Extended Data Fig. 8: FateMap reveals differences in clonal fate type outcomes between continuous and discontinuous therapy.

a. Schematic of the experimental design where we exposed single-cell-derived WM989 A6-G3 melanoma cells to continuous and discontinuous doses of targeted therapy drug vemurafenib. b. UMAP of all barcoded cells. 17,634 cells are colored by clusters determined using Seurat’s FindClusters command (“Seurat clusters, resolution = 0.6”). c. Pellet morphology for continuous (7,238 cells) and discontinuous (10,396 cells) treatment cells. Cells derived from discontinuous dosage have a larger and darker (more pigmented) pellet. This suggests that during discontinuous dosage, melanocytic cells (which are pigmented in nature) proliferate. d. On the UMAP, we recolored each cell by its expression for a select subset of genes that were identified as differentially expressed in drug resistant cells via the Seurat pipeline. e. UMAP of all barcoded cells. Cells are colored by type of dosage. f. UMAPs of representative twin clones (sharing the same barcode) that arise during discontinuous drug treatment. The twins largely end up with the same transcriptional fate type and have varying proliferative capacities. g. In discontinuous dosage, 68% of clones having high MLANA expression (log2 Expression > 2, in at least 50% of cells in a given clone) are proliferative (i.e. have clone size > 1). In continuous dosage, only 20% of clones having high MLANA expression are proliferative. h. (left) Total number of cells analyzed consisted of 60.5% discontinuous dosage samples and 39.5% continuous dosage samples. (right) The number of unique barcodes (i.e. resistant clones) displays a 3.6 fold increase in discontinuous dosage sample as compared to the continuous dosage sample. i. UMAPs of representative twin clones across the two splits of continuous and discontinuous dosing. Some twins end up in the similar transcriptional fate type while others tend to switch fate type.