Functional Heterogeneity Among Clonal Populations Derived From a Triple Negative Breast Cancer Cell Line

Abstract

Subpopulations within a single breast cancer exhibit substantial molecular heterogeneity caused by genetic and non-genetic sources of variability. However, the extent to which this diversity contributes to the functional behavior of individual tumor cells and tumor as a whole is largely unknown. The overall objective of this thesis was to establish a model in which we characterize the functional heterogeneity of clonal populations in breast cancer, track the dynamics of clonal populations within polyclonal mixtures during tumor progression and examine the contribution of interclonal cooperation on phenotypic properties associated with tumorigenesis. To accomplish this goal, we generated single cell populations (SCPs) from the triple-negative breast cancer cell line, MDA-MB-468. The SCPs displayed considerable phenotypic heterogeneity with respect to survival in suspension, colony formation in soft agar and tumorigenicity. The phenotypic heterogeneity among the SCPs was reproducible across replicates experiments suggesting the phenotypic heterogeneity is driven by the SCPs’ intrinsic properties. Genome sequencing and RNA-seq analysis revealed significant genetic diversity and differential gene expression among the SCPs. Utilizing the molecular characterization of the SCPs, we identified candidate genes and pathways that may contribute to the phenotypic heterogeneity among the SCPs. Furthermore, using a barcoding approach, we tracked the fate of individual barcoded populations within polyclonal mixtures cultured in vitro or during xenograft tumor development in the mammary gland. We found a highly reproducible pattern of expansion of distinct clones in vivo, suggesting distinct competitive advantages of individual clonal populations within distinct spatial and temporal windows. These patterns of clonal enrichment were distinct from those observed in in vitro culture conditions and highlight the stimuli or selective pressures exerted by the tumor microenvironment. Lastly, we revealed that certain clonal populations can cooperate in vitro to promote anchorage independent survival. Taken together, these results provide valuable insights into the functional heterogeneity and evolution of clonal populations of breast tumor cells and demonstrate that crosstalk between clonal populations can rescue tumor cells with conditionally weak phenotypes.