Fig. 4: SunCatcher enables functional and phenotypic analysis of individual clones and clonal dynamics.

a Functional analysis of Met1 BCs in monoculture and within the BC Pool. Column 1: proliferation rate (doubling time) of each BC over 9 days in culture, ranked from fastest to slowest. Each row represents data for the BC indicated in column 1. Column 2: Met1 BC Pool clonal dynamics in vitro, represented as fold-change (FC) in BC composition after 7 days (d) relative to initial admixture (data values shown in Table 1). Column 3: Met1 tumor clonal dynamics in vivo, represented as fold-change in BC composition at experimental endpoint relative to composition at time of injection (data values shown in Table 1). Column 4: average contribution of each BC as a percent of total BCs in each resulting tumor (n = 10). b Growth of Met1 BC Pool tumors (n = 4) and indicated individual BCs tumors (n = 6 per cohort). c Growth of indicated BC tumors (n = 6 per cohort). d Immunofluorescence images of indicated BCs stained for cytokeratin 8 (CK8, green), cytokeratin 14 (CK14, magenta), f-actin (red) (top), and epithelial cell adhesion molecule (EpCAM, green), zinc finger E-box-binding homeobox 1 (Zeb1) transcription factor (magenta), f-actin (white) (bottom). Nuclei were counterstained with DAPI (blue); Scale bars = 50 μm. Images represent 1 of 4 images per BC from 2 independent observations. e Pearson correlation matrix for individual Met1 BCs analyzed for: proliferation rate, CK8, CK14, Zeb1, EpCAM, programmed death ligand 1 (PD-L1), major histocompatibility complex type I (MHC-I) (associated with Supplementary Fig. 4 and Supplementary Tables 6–8). f Pearson correlation matrix for the 7 phenotypes assessed in vitro: proliferation rate, CK8, CK14, Zeb1, EpCAM, PD-L1, MHC-I (associated with Supplementary Tables 10, 11). Pearson correlation coefficients: CK8 v CK14 *p < 0.0215, 1-tailed, 90% CI; PD-L1 v EpCAM **p = 0.0096, 2-tailed, 90% CI; Zeb1 v EpCAM ***p = 0.0009, 1-tailed, 90% CI; MHC-I v CK14 ****p < 0.0001, 2-tailed, 90% CI. g Principal component (PC) analysis of BCs based on 9 parameters (proliferation, in vitro dynamics, in vivo dynamics, CK8, CK14, Zeb1, EpCAM, PD-L1, MHC-I) stratified by indicated percent composition of Met1 BC Pool tumors at experimental endpoint (associated with Supplementary Tables 9, 10). h Loadings plot from PCA shown in g. Source data are provided as a Source Data file.