Single-cell Regulatory Heterogeneities in Basal-like Breast Epithelia

Many biological measurements assume all the cells in a population are identical. However, no two cells are identical. How cell variation, or heterogeneity, influences biological outcomes is unclear. Cellular heterogeneity has been correlated with poorer prognoses in cancer, suggesting that heterogeneity plays a role in the progression of the disease. Understanding the role of heterogeneity is limited by the ability to identify which genes and proteins are different in the tumor population.
In this Dissertation, we build and extend computational tools to identify and quantify heterogeneously regulated genes. We apply these approaches to understand the role of heterogeneity in basal-like breast cancer, the most lethal form of breast cancer. We begin by designing a computational algorithm to quantify geometric properties of three-dimensional breast cancer spheroid in vitro assays. We use the quantitative characteristics to identify inter-cell line and intra-cell line differences in spheroid morphology. Furthermore, we use the approach to quantify the extent of heterogeneity present in basal-like breast cancer cell lines. Next, we build molecular and agent-based models to explain the heterogeneity we observe in a biomarker protein, JUND. These models helped us to understand what the triggers and consequences of JUND heterogeneity were in breast epithelial spheroids. Last, we build a statistical model of sampling to obtain single-cell level gene expression information from population measurements. We use this approach to globally quantify the frequency of cells expressing different transcriptional programs at an elevated level. We identified one gene (PIK3CD) that was rarely expressed, but critical to normal spheroid development.
In Part II of this thesis, we identified a heterogeneously expressed ligand, growth-differentiation factor 11 (GDF11). GDF11 has not been implicated in normal or pathologic breast biology. In this Dissertation, we discover that GDF11 improves the morphology of normal breast and breast cancer spheroids. We identify SMAD4 and ID2 as molecular mediators of GDF11 treatment. GDF11 blocks the ability of basal-like breast cancer cells to establish tumors in a xenograft model, suggesting the loss of GDF11 function could play a role in the progression of human basal-like breast cancer. Strikingly, we observe that human basal-like breast cancers have a defect in secretion of GDF11. This intracellular sequestration of a tumor suppressive ligand presents a new way in which cancer cells inactivate tumor suppressors.