UC Irvine

The breast epithelial system is a complex network of various cell types that work together to provide milk for the offspring. This complex network requires three distinct cell types to maintain the structure and function of the breast. This system is extremely dynamic and constantly changes in response to hormones secreted during different developmental stages. This constant change requires rapid growth and involution of the network and is where mutations and cellular dysregulation could lead to serious complications such as breast cancer. This dissertation focuses on creating a reference atlas of the normal breast epithelium and explores the pre-malignant changes that occur in human BRCA1 mutation carriers. This work utilizes single-cell RNAseq to profile the breast epithelium, which enable us to identify three main cell types, namely two distinct luminal and one basal cell type. In addition to the known basal and luminal populations, an additional luminal population was identified. This highlights the heterogeneity that exists at the cellular level in the luminal population that has been previously overlooked by bulk profiling approaches. Comparative analysis with BRCA1 mutation carrier samples reveals an expansion of a luminal progenitor population. This population is over-represented by cells from BRCA1 mutation carriers and have higher overall scEnergy, indicating greater dysregulation. Further characterization of this population reveals markers relating to stem and progenitor identities, suggesting its role as the cancer cell of origin. To perform single-cell profiling and functional assays, we needed to establish a robust method for single-cell isolation and purification. Analysis of the current method for single-cell isolation reveals that biological changes arise and these changes have long-term effects on the growth potential, thereby influencing the results of functional assays. Overall this work takes a high-resolution approach to identify cellular heterogeneity in the breast epithelium and elude the changes that occur during early cancer initiation for BRCA1 mutation carriers.