Fig. 5
From: Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq
Ten slices from a single patient (TB6393) were treated with panobinostat (3 slices), etoposide (3 slices), or vehicle (DMSO, 4 slices adjacent to drug-treated slices). a UMAP embedding of scRNA-seq profiles of ten slices colored by treatment condition. b Same as a but colored by the log-ratio of Chr. 7 to Chr. 10 average expression where a high ratio (red) indicates malignant transformation. c Same as b but colored by cell type. d Volcano plot of differential expression analysis between all transformed tumor cells from etoposide-treated slices and all adjacent vehicle-treated slices. Genes highlighted in red and blue have fold-increase or decrease, respectively, greater than two and FDR<0.05. A large set of cell cycle control markers highly downregulated in the etoposide-treated cells are labeled and highlighted in cyan. e Same as d but for panobinostat-treated transformed tumor cells showing strong induction of metallothioneins and several mature neuronal markers labeled and highlighted in orange. f Same as e but for the myeloid cells showing downregulation of the macrophage markers highlighted in cyan and strong induction of metallothioneins highlighted in orange. g Heatmap showing the normalized enrichment score (NES) from gene set enrichment analysis (GSEA) analysis. GSEA was performed using gene sets from the top 100 genes of each scHPF factor from Fig. 4 to analyze the ranked differentially expression genes between tumor or myeloid cells from each etoposide-treated slice and that of its adjacent vehicle-treated slice. scHPF factor with consistent enrichment and FDR<0.05 in at least 2 treated vs. untreated comparisons are marked with asterisk. h Same as g but showing NES from GSEA analysis for differentially expression genes between tumor or myeloid cells from each panobinostat-treated slice and that of its adjacent vehicle-treated slice