MB-231 and HCC38 TNBC breast cancer cell lines and the HCI-002 TNBC-PDX model. Clusters determined by optimized Louvain clustering. (c) UMAP projection of scRNA-seq data from the ER + MCF7 cell line and HER2 + SKBR3 cell line with optimized Louvain clustering shown. (d) Gene set enrichment analysis (GSEA) of a basal gene signature performed on transcript profiles from MCF7 Cluster 4 cells. NES, normalized enrichment score. (e) Relative scores for a basal module in MCF7 clusters. (f) Gene set enrichment analysis (GSEA) of a EMT gene signature performed on transcript profiles from SKBR3 Cluster 6 cells. NES, normalized enrichment score. (g) Relative scores for an EMT module in SKBR3 clusters. In all graphs P values are calculated using a two-sided Wilcoxon test as indicated. TNBC triple-negative breast cancer, PDX patient-derived xenograft.