Fig. 4

Characterizing single-cell drug response in BT159 GBM cells. a Schematic representation of GBM PDCL generation, drug treatment in vitro, and subsequent characterization of therapeutic response using the sSMR collection platform. Mass and growth measurements are collected after 16 h of treatment, prior to loss of cell viability, which enables downstream molecular characterization with scRNA-seq (Methods). b Plot of single-cell MAR versus mass for BT159 GBM cells treated with either DMSO (blue circles, n = 83) or RG7388 (an MDM2 inhibitor, red triangles, n = 66) for 16 h. Kernel density plots, using the same color scheme, are included in the margins for both populations. ***P < 0.001, Mann-Whitney U test. c Volcano plot showing log-transformed average expression fold change and log-transformed P-values (Bonferroni corrected) for genes upregulated (red) or downregulated (blue) in BT159 cells treated with RG7388 as compared with DMSO treatment. d Plot of mitosis scores versus buoyant mass for BT159 cells treated with DMSO (blue circles, n = 83) or RG7388 (red triangles, n = 66) for 16 h. Mitosis scores were calculated by taking the average z-score adjusted gene expression values of a panel of mitosis-related genes (n = 29, Additional file 10: Table S9; Methods). Kernel density plots, using the same color scheme, are included in the margins for both populations. ***P < 0.001, Mann-Whitney U test. e Plot of significantly enriched canonical pathways (FDR < 0.05) in RG7388-treated BT159 cells (n = 66), as determined by ingenuity pathway analysis, among genes with significant positive (black) or negative (gray) correlations with normalized MAR. (Additional file 1: Figure S4, Additional file 11: Table S10, Methods)