Figure 4
Phylogenetic reconstruction recovers previously identified subclonal lineages across a range of cancer settings. We have generated phylogenies from five scRNA-Seq data sets. The evolutionary distance for each sample condition is shown as the circles at the right of the heatmap. The color and size of the circles represent the evolutionary distance and statistical significance. The yellow (Reference) and blue (Other) heatmaps show the genotypes of the sites with phylogenetic signal K > 0.8 across cells in the phylogeny. If no sites achieved this threshold, we showed the 10 sites with highest K. (A) These cells were experimentally evolved from the parental CAMA-1 cell line to ribociclib sensitive (S) and resistant (R) cell lineages which were then grown in monoculture (alone) or mixed and grown in co-culture (R + S mixed in equal proportions). The cells induced to be drug resistant are shown as black lines in the Resistance bar. The genotypes of the sites with high association with the phylogeny are shown in the heatmap at the bottom. (B) This data set consists of tumor cells collected from ER+ breast cancer tumors before and after treatment. The color bars show the time point of each cell. The phylogeny is divided into clades of pre- (blue) and post-treatment (red) genotypes. Persister cells are delineated with dots. (C) This contains tumor cells from a multiple myeloma patient before and after chemotherapy treatment. The phylogeny is divided into clades of pre- (blue) and post-treatment (red) genotypes. Persister cells are indicated with dots. (D) This data set contains cancer cells collected from the primary or metastasis site from a multiple myeloma patient. (E) This data contains cells from the N87 gastric cancer cell line evolving under untreated conditions. Four subclonal lineages were previously reported to coexist.
