Author ORCID Identifier


Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Biostatistics, Bioinformatics and Systems Biology

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Nicholas E. Navin

Committee Member

P. Andrew Futreal

Committee Member

Bora Lim

Committee Member

Ken Chen

Committee Member

Clinton Yam


There is vast cellular heterogeneity in human breast tissues, with different transcriptional programs in the stromal, epithelial, and immune components, however, it remains unclear how their reprogramming and interplay leads to the progression of invasive phenotypes such as Triple- Negative Breast cancer (TNBC). To do define the microenvironmental alterations that occur during cancer, we first established a human breast cell atlas, a reference of normal breast cell types from disease free women. We profiled 535,941 cells from 62 women and 124,024 nuclei from 20 women revealing 11 major cell types and 52 cell states that reflect different biological functions that can be organized into 4 major spatial domains (adipose, connective, ducts, lobules). We then compared this atlas against one of the more aggressive subtypes of breast cancer, TNBC in which patients lack estrogen, progesterone, and HER2 growth receptors. Approximately 10-14% of all breast cancer patients are classified as TNBC, with a majority developing resistance to neoadjuvant chemotherapy (NAC) and having a 5-year survival of <30%. Tumor evolution and changes in components of the tumor microenvironment (TME) such as cancer associated fibroblasts (CAFs), tumor associated macrophages (TAMs), and tumor endothelial cells (TECs), have shown to play a role in tumor progression. One knowledge gap is the role macroenvironmental changes confer on chemoresistance in TNBC patients. To order to investigate the transcriptional reprogramming of the TME, we performed single cell RNA sequencing on 100 treatment-naïve TNBC biopsies and compared its ecosystem to the normal breast ecosystem captured earlier. Our data suggest reprogramming and increased proportions of certain cell states such as TECs, CAFs, and effector T cells enrichment in TNBC and positive correlation with pathological complete response. Aside from transcriptional changes in normal and late stage invasive breast cancers microenvironments, we also investigated the genomic evolution in early stage breast cancer, Ductal Carcinoma In Situ (DCIS). DCIS is the most common form of pre-invasive breast cancer and despite treatment, a small fraction (5-10%) of DCIS patients present with invasive disease many years later. A fundamental question is whether the invasive disease recurring in the same breast is established by tumor cells in the initial DCIS or represents a new unrelated disease. Whole exome sequencing of 24 longitudinally matched DCIS and recurrent invasive breast cancer revealed clonally related recurrence in ~80% patients whereas ~20% pointed towards independent evolution which was also validated by single cell DNA sequencing in a subset of 4 cases. Overall, we established a breast cell atlas that provides an invaluable reference for the research community to under how normal cell types are reprogrammed in diseases such as TNBC. We established a secondary cell atlas of TNBC patients and compared the two atlases to characterize the transcriptomic features of progression and predictive of pathological complete response in TNBC samples. Lastly, we showed that not all DCIS may be precursors to invasive cancer which paves a way for accurate risk evaluation of DCIS, treatment de-escalation strategies, and the identification of predictive biomarkers.


Single Cell Genomics, Breast Cancer, DCIS, TNBC, Tumor Microenvironment



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