Extended Data Fig. 2: In vitro model of chemotolerance in TNBC.

All the experiments were performed in MDA-MB-468 cells. a. (Left) Histogram representing the percentage of the untreated population that tolerates 5-FU. (Right) Histogram representation of the percentage of persister cells that can proliferate actively under chemotherapy treatment. b. (Left) Histogram representation of the 5-FU IC50 of untreated and chemoresistant populations. (Right) Histogram representation of the doubling time (in days) of MDA-MB-468 untreated, persister and resistant cells. (n = 3, Mean ± sd, Anova test). c. (Left) UMAP representation of scRNA-seq datasets, colored according to RNA-inferred cluster ID. (Right) Histogram representing the frequency of each cluster in the indicated samples. d. Barplot displaying the top 5 pathways activated in MM468 persister cells. e. Dot plot representing -log10(q-value) of gene enrichment studies in PDX_95 versus MDA-MB-468 (MM468). Linear regression, associated correlation score and q-value are indicated. f. UMAP plot representing scRNA-seq datasets, points are colored according to log2 gene expression signals for differentially expressed genes between persister cells from cluster R2 and untreated cells from cluster R10, log2FC and q-values are indicated above the graph. g. Histogram of the proportion of cells in the different cell cycle phases based on expression of cell cycle in the scRNA-seq datasets. For each experiment, proportions in each sample were compared to the corresponding DMSO sample using two sided Fisher’s exact test, p-value are indicated.